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Sample records for selective protein carbonylation

  1. Protein carbonylation in plants

    DEFF Research Database (Denmark)

    Møller, Ian Max; Havelund, Jesper; Rogowska-Wrzesinska, Adelina

    2017-01-01

    This chapter provides an overview of the current knowledge on protein carbonylation in plants and its role in plant physiology. It starts with a brief outline of the turnover and production sites of reactive oxygen species (ROS) in plants and the causes of protein carbonylation. This is followed...... by a description of the methods used to study protein carbonylation in plants, which is also very brief as the methods are similar to those used in studies on animals. The chapter also focuses on protein carbonylation in plants in general and in mitochondria and in seeds in particular, as case stories where...... specific carbonylated proteins have been identified. Protein carbonylation appears to accumulate at all stages of seed development and germination investigated to date. In some cases, such as seed aging, it is probably simply an accumulation of oxidative damage. However, in other cases protein...

  2. Validation of protein carbonyl measurement

    DEFF Research Database (Denmark)

    Augustyniak, Edyta; Adam, Aisha; Wojdyla, Katarzyna

    2015-01-01

    Protein carbonyls are widely analysed as a measure of protein oxidation. Several different methods exist for their determination. A previous study had described orders of magnitude variance that existed when protein carbonyls were analysed in a single laboratory by ELISA using different commercial...... protein carbonyl analysis across Europe. ELISA and Western blotting techniques detected an increase in protein carbonyl formation between 0 and 5min of UV irradiation irrespective of method used. After irradiation for 15min, less oxidation was detected by half of the laboratories than after 5min...... irradiation. Three of the four ELISA carbonyl results fell within 95% confidence intervals. Likely errors in calculating absolute carbonyl values may be attributed to differences in standardisation. Out of up to 88 proteins identified as containing carbonyl groups after tryptic cleavage of irradiated...

  3. Reciprocal carbonyl-carbonyl interactions in small molecules and proteins.

    Science.gov (United States)

    Rahim, Abdur; Saha, Pinaki; Jha, Kunal Kumar; Sukumar, Nagamani; Sarma, Bani Kanta

    2017-07-19

    Carbonyl-carbonyl n→π* interactions where a lone pair (n) of the oxygen atom of a carbonyl group is delocalized over the π* orbital of a nearby carbonyl group have attracted a lot of attention in recent years due to their ability to affect the 3D structure of small molecules, polyesters, peptides, and proteins. In this paper, we report the discovery of a "reciprocal" carbonyl-carbonyl interaction with substantial back and forth n→π* and π→π* electron delocalization between neighboring carbonyl groups. We have carried out experimental studies, analyses of crystallographic databases and theoretical calculations to show the presence of this interaction in both small molecules and proteins. In proteins, these interactions are primarily found in polyproline II (PPII) helices. As PPII are the most abundant secondary structures in unfolded proteins, we propose that these local interactions may have implications in protein folding.Carbonyl-carbonyl π* non covalent interactions affect the structure and stability of small molecules and proteins. Here, the authors carry out experimental studies, analyses of crystallographic databases and theoretical calculations to describe an additional type of carbonyl-carbonyl interaction.

  4. Advanced Oxidation Protein Products and Carbonylated Proteins as Biomarkers of Oxidative Stress in Selected Atherosclerosis-Mediated Diseases

    Directory of Open Access Journals (Sweden)

    Bogna Gryszczyńska

    2017-01-01

    Full Text Available Objectives. The main question of this study was to evaluate the intensity of oxidative protein modification shown as advanced oxidation protein products (AOPP and carbonylated proteins, expressed as protein carbonyl content (C=O in abdominal aortic aneurysms (AAA, aortoiliac occlusive disease (AIOD, and chronic kidney disease (CKD. Design and Methods. The study was carried out in a group of 35 AAA patients and 13 AIOD patients. However, CKD patients were divided into two groups: predialysis (PRE included 50 patients or hemodialysis (HD consisted of 34 patients. AOPP and C=O were measured using colorimetric assay kit, while C-reactive protein concentration was measured by high-sensitivity assay (hsCRP. Results. The concentration of AOPP in both AAA and AIOD groups was higher than in PRE and HD groups according to descending order: AAA~AIOD > HD > PRE. The content of C=O was higher in the PRE group in comparison to AIOD and AAA according to the descending order: PRE~HD > AAA~AIOD. Conclusions. AAA, AIOD, and CKD-related atherosclerosis (PRE and HD contribute to the changes in the formation of AOPP and C=O. They may promote modification of proteins in a different way, probably due to the various factors that influence oxidative stress here.

  5. Dansyl labeling and bidimensional mass spectrometry to investigate protein carbonylation.

    Science.gov (United States)

    Palmese, Angelo; De Rosa, Chiara; Marino, Gennaro; Amoresano, Angela

    2011-01-15

    Carbonylation is a non-enzymatic irreversible post-translational modification. The adduction of carbonyl groups to proteins is due to the presence of excess of ROS in cells. Carbonylation of specific amino acid side chains is one of the most abundant consequences of oxidative stress; therefore, the determination of carbonyl groups content in proteins is regarded as a reliable way to estimate the cellular damage caused by oxidative stress. This paper reports a novel RIGhT (Reporter Ion Generating Tag) (A. Amoresano, G. Monti, C. Cirulli, G. Marino. Rapid Commun. Mass Spectrom. 2006, 20, 1400) approach for selective labeling of carbonyl groups in proteins using dansylhydrazide, coupled with selective analysis by bidimensional mass spectrometry. We first applied this approach to ribonuclease A and lysozyme as model proteins. According to the so-called 'gel-free procedures', the analysis is carried out at the level of peptides following tryptic digest of the whole protein mixture. Modified RNaseA was analyzed in combined MS(2) and MS(3) scan mode, to specifically select the dansylated species taking advantage of the dansyl-specific fragmentation pathways. This combination allowed us to obtain a significant increase in signal/noise ratio and a significant increase in sensitivity of analysis, due to the reduction of duty cycle of the mass spectrometer. The unique signal obtained was correlated to peptide 1-10 of RNaseA carbonylated and labeled by dansylhydrazide. This strategy represents the first method leading to the direct identification of the carbonylation sites in proteins, thus indicating the feasibility of this strategy to investigate protein carbonylation in a proteomic approach. Copyright © 2010 John Wiley & Sons, Ltd.

  6. Protein Carbonylation and Adipocyte Mitochondrial Function*

    Science.gov (United States)

    Curtis, Jessica M.; Hahn, Wendy S.; Stone, Matthew D.; Inda, Jacob J.; Droullard, David J.; Kuzmicic, Jovan P.; Donoghue, Margaret A.; Long, Eric K.; Armien, Anibal G.; Lavandero, Sergio; Arriaga, Edgar; Griffin, Timothy J.; Bernlohr, David A.

    2012-01-01

    Carbonylation is the covalent, non-reversible modification of the side chains of cysteine, histidine, and lysine residues by lipid peroxidation end products such as 4-hydroxy- and 4-oxononenal. In adipose tissue the effects of such modifications are associated with increased oxidative stress and metabolic dysregulation centered on mitochondrial energy metabolism. To address the role of protein carbonylation in the pathogenesis of mitochondrial dysfunction, quantitative proteomics was employed to identify specific targets of carbonylation in GSTA4-silenced or overexpressing 3T3-L1 adipocytes. GSTA4-silenced adipocytes displayed elevated carbonylation of several key mitochondrial proteins including the phosphate carrier protein, NADH dehydrogenase 1α subcomplexes 2 and 3, translocase of inner mitochondrial membrane 50, and valyl-tRNA synthetase. Elevated protein carbonylation is accompanied by diminished complex I activity, impaired respiration, increased superoxide production, and a reduction in membrane potential without changes in mitochondrial number, area, or density. Silencing of the phosphate carrier or NADH dehydrogenase 1α subcomplexes 2 or 3 in 3T3-L1 cells results in decreased basal and maximal respiration. These results suggest that protein carbonylation plays a major instigating role in cytokine-dependent mitochondrial dysfunction and may be linked to the development of insulin resistance in the adipocyte. PMID:22822087

  7. Protein carbonylation and adipocyte mitochondrial function.

    Science.gov (United States)

    Curtis, Jessica M; Hahn, Wendy S; Stone, Matthew D; Inda, Jacob J; Droullard, David J; Kuzmicic, Jovan P; Donoghue, Margaret A; Long, Eric K; Armien, Anibal G; Lavandero, Sergio; Arriaga, Edgar; Griffin, Timothy J; Bernlohr, David A

    2012-09-21

    Carbonylation is the covalent, non-reversible modification of the side chains of cysteine, histidine, and lysine residues by lipid peroxidation end products such as 4-hydroxy- and 4-oxononenal. In adipose tissue the effects of such modifications are associated with increased oxidative stress and metabolic dysregulation centered on mitochondrial energy metabolism. To address the role of protein carbonylation in the pathogenesis of mitochondrial dysfunction, quantitative proteomics was employed to identify specific targets of carbonylation in GSTA4-silenced or overexpressing 3T3-L1 adipocytes. GSTA4-silenced adipocytes displayed elevated carbonylation of several key mitochondrial proteins including the phosphate carrier protein, NADH dehydrogenase 1α subcomplexes 2 and 3, translocase of inner mitochondrial membrane 50, and valyl-tRNA synthetase. Elevated protein carbonylation is accompanied by diminished complex I activity, impaired respiration, increased superoxide production, and a reduction in membrane potential without changes in mitochondrial number, area, or density. Silencing of the phosphate carrier or NADH dehydrogenase 1α subcomplexes 2 or 3 in 3T3-L1 cells results in decreased basal and maximal respiration. These results suggest that protein carbonylation plays a major instigating role in cytokine-dependent mitochondrial dysfunction and may be linked to the development of insulin resistance in the adipocyte.

  8. Ozone Effects on Protein Carbonyl Content in the Frontal ...

    Science.gov (United States)

    Oxidative stress (OS) plays an important role in susceptibility and disease in old age. Understanding age-related susceptibility is a critical part of community-based human health risk assessment of chemical exposures. There is growing concern over a common air pollutant, ozone (03), and adverse health effects including dysfunction of the pulmonary, cardiac, and nervous systems. The objective of this study was to test whether OS plays a role in the adverse effects caused by 03 exposure, and if so, if effects were age-dependent. We selected protein carbonyl as an indicator of OS because carbonyl content of cells is a useful indicator of oxidative protein damage and has been linked to chemical-induced adverse effects. Male Brown Norway rats (4, 12, and 24 months) were exposed to 03 (0,0.25 or 1 ppm) via inhalation for 6 h/day, 2 days per week for 13 weeks. Frontal cortex (FC) and cerebellum (CB) were dissected, quick frozen on dry ice, and stored at -80°C. Protein carbonyls were assayed using commercial kits. Hydrogen peroxide, a positive control, increased protein carbonyls in cortical tissue in vitro in a concentration-dependent manner. Significant effects of age on protein carbonyls in FC and a significant effect of age and 03 dose on protein carbonyls in CB were observed. In control rats, there was an age-dependent increase in protein carbonyls indicating increased OS in 12 and 24 month old rats compared to 4 month old rats. Although 03 increase

  9. Protein Carbonylation in Patients with Myelodysplastic Syndromes

    Czech Academy of Sciences Publication Activity Database

    Hlaváčková, A.; Štikarová, J.; Kotlín, R.; Chrastinová, L.; Šácha, Pavel; Májek, P.; Čermák, J.; Suttnar, J.; Dyr, J. E.

    2015-01-01

    Roč. 126, č. 23 (2015), s. 5232 ISSN 0006-4971. [Annual Meeting and Exposition of the American Society of Hematology /55./. 07.12.2013-10.12.2013, New Orleans] Institutional support: RVO:61388963 Keywords : protein carbonylation * myelodysplastic syndromes Subject RIV: CE - Biochemistry

  10. Validation of protein carbonyl measurement: A multi-centre study

    Directory of Open Access Journals (Sweden)

    Edyta Augustyniak

    2015-04-01

    Full Text Available Protein carbonyls are widely analysed as a measure of protein oxidation. Several different methods exist for their determination. A previous study had described orders of magnitude variance that existed when protein carbonyls were analysed in a single laboratory by ELISA using different commercial kits. We have further explored the potential causes of variance in carbonyl analysis in a ring study. A soluble protein fraction was prepared from rat liver and exposed to 0, 5 and 15 min of UV irradiation. Lyophilised preparations were distributed to six different laboratories that routinely undertook protein carbonyl analysis across Europe. ELISA and Western blotting techniques detected an increase in protein carbonyl formation between 0 and 5 min of UV irradiation irrespective of method used. After irradiation for 15 min, less oxidation was detected by half of the laboratories than after 5 min irradiation. Three of the four ELISA carbonyl results fell within 95% confidence intervals. Likely errors in calculating absolute carbonyl values may be attributed to differences in standardisation. Out of up to 88 proteins identified as containing carbonyl groups after tryptic cleavage of irradiated and control liver proteins, only seven were common in all three liver preparations. Lysine and arginine residues modified by carbonyls are likely to be resistant to tryptic proteolysis. Use of a cocktail of proteases may increase the recovery of oxidised peptides. In conclusion, standardisation is critical for carbonyl analysis and heavily oxidised proteins may not be effectively analysed by any existing technique.

  11. Pattern of occurrence and occupancy of carbonylation sites in proteins

    DEFF Research Database (Denmark)

    Rao, R Shyama Prasad; Møller, Ian Max

    2011-01-01

    sites. Comparison of metal-catalyzed oxidation of two closely related proteins indicates that this type of carbonylation might not be very specific in proteins. Interestingly, carbonylated sites show a very strong tendency to cluster together in the protein primary sequence hinting at some sort......Proteins are targets for modification by reactive oxygen species, and carbonylation is an important irreversible modification that increases during oxidative stress. While information on protein carbonylation is accumulating, its pattern is not yet understood. We have made a meta...

  12. Protein carbonylation associated to high-fat, high-sucrose diet and its metabolic effects.

    Science.gov (United States)

    Méndez, Lucía; Pazos, Manuel; Molinar-Toribio, Eunice; Sánchez-Martos, Vanesa; Gallardo, José M; Rosa Nogués, M; Torres, Josep L; Medina, Isabel

    2014-12-01

    The present research draws a map of the characteristic carbonylation of proteins in rats fed high-caloric diets with the aim of providing a new insight of the pathogenesis of metabolic diseases derived from the high consumption of fat and refined carbohydrates. Protein carbonylation was analyzed in plasma, liver and skeletal muscle of Sprague-Dawley rats fed a high-fat, high-sucrose (HFHS) diet by a proteomics approach based on carbonyl-specific fluorescence-labeling, gel electrophoresis and mass spectrometry. Oxidized proteins along with specific sites of oxidative damage were identified and discussed to illustrate the consequences of protein oxidation. The results indicated that long-term HFHS consumption increased protein oxidation in plasma and liver; meanwhile, protein carbonyls from skeletal muscle did not change. The increment of carbonylation by HFHS diet was singularly selective on specific target proteins: albumin from plasma and liver, and hepatic proteins such as mitochondrial carbamoyl-phosphate synthase (ammonia), mitochondrial aldehyde dehydrogenase, argininosuccinate synthetase, regucalcin, mitochondrial adenosine triphosphate synthase subunit beta, actin cytoplasmic 1 and mitochondrial glutamate dehydrogenase 1. The possible consequences that these specific protein carbonylations have on the excessive weight gain, insulin resistance and nonalcoholic fatty liver disease resulting from HFHS diet consumption are discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Selective Oxidative Carbonylation of Aniline to Diphenylurea with Ionic Liquids

    DEFF Research Database (Denmark)

    Zahrtmann, Nanette; Claver, Carmen; Godard, Cyril

    2018-01-01

    A catalytic system for the selective oxidative carbonylation of aniline to diphenylurea based on Pd complexes in combination with imidazolium ionic liquids is presented. Both oxidants, Pd complexes and ionic liquids affect the activity of the reaction while the choice of oxidant determines...

  14. Plasma protein carbonyl levels and breast cancer risk

    Czech Academy of Sciences Publication Activity Database

    Rössner ml., Pavel; Terry, M. B.; Gammon, M. D.; Agrawal, M.; Zhang, F. F.; Ferris, J.S.; Teitelbaum, S. L.; Eng, S. M.; Gaudet, M. M.; Neugut, A. I.; Santella, R. M.

    2007-01-01

    Roč. 11, č. 5 (2007), s. 1138-1148 ISSN 1582-1838 Institutional research plan: CEZ:AV0Z50390512 Keywords : oxidative stress * protein carbonyl * breast cancer Subject RIV: DN - Health Impact of the Environment Quality Impact factor: 6.807, year: 2007

  15. Protein carbonylation and metal-catalyzed protein oxidation in a cellular perspective

    DEFF Research Database (Denmark)

    Møller, Ian Max; Rogowska-Wrzesinska, Adelina; Rao, R S P

    2011-01-01

    Proteins can become oxidatively modified in many different ways, either by direct oxidation of amino acid side chains and protein backbone or indirectly by conjugation with oxidation products of polyunsaturated fatty acids and carbohydrates. While reversible oxidative modifications are thought...... to be relevant in physiological processes, irreversible oxidative modifications are known to contribute to cellular damage and disease. The most well-studied irreversible protein oxidation is carbonylation. In this work we first examine how protein carbonylation occurs via metal-catalyzed oxidation (MCO) in vivo...... and in vitro with an emphasis on cellular metal ion homeostasis and metal binding. We then review proteomic methods currently used for identifying carbonylated proteins and their sites of modification. Finally, we discuss the identified carbonylated proteins and the pattern of carbonylation sites in relation...

  16. Analysis of protein carbonylation - pitfalls and promise in commonly used methods

    DEFF Research Database (Denmark)

    Rogowska-Wrzesinska, A.; Wojdyla, K.; Nedic, O.

    2014-01-01

    that research scientists are becoming more eager to be able to measure accurately the level of oxidized protein in biological materials, and to determine the precise site of the oxidative attack on the protein, in order to get insights into the molecular mechanisms involved in the progression of diseases....... Several methods for measuring protein carbonylation have been implemented in different laboratories around the world. However, to date no methods prevail as the most accurate, reliable, and robust. The present paper aims at giving an overview of the common methods used to determine protein carbonylation...... in biological material as well as to highlight the limitations and the potential. The ultimate goal is to give quick tips for a rapid decision making when a method has to be selected and taking into consideration the advantage and drawback of the methods....

  17. Analysis of protein carbonylation-pitfalls and promise in commonly used methods

    DEFF Research Database (Denmark)

    Rogowska-Wrzesinska, Adelina; Wojdyla, K; Nedić, O

    2014-01-01

    that research scientists are becoming more eager to be able to measure accurately the level of oxidized protein in biological materials, and to determine the precise site of the oxidative attack on the protein, in order to get insights into the molecular mechanisms involved in the progression of diseases....... Several methods for measuring protein carbonylation have been implemented in different laboratories around the world. However, to date no methods prevail as the most accurate, reliable, and robust. The present paper aims at giving an overview of the common methods used to determine protein carbonylation...... in biological material as well as to highlight the limitations and the potential. The ultimate goal is to give quick tips for a rapid decision making when a method has to be selected and taking into consideration the advantage and drawback of the methods....

  18. Protein carbonylation, protein aggregation and neuronal cell death in a murine model of multiple sclerosis

    Science.gov (United States)

    Dasgupta, Anushka

    Many studies have suggested that oxidative stress plays an important role in the pathophysiology of both multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis (EAE). Yet, the mechanism by which oxidative stress leads to tissue damage in these disorders is unclear. Recent work from our laboratory has revealed that protein carbonylation, a major oxidative modification caused by severe and/or chronic oxidative stress conditions, is elevated in MS and EAE. Furthermore, protein carbonylation has been shown to alter protein structure leading to misfolding/aggregation. These findings prompted me to hypothesize that carbonylated proteins, formed as a consequence of oxidative stress and/or decreased proteasomal activity, promote protein aggregation to mediate neuronal apoptosis in vitro and in EAE. To test this novel hypothesis, I first characterized protein carbonylation, protein aggregation and apoptosis along the spinal cord during the course of myelin-oligodendrocyte glycoprotein (MOG)35-55 peptide-induced EAE in C57BL/6 mice [Chapter 2]. The results show that carbonylated proteins accumulate throughout the course of the disease, albeit by different mechanisms: increased oxidative stress in acute EAE and decreased proteasomal activity in chronic EAE. I discovered not only that there is a temporal correlation between protein carbonylation and apoptosis but also that carbonyl levels are significantly higher in apoptotic cells. A high number of juxta-nuclear and cytoplasmic protein aggregates containing the majority of the oxidized proteins are also present during the course of EAE, which seems to be due to reduced autophagy. In chapter 3, I show that when gluthathione levels are reduced to those in EAE spinal cord, both neuron-like PC12 (nPC12) cells and primary neuronal cultures accumulate carbonylated proteins and undergo cell death (both by necrosis and apoptosis). Immunocytochemical and biochemical studies also revealed a temporal

  19. A biotin enrichment strategy identifies novel carbonylated amino acids in proteins from human plasma

    DEFF Research Database (Denmark)

    Havelund, Jesper F; Wojdyla, Katarzyna; Davies, Michael J

    2017-01-01

    Protein carbonylation is an irreversible protein oxidation correlated with oxidative stress, various diseases and ageing. Here we describe a peptide-centric approach for identification and characterisation of up to 14 different types of carbonylated amino acids in proteins. The modified residues...... in vitro metal ion-catalysed oxidation. Furthermore, we assigned 133 carbonylated sites in 36 proteins in native human plasma protein samples. The optimised workflow enabled detection of 10 hitherto undetected types of carbonylated amino acids in proteins: aldehyde and ketone modifications of leucine...

  20. Protein carbonyl content: a novel biomarker for aging in HIV/AIDS patients.

    Science.gov (United States)

    Kolgiri, Vaishali; Patil, Vinayak Wamanrao

    The major complications of "treated" Human Immunodeficiency Virus (HIV) infection are cardiovascular disease, malignancy, renal disease, liver disease, bone disease, and perhaps neurological complications, which are phenomena of the normal aging process occurring at an earlier age in the HIV-infected population. The present study is aimed to explore protein carbonyl content as a biomarker for detecting oxidative DNA damage induced ART toxicity and/or accelerated aging in HIV/AIDS patients. To investigate the potential of carbonyl content as a biomarker for detecting oxidative Deoxyribonucleic acid (DNA) damage induced Antiretroviral Theraphy (ART) toxicity and/or accelerated aging in HIV/AIDS patients. In this case-control study a total 600 subjects were included. All subjects were randomly selected and grouped as HIV-negative (control group) (n=300), HIV-infected ART naive (n=100), HIV-infected on first line ART (n=100), and HIV-infected on second line ART (n=100). Seronegative control subjects were age- and sex-matched with the ART naive patients and the two other groups. Carbonyl protein was determined by the method described in Levine et al. DNA damage marker 8-OH-dG was determined using 8-hydroxy-2-deoxy Guanosine StressXpress ELA Kit by StressMarq Biosciences. Protein carbonyl content levels and oxidative DNA damage were significantly higher (paging in HIV/AIDS patients. Larger studies are warranted to elucidate the role of carbonyl content as a biomarker for premature aging in HIV/AIDS patients. Copyright © 2016 Sociedade Brasileira de Infectologia. Published by Elsevier Editora Ltda. All rights reserved.

  1. Determination of protein carbonyls in plasma, cell extracts, tissue homogenates, isolated proteins

    DEFF Research Database (Denmark)

    Weber, Daniela; Davies, Michael J.; Grune, Tilman

    2015-01-01

    Protein oxidation is involved in regulatory physiological events as well as in damage to tissues and is thought to play a key role in the pathophysiology of diseases and in the aging process. Protein-bound carbonyls represent a marker of global protein oxidation, as they are generated by multiple...

  2. Active control of methanol carbonylation selectivity over Au/carbon anode by electrochemical potential.

    Science.gov (United States)

    Funakawa, Akiyasu; Yamanaka, Ichiro; Otsuka, Kiyoshi

    2005-05-12

    Electrochemical oxidative carbonylation of methanol was studied over Au supported carbon anode in CO. The major carbonylation products were dimethyl oxalate (DMO) and dimethyl carbonate (DMC). The minor oxidation products were dimethoxy methane (DMM) and methyl formate (MF) from methanol and CO(2). Influences of various reaction conditions were studied on carbonylation activities and selectivities. The selectivities to DMO and DMC can be controlled by the electrochemical potential. Electrocatalysis of Au/carbon anode was studied by cyclic voltammetry (CV), stoichiometric reactions among Au(3+), methanol, and CO, and UV-vis spectra. The Au/carbon anode was characterized by XRD, SEM, and BE images before and after the carbonylation. These experimental facts strongly suggest that transition of oxidation states of Au affects changing of the carbonylation selectivities to DMO and DMC. Au(0) is the active species for the selective DMO formation by direct electrochemical carbonylation at low potentials (selective DMC formation by indirect electrochemical carbonylation through Au(3+)/Au(+) redox at high potentials (>+1.3 V).

  3. Protein carbonylation sites in bovine raw milk and processed milk products.

    Science.gov (United States)

    Milkovska-Stamenova, Sanja; Mnatsakanyan, Ruzanna; Hoffmann, Ralf

    2017-08-15

    During thermal treatment of milk, proteins are oxidized, which may reduce the nutritional value of milk, abolish protein functions supporting human health, especially important for newborns, and yield potentially harmful products. The side chains of several amino acids can be oxidized to reactive carbonyls, which are often used to monitor oxidative stress in organisms. Here we mapped protein carbonylation sites in raw milk and different brands of pasteurized, ultra high temperature (UHT) treated milk, and infant formulas (IFs) after digesting the precipitated proteins with trypsin. Reactive carbonyls were derivatized with O-(biotinylcarbazoylmethyl)hydroxylamine to enrich the modified peptides by avidin-biotin affinity chromatography and analyze them by nanoRP-UPLC-ESI-MS. Overall, 53 unique carbonylated peptides (37 carbonylation sites, 15 proteins) were identified. Most carbonyls were derived from dicarbonyls (mainly glyoxal). The number of carbonylation sites increased with the harsher processing from raw milk (4) to pasteurized (16) and UHT milk (16) and to IF (24). Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Plasma protein carbonyl responses to anaerobic exercise in female cyclists

    Directory of Open Access Journals (Sweden)

    M.E Afzalpour

    2016-03-01

    Full Text Available Single bouts of aerobic exercise may leads to oxidative stress due to the use of oxygen for metabolism and the generation of reactive oxygen. In athletes, oxidative stress can lead to several deleterious performance effects, such as muscular oxidative damage, muscle soreness, loss of skeletal muscle force production and/or inflammation. However, little is known regarding the severity and duration of oxidative stress arising from intensive anaerobic modes of exercise in aerobically-trained athletes. The purpose of this study was to investigate the effect of a single bout of intensive anaerobic exercise on plasma protein carbonyl (PC in aerobically-trained women. Aerobically-trained, provincial female cyclists [n = 18, age: 24.2±2.7 years; stature: 163.6±4.6 cm; body mass: 53.4±4.2 kg] were randomly assigned into either a non-exercising control (CON; n = 9 or experimental (EXP; n = 9 group that underwent a 30-second anaerobic (Wingate cycle ergometer exercise session. Blood sampling took place before exercise, immediately after the exercise (IE, and 24 hours following the exercise (24HR bout. In the EXP, results indicated significant (P ≤ 0.05 differences in PC levels between the pre-test and IE (0.010±0.0124 to 0.0149±0.0420 mmol/milt; P = 0.010, and IE and 24HR (0.0149±0.0420 to 0.0111±0.0183 mmol/milt; P = 0.013. No significant differences were observed between pre-test and 24HR (0.010±0.0124 to 0.0111±0.0183 mmol/milt; P = 0.371. These results indicate that oxidative protein damage, as indicated by PC levels, rises immediately with the onset of anaerobic exercise, but returns to resting levels within 24 hours following exercise in aerobically-trained women.

  5. Efficient and selective α-bromination of carbonyl compounds with N-bromosuccinimide under microwave

    KAUST Repository

    Guan, Xiao-Yu; Al-Misba'a, Zahra; Huang, Kuo-Wei

    2014-01-01

    A highly efficient method for the synthesis of α-halocarbonyl compounds has been achieved via selective monobromination of aromatic and aliphatic carbonyl compounds with N-bromosuccinimide catalyzed by p-toluenesulfonic acid under microwave irradiation within 30 min.

  6. Efficient and selective α-bromination of carbonyl compounds with N-bromosuccinimide under microwave

    KAUST Repository

    Guan, Xiao-Yu

    2014-02-07

    A highly efficient method for the synthesis of α-halocarbonyl compounds has been achieved via selective monobromination of aromatic and aliphatic carbonyl compounds with N-bromosuccinimide catalyzed by p-toluenesulfonic acid under microwave irradiation within 30 min.

  7. Proteomic identification of carbonylated proteins in F344 rat hippocampus after 1-bromopropane exposure

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Zhenlie [Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya 466‐8550 (Japan); Department of Toxicology, Guangdong Prevention and Treatment Center for Occupational Diseases, Guangzhou 510‐300 (China); Ichihara, Sahoko [Graduate School of Regional Innovation Studies, Mie University, Tsu 514‐8507 (Japan); Oikawa, Shinji [Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Mie 514‐8507 (Japan); Chang, Jie; Zhang, Lingyi; Subramanian, Kaviarasan; Mohideen, Sahabudeen Sheik [Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya 466‐8550 (Japan); Ichihara, Gaku, E-mail: gak@med.nagoya-u.ac.jp [Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya 466‐8550 (Japan)

    2012-08-15

    1-Bromopropane (1-BP) is neurotoxic in both experimental animals and humans. Previous proteomic analysis of rat hippocampus implicated alteration of protein expression in oxidative stress, suggesting that oxidative stress plays a role in 1-BP-induced neurotoxicity. To understand this role at the protein level, we exposed male F344 rats to 1-BP at 0, 400, or 1000 ppm for 8 h/day for 1 week or 4 weeks by inhalation and quantitated changes in hippocampal protein carbonyl using a protein carbonyl assay, two-dimensional gel electrophoresis (2-DE), immunoblotting, and matrix-assisted laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF-TOF/MS). Hippocampal reactive oxygen species and protein carbonyl were significantly increased, demonstrating 1-BP-associated induction of oxidative stress and protein damage. MALDI-TOF-TOF/MS identified 10 individual proteins with increased carbonyl modification (p < 0.05; fold-change ≥ 1.5). The identified proteins were involved in diverse biological processes including glycolysis, ATP production, tyrosine catabolism, GTP binding, guanine degradation, and neuronal metabolism of dopamine. Hippocampal triosephosphate isomerase (TPI) activity was significantly reduced and negatively correlated with TPI carbonylation (p < 0.001; r = 0.83). Advanced glycation end-product (AGE) levels were significantly elevated both in the hippocampus and plasma, and hippocampal AGEs correlated negatively with TPI activity (p < 0.001; r = 0.71). In conclusion, 1-BP-induced neurotoxicity in the rat hippocampus seems to involve oxidative damage of cellular proteins, decreased TPI activity, and elevated AGEs. -- Highlights: ► 1-BP increases hippocampal ROS levels and hippocampal and plasma protein carbonyls. ► 1-BP increases TPI carbonylation and decreases TPI activity in the hippocampus. ► 1-BP increases hippocampal and plasma AGE levels.

  8. Deuterium enrichment by selective photo-induced dissociation of an organic carbonyl compound

    International Nuclear Information System (INIS)

    Marling, J.B.

    1981-01-01

    A deuterium-enriched material is produced by selective photoinduced dissociation of a gas phase organic carbonyl compound containing at least one hydrogen atom bonded to an atom adjacent to a carbonyl group. Alkyl carbonyl compounds such as acetone, acetaldehyde, trifluoroacetic acid, cyclobutanone, cyclopentanone, methyl acetate, 3,3-dimethyl-2-butanone, 2,4-pentanedione, and 4-methyl-2-pentanone are preferred. The carbonyl compound is subjected to intense infrared radiation from one laser, or two lasers operating at different frequencies, to selectively dissociate the deuterated molecules into stable products. The undissociated compound may be redeuterated by direct aqueous liquid phase H/D exchange, or by indirect liquid phase exchange using an alkanol in an intermediate step

  9. Role of protein-bound carbonyl groups in the formation of advanced glycation endproducts.

    Science.gov (United States)

    Liggins, J; Furth, A J

    1997-08-22

    Several mechanisms have been postulated for the formation of advanced glycation endproducts (AGEs) from glycated proteins; they all feature protein-bound carbonyl intermediates. Using 2,4-dinitrophenylhydrazine (DNPH), we have detected these intermediates on bovine serum albumin, lysozyme and beta-lactoglobulin after in vitro glycation by glucose or fructose. Carbonyls were formed in parallel with AGE-fluorophores, via oxidative Maillard reactions. Neither Amadori nor Heyns products contributed to the DNPH reaction. Fluorophore and carbonyl yields were much enhanced in lipid-associated proteins, but both groups could also be detected in lipid-free proteins. When pre-glycated proteins were incubated in the absence of free sugar, carbonyl groups were rapidly lost in a first-order reaction, while fluorescence continued to develop beyond the 21 days of incubation. Another unexpected finding was that not all carbonyl groups were blocked by aminoguanidine, although there was complete inhibition of reactions leading to AGE-fluorescence. It is suggested that carbonyls acting as fluorophore precursors react readily with aminoguanidine, while others are resistant to this hydrazine, possibly because they are involved in ring closure. Factors influencing the relative rates of acyclisation and hydrazone formation are discussed, together with possible implications for antiglycation therapy.

  10. Selective transformation of carbonyl ligands to organic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cutler, A.R.

    1992-05-12

    Studies on the carbonylation of ({eta}{sup 5}-indenyl)(L)(CO)Ru-R complexes (L = CO, PPh{sub 3}; R = CH{sub 2}OMe, CH{sub 3}) have been completed. Particularly noteworthy is that the methoxymethyl complexes readily transform to their acyl derivatives under mild conditions that leave their iron congeners inert towards CO. Surprisingly, even ({eta}{sup 5}-indenyl)(PPh{sub 3}){sub 2}Ru-CH{sub 3} carbonylates and gives ({eta}{sup 5}-indenyl)(PPh{sub 3})(CO)Ru-C(O)CH{sub 3}. Mechanistic studies on the non catalyzed'' hydrosilation of the manganese acyls (CO){sub 5}Mn-C(O)CH{sub 2}R (R = H, OCH{sub 3}, CH{sub 3}) with Et{sub 3}SiH and of cobalt acetyls (CO){sub 3}(PR{sub 3})CoC(O)CH{sub 3} with several monohydrosilanes have been completed. The cobalt acetyls cleanly give ethoxysilanes (not acetaldehyde), and the manganese acyls provide {alpha}-siloxyvinyl complexes Z-(CO){sub 5}Mn-C(OSiEt{sub 3})=CHR (R = H, CH{sub 3}, OCH{sub 3}). Carbonylation and protolytic cleavage of the latter generate pyruvoyl complexes (CO){sub 5}Mn-COCOR (R = CH{sub 3}, CH{sub 2}CH{sub 3}), formally the products of net double carbonylation'' sequences. Studies in progress are concerned with how manganese complexes as diverse as (CO){sub 5}Mn-Y (Y = C(O)R, R, BR - but not SiMe{sub 3} or Mn(CO){sub 5}) and ({eta}{sup 3}-C{sub 3}H{sub 5})Mn(CO){sub 2}L (but not CpMn(CO){sub 3} or CpMn(CO){sub 2}({eta}{sup 2}HSiR{sub 3})) function as efficient hydrosilation catalysts towards Cp(CO){sub 2}FeC(O)CH{sub 3}, for example. These reactions cleanly afford fully characterized {alpha}-siloxyethyl complexes Fp-CH(OSiR{sub 3})CH{sub 3} under conditions where typically Rh(1) hydrosilation catalysts are inactive. Several of these manganese complexes also catalytically hydrosilate organic esters, including lactones, to their ethers R-CH{sub 2}OR; these novel ester reductions occur quantitatively at room temperature and appear to be general in scope.

  11. Antioxidative potential of Perna viridis and its protective role against ROS induced lipidperoxidation and protein carbonyl

    Digital Repository Service at National Institute of Oceanography (India)

    Jena, K.B.; Jagtap, T.G.; Verlecar, X.N.

    ) such as hydrogen peroxide (H2O2) and hydroxyl radical (OH•), and inhibition of lipid peroxidation (LPX) and protein carbonyl (PC). The scavenging activity of DPPH radical, H sub(2) O sub(2) and OH• radicals increased in dose dependent manner. The reducing power...

  12. Iron Dextran treatment does not induce serum protein carbonyls in the newborn pig

    Science.gov (United States)

    Oxidation of serum proteins can lead to carbonyl formation which alters their function and is often associated with stress-related diseases. Since it is recommended that all pigs reared in modern production facilities be given supplemental iron at birth to prevent anemia, and metals can catalyze th...

  13. Role of Protein Carbonylation in Skeletal Muscle Mass Loss Associated with Chronic Conditions

    Directory of Open Access Journals (Sweden)

    Esther Barreiro

    2016-05-01

    Full Text Available Muscle dysfunction, characterized by a reductive remodeling of muscle fibers, is a common systemic manifestation in highly prevalent conditions such as chronic heart failure (CHF, chronic obstructive pulmonary disease (COPD, cancer cachexia, and critically ill patients. Skeletal muscle dysfunction and impaired muscle mass may predict morbidity and mortality in patients with chronic diseases, regardless of the underlying condition. High levels of oxidants may alter function and structure of key cellular molecules such as proteins, DNA, and lipids, leading to cellular injury and death. Protein oxidation including protein carbonylation was demonstrated to modify enzyme activity and DNA binding of transcription factors, while also rendering proteins more prone to proteolytic degradation. Given the relevance of protein oxidation in the pathophysiology of many chronic conditions and their comorbidities, the current review focuses on the analysis of different studies in which the biological and clinical significance of the modifications induced by reactive carbonyls on proteins have been explored so far in skeletal muscles of patients and animal models of chronic conditions such as COPD, disuse muscle atrophy, cancer cachexia, sepsis, and physiological aging. Future research will elucidate the specific impact and sites of reactive carbonyls on muscle protein content and function in human conditions.

  14. Age-related carbonylation of fibrocartilage structural proteins drives tissue degenerative modification.

    Science.gov (United States)

    Scharf, Brian; Clement, Cristina C; Yodmuang, Supansa; Urbanska, Aleksandra M; Suadicani, Sylvia O; Aphkhazava, David; Thi, Mia M; Perino, Giorgio; Hardin, John A; Cobelli, Neil; Vunjak-Novakovic, Gordana; Santambrogio, Laura

    2013-07-25

    Aging-related oxidative stress has been linked to degenerative modifications in different organs and tissues. Using redox proteomic analysis and illustrative tandem mass spectrometry mapping, we demonstrate oxidative posttranslational modifications in structural proteins of intervertebral discs (IVDs) isolated from aging mice. Increased protein carbonylation was associated with protein fragmentation and aggregation. Complementing these findings, a significant loss of elasticity and increased stiffness was measured in fibrocartilage from aging mice. Studies using circular dichroism and intrinsic tryptophan fluorescence revealed a significant loss of secondary and tertiary structures of purified collagens following oxidation. Collagen unfolding and oxidation promoted both nonenzymatic and enzymatic degradation. Importantly, induction of oxidative modification in healthy fibrocartilage recapitulated the biochemical and biophysical modifications observed in the aging IVD. Together, these results suggest that protein carbonylation, glycation, and lipoxidation could be early events in promoting IVD degenerative changes. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Nitrite promotes protein carbonylation and Strecker aldehyde formation in experimental fermented sausages: are both events connected?

    Science.gov (United States)

    Villaverde, A; Ventanas, J; Estévez, M

    2014-12-01

    The role played by curing agents (nitrite, ascorbate) on protein oxidation and Strecker aldehyde formation is studied. To fulfill this objective, increasing concentrations of nitrite (0, 75 and 150ppm) and ascorbate (0, 250 and 500ppm) were added to sausages subjected to a 54day drying process. The concurrence of intense proteolysis, protein carbonylation and formation of Strecker aldehydes during processing of sausages suggests that α-aminoadipic semialdehyde (AAS) and γ-glutamic semialdehyde (GGS) may be implicated in the formation of Strecker aldehydes. The fact that nitrite (150ppm, ingoing amount) significantly promoted the formation of protein carbonyls at early stages of processing and the subsequent formation of Strecker aldehydes provides strength to this hypothesis. Ascorbate (125 and 250ppm) controlled the overall extent of protein carbonylation in sausages without declining the formation of Strecker aldehydes. These results may contribute to understanding the chemistry fundamentals of the positive influence of nitrite on the flavor and overall acceptability of cured muscle foods. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Dormancy alleviation by NO or HCN leading to decline of protein carbonylation levels in apple (Malus domestica Borkh.) embryos.

    Science.gov (United States)

    Krasuska, Urszula; Ciacka, Katarzyna; Dębska, Karolina; Bogatek, Renata; Gniazdowska, Agnieszka

    2014-08-15

    Deep dormancy of apple (Malus domestica Borkh.) embryos can be overcome by short-term pre-treatment with nitric oxide (NO) or hydrogen cyanide (HCN). Dormancy alleviation of embryos modulated by NO or HCN and the first step of germination depend on temporary increased production of reactive oxygen species (ROS). Direct oxidative attack on some amino acid residues or secondary reactions via reactive carbohydrates and lipids can lead to the formation of protein carbonyl derivatives. Protein carbonylation is a widely accepted covalent and irreversible modification resulting in inhibition or alteration of enzyme/protein activities. It also increases the susceptibility of proteins to proteolytic degradation. The aim of this work was to investigate protein carbonylation in germinating apple embryos, the dormancy of which was removed by pre-treatment with NO or HCN donors. It was performed using a quantitative spectrophotometric method, while patterns of carbonylated protein in embryo axes were analyzed by immunochemical techniques. The highest concentration of protein carbonyl groups was observed in dormant embryos. It declined in germinating embryos pre-treated with NO or HCN, suggesting elevated degradation of modified proteins during seedling formation. A decrease in the concentration of carbonylated proteins was accompanied by modification in proteolytic activity in germinating apple embryos. A strict correlation between the level of protein carbonyl groups and cotyledon growth and greening was detected. Moreover, direct in vitro carbonylation of BSA treated with NO or HCN donors was analyzed, showing action of both signaling molecules as protein oxidation agents. Copyright © 2014 Elsevier GmbH. All rights reserved.

  17. Selectivity of a heterogeneous rhodium catalyst for the carbonylation of monohydric alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Christensen, B; Scurrell, M S

    1977-01-01

    Selectivity of a heterogeneous rhodium catalyst for the carbonylation of monohydric alcohols with carbon monoxide in the presence of the corresponding alkyl iodides as promotors was studied in a glass reactor at approx. 0.05:1 alcohol/carbon monoxide ratio. The 1% by wt rhodium-zeolite catalyst was prepared by immersing a Linde molecular sieve zeolite Type 13X in rhodium trichloride at 80/sup 0/C for 15 hr. Methanol was converted to methyl acetate at 433/sup 0/-513/sup 0/K with selectivites > 90% even at the highest temperatures, and dimethyl ether was by-produced. In the absence of methyl iodide, the carbonylation rate decreased drastically but the dehydration was virtually unaffected. The selectivity for ethanol carbonylation decreased from 99% at 383/sup 0/K to 6% at 523/sup 0/K due to the formation of ethylene (predominant at > 470/sup 0/K) and diethyl ether. The only product of the reaction with propan-2-ol studied at 433/sup 0/ or 473/sup 0/K was propene with 100% conversion at 473/sup 0/K. These results are consistent with the relative ease of reactant dehydration on polar catalysts. Table and 13 references.

  18. Increased nitration and carbonylation of proteins in MRL +/+ mice exposed to trichloroethene: Potential role of protein oxidation in autoimmunity

    International Nuclear Information System (INIS)

    Wang Gangduo; Wang Jianling; Ma Huaxian; Khan, M. Firoze

    2009-01-01

    Even though reactive oxygen and nitrogen species (RONS) are implicated as mediators of autoimmune diseases (ADs), little is known about contribution of protein oxidation (carbonylation and nitration) in the pathogenesis of such diseases. The focus of this study was, therefore, to establish a link between protein oxidation and induction and/or exacerbation of autoimmunity. To achieve this, female MRL +/+ mice were treated with trichloroethene (TCE), an environmental contaminant known to induce autoimmune response, for 6 or 12 weeks (10 mmol/kg, i.p., every 4 th day). TCE treatment resulted in significantly increased formation of nitrotyrosine (NT) and induction of iNOS in the serum at both 6 and 12 weeks of treatment, but the response was greater at 12 weeks. Likewise, TCE treatment led to greater NT formation, and iNOS protein and mRNA expression in the livers and kidneys. Moreover, TCE treatment also caused significant increases (∼3 fold) in serum protein carbonyls (a marker of protein oxidation) at both 6 and 12 weeks. Significantly increased protein carbonyls were also observed in the livers and kidneys (2.1 and 1.3 fold, respectively) at 6 weeks, and to a greater extent at 12 weeks (3.5 and 2.1 fold, respectively) following TCE treatment. The increases in TCE-induced protein oxidation (carbonylation and nitration) were associated with significant increases in Th1 specific cytokine (IL-2, IFN-γ) release into splenocyte cultures. These results suggest an association between protein oxidation and induction/exacerbation of autoimmune response. The results present a potential mechanism by which oxidatively modified proteins could contribute to TCE-induced autoimmune response and necessitates further investigations for clearly establishing the role of protein oxidation in the pathogenesis of ADs.

  19. Carbonyl carbon transverse relaxation dispersion measurements and ms-{mu}s timescale motion in a protein hydrogen bond network

    Energy Technology Data Exchange (ETDEWEB)

    Ishima, Rieko [National Institute of Dental and Craniofacial Research, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Molecular Structural Biology Unit (United States); Baber, James; Louis, John M.; Torchia, Dennis A. [National Institute of Dental and Craniofacial Research, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Molecular Structural Biology Unit (United States)

    2004-06-15

    A constant-time, Carr-Purcell-Meiboom-Gill (CPMG) transverse relaxation, R{sub 2}, dispersion experiment for carbonyl carbons was designed and executed to detect {mu}s-ms time-scale dynamics of protein backbone carbonyl sites. Because of the large (ca. 55 Hz) C{sub {alpha}}-C' J-coupling, the carbonyl signal intensity is strongly modulated as the spacing between CPMG pulses is varied, in uniformly {sup 13}C enriched proteins, unless care is taken to minimize the perturbation of the C{sub {alpha}} magnetization by the CPMG pulses. CPMG pulse trains consisting of either a band-selective pulse, such as RE-BURP, or rectangular (with an excitation null in the C{sub {alpha}} region of the spectrum) pulses were employed in order to minimize C' signal modulation by C{sub {alpha}}-C' J-coupling. The performance of these types of CPMG refocusing pulses was assessed by computer simulation, and by comparing dispersion profiles measured for (1) uniformly [{sup 13}C,{sup 15}N, {sup 2}H] ({sup 2}H at non-labile hydrogen sites) labeled, and (2) uniformly {sup 15}N/selectively-{sup 13}C' labeled samples of HIV-1 protease bound to a potent inhibitor, DMP323. In addition, because the uniformly {sup 13}C/{sup 15}N/{sup 2}H labeled sample was well suited to measure {sup 15}N and {sup 1}H R{sub 2} dispersion as well as {sup 13}C' dispersion, conformational exchange in the inter subunit {beta}-sheet hydrogen-bond network of the inhibitor-bound protease was elucidated using relaxation dispersion data of all three types of nuclei.

  20. Carbonyl carbon transverse relaxation dispersion measurements and ms-μs timescale motion in a protein hydrogen bond network

    International Nuclear Information System (INIS)

    Ishima, Rieko; Baber, James; Louis, John M.; Torchia, Dennis A.

    2004-01-01

    A constant-time, Carr-Purcell-Meiboom-Gill (CPMG) transverse relaxation, R 2 , dispersion experiment for carbonyl carbons was designed and executed to detect μs-ms time-scale dynamics of protein backbone carbonyl sites. Because of the large (ca. 55 Hz) C α -C' J-coupling, the carbonyl signal intensity is strongly modulated as the spacing between CPMG pulses is varied, in uniformly 13 C enriched proteins, unless care is taken to minimize the perturbation of the C α magnetization by the CPMG pulses. CPMG pulse trains consisting of either a band-selective pulse, such as RE-BURP, or rectangular (with an excitation null in the C α region of the spectrum) pulses were employed in order to minimize C' signal modulation by C α -C' J-coupling. The performance of these types of CPMG refocusing pulses was assessed by computer simulation, and by comparing dispersion profiles measured for (1) uniformly [ 13 C, 15 N, 2 H] ( 2 H at non-labile hydrogen sites) labeled, and (2) uniformly 15 N/selectively- 13 C' labeled samples of HIV-1 protease bound to a potent inhibitor, DMP323. In addition, because the uniformly 13 C/ 15 N/ 2 H labeled sample was well suited to measure 15 N and 1 H R 2 dispersion as well as 13 C' dispersion, conformational exchange in the inter subunit β-sheet hydrogen-bond network of the inhibitor-bound protease was elucidated using relaxation dispersion data of all three types of nuclei

  1. Determination of protein carbonyls in plasma, cell extracts, tissue homogenates, isolated proteins: Focus on sample preparation and derivatization conditions.

    Science.gov (United States)

    Weber, Daniela; Davies, Michael J; Grune, Tilman

    2015-08-01

    Protein oxidation is involved in regulatory physiological events as well as in damage to tissues and is thought to play a key role in the pathophysiology of diseases and in the aging process. Protein-bound carbonyls represent a marker of global protein oxidation, as they are generated by multiple different reactive oxygen species in blood, tissues and cells. Sample preparation and stabilization are key steps in the accurate quantification of oxidation-related products and examination of physiological/pathological processes. This review therefore focuses on the sample preparation processes used in the most relevant methods to detect protein carbonyls after derivatization with 2,4-dinitrophenylhydrazine with an emphasis on measurement in plasma, cells, organ homogenates, isolated proteins and organelles. Sample preparation, derivatization conditions and protein handling are presented for the spectrophotometric and HPLC method as well as for immunoblotting and ELISA. An extensive overview covering these methods in previously published articles is given for researchers who plan to measure protein carbonyls in different samples. © 2015 Published by Elsevier Ltd.

  2. Cross-talk between lipid and protein carbonylation in a dynamic cardiomyocyte model of mild nitroxidative stress

    Directory of Open Access Journals (Sweden)

    Eva Griesser

    2017-04-01

    Full Text Available Reactive oxygen and nitrogen species (ROS/RNS play an important role in the regulation of cardiac function. Increase in ROS/RNS concentration results in lipid and protein oxidation and is often associated with onset and/or progression of many cardiovascular disorders. However, interplay between lipid and protein modifications has not been simultaneously studied in detail so far. Biomolecule carbonylation is one of the most common biomarkers of oxidative stress. Using a dynamic model of nitroxidative stress we demonstrated rapid changes in biomolecule carbonylation in rat cardiomyocytes. Levels of carbonylated species increased as early as 15 min upon treatment with the peroxynitrite donor, 3-morpholinosydnonimine (SIN-1, and decreased to values close to control after 16 h. Total (lipids+proteins vs. protein-specific carbonylation showed different dynamics, with a significant increase in protein-bound carbonyls at later time points. Treatment with SIN-1 in combination with inhibitors of proteasomal and autophagy/lysosomal degradation pathways allowed confirmation of a significant role of the proteasome in the degradation of carbonylated proteins, whereas lipid carbonylation increased in the presence of autophagy/lysosomal inhibitors. Electrophilic aldehydes and ketones formed by lipid peroxidation were identified and relatively quantified using LC-MS/MS. Molecular identity of reactive species was used for data-driven analysis of their protein targets. Combination of different enrichment strategies with LC-MS/MS analysis allowed identification of more than 167 unique proteins with 332 sites modified by electrophilic lipid peroxidation products. Gene ontology analysis of modified proteins demonstrated enrichment of several functional categories including proteins involved in cytoskeleton, extracellular matrix, ion channels and their regulation. Using calcium mobilization assays, the effect of nitroxidative stress on the activity of several ion

  3. Time and dose effects of cigarette smoke and acrolein on protein carbonyl formation in HaCaT keratinocytes.

    Science.gov (United States)

    Avezov, K; Reznick, A Z; Aizenbud, D

    2015-01-01

    Cigarette smoke (CS) is an important environmental source of human exposure to a highly toxic and chemically active α,β-unsaturated aldehyde: acrolein. It is capable of causing protein carbonylation and dysfunction, especially in oral tissues of smokers, constantly exposed to CS toxic constituents. The foremost damage is considered to be cumulative, but even a short exposure can be potentially harmful. The objectives of the current study were to examine the short time and dose effects of direct CS and acrolein exposure on intracellular protein carbonylation in epithelial cells. HaCaT-keratinocytes were exposed to different doses of acrolein and whole phase CS using a unique smoking simulator apparatus that mimics the exposure in smokers. The rate of intracellular protein carbonyl modification was examined 10-60 min after the exposure by Western blot. In addition, the effect of pre-incubation with a thiol scavenger N-acetylcysteine (NAC) was also assessed. We found that intracellular protein carbonyls increased as fast as 10 min after CS exposure and their concentration doubled after 20 min, with a slight elevation afterwards. Also, carbonyl levels increased gradually as CS and acrolein doses were elevated. Addition of 1 mM NAC neutralized part of the damage. We conclude that CS and acrolein intracellular protein carbonylation is dose- and time- dependent. Even a short time exposure to CS and its aldehydic constituents can be potentially harmful.

  4. Comparative Proteomic Analysis of Carbonylated Proteins from the Striatum and Cortex of Pesticide-Treated Mice

    Directory of Open Access Journals (Sweden)

    Christina Coughlan

    2015-01-01

    Full Text Available Epidemiological studies indicate exposures to the herbicide paraquat (PQ and fungicide maneb (MB are associated with increased risk of Parkinson’s disease (PD. Oxidative stress appears to be a premier mechanism that underlies damage to the nigrostriatal dopamine system in PD and pesticide exposure. Enhanced oxidative stress leads to lipid peroxidation and production of reactive aldehydes; therefore, we conducted proteomic analyses to identify carbonylated proteins in the striatum and cortex of pesticide-treated mice in order to elucidate possible mechanisms of toxicity. Male C57BL/6J mice were treated biweekly for 6 weeks with saline, PQ (10 mg/kg, MB (30 mg/kg, or the combination of PQ and MB (PQMB. Treatments resulted in significant behavioral alterations in all treated mice and depleted striatal dopamine in PQMB mice. Distinct differences in 4-hydroxynonenal-modified proteins were observed in the striatum and cortex. Proteomic analyses identified carbonylated proteins and peptides from the cortex and striatum, and pathway analyses revealed significant enrichment in a variety of KEGG pathways. Further analysis showed enrichment in proteins of the actin cytoskeleton in treated samples, but not in saline controls. These data indicate that treatment-related effects on cytoskeletal proteins could alter proper synaptic function, thereby resulting in impaired neuronal function and even neurodegeneration.

  5. Protein conjugated with aldehydes derived from lipid peroxidation as an independent parameter of the carbonyl stress in the kidney damage

    Directory of Open Access Journals (Sweden)

    Medina-Navarro Rafael

    2011-11-01

    Full Text Available Abstract Background One of the well-defined and characterized protein modifications usually produced by oxidation is carbonylation, an irreversible non-enzymatic modification of proteins. However, carbonyl groups can be introduced into proteins by non-oxidative mechanisms. Reactive carbonyl compounds have been observed to have increased in patients with renal failure. In the present work we have described a procedure designed as aldehyde capture to calculate the protein carbonyl stress derived solely from lipid peroxidation. Methods Acrolein-albumin adduct was prepared as standard at alkaline pH. Rat liver microsomal membranes and serum samples from patients with diabetic nephropathy were subjected to the aldehyde capture procedure and aldol-protein formation. Before alkalinization and incubation, samples were precipitated and redisolved in 6M guanidine. The absorbances of the samples were read with a spectrophotometer at 266 nm against a blank of guanidine. Results Evidence showed abundance of unsaturated aldehydes derived from lipid peroxidation in rat liver microsomal membranes and in the serum of diabetic patients with advanced chronic kidney disease. Carbonyl protein and aldol-proteins resulted higher in the diabetic nephropathy patients (p Conclusion The aldehyde-protein adduct represents a non oxidative component of carbonyl stress, independent of the direct amino acid oxidation and could constitute a practical and novelty strategy to measure the carbonyl stress derived solely from lipid peroxidation and particularly in diabetic nephropathy patients. In addition, we are in a position to propose an alternative explanation of why alkalinization of urine attenuates rhabdomyolysis-induced renal dysfunction.

  6. Engineered Trx2p industrial yeast strain protects glycolysis and fermentation proteins from oxidative carbonylation during biomass propagation

    Directory of Open Access Journals (Sweden)

    Gómez-Pastor Rocío

    2012-01-01

    Full Text Available Abstract Background In the yeast biomass production process, protein carbonylation has severe adverse effects since it diminishes biomass yield and profitability of industrial production plants. However, this significant detriment of yeast performance can be alleviated by increasing thioredoxins levels. Thioredoxins are important antioxidant defenses implicated in many functions in cells, and their primordial functions include scavenging of reactive oxygen species that produce dramatic and irreversible alterations such as protein carbonylation. Results In this work we have found several proteins specifically protected by yeast Thioredoxin 2 (Trx2p. Bidimensional electrophoresis and carbonylated protein identification from TRX-deficient and TRX-overexpressing cells revealed that glycolysis and fermentation-related proteins are specific targets of Trx2p protection. Indeed, the TRX2 overexpressing strain presented increased activity of the central carbon metabolism enzymes. Interestingly, Trx2p specifically preserved alcohol dehydrogenase I (Adh1p from carbonylation, decreased oligomer aggregates and increased its enzymatic activity. Conclusions The identified proteins suggest that the fermentative capacity detriment observed under industrial conditions in T73 wine commercial strain results from the oxidative carbonylation of specific glycolytic and fermentation enzymes. Indeed, increased thioredoxin levels enhance the performance of key fermentation enzymes such as Adh1p, which consequently increases fermentative capacity.

  7. Characterization of selected volatile organic compounds, polycyclic aromatic hydrocarbons and carbonyl compounds at a roadside monitoring station

    Science.gov (United States)

    Ho, K. F.; Lee, S. C.; Chiu, Gloria M. Y.

    Volatile organic compounds (VOCs), PAHs and carbonyl compounds are the major toxic components in Hong Kong. Emissions from motor vehicles have been one of the primary pollution sources in the metropolitan areas throughout Hong Kong for a long time. A 1-yr monitoring program for VOCs, PAHs and carbonyl compounds had been performed at a roadside urban station at Hong Kong Polytechnic University in order to determine the variations and correlations of each selected species (VOCs, PAHs and carbonyl compounds). This study is aimed to analyze toxic volatile organic compounds (benzene, toluene, ethylbenzene and xylene), two carbonyl compounds (formaldehyde, acetaldehyde), and selective polycyclic aromatic hydrocarbons. The monitoring program started from 16 April 1999 to 30 March 2000. Ambient VOC concentrations, many of which originate from the same sources as particulate PAHs and carbonyls compounds, show significant quantities of benzene, toluene and xylenes. Correlations and multivariate analysis of selected gaseous and particulate phase organic pollutants were performed. Source identification by principle component analysis and hierarchical cluster analysis allowed the identification of four sources (factors) for the roadside monitoring station. Factor 1 represents the effect of diesel vehicle exhaust. Factor 2 shows the contribution of aromatic compounds. Factor 3 explains photochemical products—formaldehyde and acetaldehyde. Factor 4 explains the effect of gasoline vehicle exhaust.

  8. Serum levels of carbonylated and nitrosylated proteins in mobbing victims with workplace adjustment disorders.

    Science.gov (United States)

    Di Rosa, A E; Gangemi, S; Cristani, M; Fenga, C; Saitta, S; Abenavoli, E; Imbesi, S; Speciale, A; Minciullo, P L; Spatari, G; Abbate, S; Saija, A; Cimino, F

    2009-12-01

    Today the most important problem in the work place is psychological abuse, which may affect the health because of high levels of stress and anxiety. There is evidence that most psychiatric disorders are associated with increased oxidative stress but nothing is reported about the presence of oxidative stress in mobbing victims. This study has been carried out in a group of 19 patients affected by workplace mobbing-due adjustment disorders, in comparison with 38 healthy subjects, to evaluate whether oxidative stress may be induced by mobbing. Serum levels of protein carbonyl groups and of nitrosylated proteins, biological markers of oxidative stress conditions, were higher than those measured in healthy subjects. These findings may contribute to a better understanding of the redox homeostasis dysregulation occurring in victims of workplace mobbing.

  9. Inactivation of cellular enzymes by carbonyls and protein-bound glycation/glycoxidation products

    DEFF Research Database (Denmark)

    Morgan, Philip E; Dean, Roger T; Davies, Michael Jonathan

    2002-01-01

    products. In this study, we have examined the effect of glucose and carbonyl compounds (methylglyoxal, glyoxal, glycolaldehyde, and hydroxyacetone), and glycation products arising from reaction of these materials with model proteins, on the activity of three key cellular enzymes: glyceraldehyde-3-phosphate...... dehydrogenase (GAPDH), glutathione reductase, and lactate dehydrogenase, both in isolation and in cell lysates. In contrast to glucose (1M, both fresh and aged for 8 weeks), which had no effect, marked inhibition of all three enzymes was observed with methylglyoxal and glyoxal. GAPDH was also inhibited...... by glycolaldehyde and hydroxyacetone. Incubation of these enzymes with proteins that had been preglycated with methylglyoxal, but not glucose, also resulted in significant time- and concentration-dependent inhibition with both isolated enzymes and cell lysates. This inhibition was not metal ion, oxygen, superoxide...

  10. Fish proteins as targets of ferrous-catalyzed oxidation: identification of protein carbonyls by fluorescent labeling on two-dimensional gels and MALDI-TOF/TOF mass spectrometry.

    Science.gov (United States)

    Pazos, Manuel; da Rocha, Angela Pereira; Roepstorff, Peter; Rogowska-Wrzesinska, Adelina

    2011-07-27

    Protein oxidation in fish meat is considered to affect negatively the muscle texture. An important source of free radicals taking part in this process is Fenton's reaction dependent on ferrous ions present in the tissue. The aim of this study was to investigate the susceptibility of cod muscle proteins in sarcoplasmic and myofibril fractions to in vitro metal-catalyzed oxidation and to point out protein candidates that might play a major role in the deterioration of fish quality. Extracted control proteins and proteins subjected to free radicals generated by Fe(II)/ascorbate mixture were labeled with fluorescein-5-thiosemicarbazide (FTSC) to tag carbonyl groups and separated by two-dimensional gel electrophoresis. Consecutive visualization of protein carbonyl levels by capturing the FTSC signal and total protein levels by capturing the SyproRuby staining signal allowed us to quantify the relative change in protein carbonyl levels corrected for changes in protein content. Proteins were identified using MALDI-TOF/TOF mass spectrometry and homology-based searches. The results show that freshly extracted cod muscle proteins exhibit a detectable carbonylation background and that the incubation with Fe(II)/ascorbate triggers a further oxidation of both sarcoplasmic and myofibril proteins. Different proteins exhibited various degrees of sensitivity to oxidation processes. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), nucleoside diphosphate kinase B (NDK), triosephosphate isomerase, phosphoglycerate mutase, lactate dehydrogenase, creatine kinase, and enolase were the sarcoplasmic proteins most vulnerable to ferrous-catalyzed oxidation. Moreover, NDK, phosphoglycerate mutase, and GAPDH were identified in several spots differing by their pI, and those forms showed different susceptibilities to metal-catalyzed oxidation, indicating that post-translational modifications may change the resistance of proteins to oxidative damage. The Fe(II)/ascorbate treatment significantly

  11. Selectivity control of carbonylation of methanol to dimethyl oxalate and dimethyl carbonate over gold anode by electrochemical potential.

    Science.gov (United States)

    Funakawa, Akiyasu; Yamanaka, Ichiro; Takenaka, Sakae; Otsuka, Kiyoshi

    2004-05-05

    New and unique electrocatalysis of gold for the carbonylation of methanol to dimethyl oxalate (DMO) and dimethyl carbonate (DMC) was found. The selectivity to DMO and DMC could be controlled over gold anode by electrochemical potential, as you like. Drastic changes of gold electrocatalysis was due to changes of the oxidation state of gold, Au0 or Au3+.

  12. Levels of protein hydroperoxides and carbonyl groups in guinea pigs native of high altitudes (Huancavelica, 3660 m)

    OpenAIRE

    Huayta, Roxana; Zúñiga, Haydée; Esquerre, Cynthia; Hernández, Luz; Carranza, Elizabeth

    2014-01-01

    The influence of hypobaric hypoxia on protein oxidation in lungs, heart, liver, kidneys and testicles of high altitude native guinea pigs (Huancavelica, 3660 m) in comparison to sea level (Lima, 150 m) native guinea pigs was evaluated. The concentration of protein hydroperoxides (POOH) and carbonyl groups (GC) as markers of protein oxidation, as well as total thiols (TT) concentration, powerful reducing agents that act as live antioxidants were determined. The results showed low concentration...

  13. Protein carbonyl content: a novel biomarker for aging in HIV/AIDS patients

    Directory of Open Access Journals (Sweden)

    Vaishali Kolgiri

    2017-01-01

    Conclusions: Carbonyl content may has a role as a biomarker for detecting oxidative DNA damage induced ART toxicity and/or accelerated aging in HIV/AIDS patients. Larger studies are warranted to elucidate the role of carbonyl content as a biomarker for premature aging in HIV/AIDS patients.

  14. Protein carbonyl: An oxidative stress marker in gingival crevicular fluid in healthy, gingivitis, and chronic periodontitis subjects

    Directory of Open Access Journals (Sweden)

    Avani R Pradeep

    2013-01-01

    Full Text Available Background: A defined role for reactive oxygen species (ROS in the tissue destruction that characterizes periodontitis has been described. Protein carbonyl (PC is the most widely used biomarker for oxidative damage to proteins, and reflects cellular damage induced by multiple forms of ROS. The purpose of this study is to determine the presence of PC in gingival crevicular fluid (GCF in healthy, gingivitis, and chronic periodontitis (CP subjects and to find an association, if any. Materials and Methods: A total number of 75 subjects (38 males and 37 females were selected based on their clinical parameters into three groups: Group 1 (25 healthy subjects, Group 2 (25 gingivitis subjects, and Group 3 (25 CP subjects. GCF samples were collected to estimate the levels of PC. Results: The PC concentration in GCF was highest in subjects with CP as compared to gingivitis and healthy subjects and a significant association was observed between GCF PC levels and all periodontal parameters. Conclusion: There was an increase in PC levels in GCF as the disease process progressed from healthy to gingivitis and CP, suggesting a role for increased oxidative stress in CP.

  15. The influence of oscillations on product selectivity during the palladium-catalysed phenylacetylene oxidative carbonylation reaction.

    Science.gov (United States)

    Novakovic, Katarina; Grosjean, Christophe; Scott, Stephen K; Whiting, Andrew; Willis, Mark J; Wright, Allen R

    2008-02-07

    This paper reports on the influence of oscillations on product selectivity as well as the dynamics of product formation during the palladium-catalysed phenylacetylene oxidative carbonylation reaction in a catalytic system (PdI2, KI, Air, NaOAc in methanol). The occurrence of the pH oscillations is related to PdI2 granularity and the initial pH drop after phenylacetylene addition. To achieve pH and reaction exotherm oscillations regulation of the amount of PdI2 is required, ensuring that the initial pH does not fall significantly below 1 after phenylacetylene addition. Experiments in both oscillatory and non-oscillatory pH regimes were performed in an HEL SIMULAR reaction calorimeter with the concentration-time profiles measured using a GC-MS. It is demonstrated that when operating in an oscillatory pH regime product formation may be suppressed until oscillations occur after which there is a steep increase in the formation of Z-2-phenyl-but-2-enedioic acid dimethyl ester. When operating in non-oscillatory pH mode the products are formed steadily over time with the main products being Z-2-phenyl-but-2-enedioic acid dimethyl ester, 2-phenyl-acrylic acid methyl ester and E-3-phenyl-acrylic acid methyl ester.

  16. The Effect of Temperature on Selectivity in the Oscillatory Mode of the Phenylacetylene Oxidative Carbonylation Reaction.

    Science.gov (United States)

    Parker, Julie; Novakovic, Katarina

    2017-08-05

    Reaction temperature plays a major role in product selectivity in the oscillatory mode of the palladium-catalyzed phenylacetylene oxidative carbonylation reaction. At 40 °C, dimethyl (2Z)-2-phenyl-2-butenedioate is the major product whereas at 0 °C the major product is 5,5-dimethoxy-3-phenyl-2(5H)-furanone. The occurrence of oscillations in pH coincides with an increase in the rate of phenylacetylene consumption and associated product formation. Experiments were performed isothermally in a reaction calorimeter to correlate reactant consumption and product formation with the occurrence of pH oscillations and the heat released by the reaction. An increase in the size of the pH drop in a single oscillation correlates with an increase in energy, indicating that this section of a single oscillation relates to reactant consumption. Based on these observations, a reaction pathway responsible for product formation is provided. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  17. Ester carbonyl vibration as a sensitive probe of protein local electric field.

    Science.gov (United States)

    Pazos, Ileana M; Ghosh, Ayanjeet; Tucker, Matthew J; Gai, Feng

    2014-06-10

    The ability to quantify the local electrostatic environment of proteins and protein/peptide assemblies is key to gaining a microscopic understanding of many biological interactions and processes. Herein, we show that the ester carbonyl stretching vibration of two non-natural amino acids, L-aspartic acid 4-methyl ester and L-glutamic acid 5-methyl ester, is a convenient and sensitive probe in this regard, since its frequency correlates linearly with the local electrostatic field for both hydrogen-bonding and non-hydrogen-bonding environments. We expect that the resultant frequency-electric-field map will find use in various applications. Furthermore, we show that, when situated in a non-hydrogen-bonding environment, this probe can also be used to measure the local dielectric constant (ε). For example, its application to amyloid fibrils formed by Aβ(16-22) revealed that the interior of such β-sheet assemblies has an ε value of approximately 5.6. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Analysis of protein oxidation in serum of fetal and newborn piglets and the influence of iron dextran on induction of protein carbonyls.

    Science.gov (United States)

    Methods were employed to evaluate serum biomarkers associated with protein oxidative stress and damage, to determine potential sources of metabolic stress in baby pigs. Protein carbonyls in serum were converted to dinitrophenyl (DNP) derivatives with DNP-hydrazine, precipitated with TCA, extracted i...

  19. Conduction properties of KcsA measured using brownian dynamics with flexible carbonyl groups in the selectivity filter.

    Science.gov (United States)

    Chung, Shin-Ho; Corry, Ben

    2007-07-01

    In the narrow segment of an ion conducting pathway, it is likely that a permeating ion influences the positions of the nearby atoms that carry partial or full electronic charges. Here we introduce a method of incorporating the motion of charged atoms lining the pore into Brownian dynamics simulations of ion conduction. The movements of the carbonyl groups in the selectivity filter of the KcsA channel are calculated explicitly, allowing their bond lengths, bond angles, and dihedral angels to change in response to the forces acting upon them. By systematically changing the coefficients of bond stretching and of angle bending, the carbon and oxygen atoms can be made to fluctuate from their fixed positions by varying mean distances. We show that incorporating carbonyl motion in this way does not alter the mechanism of ion conduction and only has a small influence on the computed current. The slope conductance of the channel increases by approximately 25% when the root mean-square fluctuations of the carbonyl groups are increased from 0.01 to 0.61 A. The energy profiles and the number of resident ions in the channel remain unchanged. The method we utilized here can be extended to allow the movement of glutamate or aspartate side chains lining the selectivity filters of other ionic channels.

  20. Selective transformation of carbonyl ligands to organic molecules. Progress report, September 1, 1989--November 14, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Cutler, A.R.

    1992-05-12

    Studies on the carbonylation of ({eta}{sup 5}-indenyl)(L)(CO)Ru-R complexes (L = CO, PPh{sub 3}; R = CH{sub 2}OMe, CH{sub 3}) have been completed. Particularly noteworthy is that the methoxymethyl complexes readily transform to their acyl derivatives under mild conditions that leave their iron congeners inert towards CO. Surprisingly, even ({eta}{sup 5}-indenyl)(PPh{sub 3}){sub 2}Ru-CH{sub 3} carbonylates and gives ({eta}{sup 5}-indenyl)(PPh{sub 3})(CO)Ru-C(O)CH{sub 3}. Mechanistic studies on the ``non catalyzed`` hydrosilation of the manganese acyls (CO){sub 5}Mn-C(O)CH{sub 2}R (R = H, OCH{sub 3}, CH{sub 3}) with Et{sub 3}SiH and of cobalt acetyls (CO){sub 3}(PR{sub 3})CoC(O)CH{sub 3} with several monohydrosilanes have been completed. The cobalt acetyls cleanly give ethoxysilanes (not acetaldehyde), and the manganese acyls provide {alpha}-siloxyvinyl complexes Z-(CO){sub 5}Mn-C(OSiEt{sub 3})=CHR (R = H, CH{sub 3}, OCH{sub 3}). Carbonylation and protolytic cleavage of the latter generate pyruvoyl complexes (CO){sub 5}Mn-COCOR (R = CH{sub 3}, CH{sub 2}CH{sub 3}), formally the products of net ``double carbonylation`` sequences. Studies in progress are concerned with how manganese complexes as diverse as (CO){sub 5}Mn-Y [Y = C(O)R, R, BR - but not SiMe{sub 3} or Mn(CO){sub 5}] and ({eta}{sup 3}-C{sub 3}H{sub 5})Mn(CO){sub 2}L [but not CpMn(CO){sub 3} or CpMn(CO){sub 2}({eta}{sup 2}HSiR{sub 3})] function as efficient hydrosilation catalysts towards Cp(CO){sub 2}FeC(O)CH{sub 3}, for example. These reactions cleanly afford fully characterized {alpha}-siloxyethyl complexes Fp-CH(OSiR{sub 3})CH{sub 3} under conditions where typically Rh(1) hydrosilation catalysts are inactive. Several of these manganese complexes also catalytically hydrosilate organic esters, including lactones, to their ethers R-CH{sub 2}OR; these novel ester reductions occur quantitatively at room temperature and appear to be general in scope.

  1. Determination of protein-carbonyls and ubiquitin-mediated proteolysis as biomarkers of oxidative-stress in bivalvia and anthozoa

    International Nuclear Information System (INIS)

    Walker, Stephen Thomas

    2002-01-01

    This study describes the investigation of biomarkers of oxidative-stress in the bivalves Mytilus edulis and Dosinia lupinus, together with host and symbiont tissues of the scleractinian Anthozoa Agaricia agaricites. The biomarkers used were assay of total (via spectrophotometry) and individual (via Western blotting; Oxyblot kit) protein-carbonyls (PC=Os) and content of ubiquitin protein conjugates (UPC) via Western blotting (Bivalvia and Anthozoa) and immunohistochemistry (Anthozoa only). Additional assays for Bivalvia were Trolox equivalent antioxidant capacity (TEAC); and post γ-irradiation survival rates. Experimental stressors for Bivalvia were increased seawater temperature, H 2 O 2 and 60 Co γ-radiation (latter two were used in vivo and in vitro). Comparisons of clean and polluted marine sites are included. Stressors used for Anthozoa were increased solar irradiation concomitant with elevated seawater temperature. Results and conclusions were as follows: individual samples showed considerable variation, pooling of samples improved consistency. Controls for both biomarkers had detectable background levels in each phylum, against which relatively small differences were assessed. In M. edulis, no measurable differences in PC=Os could be determined when elevated seawater temperature or dilute H 2 O 2 ( 2 O 2 (30% v/v) produced a small difference. 60 Co γ-radiation produced clearer differences via Oxyblot and spectrophotometric assays. Comparison of four different tissues from the two bivalves found considerable species-specific and tissue-specific differences. Post-irradiation mortality between species was significantly different (<0.001), D. lupinus was more susceptible than M. edulis. TEAC values generally showed a decrease following irradiation (except for digestive gland). UPCs were clearly different between tissues and between species. PC=Os can be detected by DNPH-reactivity/Western blotting assay in host A. agaricites. UPCs can be assayed via Western

  2. Determination of protein-carbonyls and ubiquitin-mediated proteolysis as biomarkers of oxidative-stress in bivalvia and anthozoa

    Energy Technology Data Exchange (ETDEWEB)

    Walker, Stephen Thomas

    2002-07-01

    This study describes the investigation of biomarkers of oxidative-stress in the bivalves Mytilus edulis and Dosinia lupinus, together with host and symbiont tissues of the scleractinian Anthozoa Agaricia agaricites. The biomarkers used were assay of total (via spectrophotometry) and individual (via Western blotting; Oxyblot kit) protein-carbonyls (PC=Os) and content of ubiquitin protein conjugates (UPC) via Western blotting (Bivalvia and Anthozoa) and immunohistochemistry (Anthozoa only). Additional assays for Bivalvia were Trolox equivalent antioxidant capacity (TEAC); and post {gamma}-irradiation survival rates. Experimental stressors for Bivalvia were increased seawater temperature, H{sub 2}O{sub 2} and {sup 60}Co {gamma}-radiation (latter two were used in vivo and in vitro). Comparisons of clean and polluted marine sites are included. Stressors used for Anthozoa were increased solar irradiation concomitant with elevated seawater temperature. Results and conclusions were as follows: individual samples showed considerable variation, pooling of samples improved consistency. Controls for both biomarkers had detectable background levels in each phylum, against which relatively small differences were assessed. In M. edulis, no measurable differences in PC=Os could be determined when elevated seawater temperature or dilute H{sub 2}O{sub 2} (<30% v/v) stressors were used, nor with between-site comparisons. Concentrated H{sub 2}O{sub 2} (30% v/v) produced a small difference. {sup 60}Co {gamma}-radiation produced clearer differences via Oxyblot and spectrophotometric assays. Comparison of four different tissues from the two bivalves found considerable species-specific and tissue-specific differences. Post-irradiation mortality between species was significantly different (<0.001), D. lupinus was more susceptible than M. edulis. TEAC values generally showed a decrease following irradiation (except for digestive gland). UPCs were clearly different between tissues and

  3. Selective transformation of carbonyl ligands to organic molecules: Progress report, 1 September 1986--31 August 1989

    Energy Technology Data Exchange (ETDEWEB)

    Cutler, A.R.

    1989-04-18

    Studies on anionic phosphido alkyl and acetyl complexes Cp(CO)(PPh/sub 2/)Fe /minus/ R/sup /minus// (1) and In(CO)(PPh/sub 2/)Fe /minus/ R/sup /minus// (2) (R = CH/sub 3/ (a), COCH/sub 3/ (b); In = /eta//sup 5/-indenyl) and their neutral phosphine derivatives Cp(CO)(PPh/sub 2/H)Fe /minus/ R (3) and In(CO)(PPh/sub 2/H)Fe /minus/ R (4) are complete. Attempts to carbonylate 1a and 2a to 1b and 2b failed; also, 3a and 4a resist carbonylation. Reacting 1b with MeI affords a neutral PPh/sub 2/Me acetyl compound 5, whereas MeOSO/sub 2/CF/sub 3/ gives the Fischer carbene complex Cp(PPh/sub 2/)(CO) Fe = C(OMe)CH/sub 3/ (6). Carbene 6 isomerizes to 5 at room temperature. Reaction conditions have been optimized for tenerating vinylidene compounds In/sub 2/(CO)/sub 3/Fe/sub 2/ ..mu..-(C = CHR) from InFe(CO)/sub 2//sup /minus// and In(CO)/sub 2/Fe /minus/ CH/sub 2/R (R = H, Me, OMe). The bimetallic carbonylation procedure for converting Fp/sup /minus//(Li/sup +/, Na/sup +/, PPN/sup +/) and In(CO)/sub 2/Fe /minus/ CH/sub 3/ to InCp(CO)/sub 3/Fe/sub 2/(COCH/sub 3//sup /minus//) and then regioselectively to FpCOCH/sub 3/ (1 atm CO) has been optimized. Studies are finished on the diastereofacial selectivity observed during reduction of the alkoxycarbenes Cp(P(OR)/sub 3/)(CO)Fe = C(OCH/sub 3/)CH/sub 3//sup +/ (R = Me, Ph) with borohydride reagents R/sub 3/BH/sup /minus// (Li/sup +/, Na/sup +/, K/sup +/) and with (PPh/sub 3/CuH)/sub 6/. A survey of the Rh(I)-catalyzed hydrosilation of a variety of iron acyl complexes has been concluded.

  4. Aldo-keto reductase family 1 B10 protein detoxifies dietary and lipid-derived alpha, beta-unsaturated carbonyls at physiological levels

    International Nuclear Information System (INIS)

    Zhong, Linlin; Liu, Ziwen; Yan, Ruilan; Johnson, Stephen; Zhao, Yupei; Fang, Xiubin; Cao, Deliang

    2009-01-01

    Alpha, beta-unsaturated carbonyls are highly reactive mutagens and carcinogens to which humans are exposed on a daily basis. This study demonstrates that aldo-keto reductase family 1 member B10 (AKR1B10) is a critical protein in detoxifying dietary and lipid-derived unsaturated carbonyls. Purified AKR1B10 recombinant protein efficiently catalyzed the reduction to less toxic alcohol forms of crotonaldehyde at 0.90 μM, 4-hydroxynonenal (HNE) at 0.10 μM, trans-2-hexanal at 0.10 μM, and trans-2,4-hexadienal at 0.05 μM, the concentrations at or lower than physiological exposures. Ectopically expressed AKR1B10 in 293T cells eliminated immediately HNE at 1 (subtoxic) or 5 μM (toxic) by converting to 1,4-dihydroxynonene, protecting the cells from HNE toxicity. AKR1B10 protein also showed strong enzymatic activity toward glutathione-conjugated carbonyls. Taken together, our study results suggest that AKR1B10 specifically expressed in the intestine is physiologically important in protecting the host cell against dietary and lipid-derived cytotoxic carbonyls.

  5. Recent advances in efficient and selective synthesis of di-, tri-, and tetrasubstituted alkenes via Pd-catalyzed alkenylation-carbonyl olefination synergy.

    Science.gov (United States)

    Negishi, Ei-ichi; Huang, Zhihong; Wang, Guangwei; Mohan, Swathi; Wang, Chao; Hattori, Hatsuhiko

    2008-11-18

    Although generally considered competitive, the alkenylation and carbonyl olefination routes to alkenes are also complementary. In this Account, we focus on these approaches for the synthesis of regio- and stereodefined di- and trisubstituted alkenes and a few examples of tetrasubstituted alkenes. We also discuss the subset of regio- and stereodefined dienes and oligoenes that are conjugated. Pd-catalyzed cross-coupling using alkenyl metals containing Zn, Al, Zr, and B (Negishi coupling and Suzuki coupling) or alkenyl halides and related alkenyl electrophiles provides a method of alkenylation with the widest applicability and predictability, with high stereo- and regioselectivity. The requisite alkenyl metals or alkenyl electrophiles are most commonly prepared through highly selective alkyne addition reactions including (i) conventional polar additions, (ii) hydrometalation, (iii) carbometalation, (iv) halometalation, and (v) other heteroatom-metal additions. Although much more limited in applicability, the Heck alkenylation offers an operationally simpler, viable alternative when it is highly selective and satisfactory. A wide variety of carbonyl olefination reactions, especially the Wittig olefination and its modifications represented by the E-selective HWE olefination and the Z-selective Still-Gennari olefination, collectively offer the major alternative to the Pd-catalyzed alkenylation. However, the carbonyl olefination method fundamentally suffers from more limited stereochemical options and generally lower stereoselectivity levels than the Pd-catalyzed alkenylation. In a number of cases, however, very high (>98%) stereoselectivity levels have been attained in the syntheses of both E and Z isomers. The complementarity of the alkenylation and carbonyl olefination routes provide synthetic chemists with valuable options. While the alkenylation involves formation of a C-C single bond to a CC bond, the carbonyl olefination converts a CO bond to a CC bond. When a

  6. Enzyme-like specificity in zeolites: a unique site position in mordenite for selective carbonylation of methanol and dimethyl ether with CO.

    Science.gov (United States)

    Boronat, Mercedes; Martínez-Sánchez, Cristina; Law, David; Corma, Avelino

    2008-12-03

    The mechanism of methanol carbonylation at different positions of zeolite MOR is investigated by quantum-chemical methods in order to discover which are the active sites that can selectively catalyze the desired reaction. It is shown that when methanol carbonylation competes with hydrocarbon formation, the first reaction occurs preferentially within 8MR channels. However, the unique selectivity for the carbonylation of methanol and dimethyl ether in mordenite is not only due to the size of the 8MR channel: neither process occurs equally at the two T3-O31 and T3-O33 positions. We show that only the T3-O33 positions are selective and that this selectivity is due to the unusual orientation of the methoxy group in relation to the 8MR channel (parallel to the cylinder axis). Only in this situation does the transition state for the attack of CO fit perfectly in the 8MR channel, while the reaction with methanol or DME is sterically impeded. This result explains why T3-O31, while also located in the 8MR channel of mordenite, is not as selective as the T3-O33 position and why ferrierite, although it contains 8MR channels, is less selective than mordenite. The competing effect of water is explained at the molecular level, and the molecular microkinetic reaction model has been established.

  7. DNA damage by carbonyl stress in human skin cells

    International Nuclear Information System (INIS)

    Roberts, Michael J.; Wondrak, Georg T.; Laurean, Daniel Cervantes; Jacobson, Myron K.; Jacobson, Elaine L.

    2003-01-01

    Reactive carbonyl species (RCS) are potent mediators of cellular carbonyl stress originating from endogenous chemical processes such as lipid peroxidation and glycation. Skin deterioration as observed in photoaging and diabetes has been linked to accumulative protein damage from glycation, but the effects of carbonyl stress on skin cell genomic integrity are ill defined. In this study, the genotoxic effects of acute carbonyl stress on HaCaT keratinocytes and CF3 fibroblasts were assessed. Administration of the α-dicarbonyl compounds glyoxal and methylglyoxal as physiologically relevant RCS inhibited skin cell proliferation, led to intra-cellular protein glycation as evidenced by the accumulation of N ε -(carboxymethyl)-L-lysine (CML) in histones, and caused extensive DNA strand cleavage as assessed by the comet assay. These effects were prevented by treatment with the carbonyl scavenger D-penicillamine. Both glyoxal and methylglyoxal damaged DNA in intact cells. Glyoxal caused DNA strand breaks while methylglyoxal produced extensive DNA-protein cross-linking as evidenced by pronounced nuclear condensation and total suppression of comet formation. Glycation by glyoxal and methylglyoxal resulted in histone cross-linking in vitro and induced oxygen-dependent cleavage of plasmid DNA, which was partly suppressed by the hydroxyl scavenger mannitol. We suggest that a chemical mechanism of cellular DNA damage by carbonyl stress occurs in which histone glycoxidation is followed by reactive oxygen induced DNA stand breaks. The genotoxic potential of RCS in cultured skin cells and its suppression by a carbonyl scavenger as described in this study have implications for skin damage and carcinogenesis and its prevention by agents selective for carbonyl stress

  8. DNA damage by carbonyl stress in human skin cells

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, Michael J.; Wondrak, Georg T.; Laurean, Daniel Cervantes; Jacobson, Myron K.; Jacobson, Elaine L

    2003-01-28

    Reactive carbonyl species (RCS) are potent mediators of cellular carbonyl stress originating from endogenous chemical processes such as lipid peroxidation and glycation. Skin deterioration as observed in photoaging and diabetes has been linked to accumulative protein damage from glycation, but the effects of carbonyl stress on skin cell genomic integrity are ill defined. In this study, the genotoxic effects of acute carbonyl stress on HaCaT keratinocytes and CF3 fibroblasts were assessed. Administration of the {alpha}-dicarbonyl compounds glyoxal and methylglyoxal as physiologically relevant RCS inhibited skin cell proliferation, led to intra-cellular protein glycation as evidenced by the accumulation of N{sup {epsilon}}-(carboxymethyl)-L-lysine (CML) in histones, and caused extensive DNA strand cleavage as assessed by the comet assay. These effects were prevented by treatment with the carbonyl scavenger D-penicillamine. Both glyoxal and methylglyoxal damaged DNA in intact cells. Glyoxal caused DNA strand breaks while methylglyoxal produced extensive DNA-protein cross-linking as evidenced by pronounced nuclear condensation and total suppression of comet formation. Glycation by glyoxal and methylglyoxal resulted in histone cross-linking in vitro and induced oxygen-dependent cleavage of plasmid DNA, which was partly suppressed by the hydroxyl scavenger mannitol. We suggest that a chemical mechanism of cellular DNA damage by carbonyl stress occurs in which histone glycoxidation is followed by reactive oxygen induced DNA stand breaks. The genotoxic potential of RCS in cultured skin cells and its suppression by a carbonyl scavenger as described in this study have implications for skin damage and carcinogenesis and its prevention by agents selective for carbonyl stress.

  9. 50 Hz electric field effects on protein carbonyl (PCO), heme oxygenase-1 (HO-1) and hydroxyproline levels

    International Nuclear Information System (INIS)

    Ozgur, Elcin; Goknur, Guler; Seyhan, Nesrin

    2008-01-01

    Full text: Non-ionizing electromagnetic field (EMF) radiation sources, such as power lines and other Extremely Low Frequency (ELF) sources have become one of the most ubiquitous components of the spectrum of the human environment, and the possibility that they may have hazardous effects on human health is a major a public concern. Although it is well documented that EMFs have biological effects, the degree to which these exposures constitute a human health hazard is not clear yet. Today relation between production of oxidative stress resulted by reactive oxygen species and electrical stimulus, also the protective effects of antioxidant treatments are mentioned in many researches. In this study, it was aimed to determine both oxidation of proteins and protein collagen levels under 50 Hz 12 kV/m vertical Electric (E) Field exposure and the N-Acetylcysteine (NAC) administration which is a well-known antioxidant. To this end, protein carbonyl levels (PCO) as bio-markers of oxidative stress and Heme oxygenase-1 (HO-1), an enzyme that catalyzes the degradation of heme analyzed to figure out the protein oxidation. Hydroxyproline level, a major component of the protein collagen was measured in order to express the level of collagen in lung tissue. Guinea pigs, weighted 250-300 g, were used in the study. A total forty male guinea pigs were randomly divided into four groups which are composed of 10 guinea pigs each for groups: 1) Group I (Sham); 2) Group II (NAC-administrated group); 3) Group III (E Field Exposure group); 4) Group IV (NAC administrated + E Field exposed group). One week exposure period for 8 hours per daily was conducted for each exposure groups (Group III, Group IV ). The electric field exposure period was from 9 a.m. to 5 p.m. After the last exposure day, the guinea pigs were anesthetized by the injection of ketamine and xylazine. The guinea pigs were killed by decapitation. Statistical analyses were carried out using SPSS software (SPSS 11.5 for windows

  10. Binding of carbonyl flavours to canola, pea and wheat proteins using GC/MS approach.

    Science.gov (United States)

    Wang, Kun; Arntfield, Susan D

    2014-08-15

    Interactions of homologous aldehydes (hexanal, heptanal, and octanal) and ketones (2-hexanone, 2-heptanone, and 2-octanone) to salt and alkaline-extracted canola and pea proteins and commercial wheat gluten were studied using GC/MS. Long-chain aldehyde flavours exhibited higher binding affinity, regardless of protein type and isolation method. Salt-extracted canola protein isolates (CPIs) revealed the highest binding capacity to all aldehydes followed by wheat gluten and salt-extracted pea protein isolates (PPIs), while binding of ketone flavours decreased in the order: PPIs>wheat gluten>CPIs. Two aldolisation products, 2-butyl-2-octenal and 2-pentyl-2-nonenal, were detected from the interactions between CPIs with hexanal and heptanal, respectively. Protein thermal behaviour in the presence of these compounds was analysed by differential scanning calorimeter, where decreased ΔH inferred potential conformational changes due to partial denaturation of PPIs. Compared to ketones, aldehyde flavours possessed much higher "unfolding capacity" (lower ΔH), which accounted for their higher binding affinities. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. [Association between carbonyl proteins and tumor necrosis factor alpha with muscle strength in young and older women: exploratory study].

    Science.gov (United States)

    Martínez Huenchullán, Sergio Francisco; Mancilla Solorza, Eladio Bernabé

    2015-01-01

    It has recently been proposed that there is a close relationship between oxidative stress and low-grade chronic inflammation. Both processes have been related separately to muscle function in older adults (OA). Nevertheless, it still has not been determined if this relationship is present particularly in OA. The objective of this study was to determine the relationship between the plasma levels of TNF-α and carbonyl proteins (CP) and muscle strength in a group of young and older women. An exploratory study was conducted on 13 older and 8 young women, in whom the plasma levels of CP and TNF-α were measured. Muscle strength was measured by handgrip test, quadriceps voluntary maximal isometric strength, arm curl, and the 30 second sit to stand test. There were no differences in the plasma levels of CP and TNF-α between the groups, but there was relationship between the biomarkers only in the OA group. A non-linear relationship was observed between CP and quadriceps voluntary maximal isometric strength only in the OA group (R(2)=36.2; P=.038). For TNF-α there were no significant association with any of the applied tests. There is an association between CP and quadriceps voluntary maximal isometric strength only in the OA group, which could indicate a deleterious action of oxidative stress on muscle function, particularly in aging. Copyright © 2015 SEGG. Published by Elsevier Espana. All rights reserved.

  12. Kinetics and Mechanism of the Gas-Phase Reaction of Selected Carbonyls with Cl Atoms between 250 and 340 K

    Science.gov (United States)

    Hasson, A. S.; Algrim, L.; Abdelhamid, A.; Tyndall, G. S.; Orlando, J. J.

    2013-12-01

    Carbonyls are important products from the gas phase degradation of most volatile organic compounds. Their atmospheric reactions therefore have a significant impact on atmospheric composition, particularly in aged air masses. While the reactions of short-chain linear carbonyls are well understood, the chemistry of larger (> C6) and branched carbonyl is more uncertain. To provide insight into these reactions, the reactions of three carbonyls (methyl isopropyl ketone, MIK; di-isopropyl ketone, DIK; and diethyl ketone, DEK) with chlorine atoms were investigated between 250 and 340 K and 1 atm in the presence and absence of NOx and an HO2 source (methanol). Experiments were performed in a photochemical reactor using a combination of long-path Fourier transform infra-red spectroscopy, proton transfer reaction mass spectrometry and gas chromatography with flame ionization detection. The kinetics were studied using the relative rate technique with butanone and isopropanol as the reference compounds. The Arrhenius expression for the three rate coefficients was determined to be k(DEK+Cl) = 3.87 x 10-11e(2 × 7 kJ/mol)/RT cm3 molecules-1 s-1 , k(MIPK+Cl) = 7.20 x 10-11e(0.2× 8 kJ/mol)/RT cm3 molecules-1 s-1 , and k(DIPK+Cl) = 3.33 x 10-10e(-3× 8 kJ/mol)/RT cm3 molecules-1 s-1 . Measured reaction products accounted for 38-72 % of the reacted carbon and were consistent with strong deactivation of the carbon atom adjacent to the carbonyl group with respect to H-atom abstraction by Cl atoms. The product distributions also provide insight into radical recycling from the organic peroxy + HO2 reaction, and the relative rates of isomerization, fragmentation and reaction with O2 for carbonyl-containing alkoxy radicals. Implications of these results will be discussed.

  13. Lack of FTSH4 Protease Affects Protein Carbonylation, Mitochondrial Morphology, and Phospholipid Content in Mitochondria of Arabidopsis: New Insights into a Complex Interplay.

    Science.gov (United States)

    Smakowska, Elwira; Skibior-Blaszczyk, Renata; Czarna, Malgorzata; Kolodziejczak, Marta; Kwasniak-Owczarek, Malgorzata; Parys, Katarzyna; Funk, Christiane; Janska, Hanna

    2016-08-01

    FTSH4 is one of the inner membrane-embedded ATP-dependent metalloproteases in mitochondria of Arabidopsis (Arabidopsis thaliana). In mutants impaired to express FTSH4, carbonylated proteins accumulated and leaf morphology was altered when grown under a short-day photoperiod, at 22°C, and a long-day photoperiod, at 30°C. To provide better insight into the function of FTSH4, we compared the mitochondrial proteomes and oxyproteomes of two ftsh4 mutants and wild-type plants grown under conditions inducing the phenotypic alterations. Numerous proteins from various submitochondrial compartments were observed to be carbonylated in the ftsh4 mutants, indicating a widespread oxidative stress. One of the reasons for the accumulation of carbonylated proteins in ftsh4 was the limited ATP-dependent proteolytic capacity of ftsh4 mitochondria, arising from insufficient ATP amount, probably as a result of an impaired oxidative phosphorylation (OXPHOS), especially complex V. In ftsh4, we further observed giant, spherical mitochondria coexisting among normal ones. Both effects, the increased number of abnormal mitochondria and the decreased stability/activity of the OXPHOS complexes, were probably caused by the lower amount of the mitochondrial membrane phospholipid cardiolipin. We postulate that the reduced cardiolipin content in ftsh4 mitochondria leads to perturbations within the OXPHOS complexes, generating more reactive oxygen species and less ATP, and to the deregulation of mitochondrial dynamics, causing in consequence the accumulation of oxidative damage. © 2016 American Society of Plant Biologists. All Rights Reserved.

  14. Ischemia-reperfusion rat model of acute pancreatitis: protein carbonyl as a putative early biomarker of pancreatic injury.

    Science.gov (United States)

    Schanaider, Alberto; de Carvalho, Thales Penna; de Oliveira Coelho, Simone; Renteria, Juan Miguel; Eleuthério, Elis Cristina Araújo; Castelo-Branco, Morgana Teixeira Lima; Madi, Kalil; Baetas-da-Cruz, Wagner; de Souza, Heitor Siffert Pereira

    2015-08-01

    Acute pancreatitis (AP) is an inflammatory disorder that can affect adjacent and/or remote organs. Some evidence indicates that the production of reactive oxygen species is able to induce AP. Protein carbonyl (PC) derivatives, which can also be generated through oxidative cleavage mechanisms, have been implicated in several diseases, but there is little or no information on this biomarker in AP. We investigated the association between some inflammatory mediators and PC, with the severity of ischemia-reperfusion AP. Wistar rats (n = 56) were randomly assigned in the following groups : control; sham, 15- or 180-min clamping of splenic artery, with 24 or 72 h of follow-up. The relationships between serum level of PC and thiobarbituric acid reactive species (TBARS) to myeloperoxidase (MPO) activity in tissue homogenates and to cytokines in culture supernatants of pancreatic samples were analyzed. MPO activity was related to the histology scores and increased in all clamping groups. Tumor necrosis factor-alpha (TNF-α), interleukin 1 beta (IL-1β), and interleukin-6 were higher in the 180-min groups. Significant correlations were found between MPO activity and the concentrations of TNF-α and IL-1β. PC levels increased in the 15-min to 24-h group. TBARS levels were not altered substantially. MPO activity and TNF-α and IL-1β concentrations in pancreatic tissue are correlated with AP severity. Serum levels of PC appear to begin to rise early in the course of the ischemia-reperfusion AP and are no longer detected at later stages in the absence of severe pancreatitis. These data suggest that PC can be an efficient tool for the diagnosis of early stages of AP.

  15. Directional Darwinian Selection in proteins.

    Science.gov (United States)

    McClellan, David A

    2013-01-01

    Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins. Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test. Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations. Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time.

  16. Optimized biotin-hydrazide enrichment and mass spectrometry analysis of peptide carbonyls

    DEFF Research Database (Denmark)

    Havelund, Jesper F.; Wojdyla, K; Jensen, O. N.

    Irreversible cell damage through protein carbonylation is the result of reaction with reactive oxygen species (ROS) and has been coupled to many diseases. The precise molecular consequences of protein carbonylation, however, are still not clear. The localization of the carbonylated amino acid is ...... modifications are isobaric to carbonylation and it is often challenging to detect the weaker signal from carbonylated peptides necessitating enrichment step. We here present an optimized method for the enrichment of carbonylated peptides....

  17. Analysis of Selected Carbonyl Compounds in Tobacco Samples by Using Pentafluorobenzylhydroxylamine Derivatization and Gas Chromatography-Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Bao Mingliang

    2014-09-01

    Full Text Available Nous avons mis au point une méthode, à la fois fiable, précise et simple, d’analyse courante des composés carbonylés, en ce compris le formaldéhyde, l’acétaldéhyde, l’acétone, le propionaldéhyde, la méthyléthylcétone (MEC, le butyraldéhyde et le crotonaldéhyde, présents à l’état de traces dans les produits de tabac ouvré. Un échantillon d’un gramme de tabac, additionné d’un mélange de carbonyles marqués d’un isotope en guise de normes internes, a été extrait par l’eau. Une part de l’extrait aqueux a subi un processus de dérivatisation à l’aide de chlorhydrate d’o-(2,3,4,5,6-pentafluorobenzyle-hydroxylamine (PFBHA. Les dérivés carbonylés obtenus à l’aide du PFBHA ont ensuite été extraits par l’hexane et analysés par chromatographie en phase gazeuse couplée à la spectrométrie de masse (GC-MS. La précision et l’exactitude de la méthode ont été évaluées au regard d’une cigarette de référence Kentucky « additionnée » 3R4F et de produits de référence sans fumée CORESTA CRP1, CRP2, CRP3 et CRP4. Eu égard aux composés carbonylés analysés, d’excellents taux de précision (5-10% et de récupération (95-107% ont été observés avec divers produits du tabac « additionnés », à l’exception de l’acroléine, qui s’est avérée instable dans tous les produits du tabac testés. L’intervalle linéaire de la méthode mise au point s’est étendu de 0,07 à 36 μg/g avec des limites de quantification variant de 0,10 à 0,15 μg/g. Grâce à la présente méthode, le formaldéhyde (0,31-6,24 μg/g et l’acétaldéhyde (0,84- 17,7 μg/g ont été décelés dans tous les produits de référence testés. L’acétone (0,55-2,12 μg/g a été trouvée dans les produits 3R4F, CRP1, CRP2 et CRP3. Des niveaux décelables de propionaldéhyde n’ont été observés que dans les produits CRP1 et CRP3. Les niveaux de MEC, butyraldéhyde et crotonaldéhyde décelés dans tous

  18. A dietary supplement improves facial photoaging and skin sebum, hydration and tonicity modulating serum fibronectin, neutrophil elastase 2, hyaluronic acid and carbonylated proteins.

    Science.gov (United States)

    Di Cerbo, Alessandro; Laurino, Carmen; Palmieri, Beniamino; Iannitti, Tommaso

    2015-03-01

    Excessive exposure to the sun can cause severe photoaging as early as the second decade of life resulting in a loss of physiological elastic fiber functions. We designed a first study to assess differences in facial skin pH, sebum, elasticity, hydration and tonicity and serum levels of fibronectin, elastin, neutrophil elastase 2, hyaluronic acid and carbonylated proteins between patients affected by facial photoaging and healthy controls. In a second study we tested the hypothesis that a dietary supplement would improve facial photoaging, also promoting changes in the above mentioned skin and serum parameters. In the first study we enrolled 30 women [age: 47.5 ± 1.6 years (mean ± standard error of the mean)] affected by moderate facial photoaging (4 cm ≤ Visual Analogue Scale (VAS)Skin Tester was used to analyze differences in facial skin parameters between patients affected by facial photoaging and healthy controls. Skin Tester was also used to assess the effect of VISCODERM Pearls on facial skin parameters and compared with placebo 2 weeks after the end of treatment. Serum levels of fibronectin, elastin, neutrophil elastase 2, hyaluronic acid and carbonylated proteins were measured by enzyme-linked immunosorbent assay in the first cohort of patients affected by facial photoaging and healthy controls and, at baseline and 2 weeks after the end of treatment, in the second cohort of patients who underwent treatment with VISCODERM Pearls and placebo. VAS photoaging score was higher in patients affected by photoaging, if compared with healthy controls (p hydration and tonicity were decreased in patients affected by photoaging, if compared with healthy controls (all p hydration and tonicity were increased in the active treatment group vs. placebo (p skin hydration, tonicity and elasticity and increased skin pH and sebum. Treatment with the dietary supplement VISCODERM Pearls significantly improved VAS photoaging score and skin hydration, sebum and tonicity 2 weeks

  19. Evaluation of the concentrations and distribution of carbonyl compounds in selected areas of a Brazilian bus terminal.

    Science.gov (United States)

    de Mendonça Ochs, Soraya; de Almeida Furtado, Leonardo; Pereira Netto, Annibal Duarte

    2015-06-01

    This study describes the determination of 30 carbonyl compounds (CCs) in three areas (bus boarding platform, passenger circulation area, and a pastry shop) of the Presidente João Goulart Bus Terminal, located at Niterói City, RJ, Brazil, and in an open area 700 m distant from the terminal. Samples were collected using SEP-PAK cartridges impregnated with 2,4-dinitrophenylhydrazine, during May to July 2012. The hydrazones formed were analyzed using rapid resolution liquid chromatography with UV detection. The studied locations showed distinct profiles of distribution of CC. The circulation area, which is influenced by different pollution sources, presented an intermediate profile between that of the pastry shop and boarding platform. Formaldehyde and acetaldehyde were the most abundant CC, but acetaldehyde predominated in the pastry shop once it is a by-product of baking yeast fermentation. Samples taken in the pastry shop and circulation area showed significant concentrations of hexanaldehyde and nonanaldehyde emitted during cooking. The pastry shop showed the largest level of total CC among the studied areas followed by the circulation area, the boarding platform, and the open area.

  20. Selective Reduction of Carbonyl Compounds with B-Phenoxydiisopinocampheylborane: Comparison of Its Reactivity to the Cyclohexoxy Derivative

    International Nuclear Information System (INIS)

    Cha, Jin Soon; Nam, Ho Tae; Jang, Seung Ho; Kwon, Sang Young; Park, Seung Jin; Kwon, Oh Oun

    2004-01-01

    Ipc 2 BOPh readily reduced a wide variety of aldehydes to the corresponding alcohols at 0 .deg. C or room temperature, whereas the other functions including ketones, acid chlorides, esters and nitriles were absolutely inert to this reagent. This chemoselectivity is actually same as that obtained by Ipc 2 BOChex. The reagent readily reduces a variety of aldehydes at room temperature, but very slowly at 0 .deg. C. It is evident that the reduction proceeds via a cyclic boatilike transition state being considered as a Meerwein-Ponndorf-Verley (MPV) type reaction. In the mechanistic point of view, the key step of such reactions must be the coordination of boron atom of reagent to the carbonyl oxygen of substrate. We believe that the reactivity of diisopino-campheylborane derivatives correlates to their Lewis acidity and steric requirement: stronger the coordination, faster the reduction rate. Accordingly, we decided to examine the reducing characteristics of B-phenoxydiisopinocampheylborane (Ipc 2 BOPh), an aromatic derivative, and compare its reactivity to that of the cyclohexoxy derivative (Ipc 2 BOC hex ), in hopes of better understanding the nature of reagent and exploring its role in organic synthesis

  1. Bovine serum albumin-catalyzed deprotonation of [1-(13)C]glycolaldehyde: protein reactivity toward deprotonation of the alpha-hydroxy alpha-carbonyl carbon.

    Science.gov (United States)

    Go, Maybelle K; Malabanan, M Merced; Amyes, Tina L; Richard, John P

    2010-09-07

    Bovine serum albumin (BSA) in D(2)O at 25 degrees C and pD 7.0 was found to catalyze the deuterium exchange reactions of [1-(13)C]glycolaldehyde ([1-(13)C]GA) to form [1-(13)C,2-(2)H]GA and [1-(13)C,2,2-di-(2)H]GA. The formation of [1-(13)C,2-(2)H]GA and [1-(13)C,2,2-di-(2)H]GA in a total yield of 51 +/- 3% was observed at early reaction times, and at later times, [1-(13)C,2-(2)H]GA was found to undergo BSA-catalyzed conversion to [1-(13)C,2,2-di-(2)H]GA. The overall second-order rate constant for these deuterium exchange reactions [(k(E))(P)] equals 0.25 M(-1) s(-1). By comparison, (k(E))(P) values of 0.04 M(-1) s(-1) [Go, M. K., Amyes, T. L., and Richard, J. P. (2009) Biochemistry 48, 5769-5778] and 0.06 M(-1) s(-1) [Go, M. K., Koudelka, A., Amyes, T. L., and Richard, J. P. (2010) Biochemistry 49, 5377-5389] have been determined for the wild-type- and K12G mutant TIM-catalyzed deuterium exchange reactions of [1-(13)C]GA, respectively, to form [1-(13)C,2,2-di-(2)H]GA. These data show that TIM and BSA exhibit a modest catalytic activity toward deprotonation of the alpha-hydroxy alpha-carbonyl carbon. We suggest that this activity is intrinsic to many globular proteins, and that it must be enhanced to demonstrate meaningful de novo design of protein catalysts of proton transfer at alpha-carbonyl carbon.

  2. Glucosinolates and isothiocyanates from broccoliseed extractsuppressproteinglycationand carbonylation

    Directory of Open Access Journals (Sweden)

    Marina Hirano,

    2018-01-01

    Full Text Available Background: Glucosinolates from brassica plants are hydrolyzed by internal or salivary myrosinase to produce isothiocyanates. Glucoraphanin, a major glucosinolate in broccoli, is hydrolyzed to sulforaphane (SFN, which exhibits antitumor and detoxification activities. Regarding the influence of broccoli and its constituents on the skin, a few studies have reported anti-inflammatory and antioxidant effects. Recently, advanced glycation end products (AGEs and carbonyl proteins have been reported to accelerate skin aging. Objective: We evaluated the effects of broccoli seed extract (BSE and glucosinolates on protein glycation and carbonylation in vitro. Methods: To evaluate the effects of BSE and its constituents, protein glycation and carbonylation were induced by mixing fructose with bovine serum albumin (BSA and then measuring production of AGEs, fructosamine, and carbonyl proteins (CP. Production of CP after mixing fatty acids with BSA was also assessed. Furthermore, the effect of BSE and its constituents on CP production by human fibroblasts (TIG103 was examined. Results: BSE suppressed the production of AGEs, fructosamine, and CP after mixing fructose and BSA. BSE also suppressed production of CP when oxidized linoleic acid was mixed with BSA. Isothiocyanates, including SFN and iberin, suppressed fructose-based CP production, but SFN had no effect on CP production stimulated by oxidized linoleic acid. In contrast, glucosinolates from BSE did not suppress fructose-based CP production, but suppressed CP production due to oxidized linoleic acid. Among the glucosinolates in BSE, glucoberteroin showed the strongest suppression of CP production. CP production in fibroblasts was also suppressed by glucosinolates, including glucoiberin and glucoberteroin. Conclusions: BSE demonstrated anti-glycation and anti-carbonylation effects on protein reactions with fructose and oxidized fatty acids. Isothiocyanates suppressed protein carbonylation induced by

  3. 50Hz Extremely Low Frequency Electromagnetic Fields Enhance Protein Carbonyl Groups Content in Cancer Cells: Effects on Proteasomal Systems

    Directory of Open Access Journals (Sweden)

    A. M. Eleuteri

    2009-01-01

    Full Text Available Electromagnetic fields are an assessed cause of prolonging free radicals lifespan. This study was carried out to investigate the influence of extremely low frequency electromagnetic fields on protein oxidation and on the 20S proteasome functionality, the complex responsible for the degradation of oxidized proteins. Caco 2 cells were exposed, for 24–72 hours, to 1 mT, 50 Hz electromagnetic fields. The treatment induced a time-dependent increase both in cell growth and in protein oxidation, more evident in the presence of TPA, while no changes in cell viability were detected. Exposing the cells to 50 Hz electromagnetic fields caused a global activation of the 20S proteasome catalytic components, particularly evident at 72 hours exposure and in the presence of TPA. The finding that EGCG, a natural antioxidant compound, counteracted the field-related pro-oxidant effects demonstrates that the increased proteasome activity was due to an enhancement in intracellular free radicals.

  4. Selection of peptides interfering with protein-protein interaction.

    Science.gov (United States)

    Gaida, Annette; Hagemann, Urs B; Mattay, Dinah; Räuber, Christina; Müller, Kristian M; Arndt, Katja M

    2009-01-01

    Cell physiology depends on a fine-tuned network of protein-protein interactions, and misguided interactions are often associated with various diseases. Consequently, peptides, which are able to specifically interfere with such adventitious interactions, are of high interest for analytical as well as medical purposes. One of the most abundant protein interaction domains is the coiled-coil motif, and thus provides a premier target. Coiled coils, which consist of two or more alpha-helices wrapped around each other, have one of the simplest interaction interfaces, yet they are able to confer highly specific homo- and heterotypic interactions involved in virtually any cellular process. While there are several ways to generate interfering peptides, the combination of library design with a powerful selection system seems to be one of the most effective and promising approaches. This chapter guides through all steps of such a process, starting with library options and cloning, detailing suitable selection techniques and ending with purification for further down-stream characterization. Such generated peptides will function as versatile tools to interfere with the natural function of their targets thereby illuminating their down-stream signaling and, in general, promoting understanding of factors leading to specificity and stability in protein-protein interactions. Furthermore, peptides interfering with medically relevant proteins might become important diagnostics and therapeutics.

  5. [carbonyl-11C]Desmethyl-WAY-100635 (DWAY) is a potent and selective radioligand for central 5-HT1A receptors in vitro and in vivo

    International Nuclear Information System (INIS)

    Pike, V.W.; McCarron, J.A.; Hirani, E.; Hume, S.P.; Osman, S.; Poole, K.G.; Wikstroem, H.; Mensonidas, M.

    1998-01-01

    In this study we set out to assess the ability of DWAY to enter brain in vivo and to elucidate its possible interaction with 5-HT 1A receptors. Desmethyl-WAY-100635 was labelled efficiently with carbon-11 in high specific radioactivity by reaction of its descyclohexanecarbonyl analogue with [carbonyl- 11 C]cyclohexanecarbonyl chloride. The product was separated in high radiochemical purity by HPLC. Rats were injected intravenously with DWAY, sacrificed and dissected to establish radioactivity content in brain tissues. At 60 min after injection, the ratios of radioactivity concentration in each brain region to that in cerebellum correlated with previous in vitro and in vivo measures of 5-HT 1A receptor density. The highest ratio was about 22 in hippocampus. Radioactivity cleared rapidly from plasma; HPLC analysis revealed that DWAY represented 55% of the radioactivity in plasma at 5 min and 33% at 30 min. Only polar radioactive metabolites were detected. Subsequently, a cynomolgus monkey was injected intravenously with DWAY and examined by PET. Maximal whole brain uptake of radioactivity was 5.7% of the administered dose at 5 min after injection. The image acquired between 9 and 90 min showed high radioactivity uptake in brain regions rich in 5-HT 1A receptors, moderate uptake in raphe nuclei and low uptake in cerebellum. A transient equilibrium was achieved in cortical regions at about 60 min, when the ratio of radioactivity concentration in frontal cortex to tcat in cerebellum reached 6. The corresponding ratio for raphe nuclei was about 3. Radioactive metabolites appeared rapidly in plasma, but these were all more polar than DWAY, which represented 52% of the radioactivity in plasma at 4 min and 20% at 55 min. In a second PET experiment, in which a cynomolgus monkey was pretreated with the selective 5-HT 1A receptor antagonist, WAY-100635, at 25 min before DWAY injection, radioactivity in all brain regions was reduced to that in cerebellum. Autoradiography of

  6. THE METAL CARBONYLS.

    Science.gov (United States)

    Blanchard, A A

    1941-10-03

    When the metal carbonyls were first discovered, their properties were startling because they seemed to violate nearly all the previously recognized generalizations of chemistry. Even to-day the existence of the carbonyls is not particularly emphasized in elementary courses of chemistry because it is rather hard to reconcile them with the first presentations of the generalizations of chemistry. Nevertheless, as the student progresses deeper into the knowledge of chemistry it becomes desirable to include the knowledge of the carbonyls both because they become more comprehensible when viewed in the light of Werner's system of coordination and because they themselves contribute to the comprehension of the Werner theory. As long ago as 1931, Reiff in his discussion of cobalt nitrosyl carbonyl recognized the correlation between the effective atomic number and the volatility of carbonyls. A more recent study of charged Werner coordination complexes, that is, of complex ions, has shown a similar role of the effective atomic number. We are standing on fairly firm ground when we point out the correlation between E.A.N. and the volatility of the carbonyl complexes and the existence of complex ions. Be it noted that we have made no postulates as to the arrangement of the electrons in quantum levels. In the inert gases the outer principal quantum group is supposed always to contain eight electrons. In the carbonyls and other Werner complexes there is no compelling reason to suppose that the electrons in the coordinating layer, be this layer of eight, ten, twelve or sixteen electrons, are not all at the same energy level. Although we have confined our discussion almost exclusively to the property of volatility, the carbonyls are very interesting from the standpoint of several other properties, for example, magnetic susceptibility and dielectric constant. Enthusiasts in the interpretation of such properties try to draw conclusions as to the condition of the electrons, sometimes

  7. Fish Proteins as Targets of Ferrous-Catalyzed Oxidation: Identification of Protein Carbonyls by Fluorescent Labeling on Two-Dimensional Gels and MALDI-TOF/TOF Mass Spectrometry

    DEFF Research Database (Denmark)

    Pazos, Manuel; da Rocha, Angela Pereira; Roepstorff, Peter

    2011-01-01

    Protein oxidation in fish meat is considered to affect negatively the muscle texture. An important source of free radicals taking part in this process is Fenton's reaction dependent on ferrous ions present in the tissue. The aim of this study was to investigate the susceptibility of cod muscle pr...

  8. DENDRIMER CONJUGATES FOR SELECTIVE OF PROTEIN AGGREGATES

    DEFF Research Database (Denmark)

    2004-01-01

    Dendrimer conjugates are presented, which are formed between a dendrimer and a protein solubilising substance. Such dendrimer conjugates are effective in the treatment of protein aggregate-related diseases (e.g. prion-related diseases). The protein solubilising substance and the dendrimer together...

  9. High throughput assay for evaluation of reactive carbonyl scavenging capacity.

    Science.gov (United States)

    Vidal, N; Cavaille, J P; Graziani, F; Robin, M; Ouari, O; Pietri, S; Stocker, P

    2014-01-01

    Many carbonyl species from either lipid peroxidation or glycoxidation are extremely reactive and can disrupt the function of proteins and enzymes. 4-hydroxynonenal and methylglyoxal are the most abundant and toxic lipid-derived reactive carbonyl species. The presence of these toxics leads to carbonyl stress and cause a significant amount of macromolecular damages in several diseases. Much evidence indicates trapping of reactive carbonyl intermediates may be a useful strategy for inhibiting or decreasing carbonyl stress-associated pathologies. There is no rapid and convenient analytical method available for the assessment of direct carbonyl scavenging capacity, and a very limited number of carbonyl scavengers have been identified to date, their therapeutic potential being highlighted only recently. In this context, we have developed a new and rapid sensitive fluorimetric method for the assessment of reactive carbonyl scavengers without involvement glycoxidation systems. Efficacy of various thiol- and non-thiol-carbonyl scavenger pharmacophores was tested both using this screening assay adapted to 96-well microplates and in cultured cells. The scavenging effects on the formation of Advanced Glycation End-product of Bovine Serum Albumin formed with methylglyoxal, 4-hydroxynonenal and glucose-glycated as molecular models were also examined. Low molecular mass thiols with an α-amino-β-mercaptoethane structure showed the highest degree of inhibitory activity toward both α,β-unsaturated aldehydes and dicarbonyls. Cysteine and cysteamine have the best scavenging ability toward methylglyoxal. WR-1065 which is currently approved for clinical use as a protective agent against radiation and renal toxicity was identified as the best inhibitor of 4-hydroxynonenal.

  10. High throughput assay for evaluation of reactive carbonyl scavenging capacity

    Directory of Open Access Journals (Sweden)

    N. Vidal

    2014-01-01

    Full Text Available Many carbonyl species from either lipid peroxidation or glycoxidation are extremely reactive and can disrupt the function of proteins and enzymes. 4-hydroxynonenal and methylglyoxal are the most abundant and toxic lipid-derived reactive carbonyl species. The presence of these toxics leads to carbonyl stress and cause a significant amount of macromolecular damages in several diseases. Much evidence indicates trapping of reactive carbonyl intermediates may be a useful strategy for inhibiting or decreasing carbonyl stress-associated pathologies. There is no rapid and convenient analytical method available for the assessment of direct carbonyl scavenging capacity, and a very limited number of carbonyl scavengers have been identified to date, their therapeutic potential being highlighted only recently. In this context, we have developed a new and rapid sensitive fluorimetric method for the assessment of reactive carbonyl scavengers without involvement glycoxidation systems. Efficacy of various thiol- and non-thiol-carbonyl scavenger pharmacophores was tested both using this screening assay adapted to 96-well microplates and in cultured cells. The scavenging effects on the formation of Advanced Glycation End-product of Bovine Serum Albumin formed with methylglyoxal, 4-hydroxynonenal and glucose-glycated as molecular models were also examined. Low molecular mass thiols with an α-amino-β-mercaptoethane structure showed the highest degree of inhibitory activity toward both α,β-unsaturated aldehydes and dicarbonyls. Cysteine and cysteamine have the best scavenging ability toward methylglyoxal. WR-1065 which is currently approved for clinical use as a protective agent against radiation and renal toxicity was identified as the best inhibitor of 4-hydroxynonenal.

  11. The importance of protein in leaf selection of folivorous primates.

    Science.gov (United States)

    Ganzhorn, Joerg U; Arrigo-Nelson, Summer J; Carrai, Valentina; Chalise, Mukesh K; Donati, Giuseppe; Droescher, Iris; Eppley, Timothy M; Irwin, Mitchell T; Koch, Flávia; Koenig, Andreas; Kowalewski, Martin M; Mowry, Christopher B; Patel, Erik R; Pichon, Claire; Ralison, Jose; Reisdorff, Christoph; Simmen, Bruno; Stalenberg, Eleanor; Starrs, Danswell; Terboven, Juana; Wright, Patricia C; Foley, William J

    2017-04-01

    Protein limitation has been considered a key factor in hypotheses on the evolution of life history and animal communities, suggesting that animals should prioritize protein in their food choice. This contrasts with the limited support that food selection studies have provided for such a priority in nonhuman primates, particularly for folivores. Here, we suggest that this discrepancy can be resolved if folivores only need to select for high protein leaves when average protein concentration in the habitat is low. To test the prediction, we applied meta-analyses to analyze published and unpublished results of food selection for protein and fiber concentrations from 24 studies (some with multiple species) of folivorous primates. To counter potential methodological flaws, we differentiated between methods analyzing total nitrogen and soluble protein concentrations. We used a meta-analysis to test for the effect of protein on food selection by primates and found a significant effect of soluble protein concentrations, but a non-significant effect for total nitrogen. Furthermore, selection for soluble protein was reinforced in forests where protein was less available. Selection for low fiber content was significant but unrelated to the fiber concentrations in representative leaf samples of a given forest. There was no relationship (either negative or positive) between the concentration of protein and fiber in the food or in representative samples of leaves. Overall our study suggests that protein selection is influenced by the protein availability in the environment, explaining the sometimes contradictory results in previous studies on protein selection. Am. J. Primatol. 79:e22550, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  12. Cotranslational protein folding reveals the selective use of ...

    Indian Academy of Sciences (India)

    to fold properly by decelerating the translation rate at these sites. Thus the cotranslational protein folding is believed to be true for many proteins and is an important selection factor for the selective codon usage to optimize proper gene expres- sion and function (Komar 2009). A web server CS and S has been created by ...

  13. Determination of Carbonyl Compounds in Cigarette Mainstream Smoke. The CORESTA 2010 Collaborative Study and Recommended Method

    Directory of Open Access Journals (Sweden)

    Intorp M

    2014-12-01

    Full Text Available A recommended method has been developed and published by CORESTA, applicable to the quantification of selected carbonyl compounds (acetaldehyde, formaldehyde, acetone, acrolein, methyl ethyl ketone, crotonaldehyde, propionaldehyde and butyraldehyde in cigarette mainstream smoke. The method involved smoke collection in impinger traps, derivatisation of carbonyls with 2,4-dinitrophenylhydrazine (DNPH, separation of carbonyl hydrazones by reversed phase high performance liquid chromatography and detection by ultra violet or diode array.

  14. A simple and highly selective ‘turn-on’ type fluorescence chemodosimeter for Hg2+ based on 1-(2-phenyl-2H-[1,2,3]triazole-4-carbonyl)thiosemicarbazide

    International Nuclear Information System (INIS)

    Lin, Hui; Shi, Wei; Tian, Yong; Ma, Fudong; Xu, Linxian; Ma, Junchi; Hui, Yonghai; Xie, Zhengfeng

    2015-01-01

    1-(2-phenyl-2H-[1,2,3]triazole-4-carbonyl)-4- (4-methylphenyl)thiosemicarbazide (M1) has been synthesized and investigated as a fluorescence chemodosimeter for Hg 2+ in dimethylsulfoxide. Highly selective ‘turn-on’ fluorescence alterations of M1 were observed upon the addition of Hg 2+ . Detection limit of Hg 2+ by M1 reaches ~3.7×10 −8 mol/L (evaluated by 3σ criteria).The coexistent metal ions rendered no obvious interference toward the optical response of M1 for Hg 2+ .The mechanism of M1 for the recognition of Hg 2+ has been investigated by FT-IR, 1 H NMR and MS analyses. - Highlights: • A type of thiosemicarbazide-derivatived compound (M1) was synthesized. • The fluorescence of M1 displayed highly selective ‘turn-on’ type fluorescence alteration with the presence of Hg 2+ . • Detection limit of ~3.7×10 −8 M for Hg 2+ can be obtained by this probing system. • Hg 2+ -induced intramolecular desulfurization and cyclization process of thiosemicarbazide moieties is the plausible probing mechanism

  15. Estimates of selection parameters in protein mutants of spring barley

    International Nuclear Information System (INIS)

    Gaul, H.; Walther, H.; Seibold, K.H.; Brunner, H.; Mikaelsen, K.

    1976-01-01

    Detailed studies have been made with induced protein mutants regarding a possible genetic advance in selection including the estimation of the genetic variation and heritability coefficients. Estimates were obtained for protein content and protein yield. The variation of mutant lines in different environments was found to be many times as large as the variation of the line means. The detection of improved protein mutants seems therefore possible only in trials with more than one environment. The heritability of protein content and protein yield was estimated in different sets of environments and was found to be low. However, higher values were found with an increasing number of environments. At least four environments seem to be necessary to obtain reliable heritability estimates. The geneticall component of the variation between lines was significant for protein content in all environmental combinations. For protein yield some environmental combinations only showed significant differences. The expected genetic advance with one selection step was small for both protein traits. Genetically significant differences between protein micromutants give, however, a first indication that selection among protein mutants with small differences seems also possible. (author)

  16. A method of detecting carbonyl compounds in tree leaves in China.

    Science.gov (United States)

    Huang, Juan; Feng, Yanli; Fu, Jiamo; Sheng, Guoying

    2010-06-01

    Carbonyl compounds have been paid more and more attention because some carbonyl species have been proven to be carcinogenic or a risk for human health. Plant leaves are both an important emission source and an important sink of carbonyl compounds. But the research on carbonyl compounds from plant leaves is very scarce. In order to make an approach to the emission mechanism of plant leaves, a new method was established to extract carbonyl compounds from fresh plant leaves. The procedure combining derivatization with ultrasonication was developed for the fast extraction of carbonyl compounds from tree leaves. Fresh leaves (Metasequoia glyptostroboides), were selected and extracted by this method. Seven carbonyl compounds, including formaldehyde, acetaldehyde, acetone, acrolein, p-tolualdehyde, m/o-tolualdehyde, and hexaldehyde were determined and quantified. The most common carbonyl species of the four tree leaves were formaldehyde, acrolein, and m/o-tolualdehyde. They accounted for 67.3% in cedar, 50.8% in sweet olive, 45.8% in dawn redwood, and 44.6% in camphor tree, respectively. Camphor tree had the highest leaf level of m/o-tolualdehyde with 15.0 +/- 3.4 microg g(-1)(fresh leaf weight), which indicated that camphor tree may be a bioindicator of the level of tolualdehyde or xylene in the atmosphere. By analyzing carbonyl compounds from different tree leaves, it is not only helpful for further studying the relationship between sink and emission of carbonyls from plants, but also helpful for exploring optimum plant population in urban greening.

  17. Selective memory generalization by spatial patterning of protein synthesis.

    Science.gov (United States)

    O'Donnell, Cian; Sejnowski, Terrence J

    2014-04-16

    Protein synthesis is crucial for both persistent synaptic plasticity and long-term memory. De novo protein expression can be restricted to specific neurons within a population, and to specific dendrites within a single neuron. Despite its ubiquity, the functional benefits of spatial protein regulation for learning are unknown. We used computational modeling to study this problem. We found that spatially patterned protein synthesis can enable selective consolidation of some memories but forgetting of others, even for simultaneous events that are represented by the same neural population. Key factors regulating selectivity include the functional clustering of synapses on dendrites, and the sparsity and overlap of neural activity patterns at the circuit level. Based on these findings, we proposed a two-step model for selective memory generalization during REM and slow-wave sleep. The pattern-matching framework we propose may be broadly applicable to spatial protein signaling throughout cortex and hippocampus. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Site-Selective Conjugation of Native Proteins with DNA

    DEFF Research Database (Denmark)

    Trads, Julie Brender; Tørring, Thomas; Gothelf, Kurt Vesterager

    2017-01-01

    Conjugation of DNA to proteins is increasingly used in academia and industry to provide proteins with tags for identification or handles for hybridization to other DNA strands. Assay technologies such as immuno-PCR and proximity ligation and the imaging technology DNA-PAINT require DNA-protein....... The introduction of a bioorthogonal handle at a specific position of a protein by recombinant techniques provides an excellent approach to site-specific conjugation, but for many laboratories and for applications where several proteins are to be labeled, the expression of recombinant proteins may be cumbersome...... conjugates. In DNA nanotechnology, the DNA handle is exploited to precisely position proteins by self-assembly. For these applications, site-selective conjugation is almost always desired because fully functional proteins are required to maintain the specificity of antibodies and the activity of enzymes...

  19. Role of the adsorbed oxygen species in the selective electrochemical reduction of CO{sub 2} to alcohols and carbonyls on copper electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Le Duff, Cecile S.; Lawrence, Matthew J.; Rodriguez, Paramaconi [School of Chemistry, University of Birmingham, Edgbaston (United Kingdom)

    2017-10-09

    The electrochemical reduction of CO{sub 2} into fuels has gained significant attention recently as source of renewable carbon-based fuels. The unique high selectivity of copper in the electrochemical reduction of CO{sub 2} to hydrocarbons has called much interest in discovering its mechanism. In order to provide significant information about the role of oxygen in the electrochemical reduction of CO{sub 2} on Cu electrodes, the conditions of the surface structure and the composition of the Cu single crystal electrodes were controlled over time. This was achieved using pulsed voltammetry, since the pulse sequence can be programmed to guarantee reproducible initial conditions for the reaction at every fraction of time and at a given frequency. In contrast to the selectivity of CO{sub 2} reduction using cyclic voltammetry and chronoamperometric methods, a large selection of oxygenated hydrocarbons was found under alternating voltage conditions. Product selectivity towards the formation of oxygenated hydrocarbon was associated to the coverage of oxygen species, which is surface-structure- and potential-dependent. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  20. Role of the adsorbed oxygen species in the selective electrochemical reduction of CO_2 to alcohols and carbonyls on copper electrodes

    International Nuclear Information System (INIS)

    Le Duff, Cecile S.; Lawrence, Matthew J.; Rodriguez, Paramaconi

    2017-01-01

    The electrochemical reduction of CO_2 into fuels has gained significant attention recently as source of renewable carbon-based fuels. The unique high selectivity of copper in the electrochemical reduction of CO_2 to hydrocarbons has called much interest in discovering its mechanism. In order to provide significant information about the role of oxygen in the electrochemical reduction of CO_2 on Cu electrodes, the conditions of the surface structure and the composition of the Cu single crystal electrodes were controlled over time. This was achieved using pulsed voltammetry, since the pulse sequence can be programmed to guarantee reproducible initial conditions for the reaction at every fraction of time and at a given frequency. In contrast to the selectivity of CO_2 reduction using cyclic voltammetry and chronoamperometric methods, a large selection of oxygenated hydrocarbons was found under alternating voltage conditions. Product selectivity towards the formation of oxygenated hydrocarbon was associated to the coverage of oxygen species, which is surface-structure- and potential-dependent. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  1. Study of selective Fischer-Tropsch catalysts synthesized by the destruction of bimetallic carbonyl complexes on activated γ-Al2O3 support

    International Nuclear Information System (INIS)

    Maksimov, Yu.V.; Matveev, V.V.; Suzdalev, I.P.; Khomenko, T.I.; Kadushin, A.A.

    1990-01-01

    The bimetallic catalysts obtained by the deposition of a Fe-Co binuclear cluster on the dehydroxylated γ-Al 2 O 3 are studied and compared to some other relative systems. These bimetallic catalysts are found to be active and selective in olefin synthesis. This is connected with the formation of Fe-Co contact which is detectable by Moessbauer spectroscopy. (orig.)

  2. Targeted Diazotransfer Reagents Enable Selective Modification of Proteins with Azides.

    Science.gov (United States)

    Lohse, Jonas; Swier, Lotteke J Y M; Oudshoorn, Ruben C; Médard, Guillaume; Kuster, Bernhard; Slotboom, Dirk-Jan; Witte, Martin D

    2017-04-19

    In chemical biology, azides are used to chemically manipulate target structures in a bioorthogonal manner for a plethora of applications ranging from target identification to the synthesis of homogeneously modified protein conjugates. While a variety of methods have been established to introduce the azido group into recombinant proteins, a method that directly converts specific amino groups in endogenous proteins is lacking. Here, we report the first biotin-tethered diazotransfer reagent DtBio and demonstrate that it selectively modifies the model proteins streptavidin and avidin and the membrane protein BioY on cell surface. The reagent converts amines in the proximity of the binding pocket to azides and leaves the remaining amino groups in streptavidin untouched. Reagents of this novel class will find use in target identification as well as the selective functionalization and bioorthogonal protection of proteins.

  3. Ruthenium(ii)-catalyzed olefination via carbonyl reductive cross-coupling.

    Science.gov (United States)

    Wei, Wei; Dai, Xi-Jie; Wang, Haining; Li, Chenchen; Yang, Xiaobo; Li, Chao-Jun

    2017-12-01

    Natural availability of carbonyl groups offers reductive carbonyl coupling tremendous synthetic potential for efficient olefin synthesis, yet the catalytic carbonyl cross-coupling remains largely elusive. We report herein such a reaction, mediated by hydrazine under ruthenium(ii) catalysis. This method enables facile and selective cross-couplings of two unsymmetrical carbonyl compounds in either an intermolecular or intramolecular fashion. Moreover, this chemistry accommodates a variety of substrates, proceeds under mild reaction conditions with good functional group tolerance, and generates stoichiometric benign byproducts. Importantly, the coexistence of KO t Bu and bidentate phosphine dmpe is vital to this transformation.

  4. Selectivity determinants of GPCR-G-protein binding

    DEFF Research Database (Denmark)

    Flock, Tilman; Hauser, Alexander S; Lund, Nadia

    2017-01-01

    of the G-protein barcode through distinct residues, like multiple keys (receptors) opening the same lock (G protein) using non-identical cuts. Considering the evolutionary history of GPCRs allows the identification of these selectivity-determining residues. These findings lay the foundation...

  5. Efficient and Selective Syntheses of (all-E)- and (6E,10Z)-2′-O-Methylmyxalamides D via Pd-Catalyzed Alkenylation—Carbonyl Olefination Synergy

    Science.gov (United States)

    Wang, Guangwei; Huang, Zhihong; Negishi, Ei-ichi

    2008-01-01

    Highly efficient and selective syntheses of both (all-E) and (6E,10Z)-isomers of 2′-O-methylmyxalamide D (2 and 3), in which the crucial conjugated pentaene moieties were assembled in ≥98% stereoselectivity through the use of two Pd-catalyzed alkenylation reactions, the Horner—Wadsworth—Emmons (HWE) olefination, and either the Corey—Schlessinger—Mills modified (CSM-modified) Peterson olefination for 2 or the Still—Gennari olefination for 3, are reported. Either 2 or 3 was prepared in 16% yield in seven steps from propargyl alcohol. PMID:18593171

  6. An Antibiotic Selection System For Protein Overproducing Bacteria

    DEFF Research Database (Denmark)

    Rennig, Maja; Nørholm, Morten

    2015-01-01

    Introduction: Protein overproduction is a major bottleneck for analyses of membrane proteins and for the construction of cell factories. Screening for optimized protein production can be very time consuming. In this study we show that the coupling of antibiotic resistance to poorly produced...... membrane proteins of Escherichia coli can be used as a fast and simple selection system for protein overproduction.Methods: We designed an expression plasmid encoding the gene of interest and an additional, inducible antibiotic resistance marker. Both genes were linked by a hairpin structure...... that translationally couples the genes. Consequently, high expressing gene variants also allow for higher production of the coupled antibiotic resistance marker. Therefore, high expressing gene variants in a library can be determined either by plating the expression library on selection plates or by growing...

  7. Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks

    Directory of Open Access Journals (Sweden)

    Sandip Chakraborty

    2016-01-01

    Full Text Available Proteins within a molecular network are expected to be subject to different selective pressures depending on their relative hierarchical positions. However, it is not obvious what genes within a network should be more likely to evolve under positive selection. On one hand, only mutations at genes with a relatively high degree of control over adaptive phenotypes (such as those encoding highly connected proteins are expected to be “seen” by natural selection. On the other hand, a high degree of pleiotropy at these genes is expected to hinder adaptation. Previous analyses of the human protein-protein interaction network have shown that genes under long-term, recurrent positive selection (as inferred from interspecific comparisons tend to act at the periphery of the network. It is unknown, however, whether these trends apply to other organisms. Here, we show that long-term positive selection has preferentially targeted the periphery of the yeast interactome. Conversely, in flies, genes under positive selection encode significantly more connected and central proteins. These observations are not due to covariation of genes’ adaptability and centrality with confounding factors. Therefore, the distribution of proteins encoded by genes under recurrent positive selection across protein-protein interaction networks varies from one species to another.

  8. Radical carbonylations using a continuous microflow system

    Directory of Open Access Journals (Sweden)

    Takahide Fukuyama

    2009-07-01

    Full Text Available Radical-based carbonylation reactions of alkyl halides were conducted in a microflow reactor under pressurized carbon monoxide gas. Good to excellent yields of carbonylated products were obtained via radical formylation, carbonylative cyclization and three-component coupling reactions, using tributyltin hydride or TTMSS as a radical mediator.

  9. Reduced protein carbonylation of cube steak and catfish fillet using antioxidative coatings containing cheddar whey, casein hydrolyzate and oolong tea extract

    Science.gov (United States)

    Hydrolysis of casein using chymotrypsin results in the formation of polypeptides (casein hydrolyzate, CH) with a hydrophobic aromatic amino acid on one end of the chain because the enzyme selectively cleaves the adjacent peptide-bond. Due to resonance of the aromatic micro-domain, thiols become redo...

  10. The effect of polyphenolic-polysaccharide conjugates from selected medicinal plants of Asteraceae family on the peroxynitrite-induced changes in blood platelet proteins.

    Science.gov (United States)

    Saluk-Juszczak, Joanna; Pawlaczyk, Izabela; Olas, Beata; Kołodziejczyk, Joanna; Ponczek, Michal; Nowak, Pawel; Tsirigotis-Wołoszczak, Marta; Wachowicz, Barbara; Gancarz, Roman

    2010-12-01

    Lots of plants belonging to Asteraceae family are very popular in folk medicine in Poland. These plants are also known as being rich in acidic polysaccharides, due to the presence of hexuronic acids or its derivatives. Our preliminary experiments have shown that the extract from Conyza canadensis L. possesses various biological activity, including antiplatelet, antiocoagulant and antioxidant properties. The aim of our study was to assess if macromolecular glycoconjugates from selected herbal plants of Asteraceae family: Achillea millefolium L., Arnica montana L., Echinacea purpurea L., Solidago virgaurea L., Chamomilla recutita (L.) Rauschert., and Conyza canadensis L. protect platelet proteins against nitrative and oxidative damage induced by peroxynitrite, which is responsible for oxidative/nitrative modifications of platelet proteins: the formation of 3-nitrotyrosine and carbonyl groups. These modifications may lead to changes of blood platelet functions and can have pathological consequences. The role of these different medicinal plants in the defence against oxidative/nitrative stress in human platelets is still unknown, therefore the oxidative damage to platelet proteins induced by peroxynitrite and protectory effects of tested conjugates by the estimation of carbonyl group level and nitrotyrosine formation (a marker of protein nitration) were studied in vitro. The antioxidative properties of the polyphenolic-polysaccharide conjugates from selected tested medicinal plants were also compared with the action of a well characterized antioxidative commercial polyphenol - resveratrol (3,4',5-trihydroxystilbene). The obtained results demonstrate that the compounds from herbal plants: A. millefolium, A. montana, E. purpurea, C. recutita, S. virgaurea, possess antioxidative properties and protect platelet proteins against peroxynitrite toxicity in vitro, similar to the glycoconjugates from C. canadensis. However, in the comparative studies, the polyphenolic

  11. Protein construct storage: Bayesian variable selection and prediction with mixtures.

    Science.gov (United States)

    Clyde, M A; Parmigiani, G

    1998-07-01

    Determining optimal conditions for protein storage while maintaining a high level of protein activity is an important question in pharmaceutical research. A designed experiment based on a space-filling design was conducted to understand the effects of factors affecting protein storage and to establish optimal storage conditions. Different model-selection strategies to identify important factors may lead to very different answers about optimal conditions. Uncertainty about which factors are important, or model uncertainty, can be a critical issue in decision-making. We use Bayesian variable selection methods for linear models to identify important variables in the protein storage data, while accounting for model uncertainty. We also use the Bayesian framework to build predictions based on a large family of models, rather than an individual model, and to evaluate the probability that certain candidate storage conditions are optimal.

  12. Semiotic Selection of Mutated or Misfolded Receptor Proteins

    DEFF Research Database (Denmark)

    Giorgi, Franco; Bruni, Luis Emilio; Maggio, Roberto

    2013-01-01

    contention that the plasma membrane acts as the locus where several contextual cues may be integrated. As such it allows the semiotic selection of those receptor configurations that provide cells with the minimum essential requirements for agency. The occurrence of protein misfolding makes it impossible...... focused on the significance and semiotic nature of the interplay between membrane receptors and the epigenetic control of gene expression, as mediated by the control of mismatched repairing and protein folding mechanisms....

  13. Methanol and carbonylation

    Energy Technology Data Exchange (ETDEWEB)

    Gauthier-Lafaye, J.; Perron, R.

    1987-01-01

    The overall focus of the book is on homogeneous catalysed processes which were seen to offer the most promising routes to C/sub 2/ oxygenates. The first three chapters review the industrial synthesis and applications of carbon monoxide such as in the manufacture of gasoline (e.g. Fischer-Tropsch, Mobil processes), organic chemicals (e.g. ethanol, acetic acid, etc.), industrial importance of C/sub 2/ oxygenates, and use of methanol as a future feedstock are discussed. The next six chapters are each concerned with the production of a particular C/sub 2/ oxygenate and a detailed analysis of the methods and catalysts used. The hydrocarbonylation of methanol occupies a large chapter (136 references) with a comparative examination of the catalysts available, and their modification to increase selectivity to either acetylaldehyde or ethanol. Following chapters examine the synthesis of ethyl acetate, acetic acid, acetic anhydride, vinyl acetate, ethylene glycol and oxalic acid.

  14. Zeolite Nanoparticles for Selective Sorption of Plasma Proteins.

    Science.gov (United States)

    Rahimi, M; Ng, E-P; Bakhtiari, K; Vinciguerra, M; Ali Ahmad, H; Awala, H; Mintova, S; Daghighi, M; Bakhshandeh Rostami, F; de Vries, M; Motazacker, M M; Peppelenbosch, M P; Mahmoudi, M; Rezaee, F

    2015-11-30

    The affinity of zeolite nanoparticles (diameter of 8-12 nm) possessing high surface area and high pore volume towards human plasma proteins has been investigated. The protein composition (corona) of zeolite nanoparticles has been shown to be more dependent on the plasma protein concentrations and the type of zeolites than zeolite nanoparticles concentration. The number of proteins present in the corona of zeolite nanoparticles at 100% plasma (in vivo state) is less than with 10% plasma exposure. This could be due to a competition between the proteins to occupy the corona of the zeolite nanoparticles. Moreover, a high selective adsorption for apolipoprotein C-III (APOC-III) and fibrinogen on the zeolite nanoparticles at high plasma concentration (100%) was observed. While the zeolite nanoparticles exposed to low plasma concentration (10%) exhibited a high selective adsorption for immunoglobulin gamma (i.e. IGHG1, IGHG2 and IGHG4) proteins. The zeolite nanoparticles can potentially be used for selectively capture of APOC-III in order to reduce the activation of lipoprotein lipase inhibition during hypertriglyceridemia treatment. The zeolite nanoparticles can be adapted to hemophilic patients (hemophilia A (F-VIII deficient) and hemophilia B (F-IX deficient)) with a risk of bleeding, and thus might be potentially used in combination with the existing therapy.

  15. A selection that reports on protein-protein interactions within a thermophilic bacterium.

    Science.gov (United States)

    Nguyen, Peter Q; Silberg, Jonathan J

    2010-07-01

    Many proteins can be split into fragments that exhibit enhanced function upon fusion to interacting proteins. While this strategy has been widely used to create protein-fragment complementation assays (PCAs) for discovering protein-protein interactions within mesophilic organisms, similar assays have not yet been developed for studying natural and engineered protein complexes at the temperatures where thermophilic microbes grow. We describe the development of a selection for protein-protein interactions within Thermus thermophilus that is based upon growth complementation by fragments of Thermotoga neapolitana adenylate kinase (AK(Tn)). Complementation studies with an engineered thermophile (PQN1) that is not viable above 75 degrees C because its adk gene has been replaced by a Geobacillus stearothermophilus ortholog revealed that growth could be restored at 78 degrees C by a vector that coexpresses polypeptides corresponding to residues 1-79 and 80-220 of AK(Tn). In contrast, PQN1 growth was not complemented by AK(Tn) fragments harboring a C156A mutation within the zinc-binding tetracysteine motif unless these fragments were fused to Thermotoga maritima chemotaxis proteins that heterodimerize (CheA and CheY) or homodimerize (CheX). This enhanced complementation is interpreted as arising from chemotaxis protein-protein interactions, since AK(Tn)-C156A fragments having only one polypeptide fused to a chemotaxis protein did not complement PQN1 to the same extent. This selection increases the maximum temperature where a PCA can be used to engineer thermostable protein complexes and to map protein-protein interactions.

  16. Mechanistic differences between methanol and dimethyl ether carbonylation in side pockets and large channels of mordenite.

    Science.gov (United States)

    Boronat, Mercedes; Martínez, Cristina; Corma, Avelino

    2011-02-21

    The activity and selectivity towards carbonylation presented by Brønsted acid sites located inside the 8MR pockets or in the main 12MR channels of mordenite is studied by means of quantum-chemical calculations, and the mechanistic differences between methanol and DME carbonylation are investigated. The selectivity towards carbonylation is higher inside the 8MR pockets, where the competitive formation of DME and hydrocarbons that finally leads to catalyst deactivation is sterically impeded. Moreover, inclusion of dispersion interactions in the calculations leads to agreement between the calculated activation barriers for the rate determining step and the experimentally observed higher reactivity of methoxy groups located inside the 8MR channels.

  17. Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory

    NARCIS (Netherlands)

    Kiewisch, K.; Jacob, C.R.; Visscher, L.

    2013-01-01

    The ability to calculate accurate electron densities of full proteins or of selected sites in proteins is a prerequisite for a fully quantum-mechanical calculation of protein-protein and protein-ligand interaction energies. Quantum-chemical subsystem methods capable of treating proteins and other

  18. Transition metal catalyzed carbonylation reactions carbonylative activation of C-X bonds

    CERN Document Server

    Beller, Matthias

    2014-01-01

    This book provides students and researchers in organic synthesis with a detailed discussion of carbonylation from the basics through to applications. It discusses the past, present and future of carbonylation reactions.

  19. Positively selected sites in cetacean myoglobins contribute to protein stability

    DEFF Research Database (Denmark)

    Dasmeh, Pouria; Serohijos, Adrian W R; Kepp, Kasper P

    2013-01-01

    Since divergence ∼50 Ma ago from their terrestrial ancestors, cetaceans underwent a series of adaptations such as a ∼10-20 fold increase in myoglobin (Mb) concentration in skeletal muscle, critical for increasing oxygen storage capacity and prolonging dive time. Whereas the O2-binding affinity...... between Mb folding stability and protein abundance, suggesting that a selection pressure for stability acts proportionally to higher expression. We also identify a major divergence event leading to the common ancestor of whales, during which major stabilization occurred. Most of the positively selected...

  20. Protein and energy metabolism in two lines of chickens selected for growth on high or low protein diets

    DEFF Research Database (Denmark)

    Chwalibog, André; Eggum, B O; Sørensen, Peter

    1983-01-01

    Genetic adaptation was investigated in broilers selected for seven generations on a normal (A) or a low (B) protein diet. Protein and energy metabolism were studied in males from these selected lines fed on a diet of intermediate protein content. All selected birds retained more nitrogen than those...

  1. Proteomic evaluation of myofibrillar carbonylation in chilled fish mince and its inhibition by catechin.

    Science.gov (United States)

    Pazos, Manuel; Maestre, Rodrigo; Gallardo, José M; Medina, Isabel

    2013-01-01

    The present study investigates the susceptibility of individual myofibrillar proteins from mackerel (Scomber scombrus) mince to undergo carbonylation reactions during chilled storage, and the antioxidant capacity of (+)-catechin to prevent oxidative processes of proteins. The carbonylation of each particular protein was quantified by combining the labelling of protein carbonyls by fluorescein-5-thiosemicarbazide (FTSC) with 1-D or 2-D gel electrophoresis. Alpha skeletal actin, glycogen phosphorylase, unnamed protein product (UNP) similar to enolase, pyruvate kinase, isoforms of creatine kinase, aldolase A and an isoform of glyceraldehyde 3-phosphate dehydrogenase (G3PDH) showed elevated oxidation in chilled non-supplemented mince. Myosin heavy chain (MHC) was not carbonylated in chilled muscle, but an extensive MHC degradation was observed in those samples. The supplementation of catechin reduced protein oxidation and lipid oxidation in a concentration-dependent manner: control>25>100≈200ppm. Therefore, the highest catechin concentrations (100 and 200ppm) exhibited the strongest antioxidant activity. Catechin (200ppm) reduced significantly carbonylation of protein spots identified as glycogen phosphorylase, pyruvate kinase muscle isozyme, isoforms of creatine kinase. Conversely, catechin was ineffective to inhibit the oxidation of actin and UNP similar to enolase. These results draw attention to the inefficiency of catechin to prevent actin oxidation, in contrast to the extremely high efficiency of catechin in inhibiting oxidation of lipids and other proteins. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Site-selective 13C labeling of proteins using erythrose

    International Nuclear Information System (INIS)

    Weininger, Ulrich

    2017-01-01

    NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with 13 C and/or 1 H, which is achieved in the most general way by using site-selectively 13 C-enriched glucose (1- and 2- 13 C) as the carbon source in bacterial expression systems. Using this strategy, multiple sites in side chains, including aromatics, become site-selectively labeled and suitable for relaxation studies. Here we systematically investigate the use of site-selectively 13 C-enriched erythrose (1-, 2-, 3- and 4- 13 C) as a suitable precursor for 13 C labeled aromatic side chains. We quantify 13 C incorporation in nearly all sites in all 20 amino acids and compare the results to glucose based labeling. In general the erythrose approach results in more selective labeling. While there is only a minor gain for phenylalanine and tyrosine side-chains, the 13 C incorporation level for tryptophan is at least doubled. Additionally, the Phe ζ and Trp η2 positions become labeled. In the aliphatic side chains, labeling using erythrose yields isolated 13 C labels for certain positions, like Ile β and His β, making these sites suitable for dynamics studies. Using erythrose instead of glucose as a source for site-selective 13 C labeling enables unique or superior labeling for certain positions and is thereby expanding the toolbox for customized isotope labeling of amino-acid side-chains.

  3. Accumulation of carbonyls accelerates the formation of pentosidine, an advanced glycation end product: carbonyl stress in uremia.

    Science.gov (United States)

    Miyata, T; Ueda, Y; Yamada, Y; Izuhara, Y; Wada, T; Jadoul, M; Saito, A; Kurokawa, K; van Ypersele de Strihou, C

    1998-12-01

    Advanced glycation end product (AGE) formation is related to hyperglycemia in diabetes but not in uremia, because plasma AGE levels do not differ between diabetic and nondiabetic hemodialysis patients. The mechanism of this phenomenon remains elusive. Previously, it was suggested that elevation of AGE levels in uremia might result from the accumulation of unknown AGE precursors. The present study evaluates the in vitro generation of pentosidine, a well identified AGE structure. Plasma samples from healthy subjects and nondiabetic hemodialysis patients were incubated under air for several weeks. Pentosidine levels were determined at intervals by HPLC assay. Pentosidine rose to a much larger extent in uremic than in control plasma. Pentosidine yield, i.e., the change in pentosidine level between 0 and 4 wk divided by 28 d, averaged 0.172 nmol/ml per d in uremic versus 0.072 nmol/ml per d in control plasma (P aminoguanidine and OPB-9195, which inhibit the Maillard reaction, lowered pentosidine yield in both uremic and control plasma. When ultrafiltrated plasma was exposed to 2,4-dinitrophenylhydrazine, the yield of hydrazones, formed by interaction with carbonyl groups, was markedly higher in uremic than in control plasma. These observations strongly suggest that the pentosidine precursors accumulated in uremic plasma are carbonyl compounds. These precursors are unrelated to glucose or ascorbic acid, whose concentration is either normal or lowered in uremic plasma. They are also unrelated to 3-deoxyglucosone, a glucose-derived dicarbonyl compound whose level is raised in uremic plasma: Its addition to normal plasma fails to increase pentosidine yield. This study reports an elevated level of reactive carbonyl compounds ("carbonyl stress") in uremic plasma. Most have a lower than 5000 Da molecular weight and are thus partly removed by hemodialysis. Their effect on pentosidine generation can be inhibited by aminoguanidine or OPB-9195. Carbonyl stress might contribute to

  4. Blood carbonyl protein measurement as a specific oxidative stress biomarker after intestinal reperfusion in rats Dosagem da proteína carbonilada sanguínea como biomarcador específico do estresse oxidativo após reperfusão intestinal em ratos

    Directory of Open Access Journals (Sweden)

    Márcio José Jamel

    2010-02-01

    Full Text Available PURPOSE: An experimental study was performed to investigate the use of protein carbonyl group as a specific biological marker for oxidative stress in a rat model of intestinal ischaemia-reperfusion. METHODS: Twenty four male Wistar rats were randomly distributed into three groups with eight animals each: Group 1 - Control group; Group 2 - Sham; Group 3 - Intestinal ischaemia by clamping ileal branches of the superior mesenteric artery for one hour, followed by another hour of reperfusion. Blood samples were taken in order to analyze the protein carbonyl level by Slot blotting assay. RESULTS: In group 3 a significant increase of protein carbonyl level was observed if compared to the homogenous levels of groups 1 and 2. CONCLUSION: From the results it may be concluded that the protein carbonylation may be used as a specific marker for measuring oxidative stress in rat intestinal reperfusion model.OBJETIVO: Realizou-se um estudo experimental com a finalidade de investigar o uso da proteína carbonilada como um marcador biológico específico do estresse oxidativo em um modelo de isquemia e reperfusão intestinal, em ratos. MÉTODOS: Vinte e quarto ratos da linhagem Wistar, machos foram distribuídos, aleatoriamente, em três grupos compostos por oito animais cada: Grupo 1 - Controle; Grupo 2 - Simulação e Grupo 3 - Submetido à isquemia, mediante clampeamento de ramos ileais da artéria mesentérica superior por uma hora, seguida de reperfusão, por igual período. Amostras sanguíneas obtidas foram utilizadas para analise dos níveis de proteína carbonilada, através do método Slot blotting. RESULTADOS: No grupo 3 houve uma elevação significante da concentração de proteína carbonilada sérica se comparada aos níveis sanguíneos homogêneos encontrados nos grupos 1 e 2. CONCLUSÃO: Fundamentado nos resultados é possível concluir que, a carbonilação protéica pode ser utilizada como um marcador específico para a mensuração do

  5. Identification of physicochemical selective pressure on protein encoding nucleotide sequences

    Directory of Open Access Journals (Sweden)

    Sainudiin Raazesh

    2006-03-01

    Full Text Available Abstract Background Statistical methods for identifying positively selected sites in protein coding regions are one of the most commonly used tools in evolutionary bioinformatics. However, they have been limited by not taking the physiochemical properties of amino acids into account. Results We develop a new codon-based likelihood model for detecting site-specific selection pressures acting on specific physicochemical properties. Nonsynonymous substitutions are divided into substitutions that differ with respect to the physicochemical properties of interest, and those that do not. The substitution rates of these two types of changes, relative to the synonymous substitution rate, are then described by two parameters, γ and ω respectively. The new model allows us to perform likelihood ratio tests for positive selection acting on specific physicochemical properties of interest. The new method is first used to analyze simulated data and is shown to have good power and accuracy in detecting physicochemical selective pressure. We then re-analyze data from the class-I alleles of the human Major Histocompatibility Complex (MHC and from the abalone sperm lysine. Conclusion Our new method allows a more flexible framework to identify selection pressure on particular physicochemical properties.

  6. Fluoride-Mediated Dephosphonylation of α-Diazo-β-carbonyl Phosphonates.

    Science.gov (United States)

    Phatake, Ravindra S; Mullapudi, Venkannababu; Wakchaure, Vivek C; Ramana, Chepuri V

    2017-01-20

    The possibility of fluoride-mediated selective dephosphonylation of α-diazo-β-carbonyl phosphonates such as the Ohira-Bestmann reagent has been proposed and executed. The resulting α-diazocarbonyl intermediates undergo a (3 + 2)-cycloaddition at room temperature with conjugated olefins and benzynes. Interestingly, under the current conditions, the resulting cycloaddition products underwent either N-acylation (with excess α-diazo-β-carbonyl phosphonates) or Michael addition (with conjugated olefins).

  7. Selective inhibition of Biotin Protein Ligase from Staphylococcus aureus*

    Science.gov (United States)

    Soares da Costa, Tatiana P.; Tieu, William; Yap, Min Y.; Pendini, Nicole R.; Polyak, Steven W.; Sejer Pedersen, Daniel; Morona, Renato; Turnidge, John D.; Wallace, John C.; Wilce, Matthew C. J.; Booker, Grant W.; Abell, Andrew D.

    2012-01-01

    There is a well documented need to replenish the antibiotic pipeline with new agents to combat the rise of drug resistant bacteria. One strategy to combat resistance is to discover new chemical classes immune to current resistance mechanisms that inhibit essential metabolic enzymes. Many of the obvious drug targets that have no homologous isozyme in the human host have now been investigated. Bacterial drug targets that have a closely related human homologue represent a new frontier in antibiotic discovery. However, to avoid potential toxicity to the host, these inhibitors must have very high selectivity for the bacterial enzyme over the human homolog. We have demonstrated that the essential enzyme biotin protein ligase (BPL) from the clinically important pathogen Staphylococcus aureus could be selectively inhibited. Linking biotin to adenosine via a 1,2,3 triazole yielded the first BPL inhibitor selective for S. aureus BPL over the human equivalent. The synthesis of new biotin 1,2,3-triazole analogues using click chemistry yielded our most potent structure (Ki 90 nm) with a >1100-fold selectivity for the S. aureus BPL over the human homologue. X-ray crystallography confirmed the mechanism of inhibitor binding. Importantly, the inhibitor showed cytotoxicity against S. aureus but not cultured mammalian cells. The biotin 1,2,3-triazole provides a novel pharmacophore for future medicinal chemistry programs to develop this new antibiotic class. PMID:22437830

  8. Selective inhibition of biotin protein ligase from Staphylococcus aureus.

    Science.gov (United States)

    Soares da Costa, Tatiana P; Tieu, William; Yap, Min Y; Pendini, Nicole R; Polyak, Steven W; Sejer Pedersen, Daniel; Morona, Renato; Turnidge, John D; Wallace, John C; Wilce, Matthew C J; Booker, Grant W; Abell, Andrew D

    2012-05-18

    There is a well documented need to replenish the antibiotic pipeline with new agents to combat the rise of drug resistant bacteria. One strategy to combat resistance is to discover new chemical classes immune to current resistance mechanisms that inhibit essential metabolic enzymes. Many of the obvious drug targets that have no homologous isozyme in the human host have now been investigated. Bacterial drug targets that have a closely related human homologue represent a new frontier in antibiotic discovery. However, to avoid potential toxicity to the host, these inhibitors must have very high selectivity for the bacterial enzyme over the human homolog. We have demonstrated that the essential enzyme biotin protein ligase (BPL) from the clinically important pathogen Staphylococcus aureus could be selectively inhibited. Linking biotin to adenosine via a 1,2,3 triazole yielded the first BPL inhibitor selective for S. aureus BPL over the human equivalent. The synthesis of new biotin 1,2,3-triazole analogues using click chemistry yielded our most potent structure (K(i) 90 nM) with a >1100-fold selectivity for the S. aureus BPL over the human homologue. X-ray crystallography confirmed the mechanism of inhibitor binding. Importantly, the inhibitor showed cytotoxicity against S. aureus but not cultured mammalian cells. The biotin 1,2,3-triazole provides a novel pharmacophore for future medicinal chemistry programs to develop this new antibiotic class.

  9. Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling

    DEFF Research Database (Denmark)

    Simonsen, Martin; Maetschke, S.R.; Ragan, M.A.

    2012-01-01

    Motivation: Phylogenetic profiling methods can achieve good accuracy in predicting protein–protein interactions, especially in prokaryotes. Recent studies have shown that the choice of reference taxa (RT) is critical for accurate prediction, but with more than 2500 fully sequenced taxa publicly......: We present three novel methods for automating the selection of RT, using machine learning based on known protein–protein interaction networks. One of these methods in particular, Tree-Based Search, yields greatly improved prediction accuracies. We further show that different methods for constituting...... phylogenetic profiles often require very different RT sets to support high prediction accuracy....

  10. Selecting highly structure-specific antibodies using structured synthetic mimics of the cystine knot protein sclerostin

    NARCIS (Netherlands)

    Back, J.W.; Frisch, C.; Van Pee, K.; Boschert, V.; van Vught, R.; Puijk, W.; Mueller, T. D.; Knappik, A.; Timmerman, P.

    2012-01-01

    Antibodies directed against specific regions of a protein have traditionally been raised against full proteins, protein domains or simple unstructured peptides, containing contiguous stretches of primary sequence. We have used a new approach of selecting antibodies against restrained peptides

  11. Protein structure and ionic selectivity in calcium channels: selectivity filter size, not shape, matters.

    Science.gov (United States)

    Malasics, Attila; Gillespie, Dirk; Nonner, Wolfgang; Henderson, Douglas; Eisenberg, Bob; Boda, Dezso

    2009-12-01

    Calcium channels have highly charged selectivity filters (4 COO(-) groups) that attract cations in to balance this charge and minimize free energy, forcing the cations (Na(+) and Ca(2+)) to compete for space in the filter. A reduced model was developed to better understand the mechanism of ion selectivity in calcium channels. The charge/space competition (CSC) mechanism implies that Ca(2+) is more efficient in balancing the charge of the filter because it provides twice the charge as Na(+) while occupying the same space. The CSC mechanism further implies that the main determinant of Ca(2+) versus Na(+) selectivity is the density of charged particles in the selectivity filter, i.e., the volume of the filter (after fixing the number of charged groups in the filter). In this paper we test this hypothesis by changing filter length and/or radius (shape) of the cylindrical selectivity filter of our reduced model. We show that varying volume and shape together has substantially stronger effects than varying shape alone with volume fixed. Our simulations show the importance of depletion zones of ions in determining channel conductance calculated with the integrated Nernst-Planck equation. We show that confining the protein side chains with soft or hard walls does not influence selectivity.

  12. Kinetics of carbonyl reductase from human brain.

    OpenAIRE

    Bohren, K M; von Wartburg, J P; Wermuth, B

    1987-01-01

    Initial-rate analysis of the carbonyl reductase-catalysed reduction of menadione by NADPH gave families of straight lines in double-reciprocal plots consistent with a sequential mechanism being obeyed. The fluorescence of NADPH was increased up to 7-fold with a concomitant shift of the emission maximum towards lower wavelength in the presence of carbonyl reductase, and both NADPH and NADP+ caused quenching of the enzyme fluorescence, indicating formation of a binary enzyme-coenzyme complex. D...

  13. Selecting for Fast Protein-Protein Association As Demonstrated on a Random TEM1 Yeast Library Binding BLIP.

    Science.gov (United States)

    Cohen-Khait, Ruth; Schreiber, Gideon

    2018-04-27

    Protein-protein interactions mediate the vast majority of cellular processes. Though protein interactions obey basic chemical principles also within the cell, the in vivo physiological environment may not allow for equilibrium to be reached. Thus, in vitro measured thermodynamic affinity may not provide a complete picture of protein interactions in the biological context. Binding kinetics composed of the association and dissociation rate constants are relevant and important in the cell. Therefore, changes in protein-protein interaction kinetics have a significant impact on the in vivo activity of the proteins. The common protocol for the selection of tighter binders from a mutant library selects for protein complexes with slower dissociation rate constants. Here we describe a method to specifically select for variants with faster association rate constants by using pre-equilibrium selection, starting from a large random library. Toward this end, we refine the selection conditions of a TEM1-β-lactamase library against its natural nanomolar affinity binder β-lactamase inhibitor protein (BLIP). The optimal selection conditions depend on the ligand concentration and on the incubation time. In addition, we show that a second sort of the library helps to separate signal from noise, resulting in a higher percent of faster binders in the selected library. Fast associating protein variants are of particular interest for drug development and other biotechnological applications.

  14. Cytoprotective Effects of Pumpkin (Cucurbita Moschata) Fruit Extract against Oxidative Stress and Carbonyl Stress.

    Science.gov (United States)

    Shayesteh, Reyhaneh; Kamalinejad, Mohammad; Adiban, Hasan; Kardan, Azin; Keyhanfar, Fariborz; Eskandari, Mohammad Reza

    2017-10-01

    Background Diabetes mellitus is a chronic endocrine disorder that is associated with significant mortality and morbidity due to microvascular and macrovascular complications. Diabetes complications accompanied with oxidative stress and carbonyl stress in different organs of human body because of the increased generation of free radicals and impaired antioxidant defense systems. In the meantime, reactive oxygen species (ROS) and reactive carbonyl species (RCS) have key mediatory roles in the development and progression of diabetes complications. Therapeutic strategies have recently focused on preventing such diabetes-related abnormalities using different natural and chemical compounds. Pumpkin ( Cucurbita moschata ) is one of the most important vegetables in the world with a broad-range of pharmacological activities such as antihyperglycemic effect. Methods In the present study, the cytoprotective effects of aqueous extract of C. moschata fruit on hepatocyte cytotoxicity induced by cumene hydroperoxide (oxidative stress model) or glyoxal (carbonylation model) were investigated using freshly isolated rat hepatocytes. Results The extract of C. moschata (50 μg/ml) excellently prevented oxidative and carbonyl stress markers, including hepatocyte lysis, ROS production, lipid peroxidation, glutathione depletion, mitochondrial membrane potential collapse, lysosomal damage, and cellular proteolysis. In addition, protein carbonylation was prevented by C. moschata in glyoxal-induced carbonyl stress. Conclusion It can be concluded that C. moschata has cytoprotective effects in oxidative stress and carbonyl stress models and this valuable vegetable can be considered as a suitable herbal product for the prevention of toxic subsequent of oxidative stress and carbonyl stress seen in chronic hyperglycemia. © Georg Thieme Verlag KG Stuttgart · New York.

  15. Proteomic and carbonylation profile analysis of rat skeletal muscles following acute swimming exercise.

    Directory of Open Access Journals (Sweden)

    Francesca Magherini

    Full Text Available Previous studies by us and other groups characterized protein expression variation following long-term moderate training, whereas the effects of single bursts of exercise are less known. Making use of a proteomic approach, we investigated the effects of acute swimming exercise (ASE on protein expression and carbonylation patterns in two hind limb muscles: the Extensor Digitorum Longus (EDL and the Soleus, mostly composed of fast-twitch and slow-twitch fibres, respectively. Carbonylation is one of the most common oxidative modifications of proteins and a marker of oxidative stress. In fact, several studies suggest that physical activity and the consequent increase in oxygen consumption can lead to increase in reactive oxygen and nitrogen species (RONS production, hence the interest in examining the impact of RONS on skeletal muscle proteins following ASE. Results indicate that protein expression is unaffected by ASE in both muscle types. Unexpectedly, the protein carbonylation level was reduced following ASE. In particular, the analysis found 31 and 5 spots, in Soleus and EDL muscles respectively, whose carbonylation is reduced after ASE. Lipid peroxidation levels in Soleus were markedly reduced as well. Most of the decarbonylated proteins are involved either in the regulation of muscle contractions or in the regulation of energy metabolism. A number of hypotheses may be advanced to account for such results, which will be addressed in future studies.

  16. Emissions of Toxic Carbonyls in an Electronic Cigarette

    Directory of Open Access Journals (Sweden)

    Guthery William

    2016-01-01

    Full Text Available Electronic cigarettes (e-cigs provide a smoke-free alternative for inhalation of nicotine without the vast array of toxic and carcinogenic combustion products produced by tobacco smoke. Elevated levels of toxic carbonyls may be generated during vaporisation; however, it is unclear whether that is indicative of a fault with the device or is due to the applied conditions of the test. A device, designed and built at this facility, was tested to determine the levels of selected toxic carbonyls. The reservoir was filled with approximately 960 mg of an e-liquid formulation containing 1.8% (w/v nicotine. Devices were puffed 200 times in blocks of 40 using a standardised regime consisting of a 55 mL puff volume; 3 s puff duration; 30 s puff interval; square wave puff profile. Confirmatory testing for nicotine and total aerosol delivery resulted in mean (n = 8 values of 10 mg (RSD 12.3% and 716 mg (RSD 11.2%, respectively. Emissions of toxic carbonyls were highly variable yet were between < 0.1% and 22.9% of expected levels from a Kentucky Reference Cigarette (K3R4F puffed 200 times under Health Canada Intense smoking conditions. It has been shown that a device built to a high specification with relatively consistent nicotine and aerosol delivery emits inconsistent levels of carbonyls. The exposure is greatly reduced when compared with lit tobacco products. However, it was observed that as the reservoirs neared depletion then emission levels were significantly higher

  17. Protein selectivity with immobilized metal ion-tacn sorbents: chromatographic studies with human serum proteins and several other globular proteins.

    Science.gov (United States)

    Jiang, W; Graham, B; Spiccia, L; Hearn, M T

    1998-01-01

    The chromatographic selectivity of the immobilized chelate system, 1,4,7-triazocyclononane (tacn), complexed with the borderline metal ions Cu2+, Cr3+, Mn2+, Co2+, Zn2+, and Ni2+ has been investigated with hen egg white lysozyme, horse heart cytochrome c, and horse skeletal muscle myoglobin, as well as proteins present in partially fractionated preparations of human plasma. The effects of ionic strength and pH of the loading and elution buffers on protein selectivities of these new immobilized metal ion affinity chromatographic (IMAC) systems have been examined. The results confirm that immobilized Mn;pl-tacn sorbents exhibit a novel type of IMAC behavior with proteins. In particular, the chromatographic properties of these immobilized M(n+)-tacn ligand systems were significantly different compared to the IMAC behavior observed with other types of immobilized tri- and tetradentate chelating ligands, such as iminodiacetic acid, O-phosphoserine, or nitrilotriacetic acid, when complexed with borderline metal ions. The experimental results have consequently been evaluated in terms of the additional contributions to the interactive processes mediated by effects other than solely the conventional lone pair Lewis soft acid-Lewis soft base coordination interactions, typically found for the IMAC of proteins with borderline and soft metal ions, such as Cu2+ or Ni2+.

  18. Predicting personal exposure to airborne carbonyls using residential measurements and time/activity data

    Science.gov (United States)

    Liu, Weili; Zhang, Junfeng (Jim); Korn, Leo R.; Zhang, Lin; Weisel, Clifford P.; Turpin, Barbara; Morandi, Maria; Stock, Tom; Colome, Steve

    As a part of the Relationships of Indoor, Outdoor, and Personal Air (RIOPA) study, 48 h integrated residential indoor, outdoor, and personal exposure concentrations of 10 carbonyls were simultaneously measured in 234 homes selected from three US cities using the Passive Aldehydes and Ketones Samplers (PAKS). In this paper, we examine the feasibility of using residential indoor concentrations to predict personal exposures to carbonyls. Based on paired t-tests, the means of indoor concentrations were not different from those of personal exposure concentrations for eight out of the 10 measured carbonyls, indicating indoor carbonyls concentrations, in general, well predicted the central tendency of personal exposure concentrations. In a linear regression model, indoor concentrations explained 47%, 55%, and 65% of personal exposure variance for formaldehyde, acetaldehyde, and hexaldehyde, respectively. The predictability of indoor concentrations on cross-individual variability in personal exposure for the other carbonyls was poorer, explainingexposure concentrations. It was found that activities related to driving a vehicle and performing yard work had significant impacts on personal exposures to a few carbonyls.

  19. Measurements of carbonyls in a 13-story building.

    Science.gov (United States)

    Báez, Armando P; Padilla, Hugo G; García, Rocío M; Belmont, Raúl D; Torres, Maria del Carmen B

    2004-01-01

    Formaldehyde and acetaldehyde are emitted by many mobile and stationary sources and secondary aldehydes are intermediates in the photo-oxidation of organic compounds in the atmosphere. These aldehydes are emitted indoors by many materials such as furniture, carpets, heating and cooling systems, an by smoking. Carbonyls, mainly formaldehyde and acetaldehyde, have been studied because of their adverse health effects. In addition, formaldehyde is a suspected carcinogen. Therefore, the concentrations of formaldehyde and acetaldehyde were determined to assess the inhalation exposure doses to carbonyls for people who work in a 13-story building and in order to evaluate the cancer hazard. Carbonyl compounds in indoor and outdoor air were measured at a 13-story building located in Mexico City. The mezzanine, fifth and tenth floors, and the third level-parking garage were selected for sampling. Samples were collected in two sampling periods, the first from April 20 to 29, 1998 and the second from December 1 to 20, 1998. Carbonyls were sampled by means of DNHP-coated cartridges at a flow rate of 1 l min(-1) from 9:00 to 19:00 hours, during 2-hour time intervals and analyzed by HPLC with hours, during 2-hour time intervals and analyzed by HPLC with UV/VIS detection. Mean carbonyl concentrations were highest in the 3rd level-parking garage, with the formaldehyde concentration being the highest ranging from 108 to 418 microg m(-3). In working areas, the highest carbonyl arithmetic mean concentrations (AM) were observed on the 5th floor. Acetone and formaldehyde concentrations were highest in April ranging from 161 to 348 microg m(-3) (AM = 226) and from 157 to 270 microg m(-3) (AM = 221), respectively. Propionaldehyde and butyraldehyde were present in smaller concentrations ranging from 2 to 25 and 1 to 28 microg m(-3), respectively, considering all the samples. Mean indoor/outdoor ratios of carbonyls ranged from 1.8 to 9.6. A reduction of inhalation exposure doses of 41% and

  20. Different Stationary Phase Selectivities and Morphologies for Intact Protein Separations

    NARCIS (Netherlands)

    Astefanei, A.; Dapic, I.; Camenzuli, M.

    The central dogma of biology proposed that one gene encodes for one protein. We now know that this does not reflect reality. The human body has approximately 20,000 protein-encoding genes; each of these genes can encode more than one protein. Proteins expressed from a single gene can vary in terms

  1. A versatile selection system for folding competent proteins using genetic complementation in a eukaryotic host

    DEFF Research Database (Denmark)

    Lyngsø, C.; Kjaerulff, S.; Muller, S.

    2010-01-01

    in vivo selection system for folded proteins. It is based on genetic complementation of the Schizosaccharomyces pombe growth marker gene invertase fused C-terminally to a protein library. The fusion proteins are directed to the secretion system, utilizing the ability of the eukaryotic protein quality...

  2. First application of supported ionic liquid phase (SILP) catalysis for continuous methanol carbonylation

    DEFF Research Database (Denmark)

    Riisager, Anders; Jørgensen, Betina; Wasserscheid, Peter

    2006-01-01

    A solid, silica-supported ionic liquid phase (SILP) rhodium iodide Monsanto-type catalyst system, [BMIM][Rh(CO)(2)I-2]-[BMIM]I -SiO2, exhibits excellent activity and selectivity towards acetyl products in fixed-bed, continuous gas-phase methanol carbonylation.......A solid, silica-supported ionic liquid phase (SILP) rhodium iodide Monsanto-type catalyst system, [BMIM][Rh(CO)(2)I-2]-[BMIM]I -SiO2, exhibits excellent activity and selectivity towards acetyl products in fixed-bed, continuous gas-phase methanol carbonylation....

  3. Spatiotemporal distribution of carbonyl compounds in China

    International Nuclear Information System (INIS)

    Ho, K.F.; Ho, Steven Sai Hang; Huang, R.-J.; Dai, W.T.; Cao, J.J.; Tian, Linwei; Deng, W.J.

    2015-01-01

    A sampling campaign was carried out at nine Chinese cities in 2010/2011. Fifteen monocarbonyls (C#= 1–9) were quantified. Temperature is the rate-determining factor of the summertime carbonyl levels. The carbonyl emissions in winter are mainly driven by the primary anthropogenic sources like automobile. A molar ratio of propionaldehyde to nonaldehyde is a barometer of the impact of atmospheric vegetation emission which suggesting that strong vegetation emissions exist in summer and high propionaldehyde abundance is caused by fossil fuel combustion in winter. Potential health risk assessment of formaldehyde and acetaldehyde was conducted and the highest cumulative risks were observed at Chengdu in summer and Wuhan in winter. Because of the strong photochemical reaction and large amount of anthropogenic emissions, high concentrations of carbonyl compounds were observed in Chengdu. The use of ethanol-blended gasoline in Wuhan is the key reason of acetaldehyde emission and action should be taken to avoid potential health risks. - Highlights: • A national wide survey of ambient carbonyl compounds were conducted in China. • Using ethanol-blended gasoline can lead to higher cancer risks. • High concentrations of HMW carbonyls (C6, C7, C8 and C9) were observed in all cities. • HMW carbonyls (C6–C9) species show a very consistent seasonal variation. • C 3 /C 9 acts as an indicator for the impact of vegetation emission in the atmosphere. - Capsule abstract: Strong vegetation emission occurs in summer atmosphere and high acetaldehyde emission due to ethanol-blended gasoline consumption in 9 Chinese cities is discouraged

  4. Catalytic reactions of synthesis gas. Part 2. Methanol carbonylation and homologation

    Energy Technology Data Exchange (ETDEWEB)

    Niemelae, M.

    1993-01-01

    The aim of the review is to evaluate the applicability of methanol hydrocarbonylation as a second test reaction to study the nondissociative activation of CO by heterogeneous rhodium and cobalt catalysts. The main emphasis in methanol (hydro)carbonylation chemistry has been on homogeneous reactions. These systems have been seen advantageous in selectivity, activity and ease of modification. The heterogenization attempts have been carried out to obtain easier separation of the catalyst and the product. The activity of cobalt, rhodium and other metals supported on different materials have been studied in heterogeneous methanol (hydro)carbonylation. The observed activities have been considerably influenced by the support. The most effective catalyst support has been activated carbon. Good carbonylation activities and selectivities have also been observed in conjunction with zeolite supports. The literature study indicates that the typical experimental conditions of methanol (hydro)carbonylation do not exceed the constructional and operational limits of the available reactor system, i.e. 500 C and 50 bar. The reaction is suitable for testing Co and Rh precursors, since both cobalt and rhodium compounds have shown carbonylation activity.

  5. Selectivity in protein degradation during sporulation of Bacillus subtilis

    International Nuclear Information System (INIS)

    Mitani, Takahiko; Kadota, Hajime

    1976-01-01

    The breakdown of cellular protein was investigated in Bacillus subtilis ATCC 6051 labeled with glycine-2- 3 H or L-phenylalanine-U- 14 C at the different stages of vegetative growth and sporulation. The growth of the culture was determined by measuring optical density at 660 nm. The heat-resistant spores were scored by plating after heating at 80 deg C for 10 minutes. A question whether the turnover of glycine-labeled protein is similar to that of phenylalanine-labeled protein was experimentally studied. The patterns obtained with the glycine-labeled protein were different from those of phenylalanine-labeled protein. This was not multiple turnover. The cellular protein which was labeled with glycine at an early stage of sporulation showed rapid degradation, but the degradation of the protein labeled with glycine at later stages did not occur at all. Another question whether the labeled glycine incorporated into cells at the different stages of growth and sporulation was present in the spore coat fraction of matured spores was studied. Experiment demonstrated that the glycine incorporated into cells at the late sporulation stage was mainly utilized for the biosynthesis of the spore coat protein. These data suggest that the spore coat protein which contains relatively large amount of glycine is rarely subject to further degradation. (Iwakiri, K.)

  6. Convenient Reduction of Carbonyl Compounds to their ...

    African Journals Online (AJOL)

    NICO

    Alcohols and their derivatives occupy an important position in organic synthesis. ... review also reveals that the reduction of carbonyl compounds ..... 1 H.B. Ji and Y.B. She, Green Oxidation and Reduction, China Petrochemi- cal Press, Beijing ...

  7. Millimeter wave spectra of carbonyl cyanide ⋆

    Science.gov (United States)

    Bteich, S.B.; Tercero, B.; Cernicharo, J.; Motiyenko, R.A.; Margulès, L.; Guillemin, J.-C.

    2016-01-01

    Context More than 30 cyanide derivatives of simple organic molecules have been detected in the interstellar medium, but only one dicarbonitrile has been found and that very recently. There is still a lack of high-resolution spectroscopic data particularly for dinitriles derivatives. The carbonyl cyanide molecule is a new and interesting candidate for astrophysical detection. It could be formed by the reaction of CO and CN radicals, or by substitution of the hydrogen atom by a cyano group in cyanoformaldehyde, HC(=O)CN, that has already been detected in the interstellar medium. Aims The available data on the rotational spectrum of carbonyl cyanide is limited in terms of quantum number values and frequency range, and does not allow accurate extrapolation of the spectrum into the millimeter-wave range. To provide a firm basis for astrophysical detection of carbonyl cyanide we studied its millimeter-wave spectrum. Methods The rotational spectrum of carbonyl cyanide was measured in the frequency range 152 - 308 GHz and analyzed using Watson’s A- and S-reduction Hamiltonians. Results The ground and first excited state of v5 vibrational mode were assigned and analyzed. More than 1100 distinct frequency lines of the ground state were fitted to produce an accurate set of rotational and centrifugal distortion constants up to the eighth order. The frequency predictions based on these constants should be accurate enough for astrophysical searches in the frequency range up to 500 GHz and for transition involving energy levels with J ≤ 100 and Ka ≤ 42. Based on the results we searched for interstellar carbonyl cyanide in available observational data without success. Thus, we derived upper limits to its column density in different sources. PMID:27738349

  8. Method for conversion of .beta.-hydroxy carbonyl compounds

    Science.gov (United States)

    Lilga, Michael A.; White, James F.; Holladay, Johnathan E.; Zacher, Alan H.; Muzatko, Danielle S.; Orth, Rick J.

    2010-03-30

    A process is disclosed for conversion of salts of .beta.-hydroxy carbonyl compounds forming useful conversion products including, e.g., .alpha.,.beta.-unsaturated carbonyl compounds and/or salts of .alpha.,.beta.-unsaturated carbonyl compounds. Conversion products find use, e.g., as feedstock and/or end-use chemicals.

  9. Protein scaffolds for selective enrichment of metal ions

    Science.gov (United States)

    He, Chuan; Zhou, Lu; Bosscher, Michael

    2016-02-09

    Polypeptides comprising high affinity for the uranyl ion are provided. Methods for binding uranyl using such proteins are likewise provided and can be used, for example, in methods for uranium purification or removal.

  10. Formation and emissions of carbonyls during and following gas-phase ozonation of indoor materials

    DEFF Research Database (Denmark)

    Poppendieck, D.G.; Hubbard, H.F.; Weschler, Charles J.

    2007-01-01

    at concentrations of 1000 ppm in the inlet stream of experimental chambers. Fifteen target carbonyls were selected and measured as building ozonation by-products (BOBPs). During the 36 h that include the 16 h ozonation and 20 h persistence phase, the total BOBP mass released from flooring and wall coverings ranged...

  11. First application of supported ionic liquid phase (SILP) catalysis for continuous methanol carbonylation.

    Science.gov (United States)

    Riisager, Anders; Jørgensen, Betina; Wasserscheid, Peter; Fehrmann, Rasmus

    2006-03-07

    A solid, silica-supported ionic liquid phase (SILP) rhodium iodide Monsanto-type catalyst system, [BMIM][Rh(CO)2I2]-[BMIM]I-SiO2, exhibits excellent activity and selectivity towards acetyl products in fixed-bed, continuous gas-phase methanol carbonylation.

  12. Selective dansylation of M protein within intact influenza virions

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, B.H.; Bennett, J.C.; Compans, R.W.

    1982-12-01

    Exposure of purified influenza virions to (/sup 14/C)dansyl chloride resulted in the covalent attachment of the dansyl chromophore to the virion. Gel electrophoresis revealed that the dansyl chromophore was specifically coupled to the internal membrane (M) protein. Purification of the M protein by gel filtration followed by cyanogen bromide cleavage and peptide fractionation revealed that four of six peptide peaks contained dansyl label. Acid hydrolysis of the separated peptide peaks followed by thin-layer chromatography revealed that dansyl label was coupled to lysine residues present in these peptides. The results of these investigations have demonstrated that the M protein molecule is the major viral polypeptide labeled when intact virions are exposed to dansyl chloride.

  13. Selective dansylation of M protein within intact influenza virions

    International Nuclear Information System (INIS)

    Robertson, B.H.; Bennett, J.C.; Compans, R.W.

    1982-01-01

    Exposure of purified influenza virions to [ 14 C]dansyl chloride resulted in the covalent attachment of the dansyl chromophore to the virion. Gel electrophoresis revealed that the dansyl chromophore was specifically coupled to the internal membrane (M) protein. Purification of the M protein by gel filtration followed by cyanogen bromide cleavage and peptide fractionation revealed that four of six peptide peaks contained dansyl label. Acid hydrolysis of the separated peptide peaks followed by thin-layer chromatography revealed that dansyl label was coupled to lysine residues present in these peptides. The results of these investigations have demonstrated that the M protein molecule is the major viral polypeptide labeled when intact virions are exposed to dansyl chloride

  14. Impaired cardiac SIRT1 activity by carbonyl stress contributes to aging-related ischemic intolerance.

    Directory of Open Access Journals (Sweden)

    Chunhu Gu

    Full Text Available Reactive aldehydes can initiate protein oxidative damage which may contribute to heart senescence. Sirtuin 1 (SIRT1 is considered to be a potential interventional target for I/R injury management in the elderly. We hypothesized that aldehyde mediated carbonyl stress increases susceptibility of aged hearts to ischemia/reperfusion (I/R injury, and elucidate the underlying mechanisms with a focus on SIRT1. Male C57BL/6 young (4-6 mo and aged (22-24 mo mice were subjected to myocardial I/R. Cardiac aldehyde dehydrogenase (ALDH2, SIRT1 activity and protein carbonyls were assessed. Our data revealed that aged heart exhibited increased endogenous aldehyde/carbonyl stress due to impaired ALDH2 activity concomitant with blunted SIRT1 activity (P<0.05. Exogenous toxic aldehydes (4-HNE exposure in isolated cardiomyocyte verified that aldehyde-induced carbonyl modification on SIRT1 impaired SIRT1 activity leading to worse hypoxia/reoxygenation (H/R injury, which could all be rescued by Alda-1 (ALDH2 activator (all P<0.05. However, SIRT1 inhibitor blocked the protective effect of Alda-1 on H/R cardiomyocyte. Interestingly, myocardial I/R leads to higher carbonylation but lower activity of SIRT1 in aged hearts than that seen in young hearts (P<0.05. The application of Alda-1 significantly reduced the carbonylation on SIRT1 and markedly improved the tolerance to in vivo I/R injury in aged hearts, but failed to protect Sirt1(+/- knockout mice against myocardial I/R injury. This was verified by Alda-1 treatment improved postischemic contractile function recovery in ex vivo perfused aged but not in Sirt1(+/- hearts. Thus, aldehyde/carbonyl stress is accelerated in aging heart. These results provide a new insight that impaired cardiac SIRT1 activity by carbonyl stress plays a critical role in the increased susceptibility of aged heart to I/R injury. ALDH2 activation can restore this aging-related myocardial ischemic intolerance.

  15. SILP catalysis in gas-phase hydroformylation and carbonylation

    Energy Technology Data Exchange (ETDEWEB)

    Riisager, A.; Fehrmann, R. [Technical Univ. of Denmark, Lyngby (Denmark). Dept. of Chemistry; Haumann, M.; Wasserscheid, P. [Univ. Erlangen-Nuernberg (Germany). Lehrstuhl fuer Chemische Reaktionstechnik

    2006-07-01

    Supported ionic liquid phase (SILP) catalysts are new materials consisting of an ionic liquid-metal catalyst solution highly dispersed on a porous support. The use of a non-volatile, ionic liquid catalyst phase in SILP catalysts results in a stable heterogeneous-type material with selectivity and efficiency like homogeneous catalysts. The silica-supported SILP Rh-bisphosphine hydroformylation catalyst exhibited good activities and excellent selectivities in gas phase hydroformylation with stability exceeding 700 hours time-on-stream. Spectroscopic and kinetic data confirmed the homogeneous nature of the catalyst. In the Rh- SILP catalysed carbonylation of methanol the formation of undesired by-products could be suppressed by variation of residence time and gas pressure. (orig.)

  16. Synthesis of dimethyl carbonate by oxidative carbonylation of methanol

    Energy Technology Data Exchange (ETDEWEB)

    Lee, B.G.; Han, M.S.; Kim, H.S.; Ahn, B.S.; Park, K.Y.

    1999-07-01

    Dimethyl carbonate (DMC) synthesis reaction by oxidative carbonylation of methanol has been studied using vapor phase flow reaction system in the presence of Cu-based catalysts. A series of Cu-based catalysts were prepared by the conventional impregnation method using activated carbon (AC) as support. The effect of various promoters and reaction conditions on the catalytic reactivities was intensively evaluated in terms of methanol conversion and DMC selectivity. The morphological change of catalysts during the reaction was also compared by X-ray diffraction and SEM analysis. Regardless of catalyst compositions, the optimal reaction temperature for oxidative carbonylation of methanol was found to be around 120--130 C. The reaction rate was too slow below 100 C, while too many by-products were produced above 150 C. Among the various catalysts employed, CuCl{sub 2}/NaOH/AC catalyst with the mole ratio of OH/Cu = 0.5--1.0 has shown the best catalytic performance, which appears to have a strong relationship with the formation of intermediate species, Cu{sub 2}(OH){sub 3}Cl.

  17. Organocatalytic Hydrophosphonylation Reaction of Carbonyl Groups.

    Science.gov (United States)

    Herrera, Raquel P

    2017-09-01

    This revision is covering the limited examples reported for a pivotal strategy in the formation of C-P bonds such as the asymmetric organocatalytic hydrophosphonylation of carbonyl groups (Pudovik reaction). The scope and limitations, and the proposed mechanisms for the scarce different possibilities of asymmetric induction are also shown. The recent evolution and future trends of this undeveloped approach are commented. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Feature selection and nearest centroid classification for protein mass spectrometry

    Directory of Open Access Journals (Sweden)

    Levner Ilya

    2005-03-01

    Full Text Available Abstract Background The use of mass spectrometry as a proteomics tool is poised to revolutionize early disease diagnosis and biomarker identification. Unfortunately, before standard supervised classification algorithms can be employed, the "curse of dimensionality" needs to be solved. Due to the sheer amount of information contained within the mass spectra, most standard machine learning techniques cannot be directly applied. Instead, feature selection techniques are used to first reduce the dimensionality of the input space and thus enable the subsequent use of classification algorithms. This paper examines feature selection techniques for proteomic mass spectrometry. Results This study examines the performance of the nearest centroid classifier coupled with the following feature selection algorithms. Student-t test, Kolmogorov-Smirnov test, and the P-test are univariate statistics used for filter-based feature ranking. From the wrapper approaches we tested sequential forward selection and a modified version of sequential backward selection. Embedded approaches included shrunken nearest centroid and a novel version of boosting based feature selection we developed. In addition, we tested several dimensionality reduction approaches, namely principal component analysis and principal component analysis coupled with linear discriminant analysis. To fairly assess each algorithm, evaluation was done using stratified cross validation with an internal leave-one-out cross-validation loop for automated feature selection. Comprehensive experiments, conducted on five popular cancer data sets, revealed that the less advocated sequential forward selection and boosted feature selection algorithms produce the most consistent results across all data sets. In contrast, the state-of-the-art performance reported on isolated data sets for several of the studied algorithms, does not hold across all data sets. Conclusion This study tested a number of popular feature

  19. Superoxide dismutase 1 is positively selected to minimize protein aggregation in great apes

    DEFF Research Database (Denmark)

    Dasmeh, Pouria; Kepp, Kasper Planeta

    2017-01-01

    Positive (adaptive) selection has recently been implied in human superoxide dismutase 1 (SOD1), a highly abundant antioxidant protein with energy signaling and antiaging functions, one of very few examples of direct selection on a human protein product (exon); the molecular drivers...... and SOD1 aggregates and triggered by aging. Our study thus marks an example of direct selection for a particular chemical phenotype (high net charge and stability) in a single human protein with possible implications for the evolution of aging....... of this selection are unknown. We mapped 30 extant SOD1 sequences to the recently established mammalian species tree and inferred ancestors, key substitutions, and signatures of selection during the protein's evolution. We detected elevated substitution rates leading to great apes (Hominidae) at ~1 per 2 million...

  20. Spatiotemporal distribution of carbonyl compounds in China.

    Science.gov (United States)

    Ho, K F; Ho, Steven Sai Hang; Huang, R-J; Dai, W T; Cao, J J; Tian, Linwei; Deng, W J

    2015-02-01

    A sampling campaign was carried out at nine Chinese cities in 2010/2011. Fifteen monocarbonyls (C# = 1-9) were quantified. Temperature is the rate-determining factor of the summertime carbonyl levels. The carbonyl emissions in winter are mainly driven by the primary anthropogenic sources like automobile. A molar ratio of propionaldehyde to nonaldehyde is a barometer of the impact of atmospheric vegetation emission which suggesting that strong vegetation emissions exist in summer and high propionaldehyde abundance is caused by fossil fuel combustion in winter. Potential health risk assessment of formaldehyde and acetaldehyde was conducted and the highest cumulative risks were observed at Chengdu in summer and Wuhan in winter. Because of the strong photochemical reaction and large amount of anthropogenic emissions, high concentrations of carbonyl compounds were observed in Chengdu. The use of ethanol-blended gasoline in Wuhan is the key reason of acetaldehyde emission and action should be taken to avoid potential health risks. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Carbonyl Compounds Generated from Electronic Cigarettes

    Directory of Open Access Journals (Sweden)

    Kanae Bekki

    2014-10-01

    Full Text Available Electronic cigarettes (e-cigarettes are advertised as being safer than tobacco cigarettes products as the chemical compounds inhaled from e-cigarettes are believed to be fewer and less toxic than those from tobacco cigarettes. Therefore, continuous careful monitoring and risk management of e-cigarettes should be implemented, with the aim of protecting and promoting public health worldwide. Moreover, basic scientific data are required for the regulation of e-cigarette. To date, there have been reports of many hazardous chemical compounds generated from e-cigarettes, particularly carbonyl compounds such as formaldehyde, acetaldehyde, acrolein, and glyoxal, which are often found in e-cigarette aerosols. These carbonyl compounds are incidentally generated by the oxidation of e-liquid (liquid in e-cigarette; glycerol and glycols when the liquid comes in contact with the heated nichrome wire. The compositions and concentrations of these compounds vary depending on the type of e-liquid and the battery voltage. In some cases, extremely high concentrations of these carbonyl compounds are generated, and may contribute to various health effects. Suppliers, risk management organizations, and users of e-cigarettes should be aware of this phenomenon.

  2. Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins.

    LENUS (Irish Health Repository)

    Morgan, Claire C

    2010-01-01

    ABSTRACT: BACKGROUND: Reproductive proteins are central to the continuation of all mammalian species. The evolution of these proteins has been greatly influenced by environmental pressures induced by pathogens, rival sperm, sexual selection and sexual conflict. Positive selection has been demonstrated in many of these proteins with particular focus on primate lineages. However, the mammalia are a diverse group in terms of mating habits, population sizes and germ line generation times. We have examined the selective pressures at work on a number of novel reproductive proteins across a wide variety of mammalia. RESULTS: We show that selective pressures on reproductive proteins are highly varied. Of the 10 genes analyzed in detail, all contain signatures of positive selection either across specific sites or in specific lineages or a combination of both. Our analysis of SP56 and Col1a1 are entirely novel and the results show positively selected sites present in each gene. Our findings for the Col1a1 gene are suggestive of a link between positive selection and severe disease type. We find evidence in our dataset to suggest that interacting proteins are evolving in symphony: most likely to maintain interacting functionality. CONCLUSION: Our in silico analyses show positively selected sites are occurring near catalytically important regions suggesting selective pressure to maximize efficient fertilization. In those cases where a mechanism of protein function is not fully understood, the sites presented here represent ideal candidates for mutational study. This work has highlighted the widespread rate heterogeneity in mutational rates across the mammalia and specifically has shown that the evolution of reproductive proteins is highly varied depending on the species and interacting partners. We have shown that positive selection and disease are closely linked in the Col1a1 gene.

  3. Palladium-catalyzed Reppe carbonylation.

    Science.gov (United States)

    Kiss, G

    2001-11-01

    PdX2L2/L/HA (A = weakly coordinating anion, L = phosphine) complexes are active catalysts in the hydroesterification of alkenes, alkynes, and conjugated dienes. Shell, the only major corporate player in the field, recently developed two very active catalyst systems tailored to the hydroesterification of either alkenes or alkynes. The hydroesterification of propyne with their Pd(OAc)2/PN/HA (PN = (2-pyridyl)diphenylphosphine, HA = strong acid with weakly coordinating anion, like methanesulfonic acid) catalyst has been declared commercially ready. However, despite the significant progress in the activity of Pd-hydroesterification catalysts, further improvements are warranted. Thus, for example, activity maintenance still seems to be an issue. Homogeneous Pd catalysts are prone to a number of deactivation reactions. Activity and stability promoters are often corrosive and add to the complexity of the system, making it less attractive. Nonetheless, the versatility of the process and its tolerance toward the functional groups of substrates should appeal especially to the makers of specialty products. Although hydroesterification yields esters from alkenes, alkynes, and dienes in fewer steps than hydroformylation does, the latter has some advantages at the current state of the art. (1) Hydroformylation catalysts, particularly some recently published phosphine-modified Rh systems, can achieve very high regioselectivity for the linear product that hydroesterification catalysts cannot match yet. By analogy with hydroformylation, bulkier ligands ought to be tested in hydroesterification to increase normal-ester selectivity. (2) Hydroformylation is proven, commercial. Hydroesterification can only replace it if it can provide significant economic incentives. Similar or just marginally better performance could not justify the cost of development of a new technology. (3) Hydroesterification requires pure CO while hydroformylation uses syngas, a mixture of CO and H2. The latter

  4. Selective backbone labelling of ILV methyl labelled proteins

    International Nuclear Information System (INIS)

    Sibille, Nathalie; Hanoulle, Xavier; Bonachera, Fanny; Verdegem, Dries; Landrieu, Isabelle; Wieruszeski, Jean-Michel; Lippens, Guy

    2009-01-01

    Adding the 13 C labelled 2-keto-isovalerate and 2-oxobutanoate precursors to a minimal medium composed of 12 C labelled glucose instead of the commonly used ( 2 D, 13 C) glucose leads not only to the 13 C labelling of (I, L, V) methyls but also to the selective 13 C labelling of the backbone C α and CO carbons of the Ile and Val residues. As a result, the backbone ( 1 H, 15 N) correlations of the Ile and Val residues and their next neighbours in the (i + 1) position can be selectively identified in HN(CA) and HN(CO) planes. The availability of a selective HSQC spectrum corresponding to the sole amide resonances of the Ile and Val residues allows connecting them to their corresponding methyls by the intra-residue NOE effect, and should therefore be applicable to larger systems

  5. Purification-Free, Target-Selective Immobilization of a Protein from Cell Lysates.

    Science.gov (United States)

    Cha, Jaehyun; Kwon, Inchan

    2018-02-27

    Protein immobilization has been widely used for laboratory experiments and industrial processes. Preparation of a recombinant protein for immobilization usually requires laborious and expensive purification steps. Here, a novel purification-free, target-selective immobilization technique of a protein from cell lysates is reported. Purification steps are skipped by immobilizing a target protein containing a clickable non-natural amino acid (p-azidophenylalanine) in cell lysates onto alkyne-functionalized solid supports via bioorthogonal azide-alkyne cycloaddition. In order to achieve a target protein-selective immobilization, p-azidophenylalanine was introduced into an exogenous target protein, but not into endogenous non-target proteins using host cells with amber codon-free genomic DNAs. Immobilization of superfolder fluorescent protein (sfGFP) from cell lysates is as efficient as that of the purified sfGFP. Using two fluorescent proteins (sfGFP and mCherry), the authors also demonstrated that the target proteins are immobilized with a minimal immobilization of non-target proteins (target-selective immobilization). © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Selecting protein families for environmental features based on manifold regularization.

    Science.gov (United States)

    Jiang, Xingpeng; Xu, Weiwei; Park, E K; Li, Guangrong

    2014-06-01

    Recently, statistics and machine learning have been developed to identify functional or taxonomic features of environmental features or physiological status. Important proteins (or other functional and taxonomic entities) to environmental features can be potentially used as biosensors. A major challenge is how the distribution of protein and gene functions embodies the adaption of microbial communities across environments and host habitats. In this paper, we propose a novel regularization method for linear regression to adapt the challenge. The approach is inspired by local linear embedding (LLE) and we call it a manifold-constrained regularization for linear regression (McRe). The novel regularization procedure also has potential to be used in solving other linear systems. We demonstrate the efficiency and the performance of the approach in both simulation and real data.

  7. Radionuclides and selected trace elements in marine protein concentrates

    Energy Technology Data Exchange (ETDEWEB)

    Beasley, T M; Jokela, T A; Eagle, R J

    1971-12-01

    The concentrations of various trace elements and radionuclides have been measured in marine protein concentrates prepared from surface feeding fishes. As with concentrates prepared from benthic fishes, the /sup 210/Pb-/sup 210/Po pair are the most significant radionuclides present. Concentrations of stable Pb, Co and Ag in certain concentrates are sufficiently high to contribute substantially to estimated current intakes of these elements.

  8. Millimeter wave spectra of carbonyl cyanide

    Science.gov (United States)

    Bteich, S. B.; Tercero, B.; Cernicharo, J.; Motiyenko, R. A.; Margulès, L.; Guillemin, J.-C.

    2016-07-01

    Context. More than 30 cyanide derivatives of simple organic molecules have been detected in the interstellar medium, but only one dicarbonitrile has been found and that very recently. There is still a lack of high-resolution spectroscopic data particularly for dinitriles derivatives. The carbonyl cyanide molecule is a new and interesting candidate for astrophysical detection. It could be formed by the reaction of CO and CN radicals, or by substitution of the hydrogen atom by a cyano group in cyanoformaldehyde, HC(=O)CN, that has already been detected in the interstellar medium. Aims: The available data on the rotational spectrum of carbonyl cyanide is limited in terms of quantum number values and frequency range, and does not allow accurate extrapolation of the spectrum into the millimeter-wave range. To provide a firm basis for astrophysical detection of carbonyl cyanide we studied its millimeter-wave spectrum. Methods: The rotational spectrum of carbonyl cyanide was measured in the frequency range 152-308 GHz and analyzed using Watson's A- and S-reduction Hamiltonians. Results: The ground and first excited state of v5 vibrational mode were assigned and analyzed. More than 1100 distinct frequency lines of the ground state were fitted to produce an accurate set of rotational and centrifugal distortion constants up to the eighth order. The frequency predictions based on these constants should be accurate enough for astrophysical searches in the frequency range up to 500 GHz and for transition involving energy levels with J ≤ 100 and Ka ≤ 42. Based on the results we searched for interstellar carbonyl cyanide in available observational data without success. Thus, we derived upper limits to its column density in different sources. This paper makes use of the following ALMA data: ADS/JAO.ALMA#2011.0.00009.SV. ALMA is a partnership of ESO (representing its member states), NSF (USA), and NINS (Japan) with NRC (Canada), NSC, and ASIAA (Taiwan), and KASI (Republic of

  9. Carbonyl Emissions from Gasoline and Diesel Motor Vehicles

    Energy Technology Data Exchange (ETDEWEB)

    Destaillats, Hugo; Jakober, Chris A.; Robert, Michael A.; Riddle, Sarah G.; Destaillats, Hugo; Charles, M. Judith; Green, Peter G.; Kleeman, Michael J.

    2007-12-01

    Carbonyls from gasoline powered light-duty vehicles (LDVs) and heavy-duty diesel powered vehicles (HDDVs) operated on chassis dynamometers were measured using an annular denuder-quartz filter-polyurethane foam sampler with O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine derivatization and chromatography-mass spectrometry analyses. Two internal standards were utilized based on carbonyl recovery, 4-fluorobenzaldehyde forcarbonyls and 6-fluoro-4-chromanone for>_C8 compounds. Gas- and particle-phase emissions for 39 aliphatic and 20 aromatic carbonyls ranged from 0.1 ? 2000 ?g/L fuel for LDVs and 1.8 - 27000 mu g/L fuel for HDDVs. Gas-phase species accounted for 81-95percent of the total carbonyls from LDVs and 86-88percent from HDDVs. Particulate carbonyls emitted from a HDDV under realistic driving conditions were similar to concentrations measured in a diesel particulate matter (PM) standard reference material. Carbonyls accounted for 19percent of particulate organic carbon (POC) emissions from low-emission LDVs and 37percent of POC emissions from three-way catalyst equipped LDVs. This identifies carbonyls as one of the largest classes of compounds in LDV PM emissions. The carbonyl fraction of HDDV POC was lower, 3.3-3.9percent depending upon operational conditions. Partitioning analysis indicates the carbonyls had not achieved equilibrium between the gas- and particle-phase under the dilution factors of 126-584 used in the current study.

  10. Protease-resistant prions selectively decrease Shadoo protein.

    Directory of Open Access Journals (Sweden)

    Joel C Watts

    2011-11-01

    Full Text Available The central event in prion diseases is the conformational conversion of the cellular prion protein (PrP(C into PrP(Sc, a partially protease-resistant and infectious conformer. However, the mechanism by which PrP(Sc causes neuronal dysfunction remains poorly understood. Levels of Shadoo (Sho, a protein that resembles the flexibly disordered N-terminal domain of PrP(C, were found to be reduced in the brains of mice infected with the RML strain of prions [1], implying that Sho levels may reflect the presence of PrP(Sc in the brain. To test this hypothesis, we examined levels of Sho during prion infection using a variety of experimental systems. Sho protein levels were decreased in the brains of mice, hamsters, voles, and sheep infected with different natural and experimental prion strains. Furthermore, Sho levels were decreased in the brains of prion-infected, transgenic mice overexpressing Sho and in infected neuroblastoma cells. Time-course experiments revealed that Sho levels were inversely proportional to levels of protease-resistant PrP(Sc. Membrane anchoring and the N-terminal domain of PrP both influenced the inverse relationship between Sho and PrP(Sc. Although increased Sho levels had no discernible effect on prion replication in mice, we conclude that Sho is the first non-PrP marker specific for prion disease. Additional studies using this paradigm may provide insight into the cellular pathways and systems subverted by PrP(Sc during prion disease.

  11. Investigation of selection methods im mutation breeding of barley for protein quantity and quality

    International Nuclear Information System (INIS)

    Ulonska, E.; Gaul, H.; Baumer, M.; Gesellschaft fuer Strahlen- und Umweltforschung m.b.H., Gruenbach

    1975-01-01

    This mutation breeding programme is investigating the qualification of micro-mutations for the selection of improved protein quality and quantity. Normally, improvement of protein content in micro-mutations is rather small. Therefore, it is important to develop methods and conditions of selection being (a) capable of measuring these small deviations in protein content and quality, and (b) simple to use. In two experiments carried out in 1971 and 1972 nitrogen fertilization was found to be the most important factor in the improvement of selection conditions. There is a highly significant negative correlation between crude protein content and the standard deviation; i.e. the higher the content of crude protein, the lower the variation coefficient. This in turn leads to an increase of genetic variation necessary for better selection progress. Nitrogen fertilization, especially during ear emergence, covers environmental influences - e.g., planting space, sowing rate, growing in different plots (6, 3, 2, 1 rows or in half-ear hills) - to a great extent. Thus, by applying high doses of nitrogen dressings comparable results can be achieved. In an overall selection experiment (testing the entire crossing and mutation material available at Weihenstephan in a stepwise selection from 1971 to 1973) and two selection experiments conducted in 1971 to 1973 with micro-mutants - variety Nota, 4 times X-rayed and the naked barley strain 1606 treated once with EMS - significant selection results were found. (author)

  12. Artificial membranes with selective nanochannels for protein transport

    KAUST Repository

    Sutisna, Burhannudin

    2016-09-05

    A poly(styrene-b-tert-butoxystyrene-b-styrene) copolymer was synthesized by anionic polymerization and hydrolyzed to poly(styrene-b-4-hydroxystyrene-b-styrene). Lamellar morphology was confirmed in the bulk after annealing. Membranes were fabricated by self-assembly of the hydrolyzed copolymer in solution, followed by water induced phase separation. A high density of pores of 4 to 5 nm diameter led to a water permeance of 40 L m−2 h−1 bar−1 and molecular weight cut-off around 8 kg mol−1. The morphology was controlled by tuning the polymer concentration, evaporation time, and the addition of imidazole and pyridine to stabilize the terpolymer micelles in the casting solution via hydrogen bond complexes. Transmission electron microscopy of the membrane cross-sections confirmed the formation of channels with hydroxyl groups beneficial for hydrogen-bond forming sites. The morphology evolution was investigated by time-resolved grazing incidence small angle X-ray scattering experiments. The membrane channels reject polyethylene glycol with a molecular size of 10 kg mol−1, but are permeable to proteins, such as lysozyme (14.3 kg mol−1) and cytochrome c (12.4 kg mol−1), due to the right balance of hydrogen bond interactions along the channels, electrostatic attraction, as well as the right pore sizes. Our results demonstrate that artificial channels can be designed for protein transport via block copolymer self-assembly using classical methods of membrane preparation.

  13. Artificial membranes with selective nanochannels for protein transport

    KAUST Repository

    Sutisna, Burhannudin; Polymeropoulos, Georgios; Mygiakis, E.; Musteata, Valentina-Elena; Peinemann, Klaus-Viktor; Smilgies, D. M.; Hadjichristidis, Nikolaos; Nunes, Suzana Pereira

    2016-01-01

    A poly(styrene-b-tert-butoxystyrene-b-styrene) copolymer was synthesized by anionic polymerization and hydrolyzed to poly(styrene-b-4-hydroxystyrene-b-styrene). Lamellar morphology was confirmed in the bulk after annealing. Membranes were fabricated by self-assembly of the hydrolyzed copolymer in solution, followed by water induced phase separation. A high density of pores of 4 to 5 nm diameter led to a water permeance of 40 L m−2 h−1 bar−1 and molecular weight cut-off around 8 kg mol−1. The morphology was controlled by tuning the polymer concentration, evaporation time, and the addition of imidazole and pyridine to stabilize the terpolymer micelles in the casting solution via hydrogen bond complexes. Transmission electron microscopy of the membrane cross-sections confirmed the formation of channels with hydroxyl groups beneficial for hydrogen-bond forming sites. The morphology evolution was investigated by time-resolved grazing incidence small angle X-ray scattering experiments. The membrane channels reject polyethylene glycol with a molecular size of 10 kg mol−1, but are permeable to proteins, such as lysozyme (14.3 kg mol−1) and cytochrome c (12.4 kg mol−1), due to the right balance of hydrogen bond interactions along the channels, electrostatic attraction, as well as the right pore sizes. Our results demonstrate that artificial channels can be designed for protein transport via block copolymer self-assembly using classical methods of membrane preparation.

  14. Exploiting translational coupling for the selection of cells producing toxic recombinant proteins from expression vectors.

    Science.gov (United States)

    Tagliavia, Marcello; Cuttitta, Angela

    2016-01-01

    High rates of plasmid instability are associated with the use of some expression vectors in Escherichia coli, resulting in the loss of recombinant protein expression. This is due to sequence alterations in vector promoter elements caused by the background expression of the cloned gene, which leads to the selection of fast-growing, plasmid-containing cells that do not express the target protein. This phenomenon, which is worsened when expressing toxic proteins, results in preparations containing very little or no recombinant protein, or even in clone loss; however, no methods to prevent loss of recombinant protein expression are currently available. We have exploited the phenomenon of translational coupling, a mechanism of prokaryotic gene expression regulation, in order to select cells containing plasmids still able to express recombinant proteins. Here we designed an expression vector in which the cloned gene and selection marker are co-expressed. Our approach allowed for the selection of the recombinant protein-expressing cells and proved effective even for clones encoding toxic proteins.

  15. From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction.

    Science.gov (United States)

    Akhter, Nasrin; Shehu, Amarda

    2018-01-19

    Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging. Repeatedly, research has shown that the protein energy functions whose minima are sought in the generation of decoys are unreliable indicators of nativeness. The prevalent approach ignores energy altogether and clusters decoys by conformational similarity. Complementary recent efforts design protein-specific scoring functions or train machine learning models on labeled decoys. In this paper, we show that an informative consideration of energy can be carried out under the energy landscape view. Specifically, we leverage local structures known as basins in the energy landscape probed by a template-free method. We propose and compare various strategies of basin-based decoy selection that we demonstrate are superior to clustering-based strategies. The presented results point to further directions of research for improving decoy selection, including the ability to properly consider the multiplicity of native conformations of proteins.

  16. From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction

    Directory of Open Access Journals (Sweden)

    Nasrin Akhter

    2018-01-01

    Full Text Available Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging. Repeatedly, research has shown that the protein energy functions whose minima are sought in the generation of decoys are unreliable indicators of nativeness. The prevalent approach ignores energy altogether and clusters decoys by conformational similarity. Complementary recent efforts design protein-specific scoring functions or train machine learning models on labeled decoys. In this paper, we show that an informative consideration of energy can be carried out under the energy landscape view. Specifically, we leverage local structures known as basins in the energy landscape probed by a template-free method. We propose and compare various strategies of basin-based decoy selection that we demonstrate are superior to clustering-based strategies. The presented results point to further directions of research for improving decoy selection, including the ability to properly consider the multiplicity of native conformations of proteins.

  17. Acute inhalation toxicity of carbonyl sulfide

    Energy Technology Data Exchange (ETDEWEB)

    Benson, J.M.; Hahn, F.F.; Barr, E.B. [and others

    1995-12-01

    Carbonyl sulfide (COS), a colorless gas, is a side product of industrial procedures sure as coal hydrogenation and gasification. It is structurally related to and is a metabolite of carbon disulfide. COS is metabolized in the body by carbonic anhydrase to hydrogen sulfide (H{sub 2}S), which is thought to be responsible for COS toxicity. No threshold limit value for COS has been established. Results of these studies indicate COS (with an LC{sub 50} of 590 ppm) is slightly less acutely toxic than H{sub 2}S (LC{sub 50} of 440 ppm).

  18. Protein structure and ionic selectivity in calcium channels: Selectivity filter size, not shape, matters

    OpenAIRE

    Malasics, Attila; Gillespie, Dirk; Nonner, Wolfgang; Henderson, Douglas; Eisenberg, Bob; Boda, Dezső

    2009-01-01

    Calcium channels have highly charged selectivity filters (4 COO− groups) that attract cations in to balance this charge and minimize free energy, forcing the cations (Na+ and Ca2+) to compete for space in the filter. A reduced model was developed to better understand the mechanism of ion selectivity in calcium channels. The charge/space competition (CSC) mechanism implies that Ca2+ is more efficient in balancing the charge of the filter because it provides twice the charge as Na+ while occupy...

  19. A single extracellular amino acid in Free Fatty Acid Receptor 2 defines antagonist species selectivity and G protein selection bias

    DEFF Research Database (Denmark)

    Sergeev, Eugenia; Hansen, Anders Højgaard; Bolognini, Daniele

    2017-01-01

    selectivity and mutational swap studies confirmed this hypothesis. Extending these studies to agonist function indicated that although the lysine - arginine variation between human and mouse orthologs had limited effect on G protein-mediated signal transduction, removal of positive charge from this residue...... produced a signalling-biased variant of Free Fatty Acid Receptor 2 in which Gi-mediated signalling by both short chain fatty acids and synthetic agonists was maintained whilst there was marked loss of agonist potency for signalling via Gq/11 and G12/13 G proteins. A single residue at the extracellular face...

  20. In vivo protein quality of selected cereal-based staple foods enriched with soybean proteins

    Directory of Open Access Journals (Sweden)

    Laura Acevedo-Pacheco

    2016-10-01

    Full Text Available Background: One way to diminish protein malnutrition in children is by enriching cereal-based flours for the manufacturing of maize tortillas, wheat flour tortillas, and yeast-leavened breads, which are widely consumed among low socio-economic groups. Objective: The aim was to determine and compare the essential amino acid (EAA scores, protein digestibility corrected amino acid scores (PDCAAS, and in vivo protein quality (protein digestibility, protein efficiency ratio (PER, biological values (BV, and net protein utilization (NPU values of regular versus soybean-fortified maize tortillas, yeast-leavened bread, and wheat flour tortillas. Design: To comparatively assess differences in protein quality among maize tortillas, wheat flour tortillas, and yeast-leavened breads, EAA compositions and in vivo studies with weanling rats were performed. The experimental diets based on regular or soybean-fortified food products were compared with a casein-based diet. Food intake, weight gains, PER, dry matter and protein digestibility, BV, NPU, and PDCAAS were assessed. The soybean-fortified tortillas contained 6% of defatted soybean flour, whereas the yeast-leavened bread flour contained 4.5% of soybean concentrate. Results: The soybean-fortified tortillas and bread contained higher amounts of lysine and tryptophan, which improved their EAA scores and PDCAAS. Rats fed diets based on soybean-fortified maize or wheat tortillas gained considerably more weight and had better BV and NPU values compared with counterparts fed with respective regular products. As a result, fortified maize tortillas and wheat flour tortillas improved PER from 0.73 to 1.64 and 0.69 to 1.77, respectively. The PER improvement was not as evident in rats fed the enriched yeast-leavened bread because the formulation contained sugar that decreased lysine availability possibly to Maillard reactions. Conclusions: The proposed enrichment of cereal-based foods with soybean proteins greatly

  1. Molecular Active Sites in Heterogeneous Ir-La/C-Catalyzed Carbonylation of Methanol to Acetates.

    Science.gov (United States)

    Kwak, Ja Hun; Dagle, Robert; Tustin, Gerald C; Zoeller, Joseph R; Allard, Lawrence F; Wang, Yong

    2014-02-06

    We report that when Ir and La halides are deposited on carbon, exposure to CO spontaneously generates a discrete molecular heterobimetallic structure, containing an Ir-La covalent bond that acts as a highly active, selective, and stable heterogeneous catalyst for the carbonylation of methanol to produce acetic acid. This catalyst exhibits a very high productivity of ∼1.5 mol acetyl/mol Ir·s with >99% selectivity to acetyl (acetic acid and methyl acetate) without detectable loss in activity or selectivity for more than 1 month of continuous operation. The enhanced activity can be mechanistically rationalized by the presence of La within the ligand sphere of the discrete molecular Ir-La heterobimetallic structure, which acts as a Lewis acid to accelerate the normally rate-limiting CO insertion in Ir-catalyzed carbonylation. Similar approaches may provide opportunities for attaining molecular (single site) behavior similar to homogeneous catalysis on heterogeneous surfaces for other industrial applications.

  2. Screening and expression of selected taxonomically conserved and unique hypothetical proteins in Burkholderia pseudomallei K96243

    Science.gov (United States)

    Akhir, Nor Azurah Mat; Nadzirin, Nurul; Mohamed, Rahmah; Firdaus-Raih, Mohd

    2015-09-01

    Hypothetical proteins of bacterial pathogens represent a large numbers of novel biological mechanisms which could belong to essential pathways in the bacteria. They lack functional characterizations mainly due to the inability of sequence homology based methods to detect functional relationships in the absence of detectable sequence similarity. The dataset derived from this study showed 550 candidates conserved in genomes that has pathogenicity information and only present in the Burkholderiales order. The dataset has been narrowed down to taxonomic clusters. Ten proteins were selected for ORF amplification, seven of them were successfully amplified, and only four proteins were successfully expressed. These proteins will be great candidates in determining the true function via structural biology.

  3. In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A.

    Directory of Open Access Journals (Sweden)

    Regina Stoltenburg

    Full Text Available A new DNA aptamer targeting Protein A is presented. The aptamer was selected by use of the FluMag-SELEX procedure. The SELEX technology (Systematic Evolution of Ligands by EXponential enrichment is widely applied as an in vitro selection and amplification method to generate target-specific aptamers and exists in various modified variants. FluMag-SELEX is one of them and is characterized by the use of magnetic beads for target immobilization and fluorescently labeled oligonucleotides for monitoring the aptamer selection progress. Structural investigations and sequence truncation experiments of the selected aptamer for Protein A led to the conclusion, that a stem-loop structure at its 5'-end including the 5'-primer binding site is essential for aptamer-target binding. Extensive interaction analyses between aptamer and Protein A were performed by methods like surface plasmon resonance, MicroScale Thermophoresis and bead-based binding assays using fluorescence measurements. The binding of the aptamer to its target was thus investigated in assays with immobilization of one of the binding partners each, and with both binding partners in solution. Affinity constants were determined in the low micromolar to submicromolar range, increasing to the nanomolar range under the assumption of avidity. Protein A provides more than one binding site for the aptamer, which may overlap with the known binding sites for immunoglobulins. The aptamer binds specifically to both native and recombinant Protein A, but not to other immunoglobulin-binding proteins like Protein G and L. Cross specificity to other proteins was not found. The application of the aptamer is directed to Protein A detection or affinity purification. Moreover, whole cells of Staphylococcus aureus, presenting Protein A on the cell surface, could also be bound by the aptamer.

  4. In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A.

    Science.gov (United States)

    Stoltenburg, Regina; Schubert, Thomas; Strehlitz, Beate

    2015-01-01

    A new DNA aptamer targeting Protein A is presented. The aptamer was selected by use of the FluMag-SELEX procedure. The SELEX technology (Systematic Evolution of Ligands by EXponential enrichment) is widely applied as an in vitro selection and amplification method to generate target-specific aptamers and exists in various modified variants. FluMag-SELEX is one of them and is characterized by the use of magnetic beads for target immobilization and fluorescently labeled oligonucleotides for monitoring the aptamer selection progress. Structural investigations and sequence truncation experiments of the selected aptamer for Protein A led to the conclusion, that a stem-loop structure at its 5'-end including the 5'-primer binding site is essential for aptamer-target binding. Extensive interaction analyses between aptamer and Protein A were performed by methods like surface plasmon resonance, MicroScale Thermophoresis and bead-based binding assays using fluorescence measurements. The binding of the aptamer to its target was thus investigated in assays with immobilization of one of the binding partners each, and with both binding partners in solution. Affinity constants were determined in the low micromolar to submicromolar range, increasing to the nanomolar range under the assumption of avidity. Protein A provides more than one binding site for the aptamer, which may overlap with the known binding sites for immunoglobulins. The aptamer binds specifically to both native and recombinant Protein A, but not to other immunoglobulin-binding proteins like Protein G and L. Cross specificity to other proteins was not found. The application of the aptamer is directed to Protein A detection or affinity purification. Moreover, whole cells of Staphylococcus aureus, presenting Protein A on the cell surface, could also be bound by the aptamer.

  5. Efficient Conversion of Oximes to the Corresponding Carbonyl Compounds with Tetrabutylammonium Chromate under Aprotic Conditions

    International Nuclear Information System (INIS)

    Pourali, Ali Reza; Goli, Arezou

    2006-01-01

    The solubility in several solvents, mildness, simple work-up and absence of side reactions provide advantages of using TBAC in deoximation reactions. This is an efficient and selective method for homogeneous deoximation of structurally different compounds under the moderately acidic and aprotic conditions in high yields. Regeneration of ketones and aldehydes from their oximes has assumed added importance since the discovery of the Barton reaction in which oximes are produced at non-activated hydrocarbon sites. Also, their synthesis from non-carbonyl compounds, such as by nitrosation of an active methylene group, nitrosation of an α-halo carbonyl compound and condensation of a nitro-alkene with an aldehyde provides a valid alternative pathway to carbonyl compounds. Therefore, there has been a continued interest in the effective regeneration of carbonyl compounds from the corresponding oximes especially under mild conditions. Oxidative and reductive methods have been found to show advantages over the classical hydrolytic methods. Although many oxidizing agents have been used, only a limited number of methods are efficient because of the low solubility of these metallic reagents in most organic solvents

  6. Weak carbonyl-methyl intermolecular interactions in acetone clusters explored by IR plus VUV spectroscopy

    International Nuclear Information System (INIS)

    Guan, Jiwen; Hu, Yongjun; Xie, Min; Bernstein, Elliot R.

    2012-01-01

    Highlights: ► The carbonyl overtone of acetone clusters is observed by IR-VUV spectroscopy. ► Acetone molecules in the dimer are stacked with an antiparallel way. ► The structure of the acetone trimer and the tetramer are the cyclic structures. ► The carbonyl groups would interact with the methyl groups in acetone clusters. ► These weak interactions are further confirmed by H/D substitution experiment. -- Abstract: Size-selected IR–VUV spectroscopy is employed to detect vibrational characteristics in the region 2850 ∼ 3550 cm −1 of neutral acetone and its clusters (CH 3 COCH 3 ) n (n = 1–4). Features around 3440 cm −1 in the spectra of acetone monomer and its clusters are assigned to the carbonyl stretch (CO) overtone. These features red-shift from 3455 to 3433 cm −1 as the size of the clusters increases from the monomer to the tetramer. Based on calculations, the experimental IR spectra in the C=O overtone region suggest that the dominant structures for the acetone trimer and tetramer should be cyclic in the supersonic expansion sample. This study also suggests that the carbonyl groups interact with the methyl groups in the acetone clusters. These weak interactions are further confirmed by the use of deuterium substitution.

  7. BLProt: Prediction of bioluminescent proteins based on support vector machine and relieff feature selection

    KAUST Repository

    Kandaswamy, Krishna Kumar

    2011-08-17

    Background: Bioluminescence is a process in which light is emitted by a living organism. Most creatures that emit light are sea creatures, but some insects, plants, fungi etc, also emit light. The biotechnological application of bioluminescence has become routine and is considered essential for many medical and general technological advances. Identification of bioluminescent proteins is more challenging due to their poor similarity in sequence. So far, no specific method has been reported to identify bioluminescent proteins from primary sequence.Results: In this paper, we propose a novel predictive method that uses a Support Vector Machine (SVM) and physicochemical properties to predict bioluminescent proteins. BLProt was trained using a dataset consisting of 300 bioluminescent proteins and 300 non-bioluminescent proteins, and evaluated by an independent set of 141 bioluminescent proteins and 18202 non-bioluminescent proteins. To identify the most prominent features, we carried out feature selection with three different filter approaches, ReliefF, infogain, and mRMR. We selected five different feature subsets by decreasing the number of features, and the performance of each feature subset was evaluated.Conclusion: BLProt achieves 80% accuracy from training (5 fold cross-validations) and 80.06% accuracy from testing. The performance of BLProt was compared with BLAST and HMM. High prediction accuracy and successful prediction of hypothetical proteins suggests that BLProt can be a useful approach to identify bioluminescent proteins from sequence information, irrespective of their sequence similarity. 2011 Kandaswamy et al; licensee BioMed Central Ltd.

  8. BLProt: Prediction of bioluminescent proteins based on support vector machine and relieff feature selection

    KAUST Repository

    Kandaswamy, Krishna Kumar; Pugalenthi, Ganesan; Hazrati, Mehrnaz Khodam; Kalies, Kai-Uwe; Martinetz, Thomas

    2011-01-01

    Background: Bioluminescence is a process in which light is emitted by a living organism. Most creatures that emit light are sea creatures, but some insects, plants, fungi etc, also emit light. The biotechnological application of bioluminescence has become routine and is considered essential for many medical and general technological advances. Identification of bioluminescent proteins is more challenging due to their poor similarity in sequence. So far, no specific method has been reported to identify bioluminescent proteins from primary sequence.Results: In this paper, we propose a novel predictive method that uses a Support Vector Machine (SVM) and physicochemical properties to predict bioluminescent proteins. BLProt was trained using a dataset consisting of 300 bioluminescent proteins and 300 non-bioluminescent proteins, and evaluated by an independent set of 141 bioluminescent proteins and 18202 non-bioluminescent proteins. To identify the most prominent features, we carried out feature selection with three different filter approaches, ReliefF, infogain, and mRMR. We selected five different feature subsets by decreasing the number of features, and the performance of each feature subset was evaluated.Conclusion: BLProt achieves 80% accuracy from training (5 fold cross-validations) and 80.06% accuracy from testing. The performance of BLProt was compared with BLAST and HMM. High prediction accuracy and successful prediction of hypothetical proteins suggests that BLProt can be a useful approach to identify bioluminescent proteins from sequence information, irrespective of their sequence similarity. 2011 Kandaswamy et al; licensee BioMed Central Ltd.

  9. Major membrane surface proteins of Mycoplasma hyopneumoniae selectively modified by covalently bound lipid

    International Nuclear Information System (INIS)

    Wise, K.S.; Kim, M.F.

    1987-01-01

    Surface protein antigens of Mycoplasma hyopneumoniae were identified by direct antibody-surface binding or by radioimmunoprecipitation of surface 125 I-labeled proteins with a series of monoclonal antibodies (MAbs). Radioimmunoprecipitation of TX-114-phase proteins from cells labeled with [ 35 S] methionine, 14 C-amino acids, or [ 3 H] palmitic acid showed that proteins p65, p50, and p44 were abundant and (with one other hydrophobic protein, p60) were selectively labeled with lipid. Alkaline hydroxylamine treatment of labeled proteins indicated linkage of lipids by amide or stable O-linked ester bonds. Proteins p65, p50, and p44 were highly immunogenic in the natural host as measured by immunoblots of TX-114-phase proteins with antisera from swine inoculated with whole organisms. These proteins were antigenically and structurally unrelated, since hyperimmune mouse antibodies to individual gel-purified proteins were monospecific and gave distinct proteolytic epitope maps. Intraspecies size variants of one surface antigen of M. hyopneumoniae were revealed by a MAb to p70 (defined in strain J, ATCC 25934), which recognized a large p73 component on strain VPP11 (ATCC 25617). In addition, MAb to internal, aqueous-phase protein p82 of strain J failed to bind an analogous antigen in strain VPP11

  10. Major membrane surface proteins of Mycoplasma hyopneumoniae selectively modified by covalently bound lipid

    Energy Technology Data Exchange (ETDEWEB)

    Wise K.S.; Kim, M.F.

    1987-12-01

    Surface protein antigens of Mycoplasma hyopneumoniae were identified by direct antibody-surface binding or by radioimmunoprecipitation of surface /sup 125/I-labeled proteins with a series of monoclonal antibodies (MAbs). Radioimmunoprecipitation of TX-114-phase proteins from cells labeled with (/sup 35/S) methionine, /sup 14/C-amino acids, or (/sup 3/H) palmitic acid showed that proteins p65, p50, and p44 were abundant and (with one other hydrophobic protein, p60) were selectively labeled with lipid. Alkaline hydroxylamine treatment of labeled proteins indicated linkage of lipids by amide or stable O-linked ester bonds. Proteins p65, p50, and p44 were highly immunogenic in the natural host as measured by immunoblots of TX-114-phase proteins with antisera from swine inoculated with whole organisms. These proteins were antigenically and structurally unrelated, since hyperimmune mouse antibodies to individual gel-purified proteins were monospecific and gave distinct proteolytic epitope maps. Intraspecies size variants of one surface antigen of M. hyopneumoniae were revealed by a MAb to p70 (defined in strain J, ATCC 25934), which recognized a large p73 component on strain VPP11 (ATCC 25617). In addition, MAb to internal, aqueous-phase protein p82 of strain J failed to bind an analogous antigen in strain VPP11.

  11. Ruthenium(ii)-catalyzed olefination via carbonyl reductive cross-coupling† †Electronic supplementary information (ESI) available: Experimental details. See DOI: 10.1039/c7sc04207h

    Science.gov (United States)

    Wei, Wei; Dai, Xi-Jie; Wang, Haining; Li, Chenchen; Yang, Xiaobo

    2017-01-01

    Natural availability of carbonyl groups offers reductive carbonyl coupling tremendous synthetic potential for efficient olefin synthesis, yet the catalytic carbonyl cross-coupling remains largely elusive. We report herein such a reaction, mediated by hydrazine under ruthenium(ii) catalysis. This method enables facile and selective cross-couplings of two unsymmetrical carbonyl compounds in either an intermolecular or intramolecular fashion. Moreover, this chemistry accommodates a variety of substrates, proceeds under mild reaction conditions with good functional group tolerance, and generates stoichiometric benign byproducts. Importantly, the coexistence of KOtBu and bidentate phosphine dmpe is vital to this transformation. PMID:29568466

  12. Integrative approaches to the prediction of protein functions based on the feature selection

    Directory of Open Access Journals (Sweden)

    Lee Hyunju

    2009-12-01

    Full Text Available Abstract Background Protein function prediction has been one of the most important issues in functional genomics. With the current availability of various genomic data sets, many researchers have attempted to develop integration models that combine all available genomic data for protein function prediction. These efforts have resulted in the improvement of prediction quality and the extension of prediction coverage. However, it has also been observed that integrating more data sources does not always increase the prediction quality. Therefore, selecting data sources that highly contribute to the protein function prediction has become an important issue. Results We present systematic feature selection methods that assess the contribution of genome-wide data sets to predict protein functions and then investigate the relationship between genomic data sources and protein functions. In this study, we use ten different genomic data sources in Mus musculus, including: protein-domains, protein-protein interactions, gene expressions, phenotype ontology, phylogenetic profiles and disease data sources to predict protein functions that are labelled with Gene Ontology (GO terms. We then apply two approaches to feature selection: exhaustive search feature selection using a kernel based logistic regression (KLR, and a kernel based L1-norm regularized logistic regression (KL1LR. In the first approach, we exhaustively measure the contribution of each data set for each function based on its prediction quality. In the second approach, we use the estimated coefficients of features as measures of contribution of data sources. Our results show that the proposed methods improve the prediction quality compared to the full integration of all data sources and other filter-based feature selection methods. We also show that contributing data sources can differ depending on the protein function. Furthermore, we observe that highly contributing data sets can be similar among

  13. Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein.

    Science.gov (United States)

    Hellberg, M E; Moy, G W; Vacquier, V D

    2000-03-01

    Male-specific proteins have increasingly been reported as targets of positive selection and are of special interest because of the role they may play in the evolution of reproductive isolation. We report the rapid interspecific divergence of cDNA encoding a major acrosomal protein of unknown function (TMAP) of sperm from five species of teguline gastropods. A mitochondrial DNA clock (calibrated by congeneric species divided by the Isthmus of Panama) estimates that these five species diverged 2-10 MYA. Inferred amino acid sequences reveal a propeptide that has diverged rapidly between species. The mature protein has diverged faster still due to high nonsynonymous substitution rates (> 25 nonsynonymous substitutions per site per 10(9) years). cDNA encoding the mature protein (89-100 residues) shows evidence of positive selection (Dn/Ds > 1) for 4 of 10 pairwise species comparisons. cDNA and predicted secondary-structure comparisons suggest that TMAP is neither orthologous nor paralogous to abalone lysin, and thus marks a second, phylogenetically independent, protein subject to strong positive selection in free-spawning marine gastropods. In addition, an internal repeat in one species (Tegula aureotincta) produces a duplicated cleavage site which results in two alternatively processed mature proteins differing by nine amino acid residues. Such alternative processing may provide a mechanism for introducing novel amino acid sequence variation at the amino-termini of proteins. Highly divergent TMAP N-termini from two other tegulines (Tegula regina and Norrisia norrisii) may have originated by such a mechanism.

  14. Widespread Positive Selection Drives Differentiation of Centromeric Proteins in the Drosophila melanogaster subgroup.

    Science.gov (United States)

    Beck, Emily A; Llopart, Ana

    2015-11-25

    Rapid evolution of centromeric satellite repeats is thought to cause compensatory amino acid evolution in interacting centromere-associated kinetochore proteins. Cid, a protein that mediates kinetochore/centromere interactions, displays particularly high amino acid turnover. Rapid evolution of both Cid and centromeric satellite repeats led us to hypothesize that the apparent compensatory evolution may extend to interacting partners in the Condensin I complex (i.e., SMC2, SMC4, Cap-H, Cap-D2, and Cap-G) and HP1s. Missense mutations in these proteins often result in improper centromere formation and aberrant chromosome segregation, thus selection for maintained function and coevolution among proteins of the complex is likely strong. Here, we report evidence of rapid evolution and recurrent positive selection in seven centromere-associated proteins in species of the Drosophila melanogaster subgroup, and further postulate that positive selection on these proteins could be a result of centromere drive and compensatory changes, with kinetochore proteins competing for optimal spindle attachment.

  15. Electromagnetic properties of carbonyl iron and their microwave ...

    Indian Academy of Sciences (India)

    Administrator

    The aim of this paper is to develop a novel thin micro- wave absorber with good absorbing performance in wide bandwidth and lightweight. So we investigated the micro- wave absorbing characterization of silicone rubber using carbonyl iron as filler. Carbonyl iron can be widely used in the field of electromagnetic shielding ...

  16. Bifunctional dendrons for multiple carbohydrate presentation via carbonyl chemistry

    Directory of Open Access Journals (Sweden)

    Davide Bini

    2014-07-01

    Full Text Available The synthesis of new dendrons of the generations 0, 1 and 2 with a double bond at the focal point and a carbonyl group at the termini has been carried out. The carbonyl group has been exploited for the multivalent conjugation to a sample saccharide by reductive amination and alkoxyamine conjugation.

  17. Carbonyl-Olefin Exchange Reaction: Present State and Outlook

    Science.gov (United States)

    Kalinova, Radostina; Jossifov, Christo

    The carbonyl-olefin exchange reaction (COER) is a new reaction between carbonyl group and olefin double bond, which has a formal similarity with the olefin metathesis (OM) - one carbon atom in the latter is replaced with an oxygen atom. Till now the new reaction is performed successfully only when the two functional groups (carbonyl group and olefin double bond) are in one molecule and are conjugated. The α, β-unsaturated carbonyl compounds (substituted propenones) are the compounds with such a structure. They polymerize giving substituted polyacetylenes. The chain propagation step of this polymerization is in fact the COER. The question arises: is it possible the COER to take place when the two functional groups are not in one molecule and are not conjugated, and could this reaction became an alternative of the existing carbonyl olefination reactions?

  18. Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein.

    Directory of Open Access Journals (Sweden)

    Aditi Gupta

    2016-03-01

    Full Text Available Epistatic interactions between residues determine a protein's adaptability and shape its evolutionary trajectory. When a protein experiences a changed environment, it is under strong selection to find a peak in the new fitness landscape. It has been shown that strong selection increases epistatic interactions as well as the ruggedness of the fitness landscape, but little is known about how the epistatic interactions change under selection in the long-term evolution of a protein. Here we analyze the evolution of epistasis in the protease of the human immunodeficiency virus type 1 (HIV-1 using protease sequences collected for almost a decade from both treated and untreated patients, to understand how epistasis changes and how those changes impact the long-term evolvability of a protein. We use an information-theoretic proxy for epistasis that quantifies the co-variation between sites, and show that positive information is a necessary (but not sufficient condition that detects epistasis in most cases. We analyze the "fossils" of the evolutionary trajectories of the protein contained in the sequence data, and show that epistasis continues to enrich under strong selection, but not for proteins whose environment is unchanged. The increase in epistasis compensates for the information loss due to sequence variability brought about by treatment, and facilitates adaptation in the increasingly rugged fitness landscape of treatment. While epistasis is thought to enhance evolvability via valley-crossing early-on in adaptation, it can hinder adaptation later when the landscape has turned rugged. However, we find no evidence that the HIV-1 protease has reached its potential for evolution after 9 years of adapting to a drug environment that itself is constantly changing. We suggest that the mechanism of encoding new information into pairwise interactions is central to protein evolution not just in HIV-1 protease, but for any protein adapting to a changing

  19. Catalyst Initiation in the Oscillatory Carbonylation Reaction

    Directory of Open Access Journals (Sweden)

    Katarina Novakovic

    2011-01-01

    Full Text Available Palladium(II iodide is used as a catalyst in the phenylacetylene oxidative carbonylation reaction that has demonstrated oscillatory behaviour in both pH and heat of reaction. In an attempt to extract the reaction network responsible for the oscillatory nature of this reaction, the system was divided into smaller parts and they were studied. This paper focuses on understanding the reaction network responsible for the initial reactions of palladium(II iodide within this oscillatory reaction. The species researched include methanol, palladium(II iodide, potassium iodide, and carbon monoxide. Several chemical reactions were considered and applied in a modelling study. The study revealed the significant role played by traces of water contained in the standard HPLC grade methanol used.

  20. Improving Classification of Protein Interaction Articles Using Context Similarity-Based Feature Selection.

    Science.gov (United States)

    Chen, Yifei; Sun, Yuxing; Han, Bing-Qing

    2015-01-01

    Protein interaction article classification is a text classification task in the biological domain to determine which articles describe protein-protein interactions. Since the feature space in text classification is high-dimensional, feature selection is widely used for reducing the dimensionality of features to speed up computation without sacrificing classification performance. Many existing feature selection methods are based on the statistical measure of document frequency and term frequency. One potential drawback of these methods is that they treat features separately. Hence, first we design a similarity measure between the context information to take word cooccurrences and phrase chunks around the features into account. Then we introduce the similarity of context information to the importance measure of the features to substitute the document and term frequency. Hence we propose new context similarity-based feature selection methods. Their performance is evaluated on two protein interaction article collections and compared against the frequency-based methods. The experimental results reveal that the context similarity-based methods perform better in terms of the F1 measure and the dimension reduction rate. Benefiting from the context information surrounding the features, the proposed methods can select distinctive features effectively for protein interaction article classification.

  1. Carbonyl complexes of rhodium with N-donor ligands: factors determining the formation of terminal versus bridging carbonyls

    NARCIS (Netherlands)

    Dzik, W.I.; Creusen, C.; de Gelder, R.; Peters, T.P.J.; Smits, J.M.M.; de Bruin, B.

    2010-01-01

    Cationic rhodium carbonyl complexes supported by a series of different N-3- and N-4-donor ligands were prepared, and their ability to form carbonyl-bridged species was evaluated. Complex [Rh(K3-bpa)(cod)r (1(+)) (bpa = bis(2-picolyBamine, cod = cis,cis-1,5-cyclooctadiene) reacts with I bar of CO to

  2. Markers of protein oxidation

    DEFF Research Database (Denmark)

    Headlam, Henrietta A; Davies, Michael Jonathan

    2004-01-01

    Exposure of proteins to radicals in the presence of O2 gives both side-chain oxidation and backbone fragmentation. These processes can be interrelated, with initial side-chain oxidation giving rise to backbone damage via transfer reactions. We have shown previously that alkoxyl radicals formed...... of this process depends on the extent of oxidation at C-3 compared with other sites. HO*, generated by gamma radiolysis, gave the highest total carbonyl yield, with protein-bound carbonyls predominating over released. In contrast, metal ion/H2O2 systems, gave more released than bound carbonyls, with this ratio...... modulated by EDTA. This is ascribed to metal ion-protein interactions affecting the sites of initial oxidation. Hypochlorous acid gave low concentrations of released carbonyls, but high yields of protein-bound material. The peroxyl radical generator 2,2'-azobis(2-amidinopropane) hydrochloride...

  3. Electrostatics promotes molecular crowding and selects the aggregation pathway in fibril-forming protein solutions

    International Nuclear Information System (INIS)

    Raccosta, S.; Martorana, V.; Manno, M.; Blanco, M.; Roberts, C.J.

    2016-01-01

    The role of intermolecular interaction in fibril-forming protein solutions and its relation with molecular conformation are crucial aspects for the control and inhibition of amyloid structures. Here, we study the fibril formation and the protein-protein interactions for two proteins at acidic ph, lysozyme and α-chymotrypsinogen. By using light scattering experiments and the Kirkwood-Buff integral approach, we show how concentration fluctuations are damped even at moderate protein concentrations by the dominant long-ranged electrostatic repulsion, which determines an effective crowded environment. In denaturing conditions, electrostatic repulsion keeps the monomeric solution in a thermodynamically metastable state, which is escaped through kinetically populated conformational sub-states. This explains how electrostatics acts as a gatekeeper in selecting a specific aggregation pathway.

  4. Use of hydrostatic pressure for modulation of protein chemical modification and enzymatic selectivity.

    Science.gov (United States)

    Makarov, Alexey A; Helmy, Roy; Joyce, Leo; Reibarkh, Mikhail; Maust, Mathew; Ren, Sumei; Mergelsberg, Ingrid; Welch, Christopher J

    2016-05-11

    Using hydrostatic pressure to induce protein conformational changes can be a powerful tool for altering the availability of protein reactive sites and for changing the selectivity of enzymatic reactions. Using a pressure apparatus, it has been demonstrated that hydrostatic pressure can be used to modulate the reactivity of lysine residues of the protein ubiquitin with a water-soluble amine-specific homobifunctional coupling agent. Fewer reactive lysine residues were observed when the reaction was carried out under elevated pressure of 3 kbar, consistent with a pressure-induced conformational change of ubiquitin that results in fewer exposed lysine residues. Additionally, modulation of the stereoselectivity of an enzymatic transamination reaction was observed at elevated hydrostatic pressure. In one case, the minor diasteromeric product formed at atmospheric pressure became the major product at elevated pressure. Such pressure-induced alterations of protein reactivity may provide an important new tool for enzymatic reactions and the chemical modification of proteins.

  5. Mature Epitope Density - A strategy for target selection based on immunoinformatics and exported prokaryotic proteins

    DEFF Research Database (Denmark)

    Santos, Anderson R; Pereira, Vanessa Bastos; Barbosa, Eudes

    2013-01-01

    . However, currently available tools do not account for the concentration of epitope products in the mature protein product and its relation to the reliability of target selection. RESULTS: We developed a computational strategy based on measuring the epitope's concentration in the mature protein, called...... Mature Epitope Density (MED). Our method, though simple, is capable of identifying promising vaccine targets. Our online software implementation provides a computationally light and reliable analysis of bacterial exoproteins and their potential for vaccines or diagnosis projects against pathogenic...... proteins were confirmed as related. There was no experimental evidence of antigenic or pathogenic contributions for three of the highest MED-scored Mtb proteins. Hence, these three proteins could represent novel putative vaccine and drug targets for Mtb. A web version of MED is publicly available online...

  6. Selective Labeling of Proteins on Living Cell Membranes Using Fluorescent Nanodiamond Probes

    Directory of Open Access Journals (Sweden)

    Shingo Sotoma

    2016-03-01

    Full Text Available The impeccable photostability of fluorescent nanodiamonds (FNDs is an ideal property for use in fluorescence imaging of proteins in living cells. However, such an application requires highly specific labeling of the target proteins with FNDs. Furthermore, the surface of unmodified FNDs tends to adsorb biomolecules nonspecifically, which hinders the reliable targeting of proteins with FNDs. Here, we combined hyperbranched polyglycerol modification of FNDs with the β-lactamase-tag system to develop a strategy for selective imaging of the protein of interest in cells. The combination of these techniques enabled site-specific labeling of Interleukin-18 receptor alpha chain, a membrane receptor, with FNDs, which eventually enabled tracking of the diffusion trajectory of FND-labeled proteins on the membrane surface.

  7. The different roles of selective autophagic protein degradation in mammalian cells.

    Science.gov (United States)

    Wang, Da-wei; Peng, Zhen-ju; Ren, Guang-fang; Wang, Guang-xin

    2015-11-10

    Autophagy is an intracellular pathway for bulk protein degradation and the removal of damaged organelles by lysosomes. Autophagy was previously thought to be unselective; however, studies have increasingly confirmed that autophagy-mediated protein degradation is highly regulated. Abnormal autophagic protein degradation has been associated with multiple human diseases such as cancer, neurological disability and cardiovascular disease; therefore, further elucidation of protein degradation by autophagy may be beneficial for protein-based clinical therapies. Macroautophagy and chaperone-mediated autophagy (CMA) can both participate in selective protein degradation in mammalian cells, but the process is quite different in each case. Here, we summarize the various types of macroautophagy and CMA involved in determining protein degradation. For this summary, we divide the autophagic protein degradation pathways into four categories: the post-translational modification dependent and independent CMA pathways and the ubiquitin dependent and independent macroautophagy pathways, and describe how some non-canonical pathways and modifications such as phosphorylation, acetylation and arginylation can influence protein degradation by the autophagy lysosome system (ALS). Finally, we comment on why autophagy can serve as either diagnostics or therapeutic targets in different human diseases.

  8. Multi-Label Learning via Random Label Selection for Protein Subcellular Multi-Locations Prediction.

    Science.gov (United States)

    Wang, Xiao; Li, Guo-Zheng

    2013-03-12

    Prediction of protein subcellular localization is an important but challenging problem, particularly when proteins may simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular localization methods are only used to deal with the single-location proteins. In the past few years, only a few methods have been proposed to tackle proteins with multiple locations. However, they only adopt a simple strategy, that is, transforming the multi-location proteins to multiple proteins with single location, which doesn't take correlations among different subcellular locations into account. In this paper, a novel method named RALS (multi-label learning via RAndom Label Selection), is proposed to learn from multi-location proteins in an effective and efficient way. Through five-fold cross validation test on a benchmark dataset, we demonstrate our proposed method with consideration of label correlations obviously outperforms the baseline BR method without consideration of label correlations, indicating correlations among different subcellular locations really exist and contribute to improvement of prediction performance. Experimental results on two benchmark datasets also show that our proposed methods achieve significantly higher performance than some other state-of-the-art methods in predicting subcellular multi-locations of proteins. The prediction web server is available at http://levis.tongji.edu.cn:8080/bioinfo/MLPred-Euk/ for the public usage.

  9. Comparative vesicle proteomics reveals selective regulation of protein expression in chestnut blight fungus by a hypovirus.

    Science.gov (United States)

    Wang, Jinzi; Wang, Fangzhen; Feng, Youjun; Mi, Ke; Chen, Qi; Shang, Jinjie; Chen, Baoshan

    2013-01-14

    The chestnut blight fungus (Cryphonectria parasitica) and hypovirus constitute a model system to study fungal pathogenesis and mycovirus-host interaction. Knowledge in this field has been gained largely from investigations at gene transcription level so far. Here we report a systematic analysis of the vesicle proteins of the host fungus with/without hypovirus infection. Thirty-three differentially expressed protein spots were identified in the purified vesicle protein samples by two-dimensional electrophoresis and mass spectrometry. Down-regulated proteins were mostly cargo proteins involved in primary metabolism and energy generation and up-regulated proteins were mostly vesicle associated proteins and ABC transporter. A virus-encoded protein p48 was found to have four forms with different molecular mass in vesicles from the virus-infected strain. While a few of the randomly selected differentially expressed proteins were in accordance with their transcription profiles, majority were not in agreement with their mRNA accumulation patterns, suggesting that an extensive post-transcriptional regulation may have occurred in the host fungus upon a hypovirus infection. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Selective radiolabeling of cell surface proteins to a high specific activity

    International Nuclear Information System (INIS)

    Thompson, J.A.; Lau, A.L.; Cunningham, D.D.

    1987-01-01

    A procedure was developed for selective radiolabeling of membrane proteins on cells to higher specific activities than possible with available techniques. Cell surface amino groups were derivatized with 125 I-(hydroxyphenyl)propionyl groups via 125 I-sulfosuccinimidyl (hydroxyphenyl)propionate ( 125 II-sulfo-SHPP). This reagent preferentially labeled membrane proteins exposed at the cell surface of erythrocytes as assessed by the degree of radiolabel incorporation into erythrocyte ghost proteins and hemoglobin. Comparison with the lactoperoxidase-[ 125 I]iodide labeling technique revealed that 125 I-sulfo-SHPP labeled cell surface proteins to a much higher specific activity and hemoglobin to a much lower specific activity. Additionally, this reagent was used for selective radiolabeling of membrane proteins on the cytoplasmic face of the plasma membrane by blocking exofacial amino groups with uniodinated sulfo-SHPP, lysing the cells, and then incubating them with 125 I-sulfo-SHPP. Exclusive labeling of either side of the plasma membrane was demonstrated by the labeling of some marker proteins with well-defined spacial orientations on erythroctyes. Transmembrane proteins such as the epidermal growth factor receptor on cultured cells could also be labeled differentially from either side of the plasma membrane

  11. Site-selective protein-modification chemistry for basic biology and drug development.

    Science.gov (United States)

    Krall, Nikolaus; da Cruz, Filipa P; Boutureira, Omar; Bernardes, Gonçalo J L

    2016-02-01

    Nature has produced intricate machinery to covalently diversify the structure of proteins after their synthesis in the ribosome. In an attempt to mimic nature, chemists have developed a large set of reactions that enable post-expression modification of proteins at pre-determined sites. These reactions are now used to selectively install particular modifications on proteins for many biological and therapeutic applications. For example, they provide an opportunity to install post-translational modifications on proteins to determine their exact biological roles. Labelling of proteins in live cells with fluorescent dyes allows protein uptake and intracellular trafficking to be tracked and also enables physiological parameters to be measured optically. Through the conjugation of potent cytotoxicants to antibodies, novel anti-cancer drugs with improved efficacy and reduced side effects may be obtained. In this Perspective, we highlight the most exciting current and future applications of chemical site-selective protein modification and consider which hurdles still need to be overcome for more widespread use.

  12. In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    OpenAIRE

    Stoltenburg, Regina; Schubert, Thomas; Strehlitz, Beate

    2015-01-01

    A new DNA aptamer targeting Protein A is presented. The aptamer was selected by use of the FluMag-SELEX procedure. The SELEX technology (Systematic Evolution of Ligands by EXponential enrichment) is widely applied as an in vitro selection and amplification method to generate target-specific aptamers and exists in various modified variants. FluMag-SELEX is one of them and is characterized by the use of magnetic beads for target immobilization and fluorescently labeled oligonucleotides for moni...

  13. A unified conformational selection and induced fit approach to protein-peptide docking.

    Directory of Open Access Journals (Sweden)

    Mikael Trellet

    Full Text Available Protein-peptide interactions are vital for the cell. They mediate, inhibit or serve as structural components in nearly 40% of all macromolecular interactions, and are often associated with diseases, making them interesting leads for protein drug design. In recent years, large-scale technologies have enabled exhaustive studies on the peptide recognition preferences for a number of peptide-binding domain families. Yet, the paucity of data regarding their molecular binding mechanisms together with their inherent flexibility makes the structural prediction of protein-peptide interactions very challenging. This leaves flexible docking as one of the few amenable computational techniques to model these complexes. We present here an ensemble, flexible protein-peptide docking protocol that combines conformational selection and induced fit mechanisms. Starting from an ensemble of three peptide conformations (extended, a-helix, polyproline-II, flexible docking with HADDOCK generates 79.4% of high quality models for bound/unbound and 69.4% for unbound/unbound docking when tested against the largest protein-peptide complexes benchmark dataset available to date. Conformational selection at the rigid-body docking stage successfully recovers the most relevant conformation for a given protein-peptide complex and the subsequent flexible refinement further improves the interface by up to 4.5 Å interface RMSD. Cluster-based scoring of the models results in a selection of near-native solutions in the top three for ∼75% of the successfully predicted cases. This unified conformational selection and induced fit approach to protein-peptide docking should open the route to the modeling of challenging systems such as disorder-order transitions taking place upon binding, significantly expanding the applicability limit of biomolecular interaction modeling by docking.

  14. Selected carbonyl compounds in the air of Silesia region

    Directory of Open Access Journals (Sweden)

    Czaplicka Marianna

    2018-01-01

    Full Text Available This study was carried out to characterize three aldehydes of health concern (formaldehyde, acetaldehyde, and acrolein at a three sites in Silesian region (Poland in January and June 2015. Aldehydes in polluted atmospheres comes from both primary and secondary sources, which limits the control strategies for these reactive compounds. Average aldehyde concentration in summer period lies in range from 3.13 μg/m3 to 10.43 μg/m3, in winter period in range from 29.0 μg/m3 to 32.2 μg/m3. Acetaldehyde was dominant compound in winter period, in summer formaldehyde concentration was highest of all determined aldehydes.

  15. Selected carbonyl compounds in the air of Silesia region

    Science.gov (United States)

    Czaplicka, Marianna; Chrobok, Michał

    2018-01-01

    This study was carried out to characterize three aldehydes of health concern (formaldehyde, acetaldehyde, and acrolein) at a three sites in Silesian region (Poland) in January and June 2015. Aldehydes in polluted atmospheres comes from both primary and secondary sources, which limits the control strategies for these reactive compounds. Average aldehyde concentration in summer period lies in range from 3.13 μg/m3 to 10.43 μg/m3, in winter period in range from 29.0 μg/m3 to 32.2 μg/m3. Acetaldehyde was dominant compound in winter period, in summer formaldehyde concentration was highest of all determined aldehydes.

  16. Carbonyl emission and toxicity profile of diesel blends with an animal-fat biodiesel and a tire pyrolysis liquid fuel.

    Science.gov (United States)

    Ballesteros, R; Guillén-Flores, J; Martínez, J D

    2014-02-01

    In this paper, two diesel fuels, an animal-fat biodiesel and two diesel blends with the animal-fat biodiesel (50vol.%) and with a tire pyrolysis liquid (TPL) fuel (5vol.%) have been tested in a 4-cylinder, 4-stroke, turbocharged, intercooled, 2.0L Nissan diesel automotive engine (model M1D) with common-rail injection system and diesel oxidation catalyst (DOC). Carbonyl emissions have been analyzed both before and after DOC and specific reactivity of carbonyl profile has been calculated. Carbonyl sampling was carried out by means of a heated line, trapping the gas in 2,4-DNPH cartridges. The eluted content was then analyzed in an HPLC system, with UV-VIS detection. Results showed, on the one hand, an increase in carbonyl emissions with the biodiesel fraction in the fuel. On the other hand, the addition of TPL to diesel also increased carbonyl emissions. These trends were occasionally different if the emissions were studied after the DOC, as it seems to be selectivity during the oxidation process. The specific reactivity was also studied, finding a decrease with the oxygen content within the fuel molecule, although the equivalent ozone emissions slightly increased with the oxygen content. Finally, the emissions toxicity was also studied, comparing them to different parameters defined by different organizations. Depending on the point of study, emissions were above or below the established limits, although acrolein exceeded them as it has the least permissive values. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Investigation of protein selectivity in multimodal chromatography using in silico designed Fab fragment variants.

    Science.gov (United States)

    Karkov, Hanne Sophie; Krogh, Berit Olsen; Woo, James; Parimal, Siddharth; Ahmadian, Haleh; Cramer, Steven M

    2015-11-01

    In this study, a unique set of antibody Fab fragments was designed in silico and produced to examine the relationship between protein surface properties and selectivity in multimodal chromatographic systems. We hypothesized that multimodal ligands containing both hydrophobic and charged moieties would interact strongly with protein surface regions where charged groups and hydrophobic patches were in close spatial proximity. Protein surface property characterization tools were employed to identify the potential multimodal ligand binding regions on the Fab fragment of a humanized antibody and to evaluate the impact of mutations on surface charge and hydrophobicity. Twenty Fab variants were generated by site-directed mutagenesis, recombinant expression, and affinity purification. Column gradient experiments were carried out with the Fab variants in multimodal, cation-exchange, and hydrophobic interaction chromatographic systems. The results clearly indicated that selectivity in the multimodal system was different from the other chromatographic modes examined. Column retention data for the reduced charge Fab variants identified a binding site comprising light chain CDR1 as the main electrostatic interaction site for the multimodal and cation-exchange ligands. Furthermore, the multimodal ligand binding was enhanced by additional hydrophobic contributions as evident from the results obtained with hydrophobic Fab variants. The use of in silico protein surface property analyses combined with molecular biology techniques, protein expression, and chromatographic evaluations represents a previously undescribed and powerful approach for investigating multimodal selectivity with complex biomolecules. © 2015 Wiley Periodicals, Inc.

  18. Selective autophagy of non-ubiquitylated targets in plants: looking for cognate receptor/adaptor proteins

    Directory of Open Access Journals (Sweden)

    Vasko eVeljanovski

    2014-06-01

    Full Text Available Cellular homeostasis is essential for the physiology of eukaryotic cells. Eukaryotic cells, including plant cells, utilize two main pathways to adjust the level of cytoplasmic components, namely the proteasomal and the lysosomal/vacuolar pathways. Macroautophagy is a lysosomal/vacuolar pathway which, until recently, was thought to be non-specific and a bulk degradation process. However, selective autophagy which can be activated in the cell under various physiological conditions, involves the specific degradation of defined macromolecules or organelles by a conserved molecular mechanism. For this process to be efficient, the mechanisms underlying the recognition and selection of the cargo to be engulfed by the double-membrane autophagosome are critical, and not yet well understood. Ubiquitin (poly-ubiquitin conjugation to the target appears to be a conserved ligand mechanism in many types of selective autophagy, and defined receptors/adaptors recognizing and regulating the autophagosomal capture of the ubiquitylated target have been characterized. However, non-proteinaceous and non-ubiquitylated cargoes are also selectively degraded by this pathway. This ubiquitin-independent selective autophagic pathway also involves receptor and/or adaptor proteins linking the cargo to the autophagic machinery. Some of these receptor/adaptor proteins including accessory autophagy-related (Atg and non-Atg proteins have been described in yeast and animal cells but not yet in plants. In this review we discuss the ubiquitin-independent cargo selection mechanisms in selective autophagy degradation of organelles and macromolecules and speculate on potential plant receptor/adaptor proteins.

  19. Application of vanadium incorporated phosphomolybdate supported on the modified kaolinin synthesis of diphenyl carbonate by oxidative carbonylation with phenol

    Directory of Open Access Journals (Sweden)

    Peng Meng

    2017-01-01

    Full Text Available Keggin-type molybdophosphoric acid, molybdophosphoric salt and vanadium incorporated molybdophosphoric salt supported on the modified kaolin (MK were investigated as redox co-catalysts for the oxidative carbonylation of phenol to diphenyl carbonate (DPC in the absence of solvent. The 20 wt.% of MnAMPV5 (one kind of vanadium incorporated molybdophosphoric salt loaded on MK showed the highest catalytic activity with the yield of 24.68% and a TON of 306, while the selectivity amounts to nearly 100% in all the carbonylation reactions. The catalysts were characterized by XRD, BET, XPS and H2-TPR. The reusability study showed that the catalysts were stable and active.

  20. A protein engineered to bind uranyl selectively and with femtomolar affinity

    Science.gov (United States)

    Zhou, Lu; Bosscher, Mike; Zhang, Changsheng; Özçubukçu, Salih; Zhang, Liang; Zhang, Wen; Li, Charles J.; Liu, Jianzhao; Jensen, Mark P.; Lai, Luhua; He, Chuan

    2014-03-01

    Uranyl (UO22+), the predominant aerobic form of uranium, is present in the ocean at a concentration of ~3.2 parts per 109 (13.7 nM) however, the successful enrichment of uranyl from this vast resource has been limited by the high concentrations of metal ions of similar size and charge, which makes it difficult to design a binding motif that is selective for uranyl. Here we report the design and rational development of a uranyl-binding protein using a computational screening process in the initial search for potential uranyl-binding sites. The engineered protein is thermally stable and offers very high affinity and selectivity for uranyl with a Kd of 7.4 femtomolar (fM) and >10,000-fold selectivity over other metal ions. We also demonstrated that the uranyl-binding protein can repeatedly sequester 30-60% of the uranyl in synthetic sea water. The chemical strategy employed here may be applied to engineer other selective metal-binding proteins for biotechnology and remediation applications.

  1. Automation of specimen selection and data acquisition for protein electron crystallography

    NARCIS (Netherlands)

    Oostergetel, G.T.; Keegstra, W.; Brisson, A.D R

    A system is presented for semi-automatic specimen selection and data acquisition for protein electron crystallography, based on a slow-scan CCD camera connected to a transmission electron microscope and control from an external computer. Areas of interest on the specimen are localised at low

  2. Characterization of hydrocarbons, halocarbons and carbonyls in the atmosphere of Hong Kong.

    Science.gov (United States)

    Guo, H; Lee, S C; Louie, P K K; Ho, K F

    2004-12-01

    Ambient air quality measurements of 156 species including 39 alkanes, 32 alkenes, 2 alkynes, 24 aromatic hydrocarbons, 43 halocarbons and 16 carbonyls, were carried out for 120 air samples collected at two sampling stations (CW and TW) in 2001 throughout Hong Kong. Spatial variations of volatile organic compounds (VOCs) in the atmosphere were investigated. Levels of most alkanes and alkenes at TW site were higher than that at the CW site, while the BTEX concentrations at the two sites were close. The BTEX ratios at CW and TW were 1.6:10.1:1.0:1.6 and 2.1:10.8:1.0:2.0, respectively. For major halogenated hydrocarbons, the mean concentrations of chloromethane, CFCs 12 and 22 did not show spatial variations at the two sites. However, site-specific differences were observed for trichloroethene and tetrachloroethene. Furthermore, there were no significant differences for carbonyls such as formaldehyde, acetaldehyde and acetone between the two sites. The levels of selected hydrocarbons in winter were 1-5 times that in summer. There were no common seasonal trends for carbonyls in Hong Kong. The ambient level of formaldehyde, the most abundant carbonyl, was higher in summer. However, levels of acetaldehyde, acetone and benzaldehyde in winter were 1.6-3.8 times that in summer. The levels of CFCs 11 and 12, and chloromethane in summer were higher than that in winter. Strong correlation of most hydrocarbons with propene and n-butane suggested that the primary contributors of hydrocarbons were vehicular emissions in Hong Kong. In addition, gasoline evaporation, use of solvents, leakage of liquefied petroleum gas (LPG), natural gas leakage and other industrial emissions, and even biogenic emissions affected the ambient levels of hydrocarbons. The sources of halocarbons were mainly materials used in industrial processes and as solvents. Correlation analysis suggested that photochemical reactions made significant contributions to the ambient levels of carbonyls in summer whereas

  3. A semi-nonparametric mixture model for selecting functionally consistent proteins.

    Science.gov (United States)

    Yu, Lianbo; Doerge, Rw

    2010-09-28

    High-throughput technologies have led to a new era of proteomics. Although protein microarray experiments are becoming more common place there are a variety of experimental and statistical issues that have yet to be addressed, and that will carry over to new high-throughput technologies unless they are investigated. One of the largest of these challenges is the selection of functionally consistent proteins. We present a novel semi-nonparametric mixture model for classifying proteins as consistent or inconsistent while controlling the false discovery rate and the false non-discovery rate. The performance of the proposed approach is compared to current methods via simulation under a variety of experimental conditions. We provide a statistical method for selecting functionally consistent proteins in the context of protein microarray experiments, but the proposed semi-nonparametric mixture model method can certainly be generalized to solve other mixture data problems. The main advantage of this approach is that it provides the posterior probability of consistency for each protein.

  4. 16th Carbonyl Metabolism Meeting: from enzymology to genomics

    Directory of Open Access Journals (Sweden)

    Maser Edmund

    2012-12-01

    Full Text Available Abstract The 16th International Meeting on the Enzymology and Molecular Biology of Carbonyl Metabolism, Castle of Ploen (Schleswig-Holstein, Germany, July 10–15, 2012, covered all aspects of NAD(P-dependent oxido-reductases that are involved in the general metabolism of xenobiotic and physiological carbonyl compounds. Starting 30 years ago with enzyme purification, structure elucidation and enzyme kinetics, the Carbonyl Society members have meanwhile established internationally recognized enzyme nomenclature systems and now consider aspects of enzyme genomics and enzyme evolution along with their roles in diseases. The 16th international meeting included lectures from international speakers from all over the world.

  5. Membrane protein damage and repair: selective loss of a quinone-protein function in chloroplast membranes

    International Nuclear Information System (INIS)

    Kyle, D.J.; Ohad, I.; Arntzen, C.J.

    1984-01-01

    A loss of electron transport capacity in chloroplast membranes was induced by high-light intensities (photoinhibition). The primary site of inhibition was at the reducing side of photosystem II (PSII) with little damage to the oxidizing side or to the reaction center core of PSII. Addition of herbicides (atrazine or diuron) partially protected the membrane from photoinhibition; these compounds displace the bound plastoquinone (designated as Q/sub B/), which functions as the secondary electron acceptor on the reducing side of PSII. Loss of function of the 32-kilodalton Q/sub B/ apoprotein was demonstrated by a loss of binding sites for [ 14 C]atraazine. We suggest that quinone anions, which may interact with molecular oxygen to produce an oxygen radical, selectively damage the apoprotein of the secondary acceptor of PSII, thus rendering it inactive and thereby blocking photosynthetic electron flow under conditions of high photon flux densities. 21 references, 4 figures, 2 tables

  6. Highly Selective Fluorescent Sensing of Proteins Based on a Fluorescent Molecularly Imprinted Nanosensor

    Directory of Open Access Journals (Sweden)

    Shuo Wang

    2013-09-01

    Full Text Available A fluorescent molecularly imprinted nanosensor was obtained by grafting imprinted polymer onto the surface of multi-wall carbon nanotubes and post-imprinting treatment with fluorescein isothiocyanate (FITC. The fluorescence of lysozyme-imprinted polymer (Lys-MIP was quenched more strongly by Lys than that of nonimprinted polymer (NIP, which indicated that the Lys-MIP could recognize Lys. The resulted imprinted material has the ability to selectively sense a target protein, and an imprinting factor of 3.34 was achieved. The Lys-MIP also showed selective detection for Lys among other proteins such as cytochrome C (Cyt C, hemoglobin (HB and bovine serum albumin (BSA due to the imprinted sites in the Lys-MIP. This approach combines the high selectivity of surface molecular imprinting technology and fluorescence, and converts binding events into detectable signals by monitoring fluorescence spectra. Therefore, it will have further applications for Lys sensing.

  7. Decarboxylative alkylation for site-selective bioconjugation of native proteins via oxidation potentials.

    Science.gov (United States)

    Bloom, Steven; Liu, Chun; Kölmel, Dominik K; Qiao, Jennifer X; Zhang, Yong; Poss, Michael A; Ewing, William R; MacMillan, David W C

    2018-02-01

    The advent of antibody-drug conjugates as pharmaceuticals has fuelled a need for reliable methods of site-selective protein modification that furnish homogeneous adducts. Although bioorthogonal methods that use engineered amino acids often provide an elegant solution to the question of selective functionalization, achieving homogeneity using native amino acids remains a challenge. Here, we explore visible-light-mediated single-electron transfer as a mechanism towards enabling site- and chemoselective bioconjugation. Specifically, we demonstrate the use of photoredox catalysis as a platform to selectivity wherein the discrepancy in oxidation potentials between internal versus C-terminal carboxylates can be exploited towards obtaining C-terminal functionalization exclusively. This oxidation potential-gated technology is amenable to endogenous peptides and has been successfully demonstrated on the protein insulin. As a fundamentally new approach to bioconjugation this methodology provides a blueprint toward the development of photoredox catalysis as a generic platform to target other redox-active side chains for native conjugation.

  8. Decarboxylative alkylation for site-selective bioconjugation of native proteins via oxidation potentials

    Science.gov (United States)

    Bloom, Steven; Liu, Chun; Kölmel, Dominik K.; Qiao, Jennifer X.; Zhang, Yong; Poss, Michael A.; Ewing, William R.; MacMillan, David W. C.

    2018-02-01

    The advent of antibody-drug conjugates as pharmaceuticals has fuelled a need for reliable methods of site-selective protein modification that furnish homogeneous adducts. Although bioorthogonal methods that use engineered amino acids often provide an elegant solution to the question of selective functionalization, achieving homogeneity using native amino acids remains a challenge. Here, we explore visible-light-mediated single-electron transfer as a mechanism towards enabling site- and chemoselective bioconjugation. Specifically, we demonstrate the use of photoredox catalysis as a platform to selectivity wherein the discrepancy in oxidation potentials between internal versus C-terminal carboxylates can be exploited towards obtaining C-terminal functionalization exclusively. This oxidation potential-gated technology is amenable to endogenous peptides and has been successfully demonstrated on the protein insulin. As a fundamentally new approach to bioconjugation this methodology provides a blueprint toward the development of photoredox catalysis as a generic platform to target other redox-active side chains for native conjugation.

  9. Catalytic performance of heterogeneous Rh/C3N4 for the carbonylation of methanol

    Science.gov (United States)

    Budiman, Anatta Wahyu; Choi, Myoung Jae; Nur, Adrian

    2018-02-01

    The excess of water in homogeneous the carbonylation of methanol system could increase the amount of by-products formed through water-gas shift reaction and could accelerate the rusting of equipment. Many scientists tried to decrease the content of water in the carbonylation of methanol system by using lithium and iodide promoter that results a moderate catalytic activity in the water content at 2wt%. The heterogenized catalyst offers several distinct advantages such as it was enables increased catalyst concentration in the reaction mixture, which is directly proportional to acetic acid production rate, without the addition of an alkali iodide salt promoter. The heterogeneous catalyst also results in reduced by-product formation. This study is aimed to produce a novel catalyst (Rh/C3N4) with a high selectivity of acetic acid in a relatively lower water and halide content. This novel catalyst performs high conversion and selectivity of acetic acid as the result of the strong ionic bonding of melamine and rhodium complex species that was caused by the presence of methyl iodide species. The CO2 in feed gas significantly decreases the catalytic activity of Rh-melamine because of its inert characteristics. The kinetic test was performed as that the first order kinetic equation. The kinetic tests revealed the reaction route of the the carbonylation of methanol in this system was performed trough the methyl acetate.

  10. Controlling the rejection of protein during membrane filtration by adding selected polyelectrolytes

    DEFF Research Database (Denmark)

    Pinelo, Manuel; Ferrer Roca, Carme; Meyer, Anne S.

    2012-01-01

    Electrostatic interactions among the charged groups on proteins and/or between proteins and other solutes significantly affect the aggregation/deposition phenomena that induce fouling and decrease permeate flux during membrane purification of proteins. Such interactions can be turned...... help enhance the performance of membrane filtration for fractionation/purification of a target protein by significantly reducing fouling and modifying rejection/selectivity.......) changing the pH, on the permeate flux and membrane transmission of bovin serum albumina (BSA) through a PVDF membrane. The addition of PS-co-AA to the feed solution resulted in significant increases of the BSA transmission at pH 7.4 as compared to the transmission of a pure BSA solution (1g...

  11. Sexual selection and the adaptive evolution of PKDREJ protein in primates and rodents.

    Science.gov (United States)

    Vicens, Alberto; Gómez Montoto, Laura; Couso-Ferrer, Francisco; Sutton, Keith A; Roldan, Eduardo R S

    2015-02-01

    PKDREJ is a testis-specific protein thought to be located on the sperm surface. Functional studies in the mouse revealed that loss of PKDREJ has effects on sperm transport and the ability to undergo an induced acrosome reaction. Thus, PKDREJ has been considered a potential target of post-copulatory sexual selection in the form of sperm competition. Proteins involved in reproductive processes often show accelerated evolution. In many cases, this rapid divergence is promoted by positive selection which may be driven, at least in part, by post-copulatory sexual selection. We analysed the evolution of the PKDREJ protein in primates and rodents and assessed whether PKDREJ divergence is associated with testes mass relative to body mass, which is a reliable proxy of sperm competition levels. Evidence of an association between the evolutionary rate of the PKDREJ gene and testes mass relative to body mass was not found in primates. Among rodents, evidence of positive selection was detected in the Pkdrej gene in the family Cricetidae but not in Muridae. We then assessed whether Pkdrej divergence is associated with episodes of sperm competition in these families. We detected a positive significant correlation between the evolutionary rates of Pkdrej and testes mass relative to body mass in cricetids. These findings constitute the first evidence of post-copulatory sexual selection influencing the evolution of a protein that participates in the mechanisms regulating sperm transport and the acrosome reaction, strongly suggesting that positive selection may act on these fertilization steps, leading to advantages in situations of sperm competition. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. New method to determine the total carbonyl functional group content in extractable particulate organic matter by tandem mass spectrometry.

    Science.gov (United States)

    Dron, J; Zheng, W; Marchand, N; Wortham, H

    2008-08-01

    A functional group analysis method was developed to determine the quantitative content of carbonyl functional groups in atmospheric particulate organic matter (POM) using constant neutral loss scanning-tandem mass spectrometry (CNLS-MS/MS). The neutral loss method consists in monitoring the loss of a neutral fragment produced by the fragmentation of a precursor ion in a collision cell. The only ions detected are the daughter ions resulting from the loss of the neutral fragment under study. Then, scanning the loss of a neutral fragment characteristic of a functional group enables the selective detection of the compounds bearing the chemical function under study within a complex mixture. The selective detection of carbonyl functional groups was achieved after derivatization with pentafluorophenylhydrazine (PFPH) by monitoring the neutral loss of C(6)F(5)N (181 amu), which was characteristic of a large panel of derivatized carbonyl compounds. The method was tested on 25 reference mixtures of different composition, all containing 24 carbonyl compounds at randomly determined concentrations. The repeatability and calibration tests were satisfying as they resulted in a relative standard deviation below 5% and a linear range between 0.01 and 0.65 mM with a calculated detection limit of 0.0035 mM. Also, the relative deviation induced by changing the composition of the mixture while keeping the total concentration of carbonyl functional groups constant was less than 20%. These reliability experiments demonstrate the high robustness of the developed procedure for accurate carbonyl functional group measurement, which was applied to atmospheric POM samples. Copyright (c) 2008 John Wiley & Sons, Ltd.

  13. Membrane proteins bind lipids selectively to modulate their structure and function.

    Science.gov (United States)

    Laganowsky, Arthur; Reading, Eamonn; Allison, Timothy M; Ulmschneider, Martin B; Degiacomi, Matteo T; Baldwin, Andrew J; Robinson, Carol V

    2014-06-05

    Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments and that lipids can bind to specific sites, for example, in potassium channels. Fundamental questions remain however regarding the extent of membrane protein selectivity towards lipids. Here we report a mass spectrometry approach designed to determine the selectivity of lipid binding to membrane protein complexes. We investigate the mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis and aquaporin Z (AqpZ) and the ammonia channel (AmtB) from Escherichia coli, using ion mobility mass spectrometry (IM-MS), which reports gas-phase collision cross-sections. We demonstrate that folded conformations of membrane protein complexes can exist in the gas phase. By resolving lipid-bound states, we then rank bound lipids on the basis of their ability to resist gas phase unfolding and thereby stabilize membrane protein structure. Lipids bind non-selectively and with high avidity to MscL, all imparting comparable stability; however, the highest-ranking lipid is phosphatidylinositol phosphate, in line with its proposed functional role in mechanosensation. AqpZ is also stabilized by many lipids, with cardiolipin imparting the most significant resistance to unfolding. Subsequently, through functional assays we show that cardiolipin modulates AqpZ function. Similar experiments identify AmtB as being highly selective for phosphatidylglycerol, prompting us to obtain an X-ray structure in this lipid membrane-like environment. The 2.3 Å resolution structure, when compared with others obtained without lipid bound, reveals distinct conformational changes that re-position AmtB residues to interact with the lipid bilayer. Our results demonstrate that resistance to unfolding correlates with specific lipid-binding events, enabling a distinction to be made between lipids that merely bind from those that modulate membrane

  14. Fast and Selective Modification of Thiol Proteins/Peptides by N-(Phenylseleno)phthalimide

    Science.gov (United States)

    Wang, Zhengfang; Zhang, Yun; Zhang, Hao; Harrington, Peter B.; Chen, Hao

    2012-03-01

    We previously reported that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used to selectively derivatize thiols for mass spectrometric analysis, and the introduced selenium tags are useful as they could survive or removed with collision-induced dissociation (CID). Described herein is the further study of the reactivity of various protein/peptide thiols toward NPSP and its application to derivatize thiol peptides in protein digests. With a modified protocol (i.e., dissolving NPSP in acetonitrile instead of aqueous solvent), we found that quantitative conversion of thiols can be obtained in seconds, using NPSP in a slight excess amount (NPSP:thiol of 1.1-2:1). Further investigation shows that the thiol reactivity toward NPSP reflects its chemical environment and accessibility in proteins/peptides. For instance, adjacent basic amino acid residues increase the thiol reactivity, probably because they could stabilize the thiolate form to facilitate the nucleophilic attack of thiol on NPSP. In the case of creatine phosphokinase, the native protein predominately has one thiol reacted with NPSP while all of four thiol groups of the denatured protein can be derivatized, in accordance with the corresponding protein conformation. In addition, thiol peptides in protein/peptide enzymatic digests can be quickly and effectively tagged by NPSP following tri- n-butylphosphine (TBP) reduction. Notably, all three thiols of the peptide QCCASVCSL in the insulin peptic digest can be modified simultaneously by NPSP. These results suggest a novel and selective method for protecting thiols in the bottom-up approach for protein structure analysis.

  15. Automated Hydrophobic Interaction Chromatography Column Selection for Use in Protein Purification

    Science.gov (United States)

    Murphy, Patrick J. M.; Stone, Orrin J.; Anderson, Michelle E.

    2011-01-01

    In contrast to other chromatographic methods for purifying proteins (e.g. gel filtration, affinity, and ion exchange), hydrophobic interaction chromatography (HIC) commonly requires experimental determination (referred to as screening or "scouting") in order to select the most suitable chromatographic medium for purifying a given protein 1. The method presented here describes an automated approach to scouting for an optimal HIC media to be used in protein purification. HIC separates proteins and other biomolecules from a crude lysate based on differences in hydrophobicity. Similar to affinity chromatography (AC) and ion exchange chromatography (IEX), HIC is capable of concentrating the protein of interest as it progresses through the chromatographic process. Proteins best suited for purification by HIC include those with hydrophobic surface regions and able to withstand exposure to salt concentrations in excess of 2 M ammonium sulfate ((NH4)2SO4). HIC is often chosen as a purification method for proteins lacking an affinity tag, and thus unsuitable for AC, and when IEX fails to provide adequate purification. Hydrophobic moieties on the protein surface temporarily bind to a nonpolar ligand coupled to an inert, immobile matrix. The interaction between protein and ligand are highly dependent on the salt concentration of the buffer flowing through the chromatography column, with high ionic concentrations strengthening the protein-ligand interaction and making the protein immobile (i.e. bound inside the column) 2. As salt concentrations decrease, the protein-ligand interaction dissipates, the protein again becomes mobile and elutes from the column. Several HIC media are commercially available in pre-packed columns, each containing one of several hydrophobic ligands (e.g. S-butyl, butyl, octyl, and phenyl) cross-linked at varying densities to agarose beads of a specific diameter 3. Automated column scouting allows for an efficient approach for determining which HIC media

  16. A Peptidomimetic Antibiotic Targets Outer Membrane Proteins and Disrupts Selectively the Outer Membrane in Escherichia coli.

    Science.gov (United States)

    Urfer, Matthias; Bogdanovic, Jasmina; Lo Monte, Fabio; Moehle, Kerstin; Zerbe, Katja; Omasits, Ulrich; Ahrens, Christian H; Pessi, Gabriella; Eberl, Leo; Robinson, John A

    2016-01-22

    Increasing antibacterial resistance presents a major challenge in antibiotic discovery. One attractive target in Gram-negative bacteria is the unique asymmetric outer membrane (OM), which acts as a permeability barrier that protects the cell from external stresses, such as the presence of antibiotics. We describe a novel β-hairpin macrocyclic peptide JB-95 with potent antimicrobial activity against Escherichia coli. This peptide exhibits no cellular lytic activity, but electron microscopy and fluorescence studies reveal an ability to selectively disrupt the OM but not the inner membrane of E. coli. The selective targeting of the OM probably occurs through interactions of JB-95 with selected β-barrel OM proteins, including BamA and LptD as shown by photolabeling experiments. Membrane proteomic studies reveal rapid depletion of many β-barrel OM proteins from JB-95-treated E. coli, consistent with induction of a membrane stress response and/or direct inhibition of the Bam folding machine. The results suggest that lethal disruption of the OM by JB-95 occurs through a novel mechanism of action at key interaction sites within clusters of β-barrel proteins in the OM. These findings open new avenues for developing antibiotics that specifically target β-barrel proteins and the integrity of the Gram-negative OM. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Instrument for Airborne Measurement of Carbonyl Sulfide, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Southwest Sciences proposes to develop small, low power instrumentation for the real-time direct measurement of carbonyl sulfide (OCS) in the atmosphere, especially...

  18. Instrument for Airborne Measurement of Carbonyl Sulfide, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — In this Phase II SBIR program, Southwest Sciences will continue the development of small, low power instrumentation for real-time direct measurement of carbonyl...

  19. Degradation of carbonyl hydroperoxides in the atmosphere and in combustion

    KAUST Repository

    Xing, Lili; Bao, Junwei Lucas; Wang, Zhandong; Zhang, Feng; Truhlar, Donald G.

    2017-01-01

    Oxygenates with carbonyl and hydroperoxy functional groups are important intermediates that are generated during the autooxidation of organic compounds in the atmosphere and during the autoignition of transport fuels. In the troposphere

  20. Differential Nanos 2 protein stability results in selective germ cell accumulation in the sea urchin.

    Science.gov (United States)

    Oulhen, Nathalie; Wessel, Gary M

    2016-10-01

    Nanos is a translational regulator required for the survival and maintenance of primordial germ cells. In the sea urchin, Strongylocentrotus purpuratus (Sp), Nanos 2 mRNA is broadly transcribed but accumulates specifically in the small micromere (sMic) lineage, in part because of the 3'UTR element GNARLE leads to turnover in somatic cells but retention in the sMics. Here we found that the Nanos 2 protein is also selectively stabilized; it is initially translated throughout the embryo but turned over in the future somatic cells and retained only in the sMics, the future germ line in this animal. This differential stability of Nanos protein is dependent on the open reading frame (ORF), and is independent of the sumoylation and ubiquitylation pathways. Manipulation of the ORF indicates that 68 amino acids in the N terminus of the Nanos protein are essential for its stability in the sMics whereas a 45 amino acid element adjacent to the zinc fingers targets its degradation. Further, this regulation of Nanos protein is cell autonomous, following formation of the germ line. These results are paradigmatic for the unique presence of Nanos in the germ line by a combination of selective RNA retention, distinctive translational control mechanisms (Oulhen et al., 2013), and now also by defined Nanos protein stability. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Propheromones that release pheromonal carbonyl compounds in light.

    Science.gov (United States)

    Liu, X; Macaulay, E D; Pickett, J A

    1984-05-01

    Pheromonal carbonyl compounds; (Z)-11-hexadecanal, (E)-citral, and 2-heptanone were treated with six alcohols to give acetals or ketals, some of which acted as propheromones by releasing the pheromonal carbonyl compounds in ultraviolet or simulated sunlight. Highest yields of pheromone were obtained from adducts prepared witho-nitrobenzyl alcohol ando-nitrophenylethane-1,2-diol. Adducts from (Z)-11-hexadecenal and these two alcohols were employed in lures to catch diamondback moths,Plutella xylostella (L.).

  2. Catalytic hydrogenation of carbonyl group for deuterated compound production

    International Nuclear Information System (INIS)

    Gluhoi, C. Andreea; Marginean, P.; Lazar, Diana; Almasan, V.

    1999-01-01

    The total deuterated isopropyl alcohol can be produced starting from acetone. The developed technology comprises two steps: Deuteration of acetone by H/D isotopic exchange between acetone and heavy water in homogeneous catalysis. Reduction of the deuterated acetone with deuterium in presence of a metal/support catalyst. H/D isotopic exchange reaction of the H atoms from CH 3 groups is easy to occur because carbonyl group weakens C-H bond (ceto-enolyc tautomery). The big difference between boiling points of acetone and water permits an easy separation of acetone by distillation method. The reduction of acetone with deuterium was performed in a dynamic reactor by passing a deuterium flow saturated with acetone vapour through a supported nickel catalyst bed. The reaction products were analysed on-line using a flame ionisation detector. The supported nickel catalysts were checked for this reaction. By using nickel over different supports the selectivity for isopropyl alcohol was about 100%. The propane was detected only as traces. The catalytic activity depends strongly on the support nature: the Ni/SiO 2 is less active, while the Ni/TiO 2 presents the larger value for the intrinsic activity. (authors)

  3. Identification and Structure-Function Analysis of Subfamily Selective G Protein-Coupled Receptor Kinase Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Homan, Kristoff T.; Larimore, Kelly M.; Elkins, Jonathan M.; Szklarz, Marta; Knapp, Stefan; Tesmer, John J.G. [Michigan; (Oxford)

    2015-02-13

    Selective inhibitors of individual subfamilies of G protein-coupled receptor kinases (GRKs) would serve as useful chemical probes as well as leads for therapeutic applications ranging from heart failure to Parkinson’s disease. To identify such inhibitors, differential scanning fluorimetry was used to screen a collection of known protein kinase inhibitors that could increase the melting points of the two most ubiquitously expressed GRKs: GRK2 and GRK5. Enzymatic assays on 14 of the most stabilizing hits revealed that three exhibit nanomolar potency of inhibition for individual GRKs, some of which exhibiting orders of magnitude selectivity. Most of the identified compounds can be clustered into two chemical classes: indazole/dihydropyrimidine-containing compounds that are selective for GRK2 and pyrrolopyrimidine-containing compounds that potently inhibit GRK1 and GRK5 but with more modest selectivity. The two most potent inhibitors representing each class, GSK180736A and GSK2163632A, were cocrystallized with GRK2 and GRK1, and their atomic structures were determined to 2.6 and 1.85 Å spacings, respectively. GSK180736A, developed as a Rho-associated, coiled-coil-containing protein kinase inhibitor, binds to GRK2 in a manner analogous to that of paroxetine, whereas GSK2163632A, developed as an insulin-like growth factor 1 receptor inhibitor, occupies a novel region of the GRK active site cleft that could likely be exploited to achieve more selectivity. However, neither compound inhibits GRKs more potently than their initial targets. This data provides the foundation for future efforts to rationally design even more potent and selective GRK inhibitors.

  4. Magnetic deep eutectic solvents molecularly imprinted polymers for the selective recognition and separation of protein

    International Nuclear Information System (INIS)

    Liu, Yanjin; Wang, Yuzhi; Dai, Qingzhou; Zhou, Yigang

    2016-01-01

    A novel and facile magnetic deep eutectic solvents (DES) molecularly imprinted polymers (MIPs) for the selective recognition and separation of Bovine hemoglobin (BHb) was prepared. The new-type DES was adopted as the functional monomer which would bring molecular imprinted technology to a new direction. The amounts of DES were optimized. The obtained magnetic DES-MIPs were characterized with fourier transform infrared spectrometry (FT-IR), thermogravimetric analysis (TGA), field emission scanning electron microscope (FESEM), dynamic light scattering (DLS), elemental analysis and vibrating sample magnetometer (VSM). The results suggested that the imprinted polymers were successfully formed and possessed a charming magnetism. The maximum adsorption capability (Q_m_a_x) and dissociation constant (K_L) were analyzed by Langmuir isotherms (R"2 = 0.9983) and the value were estimated to be 175.44 mg/g and 0.035 mg/mL for the imprinted particles. And the imprinted particles showed a high imprinting factor of 4.77. In addition, the magnetic DES-MIPs presented outstanding recognition specificity and selectivity so that it can be utilized to separate template protein from the mixture of proteins and real samples. Last but not least, the combination of deep eutectic solvents and molecular imprinted technology in this paper provides a new perspective for the recognition and separation of proteins. - Highlights: • Combined green deep eutectic solvents (DES) and molecular imprinted technology in recognition and separation of proteins. • DES was adopted as a new-type functional monomer. • The obtained magnetic DES-MIPs can separate proteins rapidly by an external magnetic field. • Adsorption and selectivity properties were discussed.

  5. Magnetic deep eutectic solvents molecularly imprinted polymers for the selective recognition and separation of protein

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yanjin [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (China); Wang, Yuzhi, E-mail: wyzss@hnu.edu.cn [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (China); Dai, Qingzhou [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (China); Zhou, Yigang [Department of Microbiology, College of Basic Medicine, Central South University, Changsha, 410083 (China)

    2016-09-14

    A novel and facile magnetic deep eutectic solvents (DES) molecularly imprinted polymers (MIPs) for the selective recognition and separation of Bovine hemoglobin (BHb) was prepared. The new-type DES was adopted as the functional monomer which would bring molecular imprinted technology to a new direction. The amounts of DES were optimized. The obtained magnetic DES-MIPs were characterized with fourier transform infrared spectrometry (FT-IR), thermogravimetric analysis (TGA), field emission scanning electron microscope (FESEM), dynamic light scattering (DLS), elemental analysis and vibrating sample magnetometer (VSM). The results suggested that the imprinted polymers were successfully formed and possessed a charming magnetism. The maximum adsorption capability (Q{sub max}) and dissociation constant (K{sub L}) were analyzed by Langmuir isotherms (R{sup 2} = 0.9983) and the value were estimated to be 175.44 mg/g and 0.035 mg/mL for the imprinted particles. And the imprinted particles showed a high imprinting factor of 4.77. In addition, the magnetic DES-MIPs presented outstanding recognition specificity and selectivity so that it can be utilized to separate template protein from the mixture of proteins and real samples. Last but not least, the combination of deep eutectic solvents and molecular imprinted technology in this paper provides a new perspective for the recognition and separation of proteins. - Highlights: • Combined green deep eutectic solvents (DES) and molecular imprinted technology in recognition and separation of proteins. • DES was adopted as a new-type functional monomer. • The obtained magnetic DES-MIPs can separate proteins rapidly by an external magnetic field. • Adsorption and selectivity properties were discussed.

  6. Vapor phase carbonylation of dimethyl ether and methyl acetate with supported transition metal catalysts

    International Nuclear Information System (INIS)

    Shikada, T.; Fujimoto, K.; Tominaga, H.O.

    1986-01-01

    The synthesis of acetic acid (AcOH) from methanol (MeOH) and carbon monoxide has been performed industrially in the liquid phase using a rhodium complex catalyst and an iodide promoter. The selectivity to AcOH is more than 99% under mild conditions (175 0 C, 28 atm). The homogeneous rhodium catalyst has been also effective for the synthesis of acetic anhydride (Ac 2 O) by carbonylation of dimethyl ether (DME) or methyl acetate (AcOMe). However, rhodium is one of the most expensive metals and its proved reserves are quite limited. It is highly desired, therefore, to develop a new catalyst as a substitute for rhodium. The authors have already reported that nickel supported on active carbon exhibits an excellent activity for the vapor phase carbonylation of MeOh in the presence of iodide promoter and under moderately pressurized conditions. In addition, corrosive attack on reactors by iodide compounds is expected to be negligible in the vapor phase system. In the present work, vapor phase carbonylation of DME and AcOMe on nickel-active carbon (Ni/A.C.) and molybdenum-active carbon (Mo/A.C.) catalysts was studied

  7. Structural insights into the neuroprotective-acting carbonyl reductase Sniffer of Drosophila melanogaster.

    Science.gov (United States)

    Sgraja, Tanja; Ulschmid, Julia; Becker, Katja; Schneuwly, Stephan; Klebe, Gerhard; Reuter, Klaus; Heine, Andreas

    2004-10-01

    In vivo studies with the fruit-fly Drosophila melanogaster have shown that the Sniffer protein prevents age-dependent and oxidative stress-induced neurodegenerative processes. Sniffer is a NADPH-dependent carbonyl reductase belonging to the enzyme family of short-chain dehydrogenases/reductases (SDRs). The crystal structure of the homodimeric Sniffer protein from Drosophila melanogaster in complex with NADP+ has been determined by multiple-wavelength anomalous dispersion and refined to a resolution of 1.75 A. The observed fold represents a typical dinucleotide-binding domain as detected for other SDRs. With respect to the cofactor-binding site and the region referred to as substrate-binding loop, the Sniffer protein shows a striking similarity to the porcine carbonyl reductase (PTCR). This loop, in both Sniffer and PTCR, is substantially shortened compared to other SDRs. In most enzymes of the SDR family this loop adopts a well-defined conformation only after substrate binding and remains disordered in the absence of any bound ligands or even if only the dinucleotide cofactor is bound. In the structure of the Sniffer protein, however, the conformation of this loop is well defined, although no substrate is present. Molecular modeling studies provide an idea of how binding of substrate molecules to Sniffer could possibly occur.

  8. Tuning a Protein-Labeling Reaction to Achieve Highly Site Selective Lysine Conjugation.

    Science.gov (United States)

    Pham, Grace H; Ou, Weijia; Bursulaya, Badry; DiDonato, Michael; Herath, Ananda; Jin, Yunho; Hao, Xueshi; Loren, Jon; Spraggon, Glen; Brock, Ansgar; Uno, Tetsuo; Geierstanger, Bernhard H; Cellitti, Susan E

    2018-04-16

    Activated esters are widely used to label proteins at lysine side chains and N termini. These reagents are useful for labeling virtually any protein, but robust reactivity toward primary amines generally precludes site-selective modification. In a unique case, fluorophenyl esters are shown to preferentially label human kappa antibodies at a single lysine (Lys188) within the light-chain constant domain. Neighboring residues His189 and Asp151 contribute to the accelerated rate of labeling at Lys188 relative to the ≈40 other lysine sites. Enriched Lys188 labeling can be enhanced from 50-70 % to >95 % by any of these approaches: lowering reaction temperature, applying flow chemistry, or mutagenesis of specific residues in the surrounding protein environment. Our results demonstrated that activated esters with fluoro-substituted aromatic leaving groups, including a fluoronaphthyl ester, can be generally useful reagents for site-selective lysine labeling of antibodies and other immunoglobulin-type proteins. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Antisense oligonucleotides targeting translation inhibitory elements in 5' UTRs can selectively increase protein levels.

    Science.gov (United States)

    Liang, Xue-Hai; Sun, Hong; Shen, Wen; Wang, Shiyu; Yao, Joyee; Migawa, Michael T; Bui, Huynh-Hoa; Damle, Sagar S; Riney, Stan; Graham, Mark J; Crooke, Rosanne M; Crooke, Stanley T

    2017-09-19

    A variety of diseases are caused by deficiencies in amounts or activity of key proteins. An approach that increases the amount of a specific protein might be of therapeutic benefit. We reasoned that translation could be specifically enhanced using trans-acting agents that counter the function of negative regulatory elements present in the 5' UTRs of some mRNAs. We recently showed that translation can be enhanced by antisense oligonucleotides (ASOs) that target upstream open reading frames. Here we report the amount of a protein can also be selectively increased using ASOs designed to hybridize to other translation inhibitory elements in 5' UTRs. Levels of human RNASEH1, LDLR, and ACP1 and of mouse ACP1 and ARF1 were increased up to 2.7-fold in different cell types and species upon treatment with chemically modified ASOs targeting 5' UTR inhibitory regions in the mRNAs encoding these proteins. The activities of ASOs in enhancing translation were sequence and position dependent and required helicase activity. The ASOs appear to improve the recruitment of translation initiation factors to the target mRNA. Importantly, ASOs targeting ACP1 mRNA significantly increased the level of ACP1 protein in mice, suggesting that this approach has therapeutic and research potentials. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Efficient Feature Selection and Classification of Protein Sequence Data in Bioinformatics

    Science.gov (United States)

    Faye, Ibrahima; Samir, Brahim Belhaouari; Md Said, Abas

    2014-01-01

    Bioinformatics has been an emerging area of research for the last three decades. The ultimate aims of bioinformatics were to store and manage the biological data, and develop and analyze computational tools to enhance their understanding. The size of data accumulated under various sequencing projects is increasing exponentially, which presents difficulties for the experimental methods. To reduce the gap between newly sequenced protein and proteins with known functions, many computational techniques involving classification and clustering algorithms were proposed in the past. The classification of protein sequences into existing superfamilies is helpful in predicting the structure and function of large amount of newly discovered proteins. The existing classification results are unsatisfactory due to a huge size of features obtained through various feature encoding methods. In this work, a statistical metric-based feature selection technique has been proposed in order to reduce the size of the extracted feature vector. The proposed method of protein classification shows significant improvement in terms of performance measure metrics: accuracy, sensitivity, specificity, recall, F-measure, and so forth. PMID:25045727

  11. Site-selective {sup 13}C labeling of proteins using erythrose

    Energy Technology Data Exchange (ETDEWEB)

    Weininger, Ulrich, E-mail: ulrich.weininger@physik.uni-halle.de [Lund University, Department of Biophysical Chemistry, Center for Molecular Protein Science (Sweden)

    2017-03-15

    NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with {sup 13}C and/or {sup 1}H, which is achieved in the most general way by using site-selectively {sup 13}C-enriched glucose (1- and 2-{sup 13}C) as the carbon source in bacterial expression systems. Using this strategy, multiple sites in side chains, including aromatics, become site-selectively labeled and suitable for relaxation studies. Here we systematically investigate the use of site-selectively {sup 13}C-enriched erythrose (1-, 2-, 3- and 4-{sup 13}C) as a suitable precursor for {sup 13}C labeled aromatic side chains. We quantify {sup 13}C incorporation in nearly all sites in all 20 amino acids and compare the results to glucose based labeling. In general the erythrose approach results in more selective labeling. While there is only a minor gain for phenylalanine and tyrosine side-chains, the {sup 13}C incorporation level for tryptophan is at least doubled. Additionally, the Phe ζ and Trp η2 positions become labeled. In the aliphatic side chains, labeling using erythrose yields isolated {sup 13}C labels for certain positions, like Ile β and His β, making these sites suitable for dynamics studies. Using erythrose instead of glucose as a source for site-selective {sup 13}C labeling enables unique or superior labeling for certain positions and is thereby expanding the toolbox for customized isotope labeling of amino-acid side-chains.

  12. Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination

    Science.gov (United States)

    Kazmier, Kelli; Alexander, Nathan S.; Meiler, Jens; Mchaourab, Hassane S.

    2010-01-01

    A hybrid protein structure determination approach combining sparse Electron Paramagnetic Resonance (EPR) distance restraints and Rosetta de novo protein folding has been previously demonstrated to yield high quality models (Alexander et al., 2008). However, widespread application of this methodology to proteins of unknown structures is hindered by the lack of a general strategy to place spin label pairs in the primary sequence. In this work, we report the development of an algorithm that optimally selects spin labeling positions for the purpose of distance measurements by EPR. For the α-helical subdomain of T4 lysozyme (T4L), simulated restraints that maximize sequence separation between the two spin labels while simultaneously ensuring pairwise connectivity of secondary structure elements yielded vastly improved models by Rosetta folding. 50% of all these models have the correct fold compared to only 21% and 8% correctly folded models when randomly placed restraints or no restraints are used, respectively. Moreover, the improvements in model quality require a limited number of optimized restraints, the number of which is determined by the pairwise connectivities of T4L α-helices. The predicted improvement in Rosetta model quality was verified by experimental determination of distances between spin labels pairs selected by the algorithm. Overall, our results reinforce the rationale for the combined use of sparse EPR distance restraints and de novo folding. By alleviating the experimental bottleneck associated with restraint selection, this algorithm sets the stage for extending computational structure determination to larger, traditionally elusive protein topologies of critical structural and biochemical importance. PMID:21074624

  13. Sequence Based Prediction of Antioxidant Proteins Using a Classifier Selection Strategy.

    Directory of Open Access Journals (Sweden)

    Lina Zhang

    Full Text Available Antioxidant proteins perform significant functions in maintaining oxidation/antioxidation balance and have potential therapies for some diseases. Accurate identification of antioxidant proteins could contribute to revealing physiological processes of oxidation/antioxidation balance and developing novel antioxidation-based drugs. In this study, an ensemble method is presented to predict antioxidant proteins with hybrid features, incorporating SSI (Secondary Structure Information, PSSM (Position Specific Scoring Matrix, RSA (Relative Solvent Accessibility, and CTD (Composition, Transition, Distribution. The prediction results of the ensemble predictor are determined by an average of prediction results of multiple base classifiers. Based on a classifier selection strategy, we obtain an optimal ensemble classifier composed of RF (Random Forest, SMO (Sequential Minimal Optimization, NNA (Nearest Neighbor Algorithm, and J48 with an accuracy of 0.925. A Relief combined with IFS (Incremental Feature Selection method is adopted to obtain optimal features from hybrid features. With the optimal features, the ensemble method achieves improved performance with a sensitivity of 0.95, a specificity of 0.93, an accuracy of 0.94, and an MCC (Matthew's Correlation Coefficient of 0.880, far better than the existing method. To evaluate the prediction performance objectively, the proposed method is compared with existing methods on the same independent testing dataset. Encouragingly, our method performs better than previous studies. In addition, our method achieves more balanced performance with a sensitivity of 0.878 and a specificity of 0.860. These results suggest that the proposed ensemble method can be a potential candidate for antioxidant protein prediction. For public access, we develop a user-friendly web server for antioxidant protein identification that is freely accessible at http://antioxidant.weka.cc.

  14. Determination of Carbonyl Compounds in Exhaled Cigarette Smoke

    Directory of Open Access Journals (Sweden)

    Moldoveanu S

    2014-12-01

    Full Text Available This paper presents the findings on a quantitative evaluation of carbonyl levels in exhaled cigarette smoke from human subjects. The cigarettes evaluated include products with 5.0 mg ‘tar’, 10.6 mg ‘tar’ and 16.2 mg ‘tar’, where ‘tar’ is defined as the weight of total wet particulate matter (TPM minus the weight of nicotine and water, and the cigarettes are smoked following U.S. Federal Trade Commission (FTC recommendations. The measured levels of carbonyls in the exhaled smoke were compared with calculated yields of carbonyls in the inhaled smoke and a retention efficiency was obtained. The number of human subjects included a total of ten smokers for the 10.6 mg ‘tar’, five for the 16.2 mg ‘tar’, and five for the 5.0 mg ‘tar’ product, each subject smoking three cigarettes. The analyzed carbonyl compounds included several aldehydes (formaldehyde, acetaldehyde, acrolein, propionaldehyde, crotonaldehyde and n-butyraldehyde, and two ketones (acetone and 2-butanone. The smoke collection from the human subjects was vacuum assisted. Exhaled smoke was collected on Cambridge pads pretreated with a solution of dinitrophenylhydrazine (DNPH followed by high performance liquid chromatography (HPLC analysis of the dinitrophenylhydrazones of the carbonyl compounds. The cigarette butts from the smokers were collected and analyzed for nicotine. The nicotine levels for the cigarette butts from the smokers were used to calculate the level of carbonyls in the inhaled smoke, based on calibration curves. These were generated separately by analyzing the carbonyls in smoke and the nicotine in the cigarette butts obtained by machine smoking under different puffing regimes. The comparison of the level of carbonyl compounds in exhaled smoke with that from the inhaled smoke showed high retention of all the carbonyls. The retention of aldehydes was above 95% for all three different ‘tar’ levels cigarettes. The ketones were retained with a

  15. Emissions of carbonyl compounds from various cookstoves in China

    International Nuclear Information System (INIS)

    Zhang, J.; Smith, K.R.; Univ. of California, Berkeley, CA

    1999-01-01

    This paper presents a new database of carbonyl emission factors for commonly used cookstoves in China. The emission factors, reported both on a fuel-mass basis (mg/kg) and on a defined cooking-task basis (mg/task), were determined using a carbon balance approach for 22 types of fuel/stove combinations. These include various stoves using different species of crop residues and wood, kerosene, and several types of coals and gases. The results show that all the tested cookstoves produced formaldehyde and acetaldehyde and that the vast majority of the biomass stoves produced additional carbonyl compounds such as acetone, acrolein, propionaldehyde, crotonaldehyde, 2-butanone, isobutyraldehyde, butyraldehyde, isovaleraldehyde, valeraldehyde, hexaldehyde, benzaldehyde, o-tolualdehyde, m,p-tolualdehyde, and 2,4-dimethylbenzaldehyde. Carbonyls other than formaldehyde and acetaldehyde, however, were rarely generated by burning coal, coal gas, and natural gas. Kerosene and LPG stoves generated more carbonyl compounds than coal, coal gas, and natural gas stoves, but less than biomass stoves. Indoor levels of carbonyl compounds for typical village houses during cooking hours, estimated using a mass balance model and the measured emission factors, can be high enough to cause acute health effects documented for formaldehyde exposure, depending upon house parameters and individuals' susceptibility

  16. Prediction of Protein Structural Class Based on Gapped-Dipeptides and a Recursive Feature Selection Approach

    Directory of Open Access Journals (Sweden)

    Taigang Liu

    2015-12-01

    Full Text Available The prior knowledge of protein structural class may offer useful clues on understanding its functionality as well as its tertiary structure. Though various significant efforts have been made to find a fast and effective computational approach to address this problem, it is still a challenging topic in the field of bioinformatics. The position-specific score matrix (PSSM profile has been shown to provide a useful source of information for improving the prediction performance of protein structural class. However, this information has not been adequately explored. To this end, in this study, we present a feature extraction technique which is based on gapped-dipeptides composition computed directly from PSSM. Then, a careful feature selection technique is performed based on support vector machine-recursive feature elimination (SVM-RFE. These optimal features are selected to construct a final predictor. The results of jackknife tests on four working datasets show that our method obtains satisfactory prediction accuracies by extracting features solely based on PSSM and could serve as a very promising tool to predict protein structural class.

  17. Protein Subcellular Localization with Gaussian Kernel Discriminant Analysis and Its Kernel Parameter Selection.

    Science.gov (United States)

    Wang, Shunfang; Nie, Bing; Yue, Kun; Fei, Yu; Li, Wenjia; Xu, Dongshu

    2017-12-15

    Kernel discriminant analysis (KDA) is a dimension reduction and classification algorithm based on nonlinear kernel trick, which can be novelly used to treat high-dimensional and complex biological data before undergoing classification processes such as protein subcellular localization. Kernel parameters make a great impact on the performance of the KDA model. Specifically, for KDA with the popular Gaussian kernel, to select the scale parameter is still a challenging problem. Thus, this paper introduces the KDA method and proposes a new method for Gaussian kernel parameter selection depending on the fact that the differences between reconstruction errors of edge normal samples and those of interior normal samples should be maximized for certain suitable kernel parameters. Experiments with various standard data sets of protein subcellular localization show that the overall accuracy of protein classification prediction with KDA is much higher than that without KDA. Meanwhile, the kernel parameter of KDA has a great impact on the efficiency, and the proposed method can produce an optimum parameter, which makes the new algorithm not only perform as effectively as the traditional ones, but also reduce the computational time and thus improve efficiency.

  18. Selection for a Zinc-Finger Protein Contributes to Seed Oil Increase during Soybean Domestication.

    Science.gov (United States)

    Li, Qing-Tian; Lu, Xiang; Song, Qing-Xin; Chen, Hao-Wei; Wei, Wei; Tao, Jian-Jun; Bian, Xiao-Hua; Shen, Ming; Ma, Biao; Zhang, Wan-Ke; Bi, Ying-Dong; Li, Wei; Lai, Yong-Cai; Lam, Sin-Man; Shui, Guang-Hou; Chen, Shou-Yi; Zhang, Jin-Song

    2017-04-01

    Seed oil is a momentous agronomical trait of soybean ( Glycine max ) targeted by domestication in breeding. Although multiple oil-related genes have been uncovered, knowledge of the regulatory mechanism of seed oil biosynthesis is currently limited. We demonstrate that the seed-preferred gene GmZF351 , encoding a tandem CCCH zinc finger protein, is selected during domestication. Further analysis shows that GmZF351 facilitates oil accumulation by directly activating WRINKLED1 , BIOTIN CARBOXYL CARRIER PROTEIN2 , 3-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III , DIACYLGLYCEROL O-ACYLTRANSFERASE1 , and OLEOSIN2 in transgenic Arabidopsis ( Arabidopsis thaliana ) seeds. Overexpression of GmZF351 in transgenic soybean also activates lipid biosynthesis genes, thereby accelerating seed oil accumulation. The ZF351 haplotype from the cultivated soybean group and the wild soybean ( Glycine soja ) subgroup III correlates well with high gene expression level, seed oil contents and promoter activity, suggesting that selection of GmZF351 expression leads to increased seed oil content in cultivated soybean. Our study provides novel insights into the regulatory mechanism for seed oil accumulation, and the manipulation of GmZF351 may have great potential in the improvement of oil production in soybean and other related crops. © 2017 American Society of Plant Biologists. All Rights Reserved.

  19. ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research.

    Science.gov (United States)

    Wang, Nanyi; Wang, Lirong; Xie, Xiang-Qun

    2017-11-27

    Molecular docking is widely applied to computer-aided drug design and has become relatively mature in the recent decades. Application of docking in modeling varies from single lead compound optimization to large-scale virtual screening. The performance of molecular docking is highly dependent on the protein structures selected. It is especially challenging for large-scale target prediction research when multiple structures are available for a single target. Therefore, we have established ProSelection, a docking preferred-protein selection algorithm, in order to generate the proper structure subset(s). By the ProSelection algorithm, protein structures of "weak selectors" are filtered out whereas structures of "strong selectors" are kept. Specifically, the structure which has a good statistical performance of distinguishing active ligands from inactive ligands is defined as a strong selector. In this study, 249 protein structures of 14 autophagy-related targets are investigated. Surflex-dock was used as the docking engine to distinguish active and inactive compounds against these protein structures. Both t test and Mann-Whitney U test were used to distinguish the strong from the weak selectors based on the normality of the docking score distribution. The suggested docking score threshold for active ligands (SDA) was generated for each strong selector structure according to the receiver operating characteristic (ROC) curve. The performance of ProSelection was further validated by predicting the potential off-targets of 43 U.S. Federal Drug Administration approved small molecule antineoplastic drugs. Overall, ProSelection will accelerate the computational work in protein structure selection and could be a useful tool for molecular docking, target prediction, and protein-chemical database establishment research.

  20. Molecular Mechanism of Selectivity among G Protein-Coupled Receptor Kinase 2 Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Thal, David M.; Yeow, Raymond Y.; Schoenau, Christian; Huber, Jochen; Tesmer, John J.G. (Sanofi); (Michigan)

    2012-07-11

    G protein-coupled receptors (GPCRs) are key regulators of cell physiology and control processes ranging from glucose homeostasis to contractility of the heart. A major mechanism for the desensitization of activated GPCRs is their phosphorylation by GPCR kinases (GRKs). Overexpression of GRK2 is strongly linked to heart failure, and GRK2 has long been considered a pharmaceutical target for the treatment of cardiovascular disease. Several lead compounds developed by Takeda Pharmaceuticals show high selectivity for GRK2 and therapeutic potential for the treatment of heart failure. To understand how these drugs achieve their selectivity, we determined crystal structures of the bovine GRK2-G{beta}{gamma} complex in the presence of two of these inhibitors. Comparison with the apoGRK2-G{beta}{gamma} structure demonstrates that the compounds bind in the kinase active site in a manner similar to that of the AGC kinase inhibitor balanol. Both balanol and the Takeda compounds induce a slight closure of the kinase domain, the degree of which correlates with the potencies of the inhibitors. Based on our crystal structures and homology modeling, we identified five amino acids surrounding the inhibitor binding site that we hypothesized could contribute to inhibitor selectivity. However, our results indicate that these residues are not major determinants of selectivity among GRK subfamilies. Rather, selectivity is achieved by the stabilization of a unique inactive conformation of the GRK2 kinase domain.

  1. Selective functional activity measurement of a PEGylated protein with a modification-dependent activity assay.

    Science.gov (United States)

    Weber, Alfred; Engelmaier, Andrea; Mohr, Gabriele; Haindl, Sonja; Schwarz, Hans Peter; Turecek, Peter L

    2017-01-05

    BAX 855 (ADYNOVATE) is a PEGylated recombinant factor VIII (rFVIII) that showed prolonged circulatory half-life compared to unmodified rFVIII in hemophilic patients. Here, the development and validation of a novel assay is described that selectively measures the activity of BAX 855 as cofactor for the serine protease factor IX, which actives factor X. This method type, termed modification-dependent activity assay, is based on PEG-specific capture of BAX 855 by an anti-PEG IgG preparation, followed by a chromogenic FVIII activity assay. The assay principle enabled sensitive measurement of the FVIII cofactor activity of BAX 855 down to the pM-range without interference by non-PEGylated FVIII. The selectivity of the capture step, shown by competition studies to primarily target the terminal methoxy group of PEG, also allowed assessment of the intactness of the attached PEG chains. Altogether, the modification-dependent activity not only enriches, but complements the group of methods to selectively, accurately, and precisely measure a PEGylated drug in complex biological matrices. In contrast to all other methods described so far, it allows measurement of the biological activity of the PEGylated protein. Data obtained demonstrate that this new method principle can be extended to protein modifications other than PEGylation and to a variety of functional activity assays. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. A genetic replacement system for selection-based engineering of essential proteins

    Science.gov (United States)

    2012-01-01

    Background Essential genes represent the core of biological functions required for viability. Molecular understanding of essentiality as well as design of synthetic cellular systems includes the engineering of essential proteins. An impediment to this effort is the lack of growth-based selection systems suitable for directed evolution approaches. Results We established a simple strategy for genetic replacement of an essential gene by a (library of) variant(s) during a transformation. The system was validated using three different essential genes and plasmid combinations and it reproducibly shows transformation efficiencies on the order of 107 transformants per microgram of DNA without any identifiable false positives. This allowed for reliable recovery of functional variants out of at least a 105-fold excess of non-functional variants. This outperformed selection in conventional bleach-out strains by at least two orders of magnitude, where recombination between functional and non-functional variants interfered with reliable recovery even in recA negative strains. Conclusions We propose that this selection system is extremely suitable for evaluating large libraries of engineered essential proteins resulting in the reliable isolation of functional variants in a clean strain background which can readily be used for in vivo applications as well as expression and purification for use in in vitro studies. PMID:22898007

  3. Selective and extensive 13C labeling of a membrane protein for solid-state NMR investigations

    International Nuclear Information System (INIS)

    Hong, M.; Jakes, K.

    1999-01-01

    The selective and extensive 13C labeling of mostly hydrophobic amino acid residues in a 25 kDa membrane protein, the colicin Ia channel domain, is reported. The novel 13C labeling approach takes advantage of the amino acid biosynthetic pathways in bacteria and suppresses the synthesis of the amino acid products of the citric acid cycle. The selectivity and extensiveness of labeling significantly simplify the solid-state NMR spectra, reduce line broadening, and should permit the simultaneous measurement of multiple structural constraints. We show the assignment of most 13C resonances to specific amino acid types based on the characteristic chemical shifts, the 13C labeling pattern, and the amino acid composition of the protein. The assignment is partly confirmed by a 2D homonuclear double-quantum-filter experiment under magic-angle spinning. The high sensitivity and spectral resolution attained with this 13C-labeling protocol, which is termed TEASE for ten-amino acid selective and extensive labeling, are demonstrated

  4. IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.

    Science.gov (United States)

    Moal, Iain H; Barradas-Bautista, Didier; Jiménez-García, Brian; Torchala, Mieczyslaw; van der Velde, Arjan; Vreven, Thom; Weng, Zhiping; Bates, Paul A; Fernández-Recio, Juan

    2017-06-15

    In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction. Atomic modeling of protein-protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100. IRaPPA has been implemented in the SwarmDock server ( http://bmm.crick.ac.uk/∼SwarmDock/ ), pyDock server ( http://life.bsc.es/pid/pydockrescoring/ ) and ZDOCK server ( http://zdock.umassmed.edu/ ), with code available on request. moal@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  5. Crude protein, fibre and phytic acid in vitro digestibility of selected legume and buckwheat samples

    Directory of Open Access Journals (Sweden)

    Petra Vojtíšková

    2013-01-01

    Full Text Available The aim of this study was to determine crude protein, fibre and phytic acid in vitro digestibility of selected legumes and buckwheat products. All analyses except the phytic acid contents were performed in the line with the Commission Regulation (EC No. 152/2009. A modified version of Holt’s Method was used for phytic acid (phytate determination. None of all samples contained more than 11% of moisture. Soybeans are rich in crude protein; they contain nearly 40% of this compound. The content of crude protein in buckwheat flours was about 14%. The highest amount of phytate was found in common beans and soybeans-about 2 g/100 g of dry matter. On the other hand, the lowest phytate content was observed in buckwheat pasta (F. esculentum groats was 1.9 g per 100 g of dry matter. In vitro digestibility was determined using an incubator Daisy and pepsin enzymes and the combination of pepsin and pancreatin. The highest coefficient of crude protein digestibility was discovered to be in peels and wholemeal flour. The greatest fibre digestibility coefficients were obtained for peels, which contain about 65% of fibre in their dry matter. When pepsin was used, a higher phytic acid digestibility coefficient for G. max, Ph. vulgaris, peels, flour, groats and broken groats was observed; while when the combination of pepsin and pancreatin was used, higher phytic acid digestibility coefficients for peas, lentil and wholemeal flour were observed.

  6. An Engineered Survival-Selection Assay for Extracellular Protein Expression Uncovers Hypersecretory Phenotypes in Escherichia coli.

    Science.gov (United States)

    Natarajan, Aravind; Haitjema, Charles H; Lee, Robert; Boock, Jason T; DeLisa, Matthew P

    2017-05-19

    The extracellular expression of recombinant proteins using laboratory strains of Escherichia coli is now routinely achieved using naturally secreted substrates, such as YebF or the osmotically inducible protein Y (OsmY), as carrier molecules. However, secretion efficiency through these pathways needs to be improved for most synthetic biology and metabolic engineering applications. To address this challenge, we developed a generalizable survival-based selection strategy that effectively couples extracellular protein secretion to antibiotic resistance and enables facile isolation of rare mutants from very large populations (i.e., 10 10-12 clones) based simply on cell growth. Using this strategy in the context of the YebF pathway, a comprehensive library of E. coli single-gene knockout mutants was screened and several gain-of-function mutations were isolated that increased the efficiency of extracellular expression without compromising the integrity of the outer membrane. We anticipate that this user-friendly strategy could be leveraged to better understand the YebF pathway and other secretory mechanisms-enabling the exploration of protein secretion in pathogenesis as well as the creation of designer E. coli strains with greatly expanded secretomes-all without the need for expensive exogenous reagents, assay instruments, or robotic automation.

  7. Acetylation of pregnane X receptor protein determines selective function independent of ligand activation

    International Nuclear Information System (INIS)

    Biswas, Arunima; Pasquel, Danielle; Tyagi, Rakesh Kumar; Mani, Sridhar

    2011-01-01

    Research highlights: → Pregnane X receptor (PXR), a major regulatory protein, is modified by acetylation. → PXR undergoes dynamic deacetylation upon ligand-mediated activation. → SIRT1 partially mediates PXR deacetylation. → PXR deacetylation per se induces lipogenesis mimicking ligand-mediated activation. -- Abstract: Pregnane X receptor (PXR), like other members of its class of nuclear receptors, undergoes post-translational modification [PTM] (e.g., phosphorylation). However, it is unknown if acetylation (a major and common form of protein PTM) is observed on PXR and, if it is, whether it is of functional consequence. PXR has recently emerged as an important regulatory protein with multiple ligand-dependent functions. In the present work we show that PXR is indeed acetylated in vivo. SIRT1 (Sirtuin 1), a NAD-dependent class III histone deacetylase and a member of the sirtuin family of proteins, partially mediates deacetylation of PXR. Most importantly, the acetylation status of PXR regulates its selective function independent of ligand activation.

  8. The Drosophila carbonyl reductase sniffer is an efficient 4-oxonon-2-enal (4ONE) reductase.

    Science.gov (United States)

    Martin, Hans-Jörg; Ziemba, Marta; Kisiela, Michael; Botella, José A; Schneuwly, Stephan; Maser, Edmund

    2011-05-30

    Studies with the fruit-fly Drosophila melanogaster demonstrated that the enzyme sniffer prevented oxidative stress-induced neurodegeneration. Mutant flies overexpressing sniffer had significantly extended life spans in a 99.5% oxygen atmosphere compared to wild-type flies. However, the molecular mechanism of this protection remained unclear. Sequence analysis and database searches identified sniffer as a member of the short-chain dehydrogenase/reductase superfamily with a 27.4% identity to the human enzyme carbonyl reductase type I (CBR1). As CBR1 catalyzes the reduction of the lipid peroxidation products 4HNE and 4ONE, we tested whether sniffer is able to metabolize these lipid derived aldehydes by carbonyl reduction. To produce recombinant enzyme, the coding sequence of sniffer was amplified from a cDNA-library, cloned into a bacterial expression vector and the His-tagged protein was purified by Ni-chelate chromatography. We found that sniffer catalyzed the NADPH-dependent carbonyl reduction of 4ONE (K(m)=24±2 μM, k(cat)=500±10 min(-1), k(cat)/K(m)=350 s(-1) mM(-1)) but not that of 4HNE. The reaction product of 4ONE reduction by sniffer was mainly 4HNE as shown by HPLC- and GC/MS analysis. Since 4HNE, though still a potent electrophile, is less neurotoxic and protein reactive than 4ONE, one mechanism by which sniffer exerts its neuroprotective effects in Drosophila after oxidative stress may be enzymatic reduction of 4ONE. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  9. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

    DEFF Research Database (Denmark)

    Lin, Michael F; Kheradpour, Pouya; Washietl, Stefan

    2011-01-01

    conservation compared to typical protein-coding genes—especially at synonymous sites. In this study, we use genome alignments of 29 placental mammals to systematically locate short regions within human ORFs that show conspicuously low estimated rates of synonymous substitution across these species. The 29......-species alignment provides statistical power to locate more than 10,000 such regions with resolution down to nine-codon windows, which are found within more than a quarter of all human protein-coding genes and contain ~2% of their synonymous sites. We collect numerous lines of evidence that the observed...... synonymous constraint in these regions reflects selection on overlapping functional elements including splicing regulatory elements, dual-coding genes, RNA secondary structures, microRNA target sites, and developmental enhancers. Our results show that overlapping functional elements are common in mammalian...

  10. Catalytic production of metal carbonyls from metal oxides

    Science.gov (United States)

    Sapienza, Richard S.; Slegeir, William A.; Foran, Michael T.

    1984-01-01

    This invention relates to the formation of metal carbonyls from metal oxides and specially the formation of molybdenum carbonyl and iron carbonyl from their respective oxides. Copper is used here in admixed form or used in chemically combined form as copper molybdate. The copper/metal oxide combination or combined copper is utilized with a solvent, such as toluene and subjected to carbon monoxide pressure of 25 atmospheres or greater at about 150.degree.-260.degree. C. The reducing metal copper is employed in catalytic concentrations or combined concentrations as CuMoO.sub.4 and both hydrogen and water present serve as promoters. It has been found that the yields by this process have been salutary and that additionally the catalytic metal may be reused in the process to good effect.

  11. Selective cell-surface labeling of the molecular motor protein prestin

    International Nuclear Information System (INIS)

    McGuire, Ryan M.; Silberg, Jonathan J.; Pereira, Fred A.; Raphael, Robert M.

    2011-01-01

    Highlights: → Trafficking to the plasma membrane is required for prestin function. → Biotin acceptor peptide (BAP) was fused to prestin through a transmembrane domain. → BAP-prestin can be metabolically labeled with biotin in HEK293 cells. → Biotin-BAP-prestin allows for selective imaging of fully trafficked prestin. → The biotin-BAP-prestin displays voltage-sensitive activity. -- Abstract: Prestin, a multipass transmembrane protein whose N- and C-termini are localized to the cytoplasm, must be trafficked to the plasma membrane to fulfill its cellular function as a molecular motor. One challenge in studying prestin sequence-function relationships within living cells is separating the effects of amino acid substitutions on prestin trafficking, plasma membrane localization and function. To develop an approach for directly assessing prestin levels at the plasma membrane, we have investigated whether fusion of prestin to a single pass transmembrane protein results in a functional fusion protein with a surface-exposed N-terminal tag that can be detected in living cells. We find that fusion of the biotin-acceptor peptide (BAP) and transmembrane domain of the platelet-derived growth factor receptor (PDGFR) to the N-terminus of prestin-GFP yields a membrane protein that can be metabolically-labeled with biotin, trafficked to the plasma membrane, and selectively detected at the plasma membrane using fluorescently-tagged streptavidin. Furthermore, we show that the addition of a surface detectable tag and a single-pass transmembrane domain to prestin does not disrupt its voltage-sensitive activity.

  12. Maximizing Selective Cleavages at Aspartic Acid and Proline Residues for the Identification of Intact Proteins

    Science.gov (United States)

    Foreman, David J.; Dziekonski, Eric T.; McLuckey, Scott A.

    2018-04-01

    A new approach for the identification of intact proteins has been developed that relies on the generation of relatively few abundant products from specific cleavage sites. This strategy is intended to complement standard approaches that seek to generate many fragments relatively non-selectively. Specifically, this strategy seeks to maximize selective cleavage at aspartic acid and proline residues via collisional activation of precursor ions formed via electrospray ionization (ESI) under denaturing conditions. A statistical analysis of the SWISS-PROT database was used to predict the number of arginine residues for a given intact protein mass and predict a m/z range where the protein carries a similar charge to the number of arginine residues thereby enhancing cleavage at aspartic acid residues by limiting proton mobility. Cleavage at aspartic acid residues is predicted to be most favorable in the m/z range of 1500-2500, a range higher than that normally generated by ESI at low pH. Gas-phase proton transfer ion/ion reactions are therefore used for precursor ion concentration from relatively high charge states followed by ion isolation and subsequent generation of precursor ions within the optimal m/z range via a second proton transfer reaction step. It is shown that the majority of product ion abundance is concentrated into cleavages C-terminal to aspartic acid residues and N-terminal to proline residues for ions generated by this process. Implementation of a scoring system that weights both ion fragment type and ion fragment area demonstrated identification of standard proteins, ranging in mass from 8.5 to 29.0 kDa. [Figure not available: see fulltext.

  13. Selective induction of cyclin B protein abrogates the G2 delay after irradiation

    International Nuclear Information System (INIS)

    Kao, G.; Muschel, R.J.; Maity, A.; Kunig, A.; McKenna, W.G.

    1996-01-01

    Purpose/Objective: Irradiation of tumor cells commonly results in G2 delay, which has been postulated to allow DNA repair and cell survival. The G2 delay after irradiation is also often marked in some cell lines by delayed expression of cyclin B protein, suggesting a role for cyclin B regulation. Investigations of these hypotheses however has been hampered by the inability to selectively perturb the G2 delay in a physiologic manner. Materials and Methods: We have devised a system, with which we are able to selectively induce cyclin B protein expression in vivo at specific points in the cell cycle, by transfecting Hela cells with an expression vector under control of a dexamethasone-inducible promoter. Experiments were subsequently performed by synchronizing, releasing, irradiating, inducing, and harvesting these cells through the cell cycle. Results: Irradiation with 5 Gy led to a pronounced G2 delay, reflected by markedly slowed progression into mitosis, concomitant with reduced expression of cyclin B protein. Induction of cyclin B after radiation in these cells abrogated the G2 delay by approximately doubling the rate at which the cells re-enter mitosis. Treatment of irradiated untransfected control cells with dexamethasone, in which cyclin B is not induced, led to minimal changes. Studies of effects of cyclin B induction on cyclin B localization (using immunofluorescence), cdc2 phosphorylation and activation will also be presented. Conclusion: This system should allow further investigations into fundamental mechanisms of cell cycle regulation after irradiation and DNA damage. This also provides direct evidence for the first time that cyclin B protein regulation may play a role in the G2 delay following irradiation in Hela cells, perhaps complementing phosphorylation events

  14. Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking.

    Science.gov (United States)

    Strecker, Claas; Meyer, Bernd

    2018-05-02

    Protein flexibility poses a major challenge to docking of potential ligands in that the binding site can adopt different shapes. Docking algorithms usually keep the protein rigid and only allow the ligand to be treated as flexible. However, a wrong assessment of the shape of the binding pocket can prevent a ligand from adapting a correct pose. Ensemble docking is a simple yet promising method to solve this problem: Ligands are docked into multiple structures, and the results are subsequently merged. Selection of protein structures is a significant factor for this approach. In this work we perform a comprehensive and comparative study evaluating the impact of structure selection on ensemble docking. We perform ensemble docking with several crystal structures and with structures derived from molecular dynamics simulations of renin, an attractive target for antihypertensive drugs. Here, 500 ns of MD simulations revealed binding site shapes not found in any available crystal structure. We evaluate the importance of structure selection for ensemble docking by comparing binding pose prediction, ability to rank actives above nonactives (screening utility), and scoring accuracy. As a result, for ensemble definition k-means clustering appears to be better suited than hierarchical clustering with average linkage. The best performing ensemble consists of four crystal structures and is able to reproduce the native ligand poses better than any individual crystal structure. Moreover this ensemble outperforms 88% of all individual crystal structures in terms of screening utility as well as scoring accuracy. Similarly, ensembles of MD-derived structures perform on average better than 75% of any individual crystal structure in terms of scoring accuracy at all inspected ensembles sizes.

  15. ORGANIC MATTER AND CRUDE PROTEIN DEGRADATION SYNCHRONY IN DIETS SELECTED BY RANGE GOATS.

    Directory of Open Access Journals (Sweden)

    Rafael Ramírez Orduña

    2010-09-01

    Full Text Available The study was carried out with the aim to asses the synchrony of organic matter and crude protein degradation in the rumen of diets selected by range goats through two years. Five esophageal cannulated adult male goats were used to collect extrusa samples during summer (August 9–13 and autumn (November 29 –December 3 of 2006, winter (February 20 – 24, spring (April 29 –May 5, summer (September 10–15 and autumn (December 4–8 of 2007 and winter (February 20 – 25 and spring (May 9 –13 of 2008. Extrusa samples were subjected to chemical analysis to determine organic matter (OM, crude protein (CP in situ and in vitro true digestibility of dry matter. OM and CP intake were estimated by total fecal collection. Effective extent of degradation of the OM and CP was calculated hourly and total 24 hours. From the hourly quantity of OM and CP degraded, a synchrony index of CP to OM was calculated, and from the total 24 hours degradation, degraded organic matter intake and crude protein intake were also estimated. Sampling date was the main effect that determined the variation of diet OM and CP degradation parameters. Degraded crude protein intake as a proportion of degraded OM was affected by sampling date and was correlated to rainfall. During winter of the first year degraded crude protein intake was below the requirements for maintenance or to promote growth for range goats weighing 40 kg. Even though, synchrony index between OM and CP degradation was affected by sampling date goats maintained a high synchrony index throughout the years.

  16. Chemical biology based on target-selective degradation of proteins and carbohydrates using light-activatable organic molecules.

    Science.gov (United States)

    Toshima, Kazunobu

    2013-05-01

    Proteins and carbohydrates play crucial roles in a wide range of biological processes, including serious diseases. The development of novel and innovative methods for selective control of specific proteins and carbohydrates functions has attracted much attention in the field of chemical biology. In this account article, the development of novel chemical tools, which can degrade target proteins and carbohydrates by irradiation with a specific wavelength of light under mild conditions without any additives, is introduced. This novel class of photochemical agents promise bright prospects for finding not only molecular-targeted bioprobes for understanding of the structure-activity relationships of proteins and carbohydrates but also novel therapeutic drugs targeting proteins and carbohydrates.

  17. Simultaneous improvement of grain yield and protein content in durum wheat by different phenotypic indices and genomic selection.

    Science.gov (United States)

    Rapp, M; Lein, V; Lacoudre, F; Lafferty, J; Müller, E; Vida, G; Bozhanova, V; Ibraliu, A; Thorwarth, P; Piepho, H P; Leiser, W L; Würschum, T; Longin, C F H

    2018-06-01

    Simultaneous improvement of protein content and grain yield by index selection is possible but its efficiency largely depends on the weighting of the single traits. The genetic architecture of these indices is similar to that of the primary traits. Grain yield and protein content are of major importance in durum wheat breeding, but their negative correlation has hampered their simultaneous improvement. To account for this in wheat breeding, the grain protein deviation (GPD) and the protein yield were proposed as targets for selection. The aim of this work was to investigate the potential of different indices to simultaneously improve grain yield and protein content in durum wheat and to evaluate their genetic architecture towards genomics-assisted breeding. To this end, we investigated two different durum wheat panels comprising 159 and 189 genotypes, which were tested in multiple field locations across Europe and genotyped by a genotyping-by-sequencing approach. The phenotypic analyses revealed significant genetic variances for all traits and heritabilities of the phenotypic indices that were in a similar range as those of grain yield and protein content. The GPD showed a high and positive correlation with protein content, whereas protein yield was highly and positively correlated with grain yield. Thus, selecting for a high GPD would mainly increase the protein content whereas a selection based on protein yield would mainly improve grain yield, but a combination of both indices allows to balance this selection. The genome-wide association mapping revealed a complex genetic architecture for all traits with most QTL having small effects and being detected only in one germplasm set, thus limiting the potential of marker-assisted selection for trait improvement. By contrast, genome-wide prediction appeared promising but its performance strongly depends on the relatedness between training and prediction sets.

  18. Specificity of molecular interactions in transient protein-protein interaction interfaces.

    Science.gov (United States)

    Cho, Kyu-il; Lee, KiYoung; Lee, Kwang H; Kim, Dongsup; Lee, Doheon

    2006-11-15

    In this study, we investigate what types of interactions are specific to their biological function, and what types of interactions are persistent regardless of their functional category in transient protein-protein heterocomplexes. This is the first approach to analyze protein-protein interfaces systematically at the molecular interaction level in the context of protein functions. We perform systematic analysis at the molecular interaction level using classification and feature subset selection technique prevalent in the field of pattern recognition. To represent the physicochemical properties of protein-protein interfaces, we design 18 molecular interaction types using canonical and noncanonical interactions. Then, we construct input vector using the frequency of each interaction type in protein-protein interface. We analyze the 131 interfaces of transient protein-protein heterocomplexes in PDB: 33 protease-inhibitors, 52 antibody-antigens, 46 signaling proteins including 4 cyclin dependent kinase and 26 G-protein. Using kNN classification and feature subset selection technique, we show that there are specific interaction types based on their functional category, and such interaction types are conserved through the common binding mechanism, rather than through the sequence or structure conservation. The extracted interaction types are C(alpha)-- H...O==C interaction, cation...anion interaction, amine...amine interaction, and amine...cation interaction. With these four interaction types, we achieve the classification success rate up to 83.2% with leave-one-out cross-validation at k = 15. Of these four interaction types, C(alpha)--H...O==C shows binding specificity for protease-inhibitor complexes, while cation-anion interaction is predominant in signaling complexes. The amine ... amine and amine...cation interaction give a minor contribution to the classification accuracy. When combined with these two interactions, they increase the accuracy by 3.8%. In the case of

  19. Selective labeling of a single organelle by using two-photon conversion of a photoconvertible fluorescent protein

    Science.gov (United States)

    Watanabe, Wataru; Shimada, Tomoko; Matsunaga, Sachihiro; Kurihara, Daisuke; Arimura, Shin-ichi; Tsutsumi, Nobuhiro; Fukui, Kiichi; Itoh, Kazuyoshi

    2008-02-01

    We present space-selective labeling of organelles by using two-photon conversion of a photoconvertible fluorescent protein with near-infrared femtosecond laser pulses. Two-photon excitation of photoconvertible fluorescent-protein, Kaede, enables space-selective labeling of organelles. We alter the fluorescence of target mitochondria in a tobacco BY-2 cell from green to red by focusing femtosecond laser pulses with a wavelength of 750 nm.

  20. Separation of Trace Amount Zn (II Using Additional Carbonyl and Carboxyl Groups Functionalized-Nano Graphene

    Directory of Open Access Journals (Sweden)

    A. Moghimi

    2013-01-01

    Full Text Available A novel and selective method for the fast determination of trace amounts of Zn(IIions in water samples has been developed.  The first additional carbonyl and carboxyl functionalized-nano graphene (SPFNano graphene. The presence of additional carbonyl and carboxyl groups located at the edge of the sheets makes GO sheets strongly hydrophilic, allowing them to readily swell and disperse in water. Based on these oxygen functionalities, different model structures of GO were used as absorbent for extraction of Zn (II   ions by solid phase extraction method. The complexes were eluted with HNO3 (2M10% V.V-1 methanol in acetone and determined the analyte by flame atomic absorption spectrometry.  The procedure is based on the selective formation of Zn (II at optimum pH by elution with organic eluents and determination by flame atomic absorption spectrometry. The method is based on complex formation on the surface of the ENVI-18 DISKTM disks modified carbonyl and carboxyl functionalized-nano graphene oxide molecules covalently bonded together followed by stripping of the retained species by minimum amounts of appropriate organic solvents. The elution is efficient and quantitative. The effect of potential interfering ions, pH, SPFNano graphene, amount, stripping solvent, and sample flow rate were also investigated. Under the optimal experimental conditions, the break-through volume was found to about 1000mL providing a preconcentration factor of 500. The maximum capacity of the disks was found to be 456± 3 µg for Zn2+.The limit of detection of the proposed method is 5ng per 1000mL.The method was applied to the extraction and recovery of Zn in different water samples.

  1. Nickel nanoparticle decorated graphene for highly selective isolation of polyhistidine-tagged proteins

    Science.gov (United States)

    Liu, Jia-Wei; Yang, Ting; Ma, Lin-Yu; Chen, Xu-Wei; Wang, Jian-Hua

    2013-12-01

    Nickel nanoparticle decorated graphene (GP-Ni) is prepared by one-pot hydrothermal reduction of graphene oxide and nickel cations by hydrazine hydrate in the presence of poly(sodium-p-styrenesulfonate) (PSS). The GP-Ni hybrid is characterized by XRD, TEM, SEM, XPS, Raman and FT-IR spectra, demonstrating the formation of poly-dispersed nickel nanoparticles with an average size of 83 nm attached on the surface of graphene sheets. The GP-Ni hybrid exhibits ferromagnetic behavior with a magnetization saturation of 31.1 emu g-1 at 10 000 Oersted (Oe). The GP-Ni also possesses favorable stability in aqueous medium and rapid magnetic response to an external magnetic field. These make it a novel magnetic adsorbent for the separation/isolation of His6-tagged recombinant proteins from a complex sample matrix (cell lysate). The targeted protein species is captured onto the surface of the GP-Ni hybrid via specific metal affinity force between polyhistidine groups and nickel nanoparticles. The SDS-PAGE assay indicates highly selective separation of His6-tagged Smt A from cell lysate. The GP-Ni hybrid displays favorable performance on the separation/isolation of His6-tagged recombinant proteins with respect to the commercial NTA-Ni2+ column.

  2. Effect of dataset selection on the topological interpretation of protein interaction networks

    Directory of Open Access Journals (Sweden)

    Robertson David L

    2005-09-01

    Full Text Available Abstract Background Studies of the yeast protein interaction network have revealed distinct correlations between the connectivity of individual proteins within the network and the average connectivity of their neighbours. Although a number of biological mechanisms have been proposed to account for these findings, the significance and influence of the specific datasets included in these studies has not been appreciated adequately. Results We show how the use of different interaction data sets, such as those resulting from high-throughput or small-scale studies, and different modelling methodologies for the derivation pair-wise protein interactions, can dramatically change the topology of these networks. Furthermore, we show that some of the previously reported features identified in these networks may simply be the result of experimental or methodological errors and biases. Conclusion When performing network-based studies, it is essential to define what is meant by the term "interaction" and this must be taken into account when interpreting the topologies of the networks generated. Consideration must be given to the type of data included and appropriate controls that take into account the idiosyncrasies of the data must be selected

  3. Handheld highly selective plasmonic chem/biosensor using engineered binding proteins for extreme conformational changes

    Science.gov (United States)

    Kosciolek, Derek J.; Sonar, Ajay; Lepak, Lori A.; Schnatz, Peter; Bendoym, Igor; Brown, Mia C.; Koder, Ronald L.; Crouse, David T.

    2017-08-01

    In this project we develop a handheld, portable, highly selective and sensitive chem/biosensor that has potential applications in both airborne and water-based environmental sensing. The device relies on a plasmonic chip of subwavelength-scale periodic gold rods engineered to resonate in the near infrared. The chip is functionalized with a novel class of proteins that exhibit large conformational changes upon binding to a specific target analyte. The subsequent change in local refractive index near the surface of the gold is one to two orders of magnitude greater than current conventional methods, which produces a readily measurable 5 to 10 percent difference in light transmission. This allows us to forgo traditional, bulky tabletop setups in favor of a compact form factor. Using commercially available optics to construct a transmission-based optical train, measured changes in bulk refractive index are presented here. While synthesis of binding protein efforts are focused on heme as analyte for proof of concept validation, the functionalized protein can be engineered to pair with a wide variety of analytes with minimal alterations to the plasmonic chip or device design. Such flexibility allows for this device to potentially meet the needs of first responders and health care professionals in a multitude of scenarios.

  4. Selectivity analysis of protein kinase CK2 inhibitors DMAT, TBB and resorufin in cisplatin-induced stress responses

    DEFF Research Database (Denmark)

    Fritz, Gerhard; Issinger, Olaf-Georg; Olsen, Birgitte Brinkmann

    2009-01-01

    Targeting protein kinases as a therapeutic approach to treat various diseases, especially cancer is currently a fast growing business. Although many inhibitors are available, exhibiting remarkable potency, the major challenge is their selectivity. Here we show that the protein kinase CK2 inhibito...

  5. Genetic polymorphism and natural selection of Duffy binding protein of Plasmodium vivax Myanmar isolates

    Science.gov (United States)

    2012-01-01

    Background Plasmodium vivax Duffy binding protein (PvDBP) plays an essential role in erythrocyte invasion and a potential asexual blood stage vaccine candidate antigen against P. vivax. The polymorphic nature of PvDBP, particularly amino terminal cysteine-rich region (PvDBPII), represents a major impediment to the successful design of a protective vaccine against vivax malaria. In this study, the genetic polymorphism and natural selection at PvDBPII among Myanmar P. vivax isolates were analysed. Methods Fifty-four P. vivax infected blood samples collected from patients in Myanmar were used. The region flanking PvDBPII was amplified by PCR, cloned into Escherichia coli, and sequenced. The polymorphic characters and natural selection of the region were analysed using the DnaSP and MEGA4 programs. Results Thirty-two point mutations (28 non-synonymous and four synonymous mutations) were identified in PvDBPII among the Myanmar P. vivax isolates. Sequence analyses revealed that 12 different PvDBPII haplotypes were identified in Myanmar P. vivax isolates and that the region has evolved under positive natural selection. High selective pressure preferentially acted on regions identified as B- and T-cell epitopes of PvDBPII. Recombination may also be played a role in the resulting genetic diversity of PvDBPII. Conclusions PvDBPII of Myanmar P. vivax isolates displays a high level of genetic polymorphism and is under selective pressure. Myanmar P. vivax isolates share distinct types of PvDBPII alleles that are different from those of other geographical areas. These results will be useful for understanding the nature of the P. vivax population in Myanmar and for development of PvDBPII-based vaccine. PMID:22380592

  6. Metal-Diazo Radicals of α-Carbonyl Diazomethanes

    Science.gov (United States)

    Li, Feifei; Xiao, Longqiang; Liu, Lijian

    2016-03-01

    Metal-diazo radicals of α-carbonyl diazomethanes are new members of the radical family and are precursors to metal-carbene radicals. Herein, using electron paramagnetic resonance spectroscopy with spin-trapping, we detect diazo radicals of α-carbonyl diazomethanes, induced by [RhICl(cod)]2, [CoII(por)] and PdCl2, at room temperature. The unique quintet signal of the Rh-diazo radical was observed in measurements of α-carbonyl diazomethane adducts of [RhICl(cod)]2 in the presence of 5,5-dimethyl-pyrroline-1-N-oxide (DMPO). DFT calculations indicated that 97.2% of spin density is localized on the diazo moiety. Co- and Pd-diazo radicals are EPR silent but were captured by DMPO to form spin adducts of DMPO-N• (triplet-of-sextets signal). The spin-trapping also provides a powerful tool for detection of metal-carbene radicals, as evidenced by the DMPO-trapped carbene radicals (DMPO-C•, sextet signal) and 2-methyl-2-nitrosopropane-carbene adducts (MNP-C•, doublet-of-triplets signal). The transformation of α-carbonyl diazomethanes to metal-carbene radicals was confirmed to be a two-step process via metal-diazo radicals.

  7. Carbonyl atmospheric reaction products of aromatic hydrocarbons in ambient air

    Science.gov (United States)

    Obermeyer, Genevieve; Aschmann, Sara M.; Atkinson, Roger; Arey, Janet

    To convert gaseous carbonyls to oximes during sampling, an XAD-4 resin denuder system pre-coated with O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine and followed by analysis with methane positive chemical ionization gas chromatography/mass spectrometry was used to measure carbonyls in ambient air samples in Riverside, CA. In conjunction with similar analyses of environmental chamber OH radical-initiated reactions of o- and p-xylene, 1,2,4-trimethylbenzene, ethylbenzene, 4-hydroxy-2-butanone and 1,4-butanediol, we identified benzaldehyde, o-, m- and p-tolualdehyde and acetophenone and the dicarbonyls glyoxal, methylglyoxal, biacetyl, ethylglyoxal, 1,4-butenedial, 3-hexene-2,5-dione, 3-oxo-butanal, 1,4-butanedial and malonaldehyde in the ambient air samples. As discussed, these carbonyls and dicarbonyls can be formed from the OH radical-initiated reactions of aromatic hydrocarbons and other volatile organic compounds emitted into the atmosphere, and we conclude that in situ atmospheric formation is a major source of these carbonyls in our Riverside, CA, ambient air samples.

  8. cyclo-addition reaction of triplet carbonyl compounds to substituted ...

    Indian Academy of Sciences (India)

    Unknown

    cited state energy of the olefin must be higher than that of the ketone so that ... the first singlet and triplet1,3 (n, π*) excited state of the carbonyl compounds.3,4 ... of the oxetane via carbon–carbon and carbon–oxygen attacks. They found the ...

  9. Olefination of carbonyl compounds: modern and classical methods

    Energy Technology Data Exchange (ETDEWEB)

    Korotchenko, V N; Nenajdenko, Valentine G; Balenkova, Elizabeth S [Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow (Russian Federation); Shastin, Aleksey V [Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region (Russian Federation)

    2004-10-31

    The published data on the methods for alkene synthesis by olefination of carbonyl compounds are generalised and systematised. The main attention is given to the use of transition metals and organoelement compounds. The review covers the data on both classical and newly developed methods that are little known to chemists at large.

  10. Olefination of carbonyl compounds: modern and classical methods

    Science.gov (United States)

    Korotchenko, V. N.; Nenajdenko, Valentine G.; Balenkova, Elizabeth S.; Shastin, Aleksey V.

    2004-10-01

    The published data on the methods for alkene synthesis by olefination of carbonyl compounds are generalised and systematised. The main attention is given to the use of transition metals and organoelement compounds. The review covers the data on both classical and newly developed methods that are little known to chemists at large.

  11. Frustrated Lewis pairs-assisted reduction of carbonyl compounds

    DEFF Research Database (Denmark)

    Marek, Ales; Pedersen, Martin Holst Friborg

    2015-01-01

    An alternative and robust method for the reduction of carbonyl groups by frustrated Lewis pairs (FLPs) is reported in this paper. With its very mild reaction conditions, good to excellent yields, absolute regioselectivity and the non-metallic character of the reagent, it provides an excellent too...

  12. Organometallic and Bioorganometallic Chemistry - Ferrocene and Metal Carbonyls

    Directory of Open Access Journals (Sweden)

    Čakić Semenčić, M.

    2011-02-01

    -substituted products. Owing to the low barrier to internal rotation around Cp-Fe-Cp axis (ω torsion angle ferrocene is characterized by D5d-symmetrical staggered and D5h-symetrical eclipsed forms. In the appropriately substituted ferrocenes, deviation from Cp coplanarity (tilt angle Θ may occur as well; e. g. ferrocenophanes are derivatives in which homo- or heteroatomic bridges spanned two Cp rings, causing appreciable deformations of ferrocene molecule (ω=0–26°; Θ=9–24°. A characteristic development of the science in the new age has been the gradual merging of what were once separate research disciplines. In such a way, on the border between classical organic and inorganic chemistry (long ago organometallic chemistry was established and in the last decades "hybridization" of biology (biochemistry and organometallic chemistry has resulted in the appearance of bioorganometallic chemistry. In short, this new discipline deals with conjugates of organometallics with biomolecules (DNA, PNA, carbohydrates, steroids, amino acids, peptides.... The principal fields of research activity in bioorganometallic chemistry are therapy, bioanalysis (sensors, molecular recognition in aqueous medium, enzymes (proteins, peptides, toxicology and environment.This article reviews only a few (interesting examples out of the immense number of bioorganometallics (classes. Many bioorganometallic drugs showed improved bioactivity in comparison with their classical anticancer and antimalarial analogues (e. g. tamoxifene → hydroxyferrocifene; chloroquine → ferroquine. Organometallic bioprobes are the molecules incorporating organometallic responding components (e. g. metal carbonyls. In the appropriately designed devices, these "molecular sensors" read out the information that is available from the molecular recognition events by FT-IR spectroscopy. Electrochemically active bioorganometallics (e. g. probes containing ferrocene are used in biosensors for detection of DNA, glucose in blood, etc. The

  13. Selection of antifungal protein-producing molds from dry-cured meat products.

    Science.gov (United States)

    Acosta, Raquel; Rodríguez-Martín, Andrea; Martín, Alberto; Núñez, Félix; Asensio, Miguel A

    2009-09-30

    To control unwanted molds in dry-cured meats it is necessary to allow the fungal development essential for the desired characteristics of the final product. Molds producing antifungal proteins could be useful to prevent hazards due to the growth of mycotoxigenic molds. The objective has been to select Penicillium spp. that produce antifungal proteins against toxigenic molds. To obtain strains adapted to these products, molds were isolated from dry-cured ham. A first screening with 281 isolates by the radial inhibition assay revealed that 166 were active against some of the toxigenic P. echinulatum, P. commune, and Aspergillusniger used as reference molds. The activity of different extracts from cultured medium was evaluated by a microspectroscopic assay. Molds producing active chloroform extracts were eliminated from further consideration. A total of 16 Penicillium isolates were screened for antifungal activity from both cell-free media and the aqueous residues obtained after chloroform extraction. The cell-free media of 10 isolates that produced a strong inhibition of the three reference molds were fractionated by FPLC on a cationic column. For protein purification, the fractions of the three molds that showed high inhibitory activity were further chromatographed on a gel filtration column, and the subfractions containing the highest absorbance peaks were assayed against the most sensitive reference molds. One subfraction each from strains AS51D and RP42C from Penicilliumchrysogenum confirmed the inhibitory activity against the reference molds. SDS-PAGE revealed a single band from each subfraction, with estimated molecular masses of 37kDa for AS51D and 9kDa for RP42C. Although further characterisation is required, both these proteins and the producing strains can be of interest to control unwanted molds on foods.

  14. ZP Domain Proteins in the Abalone Egg Coat Include a Paralog of VERL under Positive Selection That Binds Lysin and 18-kDa Sperm Proteins

    Science.gov (United States)

    Aagaard, Jan E.; Vacquier, Victor D.; MacCoss, Michael J.; Swanson, Willie J.

    2010-01-01

    Identifying fertilization molecules is key to our understanding of reproductive biology, yet only a few examples of interacting sperm and egg proteins are known. One of the best characterized comes from the invertebrate archeogastropod abalone (Haliotis spp.), where sperm lysin mediates passage through the protective egg vitelline envelope (VE) by binding to the VE protein vitelline envelope receptor for lysin (VERL). Rapid adaptive divergence of abalone lysin and VERL are an example of positive selection on interacting fertilization proteins contributing to reproductive isolation. Previously, we characterized a subset of the abalone VE proteins that share a structural feature, the zona pellucida (ZP) domain, which is common to VERL and the egg envelopes of vertebrates. Here, we use additional expressed sequence tag sequencing and shotgun proteomics to characterize this family of proteins in the abalone egg VE. We expand 3-fold the number of known ZP domain proteins present within the VE (now 30 in total) and identify a paralog of VERL (vitelline envelope zona pellucida domain protein [VEZP] 14) that contains a putative lysin-binding motif. We find that, like VERL, the divergence of VEZP14 among abalone species is driven by positive selection on the lysin-binding motif alone and that these paralogous egg VE proteins bind a similar set of sperm proteins including a rapidly evolving 18-kDa paralog of lysin, which may mediate sperm–egg fusion. This work identifies an egg coat paralog of VERL under positive selection and the candidate sperm proteins with which it may interact during abalone fertilization. PMID:19767347

  15. Selective association of a fragment of the knob protein with spectrin, actin and the red cell membrane.

    Science.gov (United States)

    Kilejian, A; Rashid, M A; Aikawa, M; Aji, T; Yang, Y F

    1991-02-01

    The knob protein of Plasmodium falciparum is essential for the formation of knob-like protrusions on the host erythrocyte membrane. A functional domain of the knob protein was identified. This peptide formed stable complexes with the two major red cell skeletal proteins, spectrin and actin. When introduced into resealed normal erythrocytes, the peptide associated selectively with the cytoplasmic surface of the membrane and formed knob-like electron dense deposits. Knobs are thought to play an important role in the immunopathology of P. falciparum infections. Our findings provide a first step towards understanding the molecular basis for selective membrane changes at knobs.

  16. Determination of the Influence of Substrate Concentration on Enzyme Selectivity Using Whey Protein Isolate and Bacillus licheniformis Protease

    NARCIS (Netherlands)

    Butré, C.I.; Sforza, S.; Gruppen, H.; Wierenga, P.A.

    2014-01-01

    Increasing substrate concentration during enzymatic protein hydrolysis results in a decrease in hydrolysis rate. To test if changes in the mechanism of hydrolysis also occur, the enzyme selectivity was determined. The selectivity is defined quantitatively as the relative rate of hydrolysis of each

  17. Complete assignment of the methionyl carbonyl carbon resonance in switch variant anti-dansyl antibodies labeled with (1- sup 13 C)methionine

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Koichi; Matsunaga, C.; Igarashi, Takako; Kim, Hahyung; Odaka, Asano; Shimada, Ichio; Arata, Yoji (Univ. of Tokyo, Hongo (Japan))

    1991-01-01

    A {sup 13}C NMR study is reported of switch variant anti-dansyl antibodies developed by Dangl et al. who had used the fluorescence-activated cell sorter to select and clone these variants. These switch variant antibodies possess the identical V{sub H}, V{sub L}, and C{sub L} domains in conjunction with different heavy chain constant regions. In the present study, switch variant antibodies of IgG1, IgG2a, and IgG2b subclasses were used along with a short-chain IgG2a antibody, in which the entire C{sub H}1 domain is deleted. The switch variant antibodies were specifically labeled with (1-{sup 13}C)methionine by growing hybridoma cells in serum-free medium. Assignments of all the methionyl carbonyl carbon resonances have been completed by using the intact antibodies along with their fragments and recombined proteins in which either heavy or light chain is labeled. A double labeling method has played a crucial role in the process of the spectral assignments. The strategy used for the assignments has been described in detail. In incorporating {sup 15}N-labeled amino acids into the antibodies for the double labeling, isotope dilution caused a serious problem except in the cases of ({alpha}-{sup 15}N)lysine and ({sup 15}N)threonine, both of which cannot become the substrate of transaminases. It was found that {beta}-chloro-L-alanine is most effective in suppressing the isotope scrambling. So far, spectral assignments by the double labeling method have been possible with {sup 15}N-labeled Ala, His, Ile, Lys, Met, Ser, Thr, Tyr, and Val. On the basis of the results of the present {sup 13}C study, possible use of the assigned carbonyl carbon resonances for the elucidation of the structure-function relationship in the antibody system has been briefly discussed.

  18. Complete assignment of the methionyl carbonyl carbon resonance in switch variant anti-dansyl antibodies labeled with [1-13C]methionine

    International Nuclear Information System (INIS)

    Kato, Koichi; Matsunaga, C.; Igarashi, Takako; Kim, Hahyung; Odaka, Asano; Shimada, Ichio; Arata, Yoji

    1991-01-01

    A 13 C NMR study is reported of switch variant anti-dansyl antibodies developed by Dangl et al. who had used the fluorescence-activated cell sorter to select and clone these variants. These switch variant antibodies possess the identical V H , V L , and C L domains in conjunction with different heavy chain constant regions. In the present study, switch variant antibodies of IgG1, IgG2a, and IgG2b subclasses were used along with a short-chain IgG2a antibody, in which the entire C H 1 domain is deleted. The switch variant antibodies were specifically labeled with [1- 13 C]methionine by growing hybridoma cells in serum-free medium. Assignments of all the methionyl carbonyl carbon resonances have been completed by using the intact antibodies along with their fragments and recombined proteins in which either heavy or light chain is labeled. A double labeling method has played a crucial role in the process of the spectral assignments. The strategy used for the assignments has been described in detail. In incorporating 15 N-labeled amino acids into the antibodies for the double labeling, isotope dilution caused a serious problem except in the cases of [α- 15 N]lysine and [ 15 N]threonine, both of which cannot become the substrate of transaminases. It was found that β-chloro-L-alanine is most effective in suppressing the isotope scrambling. So far, spectral assignments by the double labeling method have been possible with 15 N-labeled Ala, His, Ile, Lys, Met, Ser, Thr, Tyr, and Val. On the basis of the results of the present 13 C study, possible use of the assigned carbonyl carbon resonances for the elucidation of the structure-function relationship in the antibody system has been briefly discussed

  19. Selective Permeation and Organic Extraction of Recombinant Green Fluorescent Protein (gfpuv from Escherichia coli

    Directory of Open Access Journals (Sweden)

    Ishii Marina

    2002-04-01

    Full Text Available Abstract Background Transformed cells of Escherichia coli DH5-α with pGFPuv, induced by IPTG (isopropyl-β-d-thiogalactopyranoside, express the green fluorescent protein (gfpuv during growth phases. E. coli subjected to the combination of selective permeation by freezing/thawing/sonication cycles followed by the three-phase partitioning extraction (TPP method were compared to the direct application of TPP to the same culture of E. coli on releasing gfpuv from the over-expressing cells. Material and Methods Cultures (37°C/100 rpm/ 24 h; μ = 0.99 h-1 - 1.10 h-1 of transformed (pGFP Escherichia coli DH5-α, expressing the green fluorescent protein (gfpuv, absorbance at 394 nm and emission at 509 nm were sonicated in successive intervals of sonication (25 vibrations/pulse to determine the maximum amount of gfpuv released from the cells. For selective permeation, the transformed previously frozen (-75°C cells were subjected to three freeze/thaw (-20°C/ 0.83°C/min cycles interlaid by sonication (3 pulses/ 6 seconds/ 25 vibrations. The intracellular permeate with gfpuv in extraction buffer (TE solution (25 mM Tris-HCl, pH 8.0, 1 mM β-mercaptoethanol β-ME, 0.1 mM PMSF was subjected to the three-phase partitioning (TPP method with t-butanol and 1.6 M ammonium sulfate. Sonication efficiency was verified on the application to the cells previously treated by the TPP method. The intra-cell releases were mixed and eluted through methyl HIC column with a buffer solution (10 mM Tris-HCl, 10 mM EDTA, pH 8.0. Results The sonication maximum released amount obtained from the cells was 327.67 μg gfpuv/mL (20.73 μg gfpuv/mg total proteins – BSA, after 9 min of treatment. Through the selective permeation by three repeated freezing/thawing/sonication cycles applied to the cells, a close content of 241.19 μg gfpuv/mL (29.74 μg gfpuv/mg BSA was obtained. The specific mass range of gfpuv released from the same cultures, by the three-phase partitioning (TPP

  20. Degradation of carbonyl hydroperoxides in the atmosphere and in combustion

    KAUST Repository

    Xing, Lili

    2017-10-12

    Oxygenates with carbonyl and hydroperoxy functional groups are important intermediates that are generated during the autooxidation of organic compounds in the atmosphere and during the autoignition of transport fuels. In the troposphere, the degradation of carbonyl hydroperoxides leads to low-vapor-pressure polyfunctional species that be taken into in cloud and fog droplets or to the formation of secondary organic aerosols (SOAs). In combustion, the fate of carbonyl hydroperoxides is important for the performance of advanced combustion engines, especially for autoignition. A key fate of the carbonyl hydroperoxides is reac-tion with OH radicals, for which kinetics data are experimentally unavailable. Here, we study 4-hydroperoxy-2-pentanone (CH3C(=O)CH2CH(OOH)CH3) as a model compound to clarify the kinetics of OH reactions with carbonyl hydroperoxides, in par-ticular H-atom abstraction and OH addition reactions. With a combination of electronic structure calculations, we determine previ-ously missing thermochemical data, and with multipath variational transition state theory (MP-VTST), a multidimensional tunnel-ing (MT) approximation, multiple-structure anharmonicity, and torsional potential anharmonicity we obtained much more accurate rate constants than the ones that can computed by conventional single-structure harmonic transition state theory (TST) and than the empirically estimated rate constants that are currently used in atmospheric and combustion modeling. The roles of various factors in determining the rates are elucidated. The pressure-dependent rate constants for the addition reaction are computed using system-specific quantum RRK theory. The calculated temperature range is 298-2400 K, and the pressure range is 0.01–100 atm. The accu-rate thermodynamic and kinetics data determined in this work are indispensable in the global modeling of SOAs in atmospheric science and in the detailed understanding and prediction of ignition properties of hydrocarbons

  1. The effect of palatability of protein source on dietary selection in dairy calves.

    Science.gov (United States)

    Miller-Cushon, E K; Terré, M; DeVries, T J; Bach, A

    2014-07-01

    Evidence has shown that soybean meal is perceived as more palatable than canola meal by dairy calves in short-term preference tests. This study evaluated the effect of protein source on longer-term dietary selection of dairy calves. In experiment 1, 40 Holstein bull calves (11.4 ± 4.3 d of age) were randomly assigned to 1 of 2 choice diets for 6 wk: base starter pellet (S; 12% crude protein; CP) and high-protein pellet (40% CP) containing either (1) soybean meal (SB) or (2) canola meal (CM). In wk 7 to 8, all calves were offered a single pelleted diet containing the protein source to which they were previously exposed. In experiment 2, 22 Holstein bull calves (9.9 ± 4.6d of age) were offered, for 6 wk, a choice of 2 mixed pelleted diets: (1) 70% S and 30% SB (SB mix), or (2) 70% S and 30% CM (CM mix). In wk 7 to 8, calves were randomly assigned to 1 of 2 choice diets, as in experiment 1: (1) SB + S, or (2) CM + S. All feeds were provided ad libitum. Calves received 6 L/d of milk replacer [0.75 kg/d of dry matter (DM)] for the duration of both experiments. Feed intake was recorded daily and calves were weighed every 14 d. Feeds were sampled weekly to analyze DM and nutrient intake. Mixed diets in experiment 2 were analyzed for CP in wk 4 and 6 to assess feed sorting (calculated as actual CP intake as a percentage of predicted intake). In experiment 1, calves offered SB + S in wk 1 to 6 consumed more high-protein pellet than calves offered CM + S [73 vs. 42% of DM intake (DMI)] and, consequently, more CP (168 vs. 117 g/d). Solid feed DMI and average daily gain were similar between treatments. When offered a single diet in wk 7 to 8, calves offered starter containing soybean meal increased intake to a greater extent than calves offered the starter containing canola meal. In experiment 2, calves preferred the SB mix to CM mix (preference ratio: 0.7). Calves consumed more CP than predicted from SB mix in wk 4 and 6 (108 ± 2.0%), indicating that they were sorting in

  2. Low pressure carbonylation of benzyl chloride = Die carbonylierung von benzylchlorid bei niedrigen drücken

    NARCIS (Netherlands)

    Luggenhorst, H.J.; Westerterp, K.R.

    1986-01-01

    For carbonylations, metal carbonyls, particularly cobalt and iron carbonyls, are often used as catalysts. These reactions take place under rather drastic reaction conditions, e.g. 200–300 °C and 60–100 MPa. In some patents it is stated that similar reactions using the same catalysts can also be

  3. Oxidative versus Non-oxidative Decarboxylation of Amino Acids: Conditions for the Preferential Formation of Either Strecker Aldehydes or Amines in Amino Acid/Lipid-Derived Reactive Carbonyl Model Systems.

    Science.gov (United States)

    Zamora, Rosario; León, M Mercedes; Hidalgo, Francisco J

    2015-09-16

    Comparative formation of both 2-phenylethylamine and phenylacetaldehyde as a consequence of phenylalanine degradation by carbonyl compounds was studied in an attempt to understand if the amine/aldehyde ratio can be changed as a function of reaction conditions. The assayed carbonyl compounds were selected because of the presence in the chain of both electron-donating and electron-withdrawing groups and included alkenals, alkadienals, epoxyalkenals, oxoalkenals, and hydroxyalkenals as well as lipid hydroperoxides. The obtained results showed that the 2-phenylethylamine/phenylacetaldehyde ratio depended upon both the carbonyls and the reaction conditions. Thus, it can be increased using electron-donating groups in the chain of the carbonyl compound, small amounts of carbonyl compound, low oxygen content, increasing the pH, or increasing the temperature at pH 6. Opposed conditions (use of electron-withdrawing groups in the chain of the carbonyl compound, large amounts of carbonyl compound, high oxygen contents, low pH values, and increasing temperatures at low pH values) would decrease the 2-phenylethylamine/phenylacetaldehyde ratio, and the formation of aldehydes over amines in amino acid degradations would be favored.

  4. Measurement of conformational constraints in an elastin-mimetic protein by residue-pair selected solid-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Mei [Iowa State University, Department of Chemistry (United States)], E-mail: mhong@iastate.edu; McMillan, R. Andrew; Conticello, Vincent P. [Emory University, Department of Chemistry (United States)

    2002-02-15

    We introduce a solid-state NMR technique for selective detection of a residue pair in multiply labeled proteins to obtain site-specific structural constraints. The method exploits the frequency-offset dependence of cross polarization to achieve {sup 13}CO{sub i} {sup {yields}} {sup 15}N{sub i} {sup {yields}} {sup 13}C{alpha}{sub i} transfer between two residues. A {sup 13}C, {sup 15}N-labeled elastin mimetic protein (VPGVG){sub n} is used to demonstrate the method. The technique selected the Gly3 C{alpha} signal while suppressing the Gly5 C{alpha} signal, and allowed the measurement of the Gly3 C{alpha} chemical shift anisotropy to derive information on the protein conformation. This residue-pair selection technique should simplify the study of protein structure at specific residues.

  5. Measurement of conformational constraints in an elastin-mimetic protein by residue-pair selected solid-state NMR

    International Nuclear Information System (INIS)

    Hong, Mei; McMillan, R. Andrew; Conticello, Vincent P.

    2002-01-01

    We introduce a solid-state NMR technique for selective detection of a residue pair in multiply labeled proteins to obtain site-specific structural constraints. The method exploits the frequency-offset dependence of cross polarization to achieve 13 CO i → 15 N i → 13 Cα i transfer between two residues. A 13 C, 15 N-labeled elastin mimetic protein (VPGVG) n is used to demonstrate the method. The technique selected the Gly3 Cα signal while suppressing the Gly5 Cα signal, and allowed the measurement of the Gly3 Cα chemical shift anisotropy to derive information on the protein conformation. This residue-pair selection technique should simplify the study of protein structure at specific residues

  6. Integration of carboxyl modified magnetic particles and aqueous two-phase extraction for selective separation of proteins.

    Science.gov (United States)

    Gai, Qingqing; Qu, Feng; Zhang, Tao; Zhang, Yukui

    2011-07-15

    Both of the magnetic particle adsorption and aqueous two-phase extraction (ATPE) were simple, fast and low-cost method for protein separation. Selective proteins adsorption by carboxyl modified magnetic particles was investigated according to protein isoelectric point, solution pH and ionic strength. Aqueous two-phase system of PEG/sulphate exhibited selective separation and extraction for proteins before and after magnetic adsorption. The two combination ways, magnetic adsorption followed by ATPE and ATPE followed by magnetic adsorption, for the separation of proteins mixture of lysozyme, bovine serum albumin, trypsin, cytochrome C and myloglobin were discussed and compared. The way of magnetic adsorption followed by ATPE was also applied to human serum separation. Copyright © 2011 Elsevier B.V. All rights reserved.

  7. Selective small-chemical inhibitors of protein arginine methyltransferase 5 with anti-lung cancer activity.

    Directory of Open Access Journals (Sweden)

    Gui-Mei Kong

    Full Text Available Protein arginine methyltransferase 5 (PRMT5 plays critical roles in a wide variety of biological processes, including tumorigenesis. By screening a library of small chemical compounds, we identified eight compounds that selectively inhibit the PRMT5 enzymatic activity, with IC50 values ranging from 0.1 to 6 μM. Molecular docking simulation and site-directed mutagenesis indicated that identified compounds target the substrate-binding site in PRMT5. Treatment of lung cancer cells with identified inhibitors led to inhibition of the symmetrical arginine methylation of SmD3 and histones and the cellular proliferation. Oral administration of the inhibitor demonstrated antitumor activity in a lung tumor xenograft model. Thus, identified PRMT5-specific small-molecule inhibitors would help elucidate the biological roles of PRMT5 and serve as lead compounds for future drug development.

  8. Border control: selectivity of chloroplast protein import and regulation at the TOC-complex.

    Science.gov (United States)

    Demarsy, Emilie; Lakshmanan, Ashok M; Kessler, Felix

    2014-01-01

    Plants have evolved complex and sophisticated molecular mechanisms to regulate their development and adapt to their surrounding environment. Particularly the development of their specific organelles, chloroplasts and other plastid-types, is finely tuned in accordance with the metabolic needs of the cell. The normal development and functioning of plastids require import of particular subsets of nuclear encoded proteins. Most preproteins contain a cleavable sequence at their N terminal (transit peptide) serving as a signal for targeting to the organelle and recognition by the translocation machinery TOC-TIC (translocon of outer membrane complex-translocon of inner membrane complex) spanning the dual membrane envelope. The plastid proteome needs constant remodeling in response to developmental and environmental factors. Therefore selective regulation of preprotein import plays a crucial role in plant development. In this review we describe the diversity of transit peptides and TOC receptor complexes, and summarize the current knowledge and potential directions for future research concerning regulation of the different Toc isoforms.

  9. Regulation of expression of a select group of Bacillus anthracis spore coat proteins.

    Science.gov (United States)

    Aronson, Arthur

    2018-04-01

    The spore coat of Bacilli is a relatively complex structure comprised of about 70 species of proteins in 2 or 3 layers. While some are involved in assembly or protection, the regulation of many are not well defined so lacZ transcriptional fusions were constructed to six Bacillus anthracis spore coat genes in order to gain insight into their possible functions. The genes were selected on the basis of the location of the encoded proteins within the coat and distribution among spore forming species. Conditions tested were temperature and media either as solid or liquid. The most extensive differences were for the relatively well expressed fusions to the cotH and cotM genes, which were greatest at 30°C on plates of a nutrient rich medium. The cotJ operon was moderately expressed under all conditions although somewhat higher on enriched plates at 30°C. Cot S was low under all conditions except for a substantial increase in biofilm medium. Cot∝ and cotF were essentially invariant with a somewhat greater expression in the more enriched medium. The capacity of a subset of coat genes to respond to various conditions reflects a flexibility in spore coat structure that may be necessary for adaptation to environmental challenges. This could account, at least in part, for the complexity of this structure.

  10. Selective effects of whey protein concentrate on glutathione levels and apoptosis in rats with mammary tumors.

    Science.gov (United States)

    Cheng, Shih-Hsuan; Tseng, Yang-Ming; Wu, Szu-Hsien; Tsai, Shih-Meng; Tsai, Li-Yu

    2017-09-01

    Glutathione (GSH) plays an important role in antioxidant defense and regulation of apoptosis. GSH deficiency is related to many diseases, including cancer, and increased GSH levels in cancer cells are associated with chemotherapy resistance because of resistance to apoptosis. In this study, we investigated the effects of whey protein concentrate (WPC), a precursor of GSH, in rats with mammary tumors induced by treatment with 7,12-dimethylbenz(a)anthracene (DMBA). DMBA treatment results in cellular changes that mimic the initiation and promotion of carcinogenesis of breast tissue. We aimed to examine the possible preventive effects of diets containing whey protein on DMBA-induced mammary tumors in rats. The results indicate that WPC (0.334 g/kg) supplementation significantly increased the liver GSH levels by 92%, and were accompanied by low Bax/Bcl-2 ratio (from 5 to 3) and cleaved caspase-3/procaspase-3 ratio (from 2.4 to 1.2) in DMBA-treated rats. Furthermore, tumor GSH levels were decreased by 47% in WPC-supplemented rats, which resulted in increased Bax/Bcl-2 ratio (from 0.9 to 2) and cleaved caspase-3/procaspase-3 ratio (from 1.1 to 2.7). In conclusion, supplementation with WPC could selectively deplete tumor GSH levels and, therefore, WPC supplementation might be a promising strategy to overcome treatment resistance in cancer therapy. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Natural selection in avian protein-coding genes expressed in brain.

    Science.gov (United States)

    Axelsson, Erik; Hultin-Rosenberg, Lina; Brandström, Mikael; Zwahlén, Martin; Clayton, David F; Ellegren, Hans

    2008-06-01

    The evolution of birds from theropod dinosaurs took place approximately 150 million years ago, and was associated with a number of specific adaptations that are still evident among extant birds, including feathers, song and extravagant secondary sexual characteristics. Knowledge about the molecular evolutionary background to such adaptations is lacking. Here, we analyse the evolution of > 5000 protein-coding gene sequences expressed in zebra finch brain by comparison to orthologous sequences in chicken. Mean d(N)/d(S) is 0.085 and genes with their maximal expression in the eye and central nervous system have the lowest mean d(N)/d(S) value, while those expressed in digestive and reproductive tissues exhibit the highest. We find that fast-evolving genes (those which have higher than expected rate of nonsynonymous substitution, indicative of adaptive evolution) are enriched for biological functions such as fertilization, muscle contraction, defence response, response to stress, wounding and endogenous stimulus, and cell death. After alignment to mammalian orthologues, we identify a catalogue of 228 genes that show a significantly higher rate of protein evolution in the two bird lineages than in mammals. These accelerated bird genes, representing candidates for avian-specific adaptations, include genes implicated in vocal learning and other cognitive processes. Moreover, colouration genes evolve faster in birds than in mammals, which may have been driven by sexual selection for extravagant plumage characteristics.

  12. Selection of unadapted, pathogenic SHIVs encoding newly transmitted HIV-1 envelope proteins.

    Science.gov (United States)

    Del Prete, Gregory Q; Ailers, Braiden; Moldt, Brian; Keele, Brandon F; Estes, Jacob D; Rodriguez, Anthony; Sampias, Marissa; Oswald, Kelli; Fast, Randy; Trubey, Charles M; Chertova, Elena; Smedley, Jeremy; LaBranche, Celia C; Montefiori, David C; Burton, Dennis R; Shaw, George M; Markowitz, Marty; Piatak, Michael; KewalRamani, Vineet N; Bieniasz, Paul D; Lifson, Jeffrey D; Hatziioannou, Theodora

    2014-09-10

    Infection of macaques with chimeric viruses based on SIVMAC but expressing the HIV-1 envelope (Env) glycoproteins (SHIVs) remains the most powerful model for evaluating prevention and therapeutic strategies against AIDS. Unfortunately, only a few SHIVs are currently available. Furthermore, their generation has required extensive adaptation of the HIV-1 Env sequences in macaques so they may not accurately represent HIV-1 Env proteins circulating in humans, potentially limiting their translational utility. We developed a strategy for generating large numbers of SHIV constructs expressing Env proteins from newly transmitted HIV-1 strains. By inoculating macaques with cocktails of multiple SHIV variants, we selected SHIVs that can replicate and cause AIDS-like disease in immunologically intact rhesus macaques without requiring animal-to-animal passage. One of these SHIVs could be transmitted mucosally. We demonstrate the utility of the SHIVs generated by this method for evaluating neutralizing antibody administration as a protection against mucosal SHIV challenge. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Blocking peptides against HBV: PreS1 protein selected from a phage display library

    International Nuclear Information System (INIS)

    Wang, Wei; Liu, Yang; Zu, Xiangyang; Jin, Rui; Xiao, Gengfu

    2011-01-01

    Highlights: → Successfully selected specific PreS1-interacting peptides by using phage displayed library. → Alignment of the positive phage clones revealed a consensus PreS1 binding motif. → A highly enriched peptide named P7 had a strong binding ability for PreS1. → P7 could block PreS1 attachment. -- Abstract: The PreS1 protein is present on the outermost part of the hepatitis B virus (HBV) surface and has been shown to have a pivotal function in viral infectivity and assembly. The development of reagents with high affinity and specificity for PreS1 is of great significance for early diagnosis and treatment of HBV infection. A phage display library of dodecapeptide was screened for interactions with purified PreS1 protein. Alignment of the positive phage clones revealed a putative consensus PreS1 binding motif of HX n HX m HP/R. Moreover, a peptide named P7 (KHMHWHPPALNT) was highly enriched and occurred with a surprisingly high frequency of 72%. A thermodynamic study revealed that P7 has a higher binding affinity to PreS1 than the other peptides. Furthermore, P7 was able to abrogate the binding of HBV virions to the PreS1 antibody, suggesting that P7 covers key functional sites on the native PreS1 protein. This newly isolated peptide may, therefore, be a new therapeutic candidate for the treatment of HBV. The consensus motif could be modified to deliver imaging, diagnostic, and therapeutic agents to tissues affected by HBV.

  14. Blocking peptides against HBV: PreS1 protein selected from a phage display library

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Wei; Liu, Yang; Zu, Xiangyang; Jin, Rui [State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China); Xiao, Gengfu, E-mail: xiaogf@wh.iov.cn [State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China)

    2011-09-09

    Highlights: {yields} Successfully selected specific PreS1-interacting peptides by using phage displayed library. {yields} Alignment of the positive phage clones revealed a consensus PreS1 binding motif. {yields} A highly enriched peptide named P7 had a strong binding ability for PreS1. {yields} P7 could block PreS1 attachment. -- Abstract: The PreS1 protein is present on the outermost part of the hepatitis B virus (HBV) surface and has been shown to have a pivotal function in viral infectivity and assembly. The development of reagents with high affinity and specificity for PreS1 is of great significance for early diagnosis and treatment of HBV infection. A phage display library of dodecapeptide was screened for interactions with purified PreS1 protein. Alignment of the positive phage clones revealed a putative consensus PreS1 binding motif of HX{sub n}HX{sub m}HP/R. Moreover, a peptide named P7 (KHMHWHPPALNT) was highly enriched and occurred with a surprisingly high frequency of 72%. A thermodynamic study revealed that P7 has a higher binding affinity to PreS1 than the other peptides. Furthermore, P7 was able to abrogate the binding of HBV virions to the PreS1 antibody, suggesting that P7 covers key functional sites on the native PreS1 protein. This newly isolated peptide may, therefore, be a new therapeutic candidate for the treatment of HBV. The consensus motif could be modified to deliver imaging, diagnostic, and therapeutic agents to tissues affected by HBV.

  15. Positive evolutionary selection of an HD motif on Alzheimer precursor protein orthologues suggests a functional role.

    Science.gov (United States)

    Miklós, István; Zádori, Zoltán

    2012-02-01

    HD amino acid duplex has been found in the active center of many different enzymes. The dyad plays remarkably different roles in their catalytic processes that usually involve metal coordination. An HD motif is positioned directly on the amyloid beta fragment (Aβ) and on the carboxy-terminal region of the extracellular domain (CAED) of the human amyloid precursor protein (APP) and a taxonomically well defined group of APP orthologues (APPOs). In human Aβ HD is part of a presumed, RGD-like integrin-binding motif RHD; however, neither RHD nor RXD demonstrates reasonable conservation in APPOs. The sequences of CAEDs and the position of the HD are not particularly conserved either, yet we show with a novel statistical method using evolutionary modeling that the presence of HD on CAEDs cannot be the result of neutral evolutionary forces (pHD motif is underrepresented in the proteomes of all species of the animal kingdom. Position migration can be explained by high probability occurrence of multiple copies of HD on intermediate sequences, from which only one is kept by selective evolutionary forces, in a similar way as in the case of the "transcription binding site turnover." CAED of all APP orthologues and homologues are predicted to bind metal ions including Amyloid-like protein 1 (APLP1) and Amyloid-like protein 2 (APLP2). Our results suggest that HDs on the CAEDs are most probably key components of metal-binding domains, which facilitate and/or regulate inter- or intra-molecular interactions in a metal ion-dependent or metal ion concentration-dependent manner. The involvement of naturally occurring mutations of HD (Tottori (D7N) and English (H6R) mutations) in early onset Alzheimer's disease gives additional support to our finding that HD has an evolutionary preserved function on APPOs.

  16. A novel typing method for Streptococcus pneumoniae using selected surface proteins

    Directory of Open Access Journals (Sweden)

    Arnau eDomenech

    2016-03-01

    Full Text Available The diverse pneumococcal diseases are associated with different pneumococcal lineages, or clonal complexes. Nevertheless, intra-clonal genomic variability, which influences pathogenicity, has been reported for surface virulence factors. These factors constitute the communication interface between the pathogen and its host and their corresponding genes are subjected to strong selective pressures affecting functionality and immunogenicity. First, the presence and allelic dispersion of 97 outer protein families were screened in 19 complete pneumococcal genomes. Seventeen families were deemed variable and were then examined in 216 draft genomes. This procedure allowed the generation of binary vectors with 17 positions and the classification of strains into surfotypes. They represent the outer protein subsets with the highest inter-strain discriminative power. A total of 116 non-redundant surfotypes were identified. Those sharing a critical number of common protein features were hierarchically clustered into 18 surfogroups. Most clonal complexes with comparable epidemiological characteristics belonged to the same or similar surfogroups. However, the very large CC156 clonal complex was dispersed over several surfogroups. In order to establish a relationship between surfogroup and pathogenicity, the surfotypes of 95 clinical isolates with different serogroup/serotype combinations were analysed. We found a significant correlation between surfogroup and type of pathogenic behaviour (primary invasive, opportunistic invasive and non-invasive. We conclude that the virulent behaviour of S. pneumoniae is related to the activity of collections of, rather than individual, surface virulence factors. Since surfotypes evolve faster than MLSTs and directly reflect virulence potential, this novel typing protocol is appropriate for the identification of emerging clones.

  17. Rats free to select between pure protein and a fat-carbohydrate mix ingest high-protein mixed meals during the dark period and protein meals during the light period.

    Science.gov (United States)

    Makarios-Lahham, Lina; Roseau, Suzanne M; Fromentin, Gilles; Tome, Daniel; Even, Patrick C

    2004-03-01

    Rats that are allowed to select their diets [dietary self- selection (DSS)] often ingest >30% of their daily energy in the form of protein. Such an intake may seem unhealthy, but the consistency of this choice suggests that it is motivated by physiologic drives. To gain a clearer understanding of how protein selection is structured during DSS, we adapted 12 rats to a standard diet (14% Protein) and then allowed them to choose between two diets, i.e., total milk protein (P) and a mix of carbohydrates and lipids (FC). The protein intake during DSS rose above 40%; assuming an intermeal interval of 10 min, 70% of the energy intake occurred with meals that included both P and FC, with the sequence of FC followed by P preferred to the sequence of P followed by FC (70 vs. 30%, P energy intake during the light period was reduced to only 10% of the daily energy intake [vs. 30% with the control P14 diet or a with a high-protein diet (50%)], and 90% of the intake was in the form of pure protein meals. In complementary studies, we verified that the high protein intake also occurred when rats were offered casein and whey and was not due to the high palatability of the milk protein. We conclude that a specific feeding pattern accompanies high protein intake in rats allowed DSS. The mechanisms underlying this behavior and its potential beneficial/adverse consequences over the long term still must be clarified.

  18. Carbonylation as a key reaction in anaerobic acetone activation by Desulfococcus biacutus.

    Science.gov (United States)

    Gutiérrez Acosta, Olga B; Hardt, Norman; Schink, Bernhard

    2013-10-01

    Acetone is activated by aerobic and nitrate-reducing bacteria via an ATP-dependent carboxylation reaction to form acetoacetate as the first reaction product. In the activation of acetone by sulfate-reducing bacteria, acetoacetate has not been found to be an intermediate. Here, we present evidence of a carbonylation reaction as the initial step in the activation of acetone by the strictly anaerobic sulfate reducer Desulfococcus biacutus. In cell suspension experiments, CO was found to be a far better cosubstrate for acetone activation than CO2. The hypothetical reaction product, acetoacetaldehyde, is extremely reactive and could not be identified as a free intermediate. However, acetoacetaldehyde dinitrophenylhydrazone was detected by mass spectrometry in cell extract experiments as a reaction product of acetone, CO, and dinitrophenylhydrazine. In a similar assay, 2-amino-4-methylpyrimidine was formed as the product of a reaction between acetoacetaldehyde and guanidine. The reaction depended on ATP as a cosubstrate. Moreover, the specific activity of aldehyde dehydrogenase (coenzyme A [CoA] acylating) tested with the putative physiological substrate was found to be 153 ± 36 mU mg(-1) protein, and its activity was specifically induced in extracts of acetone-grown cells. Moreover, acetoacetyl-CoA was detected (by mass spectrometry) after the carbonylation reaction as the subsequent intermediate after acetoacetaldehyde was formed. These results together provide evidence that acetoacetaldehyde is an intermediate in the activation of acetone by sulfate-reducing bacteria.

  19. Plant protein and secondary metabolites influence diet selection in a mammalian specialist herbivore

    Science.gov (United States)

    Ulappa, Amy C.; Kelsey, Rick G.; Frye, Graham G.; Rachlow, Janet L.; Shipley, Lisa A.; Bond, Laura; Pu, Xinzhu; Forbey, Jennifer Sorensen

    2015-01-01

    For herbivores, nutrient intake is limited by the relatively low nutritional quality of plants and high concentrations of potentially toxic defensive compounds (plant secondary metabolites, PSMs) produced by many plants. In response to phytochemical challenges, some herbivores selectively forage on plants with higher nutrient and lower PSM concentrations relative to other plants. Pygmy rabbits (Brachylagus idahoensis) are dietary specialists that feed on sagebrush (Artemisia spp.) and forage on specific plants more than others within a foraging patch. We predicted that the plants with evidence of heavy foraging (browsed plants) would be of higher dietary quality than plants that were not browsed (unbrowsed). We used model selection to determine which phytochemical variables best explained the difference between browsed and unbrowsed plants. Higher crude protein increased the odds that plants would be browsed by pygmy rabbits and the opposite was the case for certain PSMs. Additionally, because pygmy rabbits can occupy foraging patches (burrows) for consecutive years, their browsing may influence the nutritional and PSM constituents of plants at the burrows. In a post hoc analysis, we did not find a significant relationship between phytochemical concentrations, browse status and burrow occupancy length. We concluded that pygmy rabbits use nutritional and chemical cues while making foraging decisions. PMID:26366011

  20. Automated selected reaction monitoring software for accurate label-free protein quantification.

    Science.gov (United States)

    Teleman, Johan; Karlsson, Christofer; Waldemarson, Sofia; Hansson, Karin; James, Peter; Malmström, Johan; Levander, Fredrik

    2012-07-06

    Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently removes interfering signals from contaminating peptides to estimate the true signal of the targeted peptides. We evaluated the algorithm on a published multisite data set and achieved results in line with manual data analysis. In complex peptide mixtures from whole proteome digests of Streptococcus pyogenes we achieved a technical variability across the entire proteome abundance range of 6.5-19.2%, which was considerably below the total variation across biological samples. Our results show that the label-free SRM workflow with automated data analysis is feasible for large-scale biological studies, opening up new possibilities for quantitative proteomics and systems biology.

  1. Selectively dispersed isotope labeling for protein structure determination by magic angle spinning NMR

    Energy Technology Data Exchange (ETDEWEB)

    Eddy, Matthew T. [Massachusetts Institute of Technology, Department of Chemistry (United States); Belenky, Marina [Brandeis University, Department of Chemistry (United States); Sivertsen, Astrid C. [Massachusetts Institute of Technology, Francis Bitter Magnet Laboratory (United States); Griffin, Robert G. [Massachusetts Institute of Technology, Department of Chemistry (United States); Herzfeld, Judith, E-mail: herzfeld@brandeis.edu [Brandeis University, Department of Chemistry (United States)

    2013-10-15

    The power of nuclear magnetic resonance spectroscopy derives from its site-specific access to chemical, structural and dynamic information. However, the corresponding multiplicity of interactions can be difficult to tease apart. Complimentary approaches involve spectral editing on the one hand and selective isotope substitution on the other. Here we present a new 'redox' approach to the latter: acetate is chosen as the sole carbon source for the extreme oxidation numbers of its two carbons. Consistent with conventional anabolic pathways for the amino acids, [1-{sup 13}C] acetate does not label {alpha} carbons, labels other aliphatic carbons and the aromatic carbons very selectively, and labels the carboxyl carbons heavily. The benefits of this labeling scheme are exemplified by magic angle spinning spectra of microcrystalline immunoglobulin binding protein G (GB1): the elimination of most J-couplings and one- and two-bond dipolar couplings provides narrow signals and long-range, intra- and inter-residue, recoupling essential for distance constraints. Inverse redox labeling, from [2-{sup 13}C] acetate, is also expected to be useful: although it retains one-bond couplings in the sidechains, the removal of CA-CO coupling in the backbone should improve the resolution of NCACX spectra.

  2. Kinetic Basis of Nucleotide Selection Employed by a Protein Template-Dependent DNA Polymerase†

    Science.gov (United States)

    Brown, Jessica A.; Fowler, Jason D.; Suo, Zucai

    2010-01-01

    Rev1, a Y-family DNA polymerase, contributes to spontaneous and DNA damage-induced mutagenic events. In this paper, we have employed pre-steady state kinetic methodology to establish a kinetic basis for nucleotide selection by human Rev1, a unique nucleotidyl transferase that uses a protein template-directed mechanism to preferentially instruct dCTP incorporation. This work demonstrated that the high incorporation efficiency of dCTP is dependent on both substrates: an incoming dCTP and a templating base dG. The extremely low base substitution fidelity of human Rev1 (100 to 10-5) was due to the preferred misincorporation of dCTP with templating bases dA, dT, and dC over correct dNTPs. Using non-natural nucleotide analogs, we showed that hydrogen bonding interactions between residue R357 of human Rev1 and an incoming dNTP are not essential for DNA synthesis. Lastly, human Rev1 discriminates between ribonucleotides and deoxyribonucleotides mainly by reducing the rate of incorporation, and the sugar selectivity of human Rev1 is sensitive to both the size and orientation of the 2′-substituent of a ribonucleotide. PMID:20518555

  3. A potential new selection criterion for breeding winter barley optimal protein and amino acid profiles for liquid pig feed

    DEFF Research Database (Denmark)

    Christensen, Jesper Bjerg; Blaabjerg, Karoline; Poulsen, Hanne Damgaard

    The hypothesis is that cereal proteases in liquid feed degrade and convert water insoluble storage protein into water soluble protein, which may improve the digestibility of protein in pigs compared with dry feeding. Protein utilization is increased by matching the amino acid (AAs) content...... of the diet as close as possible to the pigs’ requirement. By improving the availability of isoleucine, leucine, histidine and phenylalanine, which are limiting and commercial unavailable, the amount of crude protein in the pig feed can be reduced, resulting in a decreased excretion of nitrogen. The aim...... of glutamic acid revealed differences between the cultivars and the solubilised protein at all three times. These preliminary results may indicate that improvements of the nitrogen utilization in pigs fed soaked winter barley depends on the choice of cultivar and soaking time, and may serve as a new selection...

  4. Generation of a selectively cytotoxic fusion protein against p53 mutated cancers

    International Nuclear Information System (INIS)

    Kousparou, Christina A; Yiacoumi, Efthymia; Deonarain, Mahendra P; Epenetos, Agamemnon A

    2012-01-01

    A significant number of cancers are caused by defects in p21 causing functional defects in p21 or p53 tumour-suppressor proteins. This has led to many therapeutic approaches including restoration by gene therapy with wild-type p53 or p21 using viral or liposomal vectors, which have toxicity or side-effect limitations. We set out to develop a safer, novel fusion protein which has the ability to reconstitute cancer cell lines with active p21 by protein transduction. The fusion protein was produced from the cell-translocating peptide Antennapedia (Antp) and wild-type, full-length p21 (Antp-p21). This was expressed and refolded from E. coli and tested on a variety of cell lines and tumours (in a BALB/c nude xenograft model) with differing p21 or p53 status. Antp-p21 penetrated and killed cancer cells that do not express wild type p53 or p21. This included cells that were matched to cogenic parental cell lines. Antp-p21 killed cancer cells selectively that were malignant as a result of mutations or nuclear exclusion of the p53 and p21 genes and over-expression of MDM2. Non-specific toxicity was excluded by showing that Antp-p21 penetrated but did not kill p53- or p21- wild-type cells. Antp-p21 was not immunogenic in normal New Zealand White rabbits. Recombinant Antp peptide alone was not cytotoxic, showing that killing was due to the transduction of the p21 component of Antp-p21. Antp-p21 was shown to penetrate cancer cells engrafted in vivo and resulted in tumour eradication when administered with conventionally-used chemotherapeutic agents, which alone were unable to produce such an effect. Antp-p21 may represent a new and promising targeted therapy for patients with p53-associated cancers supporting the concept that rational design of therapies directed against specific cancer mutations will play a part in the future of medical oncology

  5. Generation of a selectively cytotoxic fusion protein against p53 mutated cancers

    Directory of Open Access Journals (Sweden)

    Kousparou Christina A

    2012-08-01

    Full Text Available Abstract Background A significant number of cancers are caused by defects in p21 causing functional defects in p21 or p53 tumour-suppressor proteins. This has led to many therapeutic approaches including restoration by gene therapy with wild-type p53 or p21 using viral or liposomal vectors, which have toxicity or side-effect limitations. We set out to develop a safer, novel fusion protein which has the ability to reconstitute cancer cell lines with active p21 by protein transduction. Methods The fusion protein was produced from the cell-translocating peptide Antennapedia (Antp and wild-type, full-length p21 (Antp-p21. This was expressed and refolded from E. coli and tested on a variety of cell lines and tumours (in a BALB/c nude xenograft model with differing p21 or p53 status. Results Antp-p21 penetrated and killed cancer cells that do not express wild type p53 or p21. This included cells that were matched to cogenic parental cell lines. Antp-p21 killed cancer cells selectively that were malignant as a result of mutations or nuclear exclusion of the p53 and p21 genes and over-expression of MDM2. Non-specific toxicity was excluded by showing that Antp-p21 penetrated but did not kill p53- or p21- wild-type cells. Antp-p21 was not immunogenic in normal New Zealand White rabbits. Recombinant Antp peptide alone was not cytotoxic, showing that killing was due to the transduction of the p21 component of Antp-p21. Antp-p21 was shown to penetrate cancer cells engrafted in vivo and resulted in tumour eradication when administered with conventionally-used chemotherapeutic agents, which alone were unable to produce such an effect. Conclusions Antp-p21 may represent a new and promising targeted therapy for patients with p53-associated cancers supporting the concept that rational design of therapies directed against specific cancer mutations will play a part in the future of medical oncology.

  6. Stapled Voltage-Gated Calcium Channel (CaV) α-Interaction Domain (AID) Peptides Act As Selective Protein-Protein Interaction Inhibitors of CaV Function.

    Science.gov (United States)

    Findeisen, Felix; Campiglio, Marta; Jo, Hyunil; Abderemane-Ali, Fayal; Rumpf, Christine H; Pope, Lianne; Rossen, Nathan D; Flucher, Bernhard E; DeGrado, William F; Minor, Daniel L

    2017-06-21

    For many voltage-gated ion channels (VGICs), creation of a properly functioning ion channel requires the formation of specific protein-protein interactions between the transmembrane pore-forming subunits and cystoplasmic accessory subunits. Despite the importance of such protein-protein interactions in VGIC function and assembly, their potential as sites for VGIC modulator development has been largely overlooked. Here, we develop meta-xylyl (m-xylyl) stapled peptides that target a prototypic VGIC high affinity protein-protein interaction, the interaction between the voltage-gated calcium channel (Ca V ) pore-forming subunit α-interaction domain (AID) and cytoplasmic β-subunit (Ca V β). We show using circular dichroism spectroscopy, X-ray crystallography, and isothermal titration calorimetry that the m-xylyl staples enhance AID helix formation are structurally compatible with native-like AID:Ca V β interactions and reduce the entropic penalty associated with AID binding to Ca V β. Importantly, electrophysiological studies reveal that stapled AID peptides act as effective inhibitors of the Ca V α 1 :Ca V β interaction that modulate Ca V function in an Ca V β isoform-selective manner. Together, our studies provide a proof-of-concept demonstration of the use of protein-protein interaction inhibitors to control VGIC function and point to strategies for improved AID-based Ca V modulator design.

  7. Phenolic carbonyls undergo rapid aqueous photodegradation to form low-volatility, light-absorbing products

    Science.gov (United States)

    Smith, Jeremy D.; Kinney, Haley; Anastasio, Cort

    2016-02-01

    We investigated the aqueous photochemistry of six phenolic carbonyls - vanillin, acetovanillone, guaiacyl acetone, syringaldehyde, acetosyringone, and coniferyl aldehyde - that are emitted from wood combustion. The phenolic carbonyls absorb significant amounts of solar radiation and decay rapidly via direct photodegradation, with lifetimes (τ) of 13-140 min under Davis, CA winter solstice sunlight at midday (solar zenith angle = 62°). The one exception is guaiacyl acetone, where the carbonyl group is not directly connected to the aromatic ring: This species absorbs very little sunlight and undergoes direct photodegradation very slowly (τ > 103 min). We also found that the triplet excited states (3C*) of the phenolic carbonyls rapidly oxidize syringol (a methoxyphenol without a carbonyl group), on timescales of 1-5 h for solutions containing 5 μM phenolic carbonyl. The direct photodegradation of the phenolic carbonyls, and the oxidation of syringol by 3C*, both efficiently produce low volatility products, with SOA mass yields ranging from 80 to 140%. Contrary to most aliphatic carbonyls, under typical fog conditions we find that the primary sink for the aromatic phenolic carbonyls is direct photodegradation in the aqueous phase. In areas of significant wood combustion, phenolic carbonyls appear to be small but significant sources of aqueous SOA: over the course of a few hours, nearly all of the phenolic carbonyls will be converted to SOA via direct photodegradation, enhancing the POA mass from wood combustion by approximately 3-5%.

  8. Intracellular delivery of cell-penetrating peptide-transcriptional factor fusion protein and its role in selective osteogenesis

    Science.gov (United States)

    Suh, Jin Sook; Lee, Jue Yeon; Choi, Yoon Jung; You, Hyung Keun; Hong, Seong-Doo; Chung, Chong Pyoung; Park, Yoon Jeong

    2014-01-01

    Protein-transduction technology has been attempted to deliver macromolecular materials, including protein, nucleic acids, and polymeric drugs, for either diagnosis or therapeutic purposes. Herein, fusion protein composed of an arginine-rich cell-penetrating peptide, termed low-molecular-weight protamine (LMWP), and a transcriptional coactivator with a PDZ-binding motif (TAZ) protein was prepared and applied in combination with biomaterials to increase bone-forming capacity. TAZ has been recently identified as a specific osteogenic stimulating transcriptional coactivator in human mesenchymal stem cell (hMSC) differentiation, while simultaneously blocking adipogenic differentiation. However, TAZ by itself cannot penetrate the cells, and thus needs a transfection tool for translocalization. The LMWP-TAZ fusion proteins were efficiently translocalized into the cytosol of hMSCs. The hMSCs treated with cell-penetrating LMWP-TAZ exhibited increased expression of osteoblastic genes and protein, producing significantly higher quantities of mineralized matrix compared to free TAZ. In contrast, adipogenic differentiation of the hMSCs was blocked by treatment of LMWP-TAZ fusion protein, as reflected by reduced marker-protein expression, adipocyte fatty acid-binding protein 2, and peroxisome proliferator-activated receptor-γ messenger ribonucleic acid levels. LMWP-TAZ was applied in alginate gel for the purpose of localization and controlled release. The LMWP-TAZ fusion protein-loaded alginate gel matrix significantly increased bone formation in rabbit calvarial defects compared with alginate gel matrix mixed with free TAZ protein. The protein transduction of TAZ fused with cell-penetrating LMWP peptide was able selectively to stimulate osteogenesis in vitro and in vivo. Taken together, this fusion protein-transduction technology for osteogenic protein can thus be applied in combination with biomaterials for tissue regeneration and controlled release for tissue

  9. Effect of beta-hydroxy-beta-methylbutyrate (HMB) on protein metabolism in whole body and in selected tissues.

    Science.gov (United States)

    Holecek, M; Muthny, T; Kovarik, M; Sispera, L

    2009-01-01

    Beta-hydroxy-beta-methylbutyrate (HMB) is a leucine metabolite with protein anabolic effect. The aim of the study was to examine the role of exogenous HMB on leucine and protein metabolism in whole body and selected tissues. Rats were administered by HMB (0.1 g/kg b.w.) or by saline. The parameters of whole-body protein metabolism were evaluated 24 h later using L-[1-14C]leucine and L-[3,4,5-3H]phenylalanine. Changes in proteasome dependent proteolysis and protein synthesis were determined according the "chymotrypsin-like" enzyme activity and labeled leucine and phenylalanine incorporation into the protein. A decrease in leucine clearance and whole-body protein turnover (i.e., a decrease in whole-body proteolysis and protein synthesis) was observed in HMB treated rats. Proteasome-dependent proteolysis decreased significantly in skeletal muscle, changes in heart, liver, jejunum, colon, kidney, and spleen were insignificant. Decrease in protein synthesis was observed in the heart, colon, kidney, and spleen, while an increase was observed in the liver. There were no significant changes in leucine oxidation. We conclude that protein anabolic effect of HMB in skeletal muscle is related to inhibition of proteolysis in proteasome. Alterations in protein synthesis in visceral tissues may affect several important functions and the metabolic status of the whole body.

  10. Catalytic synthesis of aromatic diisocyanates by means of carbonylation of nitrocompounds with carbon monoxide

    Energy Technology Data Exchange (ETDEWEB)

    Nefedov, B K; Manov-Yuvenskii, V I; Khoshdurdev, Kh O; Novikov, S S [AN SSSR, Moscow. Inst. Organicheskoj Khimii

    1977-02-11

    The development of an active and selective heterogeneous catalyst for synthesis of aromatic diisocyanates has been studied. The catalytic ability of the catalyst PdO-MoO/sub 3/-Fe/sub 2/O/sub 3/ deposited on ..gamma..-Al/sub 2/O/sub 3/ has been investigated in the reactions of carbonylation of aromatic dinitrocompounds with carbon oxide. The effect of the catalyst composition, method of catalyst production, reaction temperature and pressure on the catalytic ability have been studied. It has been established that the catalyst PdO-MoO/sub 3/-Fe/sub 2/O/sub 3/(2-6:1:1) deposited on ..gamma..-Al/sub 2/O/sub 3/ is highly active and selective in the reactions of carbonilation of aromatic dinitrocompounds at 210 deg and 300 atm. It has been used for synthesis of aromatic diisocyanates in yield 32-75%.

  11. Anchoring selenido-carbonyl ruthenium clusters to functionalized silica xerogels

    International Nuclear Information System (INIS)

    Cauzzi, Daniele; Graiff, Claudia; Pattacini, Roberto; Predieri, Giovanni; Tiripicchio, Antonio

    2003-01-01

    Silica Xerogels containing carbonyl Ru 3 Se 2 nido clusters were prepared in three different ways. The simple dispersion of [Ru 3 (μ 3 -Se) 2 (CO) 7 (PPh 3 ) 2 ] via sol gel process produces an inhomogeneous material; by contrast, homogeneous xerogels were obtained by reaction of [Ru 3 (μ 3 -Se) 2 (CO) 8 (PPh 3 )] with functionalized xerogels containing grafted diphenylphosphine moieties and by reaction of [Ru 3 (CO) 12 ] with a xerogel containing grafted phosphine-selenide groups. The reaction between [Ru 3 (CO) 12 ] and dodecyl diphenylphosphine selenide led to the formation of four selenido carbonyl clusters, which are soluble in hydrocarbon solvents and can be deposited as thin films from their solution by slow evaporation. (author)

  12. Reactions of α-phosphorylated carbonyl compounds with amino alcohols

    International Nuclear Information System (INIS)

    Moskva, V.V.; Sitdikova, T.Sh.; Zykova, T.V.; Alparova, M.V.; Shagvaleev, F.Sh.

    1986-01-01

    2-Aminoethanol reacts with carbonyl compounds with the formation, depending on the structure of the latter, either of a mixture of azomethines and oxazolidines, or of only azomethines. In the development of investigations on the reactivity of α-phosphorylated carbonyl compounds the authors studied the reactions of a number of amino alcohols with phosphorylated acetaldehyde and acetone. In both cases they observed the formation of compounds of enamine structure, oxazolidines and azomethines were not observed. By means of NMR spectroscopy they established clearly the formation of the E-isomeric products. The 1 H, 31 P, and 13 C NMR spectra were recorded on a WP-80 spectrometer. Chemical shifts of protons and 13 C nuclei are given relative to TMS, and phosphorus nuclei relative to orthophosphoric acid

  13. Synthetic and mechanistic aspects of titanium-mediated carbonyl olefinations

    Energy Technology Data Exchange (ETDEWEB)

    Petasis, N.A.; Staszewski, J.P.; Hu, Yong-Han; Lu, Shao-Po [Univ. of Southern California, Los Angeles, CA (United States)

    1995-12-31

    A new method for the olefination of carbonyl compounds with dimethyl titanocene, and other related bishydrocarbyl titanocene derivatives has been recently developed in the author`s laboratories. This process is experimentally convenient and works with various types of carbonyl compounds, including aldehydes, ketones, esters, lactones, carbonates, anhydrides, amides, imides, lactams, thioesters, selenoesters, and acylsilanes. More recent studies have focused on the scope and utility of this reaction, including mechanistic studies and synthetic applications. In addition to varying the reaction conditions, the authors have examined several mixed titanocene derivatives and have found ways for carrying out this type of olefination at room temperature, such as the use of tris(trimethylsilyl) titanacyclobutene. The authors have also employed this reaction in the modification of carbohydrates and cyclobutenediones. This olefination was also followed-up with subsequent transformations to produce carbocycles and heterocycles, including tetrahydrofurans and tetrahydropyrans.

  14. A three-membered ring approach to carbonyl olefination.

    Science.gov (United States)

    Niyomchon, Supaporn; Oppedisano, Alberto; Aillard, Paul; Maulide, Nuno

    2017-10-23

    The carbon-carbon double bond, with its diverse and multifaceted reactivity, occupies a prominent position in organic synthesis. Although a variety of simple alkenes are readily available, the mild and chemoselective introduction of a unit of unsaturation into a functionalized organic molecule remains an ongoing area of research, and the olefination of carbonyl compounds is a cornerstone of such approaches. Here we show the direct olefination of hydrazones via the intermediacy of three-membered ring species generated by addition of sulfoxonium ylides, departing from the general dogma of alkenes synthesis from carbonyls. Moreover, the mild reaction conditions and operational simplicity of the transformation render the methodology appealing from a practical point of view.

  15. Identification of potential nuclear reprogramming and differentiation factors by a novel selection method for cloning chromatin-binding proteins

    International Nuclear Information System (INIS)

    Wang Liu; Zheng Aihua; Yi Ling; Xu Chongren; Ding Mingxiao; Deng Hongkui

    2004-01-01

    Nuclear reprogramming is critical for animal cloning and stem cell creation through nuclear transfer, which requires extensive remodeling of chromosomal architecture involving dramatic changes in chromatin-binding proteins. To understand the mechanism of nuclear reprogramming, it is critical to identify chromatin-binding factors specify the reprogramming process. In this report, we have developed a high-throughput selection method, based on T7 phage display and chromatin immunoprecipitation, to isolate chromatin-binding factors expressed in mouse embryonic stem cells using primary mouse embryonic fibroblast chromatin. Seven chromatin-binding proteins have been isolated by this method. We have also isolated several chromatin-binding proteins involved in hepatocyte differentiation. Our method provides a powerful tool to rapidly and selectively identify chromatin-binding proteins. The method can be used to study epigenetic modification of chromatin during nuclear reprogramming, cell differentiation, and transdifferentiation

  16. Toward Green Acylation of (Heteroarenes: Palladium-Catalyzed Carbonylation of Olefins to Ketones

    Directory of Open Access Journals (Sweden)

    Jie Liu

    2017-11-01

    Full Text Available Green Friedel–Crafts acylation reactions belong to the most desired transformations in organic chemistry. The resulting ketones constitute important intermediates, building blocks, and functional molecules in organic synthesis as well as for the chemical industry. Over the past 60 years, advances in this topic have focused on how to make this reaction more economically and environmentally friendly by using green acylating conditions, such as stoichiometric acylations and catalytic homogeneous and heterogeneous acylations. However, currently well-established methodologies for their synthesis either produce significant amounts of waste or proceed under harsh conditions, limiting applications. Here, we present a new protocol for the straightforward and selective introduction of acyl groups into (hetero­arenes without directing groups by using available olefins with inexpensive CO. In the presence of commercial palladium catalysts, inter- and intramolecular carbonylative C–H functionalizations take place with good regio- and chemoselectivity. Compared to classical Friedel–Crafts chemistry, this novel methodology proceeds under mild reaction conditions. The general applicability of this methodology is demonstrated by the direct carbonylation of industrial feedstocks (ethylene and diisobutene as well as of natural products (eugenol and safrole. Furthermore, synthetic applications to drug molecules are showcased.

  17. Nucleophilic tetrafluoroethylation of carbonyl compounds with fluorinated sulfones

    Czech Academy of Sciences Publication Activity Database

    Václavík, Jiří; Chernykh, Yana; Jurásek, Bronislav; Beier, Petr

    2015-01-01

    Roč. 169, Jan (2015), s. 24-31 ISSN 0022-1139 R&D Projects: GA ČR GAP207/11/0421 Grant - others:GA MŠk(CZ) ED3.2.00/08.0144; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : fluorine * tetrafluoroethylation * sulfones * nucleophilic addition * carbonyl compounds Subject RIV: CC - Organic Chemistry Impact factor: 2.213, year: 2015

  18. Magnetophoretic manipulation in microsystem using carbonyl iron-polydimethylsiloxane microstructures

    OpenAIRE

    Faivre, Magalie; Gelszinnis, Renaud; Degouttes, Jérôme; Terrier, Nicolas; Rivière, Charlotte; Ferrigno, Rosaria; Deman, Anne-Laure

    2014-01-01

    This paper reports the use of a recent composite material, noted hereafter i-PDMS, made of carbonyl iron microparticles mixed in a PolyDiMethylSiloxane (PDMS) matrix, for magnetophoretic functions such as capture and separation of magnetic species. We demonstrated that this composite which combine the advantages of both components, can locally generate high gradients of magnetic field when placed between two permanent magnets. After evaluating the magnetic susceptibility of the material as a ...

  19. Formylbenzene diazonium hexafluorophosphate reagent for tyrosine-selective modification of proteins and the introduction of a bioorthogonal aldehyde.

    Science.gov (United States)

    Gavrilyuk, Julia; Ban, Hitoshi; Nagano, Masanobu; Hakamata, Wataru; Barbas, Carlos F

    2012-12-19

    4-Formylbenzene diazonium hexafluorophosphate (FBDP) is a novel bench-stable crystalline diazonium salt that reacts selectively with tyrosine to install a bioorthogonal aldehyde functionality. Model studies with N-acyl-tyrosine methylamide allowed us to identify conditions optimal for tyrosine ligation reactions with small peptides and proteins. FBDP-based conjugation was used for the facile introduction of small molecule tags, poly(ethylene glycol) chains (PEGylation), and functional small molecules onto model proteins and to label the surface of living cells.

  20. The SARS coronavirus spike glycoprotein is selectively recognized by lung surfactant protein D and activates macrophages

    DEFF Research Database (Denmark)

    Leth-Larsen, Rikke; Zhong, Fei; Chow, Vincent T K

    2007-01-01

    Da glycosylated protein. It was not secreted in the presence of tunicamycin and was detected as a 130 kDa protein in the cell lysate. The purified S-protein bound to Vero but not 293T cells and was itself recognized by lung surfactant protein D (SP-D), a collectin found in the lung alveoli. The binding required...

  1. Enzastaurin (LY317615), a Protein Kinase C Beta Selective Inhibitor, Enhances Antiangiogenic Effect of Radiation

    International Nuclear Information System (INIS)

    Willey, Christopher D.; Xiao Dakai; Tu Tianxiang; Kim, Kwang Woon; Moretti, Luigi; Niermann, Kenneth J.; Tawtawy, Mohammed N.; Quarles, Chad C. Ph.D.; Lu Bo

    2010-01-01

    Purpose: Angiogenesis has generated interest in oncology because of its important role in cancer growth and progression, particularly when combined with cytotoxic therapies, such as radiotherapy. Among the numerous pathways influencing vascular growth and stability, inhibition of protein kinase B(Akt) or protein kinase C(PKC) can influence tumor blood vessels within tumor microvasculature. Therefore, we wanted to determine whether PKC inhibition could sensitize lung tumors to radiation. Methods and Materials: The combination of the selective PKCβ inhibitor Enzastaurin (ENZ, LY317615) and ionizing radiation were used in cell culture and a mouse model of lung cancer. Lung cancer cell lines and human umbilical vascular endothelial cells (HUVEC) were examined using immunoblotting, cytotoxic assays including cell proliferation and clonogenic assays, and Matrigel endothelial tubule formation. In vivo, H460 lung cancer xenografts were examined for tumor vasculature and proliferation using immunohistochemistry. Results: ENZ effectively radiosensitizes HUVEC within in vitro models. Furthermore, concurrent ENZ treatment of lung cancer xenografts enhanced radiation-induced destruction of tumor vasculature and proliferation by IHC. However, tumor growth delay was not enhanced with combination treatment compared with either treatment alone. Analysis of downstream effectors revealed that HUVEC and the lung cancer cell lines differed in their response to ENZ and radiation such that only HUVEC demonstrate phosphorylated S6 suppression, which is downstream of mTOR. When ENZ was combined with the mTOR inhibitor, rapamycin, in H460 lung cancer cells, radiosensitization was observed. Conclusion: PKC appears to be crucial for angiogenesis, and its inhibition by ENZ has potential to enhance radiotherapy in vivo.

  2. Mitogen activated protein kinases selectively regulate palytoxin-stimulated gene expression in mouse keratinocytes

    International Nuclear Information System (INIS)

    Zeliadt, Nicholette A.; Warmka, Janel K.; Wattenberg, Elizabeth V.

    2003-01-01

    We have been investigating how the novel skin tumor promoter palytoxin transmits signals through mitogen activated protein kinases (MAPKs). Palytoxin activates three major MAPKs, extracellular signal-regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and p38, in a keratinocyte cell line derived from initiated mouse skin (308). We previously showed that palytoxin requires ERK to increase matrix metalloproteinase-13 (MMP-13) gene expression, an enzyme implicated in carcinogenesis. Diverse stimuli require JNK and p38 to increase MMP-13 gene expression, however. We therefore used the JNK and p38 inhibitors SP 600125 and SB 202190, respectively, to investigate the role of these MAPKs in palytoxin-induced MMP-13 gene expression. Surprisingly, palytoxin does not require JNK and p38 to increase MMP-13 gene expression. Accordingly, ERK activation, independent of palytoxin and in the absence of JNK and p38 activation, is sufficient to induce MMP-13 gene expression in 308 keratinocytes. Dexamethasone, a synthetic glucocorticoid that inhibits activator protein-1 (AP-1), blocked palytoxin-stimulated MMP-13 gene expression. Therefore, the AP-1 site present in the promoter of the MMP-13 gene appears to be functional and to play a key role in palytoxin-stimulated gene expression. Previous studies showed that palytoxin simulates an ERK-dependent selective increase in the c-Fos content of AP-1 complexes that bind to the promoter of the MMP-13 gene. JNK and p38 can also modulate c-Fos. Palytoxin does not require JNK or p38 to increase c-Fos binding, however. Altogether, these studies indicate that ERK plays a distinctly essential role in transmitting palytoxin-stimulated signals to specific nuclear targets in keratinocytes derived from initiated mouse skin

  3. Thioredoxin Selectivity for Thiol-based Redox Regulation of Target Proteins in Chloroplasts*

    Science.gov (United States)

    Yoshida, Keisuke; Hara, Satoshi; Hisabori, Toru

    2015-01-01

    Redox regulation based on the thioredoxin (Trx) system is believed to ensure light-responsive control of various functions in chloroplasts. Five Trx subtypes have been reported to reside in chloroplasts, but their functional diversity in the redox regulation of Trx target proteins remains poorly clarified. To directly address this issue, we studied the Trx-dependent redox shifts of several chloroplast thiol-modulated enzymes in vitro and in vivo. In vitro assays using a series of Arabidopsis recombinant proteins provided new insights into Trx selectivity for the redox regulation as well as the underpinning for previous suggestions. Most notably, by combining the discrimination of thiol status with mass spectrometry and activity measurement, we identified an uncharacterized aspect of the reductive activation of NADP-malate dehydrogenase; two redox-active Cys pairs harbored in this enzyme were reduced via distinct utilization of Trxs even within a single polypeptide. In our in vitro assays, Trx-f was effective in reducing all thiol-modulated enzymes analyzed here. We then investigated the in vivo physiological relevance of these in vitro findings, using Arabidopsis wild-type and Trx-f-deficient plants. Photoreduction of fructose-1,6-bisphosphatase was partially impaired in Trx-f-deficient plants, but the global impact of Trx-f deficiency on the redox behaviors of thiol-modulated enzymes was not as striking as expected from the in vitro data. Our results provide support for the in vivo functionality of the Trx system and also highlight the complexity and plasticity of the chloroplast redox network. PMID:25878252

  4. Defects in tor regulatory complexes retard aging and carbonyl/oxidative stress development in yeast Sассharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    B. V. Homza

    2014-02-01

    Full Text Available TOR signaling pathway first described in yeast S. сerevisiae is the highly conserved regulator of eukaryotic cell growth, aging and stress resistance. The effect of nitrogen sources, in particular amino acids, on the activity of TOR signaling pathway is well studied, however its relation to carbohydrates is poor understood. The aim of the present study is expanding of our understanding of potential role of TOR regulatory complexes in development of carbonyl/oxidative stress that can result from yeast cultivation on glucose and fructose. It has been shown that the level of α-dicarbonyl compounds and protein carbonyl groups increased with time of yeast cultivation and was higher in cells grown on fructose that demonstrated their accelerated aging and carbonyl/oxidative stress development as compared with cells grown on glucose. The strains defective in TOR proteins cultivated in the presence of glucose as well as fructose demonstrated lower markers of the stress and aging than parental strain. Thus these data confirmed the previous conclusion on fructose more potent ability to cause carbonyl/oxidative stress and accelerated aging in S. cerevisiae as compared with glucose. However, defects in TOR regulatory complexes retard aging and development of the stress in yeast independent on the type of carbohydrate in the cultivation medium.

  5. Levels of Crotonaldehyde and 4-hydroxy-(E-2-nonenal and Expression of Genes Encoding Carbonyl-Scavenging Enzyme at Critical Node During Rice Seed Aging

    Directory of Open Access Journals (Sweden)

    Fu Shenzao

    2018-05-01

    Full Text Available Abstract:: The critical node (CN is an important stage during seed aging, which is related to effective genebank conservation. Previous studies have demonstrated that proteins undergo carbonylated modification at the CN in rice, indicating oxidative damage. However, the levels of reactive carbonyl species (RCS and the associated scavenging system at the CN are largely unknown. In this study, we optimized methods for the extraction and analysis of RCS from dry rice embryos. In order to acquire seeds at the CN, rice seeds were subjected to natural conditions for 7, 9, 11 and 13 months, and the seed germination rates were reduced to 90%, 82%, 71% and 57%, respectively. We chose the stage with seed germination rate of 82% as the CN according to the rice seed vigor loss curve. The levels of crotonaldehyde and 4-hydroxy-(E-2-nonenal (HNE were significantly increased at the CN. In addition, genes encoding carbonyl-scavenging enzyme, including OsALDHs and OsAKRs, were significantly down-regulated at the CN, and reductions in the expression of OsALDH2-2, OsALDH2-5, OsALDH3-4, OsALDH7, OsAKR1 and OsAKR2 in particular could be responsible for RCS accumulation. Thus, the accumulations of crotonaldehyde and HNE and down-regulation of genes encoding carbonyl-scavenging enzyme might be related to an accelerating loss of seed viability at the CN. Key words: carbonyl-scavenging system, reactive carbonyl species, seed aging, crotonaldehyde, critical node, rice storage

  6. DNABP: Identification of DNA-Binding Proteins Based on Feature Selection Using a Random Forest and Predicting Binding Residues.

    Science.gov (United States)

    Ma, Xin; Guo, Jing; Sun, Xiao

    2016-01-01

    DNA-binding proteins are fundamentally important in cellular processes. Several computational-based methods have been developed to improve the prediction of DNA-binding proteins in previous years. However, insufficient work has been done on the prediction of DNA-binding proteins from protein sequence information. In this paper, a novel predictor, DNABP (DNA-binding proteins), was designed to predict DNA-binding proteins using the random forest (RF) classifier with a hybrid feature. The hybrid feature contains two types of novel sequence features, which reflect information about the conservation of physicochemical properties of the amino acids, and the binding propensity of DNA-binding residues and non-binding propensities of non-binding residues. The comparisons with each feature demonstrated that these two novel features contributed most to the improvement in predictive ability. Furthermore, to improve the prediction performance of the DNABP model, feature selection using the minimum redundancy maximum relevance (mRMR) method combined with incremental feature selection (IFS) was carried out during the model construction. The results showed that the DNABP model could achieve 86.90% accuracy, 83.76% sensitivity, 90.03% specificity and a Matthews correlation coefficient of 0.727. High prediction accuracy and performance comparisons with previous research suggested that DNABP could be a useful approach to identify DNA-binding proteins from sequence information. The DNABP web server system is freely available at http://www.cbi.seu.edu.cn/DNABP/.

  7. Intracellular delivery of cell-penetrating peptide-transcriptional factor fusion protein and its role in selective osteogenesis

    Directory of Open Access Journals (Sweden)

    Suh JS

    2014-03-01

    alginate gel for the purpose of localization and controlled release. The LMWP-TAZ fusion protein-loaded alginate gel matrix significantly increased bone formation in rabbit calvarial defects compared with alginate gel matrix mixed with free TAZ protein. The protein transduction of TAZ fused with cell-penetrating LMWP peptide was able selectively to stimulate osteogenesis in vitro and in vivo. Taken together, this fusion protein-transduction technology for osteogenic protein can thus be applied in combination with biomaterials for tissue regeneration and controlled release for tissue-engineering purposes. Keywords: protein transduction, low-molecular-weight protamine (LMWP, transcriptional coactivator with PDZ-binding motif (TAZ, selective osteogenesis, bone-tissue engineering

  8. Carbonyl compounds in gas and particle phases of mainstream cigarette smoke

    Energy Technology Data Exchange (ETDEWEB)

    Pang, Xiaobing, E-mail: pangxbyuanj@gmail.com [Department of Chemistry, University of York, Heslington, York, YO10 5DD (United Kingdom); Lewis, Alastair C., E-mail: ally.lewis@york.ac.uk [National Centre for Atmospheric Science, University of York, Heslington, York, YO10 5DD (United Kingdom)

    2011-11-01

    Carbonyl compounds (carbonyls) are important constituents of cigarette smoke and some are toxic and may be carcinogenic or mutagenic to humans. In this study carbonyl emissions in the gas and particle phases of mainstream cigarette smoke were assessed by GC-MS with pentafluorophenyl hydrazine (PFPH) derivatization. Seven brands of cigarettes and one brand of cigar common in the UK market and having differing nicotine, tar and carbon monoxide yields were investigated. Sixteen carbonyl components were identified in gaseous emissions and twenty in the particle phase. In the gaseous emissions, acetaldehyde presented as the predominant species, followed by formaldehyde, 2-propenal, and pentanal. In the particulate emissions, 1-hydroxy-2-propanone was the most abundant followed by formaldehyde, benzaldehyde, and 2,5-dimethylbenzaldehyde. Significant differences were found in carbonyl emissions among the brands of cigarettes. The gaseous carbonyl emissions varied in the range of 216-405 {mu}g cigarette{sup -1} ({mu}g cig{sup -1}) and the particulate carbonyl emissions varied in the range of 23-127 {mu}g cig{sup -1}. Positive correlations were found between the total emission of carbonyls, tar yield and carbon monoxide yield. Similar gas/particle (G/P) partitioning ratios of carbonyls were found among all cigarettes, which implies that G/P partitions of carbonyls in smoke mainly depend on the physical properties of the carbonyls. The gaseous carbonyl emissions were enhanced by 40% to 130% when some of the water, accounting for 8-12% of cigarettes in mass, was removed from the tobacco. Non-filtered cigarettes showed significantly higher carbonyl emissions compared to their filtered equivalents. Carbonyl particulate accounted for 11-19% by mass of total particulate matter from tobacco smoke. The cigar generated 806 {mu}g cig{sup -1} gaseous and 141 {mu}g cig{sup -1} particulate carbonyls, which is 2-4 times greater than the cigarettes. - Highlights: {yields} Carbonyl

  9. Carbonyl compounds in gas and particle phases of mainstream cigarette smoke

    International Nuclear Information System (INIS)

    Pang, Xiaobing; Lewis, Alastair C.

    2011-01-01

    Carbonyl compounds (carbonyls) are important constituents of cigarette smoke and some are toxic and may be carcinogenic or mutagenic to humans. In this study carbonyl emissions in the gas and particle phases of mainstream cigarette smoke were assessed by GC-MS with pentafluorophenyl hydrazine (PFPH) derivatization. Seven brands of cigarettes and one brand of cigar common in the UK market and having differing nicotine, tar and carbon monoxide yields were investigated. Sixteen carbonyl components were identified in gaseous emissions and twenty in the particle phase. In the gaseous emissions, acetaldehyde presented as the predominant species, followed by formaldehyde, 2-propenal, and pentanal. In the particulate emissions, 1-hydroxy-2-propanone was the most abundant followed by formaldehyde, benzaldehyde, and 2,5-dimethylbenzaldehyde. Significant differences were found in carbonyl emissions among the brands of cigarettes. The gaseous carbonyl emissions varied in the range of 216-405 μg cigarette -1 (μg cig -1 ) and the particulate carbonyl emissions varied in the range of 23-127 μg cig -1 . Positive correlations were found between the total emission of carbonyls, tar yield and carbon monoxide yield. Similar gas/particle (G/P) partitioning ratios of carbonyls were found among all cigarettes, which implies that G/P partitions of carbonyls in smoke mainly depend on the physical properties of the carbonyls. The gaseous carbonyl emissions were enhanced by 40% to 130% when some of the water, accounting for 8-12% of cigarettes in mass, was removed from the tobacco. Non-filtered cigarettes showed significantly higher carbonyl emissions compared to their filtered equivalents. Carbonyl particulate accounted for 11-19% by mass of total particulate matter from tobacco smoke. The cigar generated 806 μg cig -1 gaseous and 141 μg cig -1 particulate carbonyls, which is 2-4 times greater than the cigarettes. - Highlights: → Carbonyl emission factors in both gas (16 species) and

  10. Ambient levels of carbonyl compounds and their sources in Guangzhou, China

    Science.gov (United States)

    Feng, Yanli; Wen, Sheng; Chen, Yingjun; Wang, Xinming; Lü, Huixiong; Bi, Xinhui; Sheng, Guoying; Fu, Jiamo

    Ambient levels of carbonyl compounds and their possible sources, vehicular exhaust and cooking exhaust, were studied at seven places in Guangzhou, including five districts (a residential area, an industrial area, a botanical garden, a downtown area and a semi-rural area), a bus station and a restaurant during the period of June-September 2003. Nineteen carbonyl compounds were identified in the ambient air, of which acetone was the most abundant carbonyl, followed by formaldehyde and acetaldehyde. Only little changes were found in carbonyl concentration levels in the five different districts because of their dispersion and mixture in the atmosphere in summer. The lower correlations between the carbonyls' concentrations might result from the mixture of carbonyls derived from different sources, including strong photochemical reactions at noon in summer. Formaldehyde and acetaldehyde were the main carbonyls in bus station, while straight-chain carbonyls were comparatively abundant in cooking exhaust. Besides vehicular exhaust, cooking might be another major source of carbonyl compounds in Guangzhou City, especially for high molecular weight carbonyls.

  11. Determination of Carbonyl Functional Groups in Bio-oils by Potentiometric Titration: The Faix Method.

    Science.gov (United States)

    Black, Stuart; Ferrell, Jack R

    2017-02-07

    Carbonyl compounds present in bio-oils are known to be responsible for bio-oil property changes upon storage and during upgrading. Specifically, carbonyls cause an increase in viscosity (often referred to as 'aging') during storage of bio-oils. As such, carbonyl content has previously been used as a method of tracking bio-oil aging and condensation reactions with less variability than viscosity measurements. Additionally, carbonyls are also responsible for coke formation in bio-oil upgrading processes. Given the importance of carbonyls in bio-oils, accurate analytical methods for their quantification are very important for the bio-oil community. Potentiometric titration methods based on carbonyl oximation have long been used for the determination of carbonyl content in pyrolysis bio-oils. Here, we present a modification of the traditional carbonyl oximation procedures that results in less reaction time, smaller sample size, higher precision, and more accurate carbonyl determinations. While traditional carbonyl oximation methods occur at room temperature, the Faix method presented here occurs at an elevated temperature of 80 °C.

  12. Reactive carbonyl compounds impair wound healing by vimentin collapse and loss of the primary cilium.

    Science.gov (United States)

    Rodríguez-Ribera, Lara; Slattery, Craig; Mc Morrow, Tara; Marcos, Ricard; Pastor, Susana

    2017-10-01

    In renal pathologies tubulo-interstitial fibrosis results from an aberrant wound-healing ability where the normal epithelial tissue is substituted for scar tissue caused by accumulation of extracellular matrix proteins (ECM). During the wound-healing process, epithelial cells may undergo epithelial-mesenchymal transition (EMT) acquiring a mesenchymal-like phenotype that allows cells to migrate and re-epithelialize the wound site. It has been reported that chronic inflammation and uremic milieu are involved in wound-healing and enhanced kidney damage in chronic kidney disease (CKD) patients. In this study we evaluated reactive carbonyl compounds (RCC) effects on renal wound healing. The compounds resulting from carbonyl stress evaluated in this study were glyoxal (GO), methylglyoxal (MGO), malondialdehyde (MDA) and 4-hydroxy-hexenal (HHE). Wound repair ability was evaluated by the wound healing assay using HK-2 cells. EMT was evaluated by morphological, protein and transcriptional changes using microscopy, western blot, zymography and RT-qPCR. Changes in the vimentin network and primary cilia were assessed by immunofluorescence. Our data demonstrated that MDA and GO delay wound closure mediated by vimentin disruption, which caused collagen I mRNA decrease, and deciliation. In contrast, HHE treatment (and MGO to a minor degree) induced morphological changes and increased mesenchymal marker expression and gelatinase activity in HK-2 cells. In this study, we have demonstrated for the first time that exposure to RCC differentially affects wound healing in proximal tubular epithelia. A better comprehension of effects of uremic toxins on wound healing and fibrosis and migration is necessary to seek mechanisms to slow down renal fibrosis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Protein Tyrosine Nitration : Selectivity, Physicochemical and Biological Consequences, Denitration, and Proteomics Methods for the Identification of Tyrosine-Nitrated Proteins

    NARCIS (Netherlands)

    Abello, Nicolas; Kerstjens, Huib A. M.; Postma, Dirkje S.; Bischoff, Rainer

    Protein tyrosine nitration (PTN) is a post-translational modification occurring under the action of a nitrating agent. Tyrosine is modified in the 3-position of the phenolic ring through the addition of a nitro group (NO(2)). In the present article, we review the main nitration reactions and

  14. Selective protein adduct formation of diclofenac glucuronide is critically dependent on the rat canalicular conjugate export pump (Mrp2)

    NARCIS (Netherlands)

    Seitz, S.; Kretz-Rommel, A.; Oude Elferink, R. P.; Boelsterli, U. A.

    1998-01-01

    Previous work demonstrates that the reactive acyl glucuronide of the nonsteroidal antiinflammatory drug diclofenac forms selective protein adducts in the liver, which may play a causal role in the pathogenesis of diclofenac-associated liver toxicity. Because glucuronide conjugates can be exported

  15. Evolution of species-specific major seminal fluid proteins in placental mammals by gene death and positive selection

    NARCIS (Netherlands)

    Meslin, C.; Laurin, M.; Callebaut, I.; Druart, X.; Monget, P.

    2015-01-01

    The seminal fluid is a complex substance composed of a variety of secreted proteins and has been shown to play an important role in the fertilisation process in mammals and also in Drosophila. Several genes under positive selection have been documented in some rodents and primates. Our study

  16. Selective Incorporation of Nitrile-Based Infrared Probes into Proteins via Cysteine Alkylation

    Science.gov (United States)

    Jo, Hyunil; Culik, Robert M.; Korendovych, Ivan V.; DeGrado, William F.; Gai, Feng

    2010-01-01

    The nitrile stretching vibration is increasingly used as a sensitive infrared probe of local protein environments. However, site-specific incorporation of a nitrile moiety into proteins is difficult. Here we show that various aromatic nitriles can be easily incorporated into peptides and proteins via either thiol alkylation or arylation reaction. PMID:21077670

  17. Selective Incorporation of Nitrile-Based Infrared Probes into Proteins via Cysteine Alkylation

    OpenAIRE

    Jo, Hyunil; Culik, Robert M.; Korendovych, Ivan V.; DeGrado, William F.; Gai, Feng

    2010-01-01

    The nitrile stretching vibration is increasingly used as a sensitive infrared probe of local protein environments. However, site-specific incorporation of a nitrile moiety into proteins is difficult. Here we show that various aromatic nitriles can be easily incorporated into peptides and proteins via either thiol alkylation or arylation reaction.

  18. Regulation and Selectivity of Exchange Factors for G-proteins of the Ras-family

    NARCIS (Netherlands)

    Popovic, M.

    2013-01-01

    Small G-proteins are important regulators of the cellular signaling pathways. Among them, members of the Ras family of small G-proteins regulate processes such as cell differentiation, growth, migration, transport and adhesion, and their deregulation may lead to various diseases. Small G-proteins

  19. Peptidomics of Peptic Digest of Selected Potato Tuber Proteins: Post-Translational Modifications and Limited Cleavage Specificity.

    Science.gov (United States)

    C K Rajendran, Subin R; Mason, Beth; Udenigwe, Chibuike C

    2016-03-23

    Bioinformatic tools are useful in predicting bioactive peptides from food proteins. This study was focused on using bioinformatics and peptidomics to evaluate the specificity of peptide release and post-translational modifications (PTMs) in a peptic digest of potato protein isolate. Peptides in the protein hydrolysate were identified by LC-MS/MS and subsequently aligned to their parent potato tuber proteins. Five major proteins were selected for further analysis, namely, lipoxygenase, α-1,4-glucan phosphorylase, annexin, patatin, and polyubiquitin, based on protein coverage, abundance, confidence levels, and function. Comparison of the in silico peptide profile generated with ExPASy PeptideCutter and experimental peptidomics data revealed several differences. The experimental peptic cleavage sites were found to vary in number and specificity from PeptideCutter predictions. Average peptide chain length was also found to be higher than predicted with hexapeptides as the smallest detected peptides. Moreover, PTMs, particularly Met oxidation and Glu/Asp deamidation, were observed in some peptides, and these were unaccounted for during in silico analysis. PTMs can be formed during aging of potato tubers, or as a result of processing conditions during protein isolation and hydrolysis. The findings provide insights on the limitations of current bioinformatics tools for predicting bioactive peptide release from proteins, and on the existence of structural modifications that can alter the peptide bioactivity and functionality.

  20. Cardiac protein expression patterns are associated with distinct inborn exercise capacity in non-selectively bred rats

    Directory of Open Access Journals (Sweden)

    L.P. Ribeiro

    2018-01-01

    Full Text Available In the present study, we successfully demonstrated for the first time the existence of cardiac proteomic differences between non-selectively bred rats with distinct intrinsic exercise capacities. A proteomic approach based on two-dimensional gel electrophoresis coupled to mass spectrometry was used to study the left ventricle (LV tissue proteome of rats with distinct intrinsic exercise capacity. Low running performance (LRP and high running performance (HRP rats were categorized by a treadmill exercise test, according to distance run to exhaustion. The running capacity of HRPs was 3.5-fold greater than LRPs. Protein profiling revealed 29 differences between HRP and LRP rats (15 proteins were identified. We detected alterations in components involved in metabolism, antioxidant and stress response, microfibrillar and cytoskeletal proteins. Contractile proteins were upregulated in the LVs of HRP rats (α-myosin heavy chain-6, myosin light chain-1 and creatine kinase, whereas the LVs of LRP rats exhibited upregulation in proteins associated with stress response (aldehyde dehydrogenase 2, α-crystallin B chain and HSPβ-2. In addition, the cytoskeletal proteins desmin and α-actin were upregulated in LRPs. Taken together, our results suggest that the increased contractile protein levels in HRP rats partly accounted for their improved exercise capacity, and that proteins considered risk factors to the development of cardiovascular disease were expressed in higher amounts in LRP animals.

  1. Proteotoxic stress induces phosphorylation of p62/SQSTM1 by ULK1 to regulate selective autophagic clearance of protein aggregates.

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    Junghyun Lim

    Full Text Available Disruption of proteostasis, or protein homeostasis, is often associated with aberrant accumulation of misfolded proteins or protein aggregates. Autophagy offers protection to cells by removing toxic protein aggregates and injured organelles in response to proteotoxic stress. However, the exact mechanism whereby autophagy recognizes and degrades misfolded or aggregated proteins has yet to be elucidated. Mounting evidence demonstrates the selectivity of autophagy, which is mediated through autophagy receptor proteins (e.g. p62/SQSTM1 linking autophagy cargos and autophagosomes. Here we report that proteotoxic stress imposed by the proteasome inhibition or expression of polyglutamine expanded huntingtin (polyQ-Htt induces p62 phosphorylation at its ubiquitin-association (UBA domain that regulates its binding to ubiquitinated proteins. We find that autophagy-related kinase ULK1 phosphorylates p62 at a novel phosphorylation site S409 in UBA domain. Interestingly, phosphorylation of p62 by ULK1 does not occur upon nutrient starvation, in spite of its role in canonical autophagy signaling. ULK1 also phosphorylates S405, while S409 phosphorylation critically regulates S405 phosphorylation. We find that S409 phosphorylation destabilizes the UBA dimer interface, and increases binding affinity of p62 to ubiquitin. Furthermore, lack of S409 phosphorylation causes accumulation of p62, aberrant localization of autophagy proteins and inhibition of the clearance of ubiquitinated proteins or polyQ-Htt. Therefore, our data provide mechanistic insights into the regulation of selective autophagy by ULK1 and p62 upon proteotoxic stress. Our study suggests a potential novel drug target in developing autophagy-based therapeutics for the treatment of proteinopathies including Huntington's disease.

  2. Structural optimization and structure-functional selectivity relationship studies of G protein-biased EP2 receptor agonists.

    Science.gov (United States)

    Ogawa, Seiji; Watanabe, Toshihide; Moriyuki, Kazumi; Goto, Yoshikazu; Yamane, Shinsaku; Watanabe, Akio; Tsuboi, Kazuma; Kinoshita, Atsushi; Okada, Takuya; Takeda, Hiroyuki; Tani, Kousuke; Maruyama, Toru

    2016-05-15

    The modification of the novel G protein-biased EP2 agonist 1 has been investigated to improve its G protein activity and develop a better understanding of its structure-functional selectivity relationship (SFSR). The optimization of the substituents on the phenyl ring of 1, followed by the inversion of the hydroxyl group on the cyclopentane moiety led to compound 9, which showed a 100-fold increase in its G protein activity compared with 1 without any increase in β-arrestin recruitment. Furthermore, SFSR studies revealed that the combination of meta and para substituents on the phenyl moiety was crucial to the functional selectivity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Evidence of positive selection at codon sites localized in extracellular domains of mammalian CC motif chemokine receptor proteins

    Directory of Open Access Journals (Sweden)

    Metzger Kelsey J

    2010-05-01

    Full Text Available Abstract Background CC chemokine receptor proteins (CCR1 through CCR10 are seven-transmembrane G-protein coupled receptors whose signaling pathways are known for their important roles coordinating immune system responses through targeted trafficking of white blood cells. In addition, some of these receptors have been identified as fusion proteins for viral pathogens: for example, HIV-1 strains utilize CCR5, CCR2 and CCR3 proteins to obtain cellular entry in humans. The extracellular domains of these receptor proteins are involved in ligand-binding specificity as well as pathogen recognition interactions. In mammals, the majority of chemokine receptor genes are clustered together; in humans, seven of the ten genes are clustered in the 3p21-24 chromosome region. Gene conversion events, or exchange of DNA sequence between genes, have been reported in chemokine receptor paralogs in various mammalian lineages, especially between the cytogenetically closely located pairs CCR2/5 and CCR1/3. Datasets of mammalian orthologs for each gene were analyzed separately to minimize the potential confounding impact of analyzing highly similar sequences resulting from gene conversion events. Molecular evolution approaches and the software package Phylogenetic Analyses by Maximum Likelihood (PAML were utilized to investigate the signature of selection that has acted on the mammalian CC chemokine receptor (CCR gene family. The results of neutral vs. adaptive evolution (positive selection hypothesis testing using Site Models are reported. In general, positive selection is defined by a ratio of nonsynonymous/synonymous nucleotide changes (dN/dS, or ω >1. Results Of the ten mammalian CC motif chemokine receptor sequence datasets analyzed, only CCR2 and CCR3 contain amino acid codon sites that exhibit evidence of positive selection using site based hypothesis testing in PAML. Nineteen of the twenty codon sites putatively indentified as likely to be under positive

  4. A Venom Gland Extracellular Chitin-Binding-Like Protein from Pupal Endoparasitoid Wasps, Pteromalus Puparum, Selectively Binds Chitin

    Directory of Open Access Journals (Sweden)

    Yu Zhu

    2015-11-01

    Full Text Available Chitin-binding proteins (CBPs are present in many species and they act in a variety of biological processes. We analyzed a Pteromalus puparum venom apparatus proteome and transcriptome and identified a partial gene encoding a possible CBP. Here, we report cloning a full-length cDNA of a sequence encoding a chitin-binding-like protein (PpCBP from P. puparum, a pupal endoparasitoid of Pieris rapae. The cDNA encoded a 96-amino-acid protein, including a secretory signal peptide and a chitin-binding peritrophin-A domain. Phylogenetic analysis of chitin binding domains (CBDs of cuticle proteins and peritrophic matrix proteins in selected insects revealed that the CBD of PpCBP clustered with the CBD of Nasonia vitripennis. The PpCBP is specifically expressed in the venom apparatus of P. puparum, mostly in the venom gland. PpCBP expression was highest at day one after adult eclosion and much lower for the following five days. We produced a recombinant PpCBP and binding assays showed the recombinant protein selectively binds chitin but not cellulose in vitro. We infer that PpCBP serves a structural role in the venom reservoir, or may be injected into the host to help wound healing of the host exoskeleton.

  5. Effect of Gamma Radiation and Electron Beam on Microbiological Quality and Protein Patterns of 4 Selected Beans

    International Nuclear Information System (INIS)

    Chookaew, S.; Eamsir, J.; Pewlong, W.; Sajjabut, S.

    2014-01-01

    The aim of the present study was to evaluate the effect of gamma ray and electron beam on microbiological quality and protein pattern of four selected beans: mung beans, soy beans, peanuts and black beans. All beans samples were exposed to irradiation at doses of 0, 0.5, 1, and 2 kGy before evaluated for their microbiological quality using AOAC method and protein analysis by gel electrophoresis. Results showed that the amount of bacteria, yeast and mold of irradiated mung beans and peanuts were reduced, whereas these microbiological quality values remained relatively the same for irradiated soy beans and black beans compared to non-irradiated samples. In terms of protein analysis, the protein patterns of the irradiated beans were of the same quality as the non-irradiated samples. To further tested the effect of irradiation on the bean's protein at higher doses, all four selected beans were exposed to gamma ray at 10, 50, 100, 150 and 200 kGy. We found that the protein patterns of mung beans, peanuts and black beans were altered at doses above 50 kGy.

  6. Pharmacological targeting of valosin containing protein (VCP) induces DNA damage and selectively kills canine lymphoma cells

    International Nuclear Information System (INIS)

    Nadeau, Marie-Ève; Rico, Charlène; Tsoi, Mayra; Vivancos, Mélanie; Filimon, Sabin; Paquet, Marilène; Boerboom, Derek

    2015-01-01

    Valosin containing protein (VCP) is a critical mediator of protein homeostasis and may represent a valuable therapeutic target for several forms of cancer. Overexpression of VCP occurs in many cancers, and often in a manner correlating with malignancy and poor outcome. Here, we analyzed VCP expression in canine lymphoma and assessed its potential as a therapeutic target for this disease. VCP expression in canine lymphomas was evaluated by immunoblotting and immunohistochemistry. The canine lymphoma cell lines CLBL-1, 17–71 and CL-1 were treated with the VCP inhibitor Eeyarestatin 1 (EER-1) at varying concentrations and times and were assessed for viability by trypan blue exclusion, apoptosis by TUNEL and caspase activity assays, and proliferation by propidium iodide incorporation and FACS. The mechanism of EER-1 action was determined by immunoblotting and immunofluorescence analyses of Lys48 ubiquitin and markers of ER stress (DDIT3), autophagy (SQSTM1, MAP1LC3A) and DNA damage (γH2AFX). TRP53/ATM-dependent signaling pathway activity was assessed by immunoblotting for TRP53 and phospho-TRP53 and real-time RT-PCR measurement of Cdkn1a mRNA. VCP expression levels in canine B cell lymphomas were found to increase with grade. EER-1 treatment killed canine lymphoma cells preferentially over control peripheral blood mononuclear cells. EER-1 treatment of CLBL-1 cells was found to both induce apoptosis and cell cycle arrest in G1. Unexpectedly, EER-1 did not appear to act either by inducing ER stress or inhibiting the aggresome-autophagy pathway. Rather, a rapid and dramatic increase in γH2AFX expression was noted, indicating that EER-1 may act by promoting DNA damage accumulation. Increased TRP53 phosphorylation and Cdkn1a mRNA levels indicated an activation of the TRP53/ATM DNA damage response pathway in response to EER-1, likely contributing to the induction of apoptosis and cell cycle arrest. These results correlate VCP expression with malignancy in canine B cell

  7. Dynamic Proteomics Emphasizes the Importance of Selective mRNA Translation and Protein Turnover during Arabidopsis Seed Germination*

    Science.gov (United States)

    Galland, Marc; Huguet, Romain; Arc, Erwann; Cueff, Gwendal; Job, Dominique; Rajjou, Loïc

    2014-01-01

    During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [35S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment. PMID:24198433

  8. Affinity selection-mass spectrometry and its emerging application to the high throughput screening of G protein-coupled receptors.

    Science.gov (United States)

    Whitehurst, Charles E; Annis, D Allen

    2008-07-01

    Advances in combinatorial chemistry and genomics have inspired the development of novel affinity selection-based screening techniques that rely on mass spectrometry to identify compounds that preferentially bind to a protein target. Of the many affinity selection-mass spectrometry techniques so far documented, only a few solution-based implementations that separate target-ligand complexes away from unbound ligands persist today as routine high throughput screening platforms. Because affinity selection-mass spectrometry techniques do not rely on radioactive or fluorescent reporters or enzyme activities, they can complement traditional biochemical and cell-based screening assays and enable scientists to screen targets that may not be easily amenable to other methods. In addition, by employing mass spectrometry for ligand detection, these techniques enable high throughput screening of massive library collections of pooled compound mixtures, vastly increasing the chemical space that a target can encounter during screening. Of all drug targets, G protein coupled receptors yield the highest percentage of therapeutically effective drugs. In this manuscript, we present the emerging application of affinity selection-mass spectrometry to the high throughput screening of G protein coupled receptors. We also review how affinity selection-mass spectrometry can be used as an analytical tool to guide receptor purification, and further used after screening to characterize target-ligand binding interactions, enabling the classification of orthosteric and allosteric binders.

  9. Structure of the Regulator of G Protein Signaling 8 (RGS8)-Gαq Complex: MOLECULAR BASIS FOR Gα SELECTIVITY.

    Science.gov (United States)

    Taylor, Veronica G; Bommarito, Paige A; Tesmer, John J G

    2016-03-04

    Regulator of G protein signaling (RGS) proteins interact with activated Gα subunits via their RGS domains and accelerate the hydrolysis of GTP. Although the R4 subfamily of RGS proteins generally accepts both Gαi/o and Gαq/11 subunits as substrates, the R7 and R12 subfamilies select against Gαq/11. In contrast, only one RGS protein, RGS2, is known to be selective for Gαq/11. The molecular basis for this selectivity is not clear. Previously, the crystal structure of RGS2 in complex with Gαq revealed a non-canonical interaction that could be due to interfacial differences imposed by RGS2, the Gα subunit, or both. To resolve this ambiguity, the 2.6 Å crystal structure of RGS8, an R4 subfamily member, was determined in complex with Gαq. RGS8 adopts the same pose on Gαq as it does when bound to Gαi3, indicating that the non-canonical interaction of RGS2 with Gαq is due to unique features of RGS2. Based on the RGS8-Gαq structure, residues in RGS8 that contact a unique α-helical domain loop of Gαq were converted to those typically found in R12 subfamily members, and the reverse substitutions were introduced into RGS10, an R12 subfamily member. Although these substitutions perturbed their ability to stimulate GTP hydrolysis, they did not reverse selectivity. Instead, selectivity for Gαq seems more likely determined by whether strong contacts can be maintained between α6 of the RGS domain and Switch III of Gαq, regions of high sequence and conformational diversity in both protein families. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. An α-Helix-Mimicking 12,13-Helix: Designed α/β/γ-Foldamers as Selective Inhibitors of Protein-Protein Interactions.

    Science.gov (United States)

    Grison, Claire M; Miles, Jennifer A; Robin, Sylvie; Wilson, Andrew J; Aitken, David J

    2016-09-05

    A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein-protein interactions (PPIs). In this work, trans-2-aminocyclobutanecarboxylic acid (tACBC) was used as the key β-amino acid component in the design of α/β/γ-peptides to structurally mimic a native α-helix. Suitably functionalized α/β/γ-peptides assume an α-helix-mimicking 12,13-helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild-type α-peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  11. Plant-derived phenolics inhibit the accrual of structurally characterised protein and lipid oxidative modifications.

    Directory of Open Access Journals (Sweden)

    Arantza Soler-Cantero

    Full Text Available Epidemiological data suggest that plant-derived phenolics beneficial effects include an inhibition of LDL oxidation. After applying a screening method based on 2,4-dinitrophenyl hydrazine-protein carbonyl reaction to 21 different plant-derived phenolic acids, we selected the most antioxidant ones. Their effect was assessed in 5 different oxidation systems, as well as in other model proteins. Mass-spectrometry was then used, evidencing a heterogeneous effect on the accumulation of the structurally characterized protein carbonyl glutamic and aminoadipic semialdehydes as well as for malondialdehyde-lysine in LDL apoprotein. After TOF based lipidomics, we identified the most abundant differential lipids in Cu(++-incubated LDL as 1-palmitoyllysophosphatidylcholine and 1-stearoyl-sn-glycero-3-phosphocholine. Most of selected phenolic compounds prevented the accumulation of those phospholipids and the cellular impairment induced by oxidized LDL. Finally, to validate these effects in vivo, we evaluated the effect of the intake of a phenolic-enriched extract in plasma protein and lipid modifications in a well-established model of atherosclerosis (diet-induced hypercholesterolemia in hamsters. This showed that a dietary supplement with a phenolic-enriched extract diminished plasma protein oxidative and lipid damage. Globally, these data show structural basis of antioxidant properties of plant-derived phenolic acids in protein oxidation that may be relevant for the health-promoting effects of its dietary intake.

  12. Carbonyl Compounds Produced by Vaporizing Cannabis Oil Thinning Agents.

    Science.gov (United States)

    Troutt, William D; DiDonato, Matthew D

    2017-11-01

    Cannabis use has increased in the United States, particularly the use of vaporized cannabis oil, which is often mixed with thinning agents for use in vaporizing devices. E-cigarette research shows that heated thinning agents produce potentially harmful carbonyls; however, similar studies have not been conducted (1) with agents that are commonly used in the cannabis industry and (2) at temperatures that are appropriate for cannabis oil vaporization. The goal of this study was to determine whether thinning agents used in the cannabis industry produce potentially harmful carbonyls when heated to a temperature that is appropriate for cannabis oil vaporization. Four thinning agents (propylene glycol [PG], vegetable glycerin [VG], polyethylene glycol 400 [PEG 400], and medium chain triglycerides [MCT]) were heated to 230°C and the resulting vapors were tested for acetaldehyde, acrolein, and formaldehyde. Each agent was tested three times. Testing was conducted in a smoking laboratory. Carbonyl levels were measured in micrograms per puff block. Analyses showed that PEG 400 produced significantly higher levels of acetaldehyde and formaldehyde than PG, MCT, and VG. Formaldehyde production was also significantly greater in PG compared with MCT and VG. Acrolein production did not differ significantly across the agents. PG and PEG 400 produced high levels of acetaldehyde and formaldehyde when heated to 230°C. Formaldehyde production from PEG 400 isolate was particularly high, with one inhalation accounting for 1.12% of the daily exposure limit, nearly the same exposure as smoking one cigarette. Because PG and PEG 400 are often mixed with cannabis oil, individuals who vaporize cannabis oil products may risk exposure to harmful formaldehyde levels. Although more research is needed, consumers and policy makers should consider these potential health effects before use and when drafting cannabis-related legislation.

  13. Chloroform-assisted phenol extraction improving proteome profiling of maize embryos through selective depletion of high-abundance storage proteins.

    Directory of Open Access Journals (Sweden)

    Erhui Xiong

    Full Text Available The presence of abundant storage proteins in plant embryos greatly impedes seed proteomics analysis. Vicilin (or globulin-1 is the most abundant storage protein in maize embryo. There is a need to deplete the vicilins from maize embryo extracts for enhanced proteomics analysis. We here reported a chloroform-assisted phenol extraction (CAPE method for vicilin depletion. By CAPE, maize embryo proteins were first extracted in an aqueous buffer, denatured by chloroform and then subjected to phenol extraction. We found that CAPE can effectively deplete the vicilins from maize embryo extract, allowing the detection of low-abundance proteins that were masked by vicilins in 2-DE gel. The novelty of CAPE is that it selectively depletes abundant storage proteins from embryo extracts of both monocot (maize and dicot (soybean and pea seeds, whereas other embryo proteins were not depleted. CAPE can significantly improve proteome profiling of embryos and extends the application of chloroform and phenol extraction in plant proteomics. In addition, the rationale behind CAPE depletion of abundant storage proteins was explored.

  14. Selection for Protein Kinetic Stability Connects Denaturation Temperatures to Organismal Temperatures and Provides Clues to Archaean Life.

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    M Luisa Romero-Romero

    Full Text Available The relationship between the denaturation temperatures of proteins (Tm values and the living temperatures of their host organisms (environmental temperatures: TENV values is poorly understood. Since different proteins in the same organism may show widely different Tm's, no simple universal relationship between Tm and TENV should hold, other than Tm≥TENV. Yet, when analyzing a set of homologous proteins from different hosts, Tm's are oftentimes found to correlate with TENV's but this correlation is shifted upward on the Tm axis. Supporting this trend, we recently reported Tm's for resurrected Precambrian thioredoxins that mirror a proposed environmental cooling over long geological time, while remaining a shocking ~50°C above the proposed ancestral ocean temperatures. Here, we show that natural selection for protein kinetic stability (denaturation rate can produce a Tm↔TENV correlation with a large upward shift in Tm. A model for protein stability evolution suggests a link between the Tm shift and the in vivo lifetime of a protein and, more specifically, allows us to estimate ancestral environmental temperatures from experimental denaturation rates for resurrected Precambrian thioredoxins. The TENV values thus obtained match the proposed ancestral ocean cooling, support comparatively high Archaean temperatures, and are consistent with a recent proposal for the environmental temperature (above 75°C that hosted the last universal common ancestor. More generally, this work provides a framework for understanding how features of protein stability reflect the environmental temperatures of the host organisms.

  15. Determination of carbonyl compounds in air by HPLC

    International Nuclear Information System (INIS)

    Garcia, S.; Perez, R.M.; Campos, A.; Gonzalez, D.

    1995-09-01

    A method for the determination of seven carbonyl compounds in air is presented. The procedure involve sampling of air by a Sep-Pak cartridge impregnated with 2,4-dinitrophenylhydrazine. Elution was done with 3 mL of acetonitrile and the eluate was diluted to 5 mL. The analysis was done by HPLC with UV detection and external standard method quantification. It has been achieved relative standard deviations about 5% and detection limits of 80 ng/cartridge for formaldehyde, acetaldehyde and acetone+acrolein. Three different types of samples (rural, urban, petrol emission) were successfully analyzed

  16. Determination of carbonyl compounds in air by HPLC

    International Nuclear Information System (INIS)

    Garcia, S.; Perez, R.M.; Campos, A.; Gonzalez, D.

    1995-01-01

    A method for the determination of seven carbonyl compounds in air is presented. The procedure involve sampling of air by a Sep-Pak Cartridge impregnated with 2,4-dinitrophenylhydrazine. Elution was done with 3 mL of acetonitrile and the eluate was diluted to 5 mL. The analysis was done by HPLC with UV detection and external standard method quantification. It has been achieved relative standard deviations about 5% and detection limits of 80 ng/cartridge for formaldehyde, acetaldehyde and acetoacetonitrile. Three different types of samples (rural, urban, petrol emission) were successfully analyzed. (Author) 12 refs

  17. Magnetic properties of carbonyl iron particles in magnetorheological fluids

    International Nuclear Information System (INIS)

    Gorodkin, S R; James, R O; Kordonski, W I

    2009-01-01

    Knowledge of the magnetic properties of dispersed magnetic particles is a prerequisite to the design an MR fluid with desired performance. A term specific susceptibility is introduced for characterization of particle susceptibility. The study was performed with the Bartington MS2B magnetic susceptibility system on small samples volume. Specific magnetic susceptibility of iron particles was found to be a linear function of median particle size. Structural change in the fluid, including particle organization, led to susceptibility drift and may affect fluid performance. It was shown that susceptibility data can be used for evaluation of the concentration of carbonyl iron particles in MR fluids.

  18. PredPPCrys: accurate prediction of sequence cloning, protein production, purification and crystallization propensity from protein sequences using multi-step heterogeneous feature fusion and selection.

    Directory of Open Access Journals (Sweden)

    Huilin Wang

    Full Text Available X-ray crystallography is the primary approach to solve the three-dimensional structure of a protein. However, a major bottleneck of this method is the failure of multi-step experimental procedures to yield diffraction-quality crystals, including sequence cloning, protein material production, purification, crystallization and ultimately, structural determination. Accordingly, prediction of the propensity of a protein to successfully undergo these experimental procedures based on the protein sequence may help narrow down laborious experimental efforts and facilitate target selection. A number of bioinformatics methods based on protein sequence information have been developed for this purpose. However, our knowledge on the important determinants of propensity for a protein sequence to produce high diffraction-quality crystals remains largely incomplete. In practice, most of the existing methods display poorer performance when evaluated on larger and updated datasets. To address this problem, we constructed an up-to-date dataset as the benchmark, and subsequently developed a new approach termed 'PredPPCrys' using the support vector machine (SVM. Using a comprehensive set of multifaceted sequence-derived features in combination with a novel multi-step feature selection strategy, we identified and characterized the relative importance and contribution of each feature type to the prediction performance of five individual experimental steps required for successful crystallization. The resulting optimal candidate features were used as inputs to build the first-level SVM predictor (PredPPCrys I. Next, prediction outputs of PredPPCrys I were used as the input to build second-level SVM classifiers (PredPPCrys II, which led to significantly enhanced prediction performance. Benchmarking experiments indicated that our PredPPCrys method outperforms most existing procedures on both up-to-date and previous datasets. In addition, the predicted crystallization

  19. Uniform and selective deuteration in two-dimensional NMR of proteins

    International Nuclear Information System (INIS)

    LeMaster, D.M.

    1990-01-01

    This paper reports on the practicality of isotopic labeling, particularly deuteration, that has received considerable impetus from advances in molecular biology, which have allowed ready production of NMR quantities of labeled proteins. Protein expression in Escherichia coli allows use of the considerable metabolic genetics known for the organism in shaping the biosynthetic process to meet the labeling demands of the NMR experiments. In addition to deuteration's common use in spectral assignment problems, it also offers considerable potential for enhancing the quality of the nuclear Overhauser effect (NOE) distance and dihedral angle constraints used for solution structural analysis of proteins. Recent reviews emphasize the sample preparation and spectral benefits of protein deuteration

  20. Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates.

    Directory of Open Access Journals (Sweden)

    Jia-Yu Chen

    2015-07-01

    Full Text Available While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs, the transition process remains poorly understood. Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise splicing structures and specific tissue expression profiles. Whole-genome sequencing of dozens of rhesus macaque animals revealed that these lncRNAs are generally not more selectively constrained than other lncRNA loci. The existence of these newly-originated de novo proteins is also not beyond anticipation under neutral expectation, as they generally have longer theoretical lifespan than their current age, due to their GC-rich sequence property enabling stable ORFs with lower chance of non-sense mutations. Interestingly, although the emergence and retention of these de novo genes are likely driven by neutral forces, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution, which may contribute to human-specific genetic novelties by taking advantage of existed genomic contexts.

  1. Prediction of protein modification sites of pyrrolidone carboxylic acid using mRMR feature selection and analysis.

    Directory of Open Access Journals (Sweden)

    Lu-Lu Zheng

    Full Text Available Pyrrolidone carboxylic acid (PCA is formed during a common post-translational modification (PTM of extracellular and multi-pass membrane proteins. In this study, we developed a new predictor to predict the modification sites of PCA based on maximum relevance minimum redundancy (mRMR and incremental feature selection (IFS. We incorporated 727 features that belonged to 7 kinds of protein properties to predict the modification sites, including sequence conservation, residual disorder, amino acid factor, secondary structure and solvent accessibility, gain/loss of amino acid during evolution, propensity of amino acid to be conserved at protein-protein interface and protein surface, and deviation of side chain carbon atom number. Among these 727 features, 244 features were selected by mRMR and IFS as the optimized features for the prediction, with which the prediction model achieved a maximum of MCC of 0.7812. Feature analysis showed that all feature types contributed to the modification process. Further site-specific feature analysis showed that the features derived from PCA's surrounding sites contributed more to the determination of PCA sites than other sites. The detailed feature analysis in this paper might provide important clues for understanding the mechanism of the PCA formation and guide relevant experimental validations.

  2. Anticariogenic and Hemolytic Activity of Selected Seed Protein Extracts In vitro conditions.

    Directory of Open Access Journals (Sweden)

    Kalpesh B Ishnava

    2014-10-01

    Full Text Available This study aimed to assess the anticariogenic and hemolytic activity of crude plant seed protein extracts against tooth decaying bacteria.The proteins from seeds of 12 different plants were extracted and used for antimicrobial assay against six different organisms. The extraction was carried out in 10mM of sodium phosphate buffer (pH 7.0. Protein concentrations were determined as described by Bradford method. Anticariogenic activity was studied by agar well diffusion method and Minimum Inhibitory Concentration (MIC was evaluated by the two-fold serial broth dilution method. Hemolytic activity, treatment of proteinase K and Kinetic study in Mimusops elengi crude seed protein extract.The anticariogenic assay demonstrated the activity of Mimusops elengi against Staphylococcus aureus and Streptococcus pyogenes. A minor activity of Glycine wightii against Streptococcus mutans was also found. The protein content of Mimusops elengi seed protein extract was 5.84mg/ml. The MIC values for Staphylococcus aureus and Streptococcus pyogenes against Mimusops elengi seed protein extract were 364.36μg/ml and 182.19μg/ml, respectively. Kinetic study further elucidated the mode of inhibition in the presence of the Mimusops elengi plant seed protein with respect to time. The concentration of crude extract which gave 50% hemolysis compared to Triton X-100 treatment (HC50 value was 1.58 mg/ml; which is more than five times larger than that of the MIC. Treatment with proteinase K of the Mimusops elengi seed protein resulted in absence of the inhibition zone; which clearly indicates that the activity was only due to protein.Our results showed the prominence of Mimusops elengi plant seed protein extract as an effective herbal medication against tooth decaying bacteria.

  3. Palatability of water-soluble extracts of protein sources and replacement of fishmeal by a selected mixture of protein sources for juvenile turbot ( Scophthalmus maximus)

    Science.gov (United States)

    Dong, Chun; He, Gen; Mai, Kangsen; Zhou, Huihui; Xu, Wei

    2016-06-01

    Poor palatability is a limiting factor for replacing fishmeal with other protein sources in aquaculture. The water-soluble molecules with low molecular weights are the major determinants of the palatability of diets. The present study was conducted to investigate the palatability of water-soluble extracts from single protein source (single extract pellets) and the mixture of these extracts with different proportions (blended extract pellets) in juvenile turbot ( Scophthalmus maximus). Then according to the palatability of blended extract pellets, an optimal mixture proportion was selected, and a new protein source made from raw protein materials with the selected proportion was formulated to replace fishmeal. Summarily, the palatability of single extract pellets for turbot was descendent from fishmeal to pet-food grade poultry by-product meal, wheat gluten meal, soybean meal, peanut meal, meat and bone meal, and corn gluten meal. Subsequently, according to the palatability of single extract pellets, 52 kinds of blended extract pellets were designed to test their palatability. The results showed that the pellets presented remarkably different palatability, and the optimal one was diet 52 (wheat gluten meal: pet-food grade poultry by-product meal: meat and bone meal: corn gluten meal = 1:6:1:2). The highest ingestion ratio (the number of pellets ingested/the number of pellets fed) was 0.73 ± 0.03, which was observed in Diet 52. Then five isonitrogenous (52% crude protein) and isocaloric (20 kJ g-1 gross energy) diets were formulated by replacing 0 (control), 35%, 50%, 65% and 80% of fishmeal with No.52 blending proportion. After a 10-weeks feeding trial, a consistent feed intake was found among all replacement treatments. Replacement level of fishmeal up to 35% did not significantly influence final body weight, specific growth rate, feed efficiency ratio, and protein efficiency ratio of turbot. Therefore, the water-soluble extracts of protein sources play an

  4. Use of nuclear techniques for mutation and selection of fungi for high protein yield utilizing carbon from inexpensive agricultural waste

    International Nuclear Information System (INIS)

    Georgopulos, S.

    1976-12-01

    The report briefly describes work carried out on the following subjects: Determination of protein in fungal strains (including Fusarium and Aspergillus niger); induction and selection of mutants (Aspergillus niger) giving higher yields of biomass and/or higher protein content; ability of fungi (Candida tropicalis) to utilize water extracts of carob bean pods; growth of Fusarium monoliforme at the expense of carob sugars; the use of alternate oxidase-negative mutants (of Ustilago maydis), for better utilization of substrates for growth (electron transport pathways in reoxidation of reduced coenzymes); kinetics of batch and continuous cultivation of Fusarium moniliforme (cultivated on aqueous carob extracts)

  5. Biotin-tagged proteins: Reagents for efficient ELISA-based serodiagnosis and phage display-based affinity selection.

    Science.gov (United States)

    Verma, Vaishali; Kaur, Charanpreet; Grover, Payal; Gupta, Amita; Chaudhary, Vijay K

    2018-01-01

    The high-affinity interaction between biotin and streptavidin has opened avenues for using recombinant proteins with site-specific biotinylation to achieve efficient and directional immobilization. The site-specific biotinylation of proteins carrying a 15 amino acid long Biotin Acceptor Peptide tag (BAP; also known as AviTag) is effected on a specific lysine either by co-expressing the E. coli BirA enzyme in vivo or by using purified recombinant E. coli BirA enzyme in the presence of ATP and biotin in vitro. In this paper, we have designed a T7 promoter-lac operator-based expression vector for rapid and efficient cloning, and high-level cytosolic expression of proteins carrying a C-terminal BAP tag in E. coli with TEV protease cleavable N-terminal deca-histidine tag, useful for initial purification. Furthermore, a robust three-step purification pipeline integrated with well-optimized protocols for TEV protease-based H10 tag removal, and recombinant BirA enzyme-based site-specific in vitro biotinylation is described to obtain highly pure biotinylated proteins. Most importantly, the paper demonstrates superior sensitivities in indirect ELISA with directional and efficient immobilization of biotin-tagged proteins on streptavidin-coated surfaces in comparison to passive immobilization. The use of biotin-tagged proteins through specific immobilization also allows more efficient selection of binders from a phage-displayed naïve antibody library. In addition, for both these applications, specific immobilization requires much less amount of protein as compared to passive immobilization and can be easily multiplexed. The simplified strategy described here for the production of highly pure biotin-tagged proteins will find use in numerous applications, including those, which may require immobilization of multiple proteins simultaneously on a solid surface.

  6. The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions

    NARCIS (Netherlands)

    Leliveld, S. R.; Dame, R.T.; Wuite, G.J.L.; Stitz, L.; Korth, C.

    2006-01-01

    Insertion of additional octarepeats into the prion protein gene has been genetically linked to familial Creutzfeldt Jakob disease and hence to de novo generation of infectious prions. The pivotal event during prion formation is the conversion of the normal prion protein (PrP

  7. Selective inhibition of influenza virus protein synthesis by inhibitors of DNA function

    International Nuclear Information System (INIS)

    Minor, P.D.; Dimmock, N.J.

    1977-01-01

    Various known inhibitors of cellular DNA function were shown to inhibit cellular RNA synthesis and influenza (fowl plague) virus multiplication. The drugs were investigated for their effect upon the synthesis of influenza virus proteins. According to this effect they could be classified with previously studied compounds as follows: Group I (ethidium bromide, proflavine, and N-nitroquinoline-N-oxide) inhibited both viral and cellular protein synthesis; Group II (nogalomycin, daunomycin and α-amanitin) inhibited viral but not cellular protein synthesis, and all viral proteins were inhibited coordinately; Group III (mithramycin, echinomycin, and actinomycin D) inhibited all viral but not cellular protein synthesis at high concentrations, but at a lower critical concentration inhibited the synthesis of viral haemagglutinin, neuraminidase, and M protein preferentially; Group IV(uv irradiation and camptothecin) inhibited the synthesis of viral haemagglutinin, neuraminidase, and M protein, but not other viral proteins, even at high doses. The mode of action of these inhibitors is discussed in relation to the mechanism of the nuclear events upon which influenza virus multiplication is dependent

  8. A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking

    NARCIS (Netherlands)

    Trellet, M.; Melquiond, A.S.J.; Bonvin, A.M.J.J.

    2013-01-01

    Protein-peptide interactions are vital for the cell. They mediate, inhibit or serve as structural components in nearly 40% of all macromolecular interactions, and are often associated with diseases, making them interesting leads for protein drug design. In recent years, large-scale technologies have

  9. Use of synthetic biology techniques to site-selective introduce posttranslational modifactions in proteins

    NARCIS (Netherlands)

    Bosmans, R.P.G.; Brunsveld, L.; Ryadnov, M.; Brunsveld, L.; Suga, H.

    2014-01-01

    Unravelling the influence of posttranslational modifications (PTMs) on protein functioning is of key interest to get understanding how complex cellular networks are regulated. The current biological toolbox to synthesize these modified proteins in a single form in decent quantities is insufficient,

  10. Feature Selection and the Class Imbalance Problem in Predicting Protein Function from Sequence

    NARCIS (Netherlands)

    Al-Shahib, A.; Breitling, R.; Gilbert, D.

    2005-01-01

    Abstract: When the standard approach to predict protein function by sequence homology fails, other alternative methods can be used that require only the amino acid sequence for predicting function. One such approach uses machine learning to predict protein function directly from amino acid sequence

  11. Selective labeling of pulmonary surfactant protein SP-C in organic solution

    DEFF Research Database (Denmark)

    Plasencia, I; Cruz, A; López-Lacomba, J L

    2001-01-01

    Pulmonary surfactant protein SP-C has been isolated from porcine lungs and treated with dansyl isothiocyanate in chloroform:methanol 2:1 (v/v) solutions,under conditions optimized to introduce a single dansyl group covalently attached to the N-terminalamine group of the protein without loss of its...

  12. Evaluation of activity of selected antioxidants on proteins in solution and in emulsions

    DEFF Research Database (Denmark)

    Baron, Caroline; Berner, Lis; Skibsted, L.H.

    2005-01-01

    that Trolox always provided better protection of the protein than tocopherol and the carotenoids in both the BSA and the BSA/LnMe systems. In conclusion, prevention of protein oxidation using a water-soluble antioxidant has a protective effect on the lipid fraction and this approach deserves further attention...

  13. Exploring variation in pea protein composition by natural selection and genetic transformation

    NARCIS (Netherlands)

    Tzitzikas, E.

    2005-01-01

    Pea (Pisumsativum L.) seeds are a rich and valuable source of proteins, which can have potential for food industrial applications. Pea storage proteins are classified into two major classes: the salt-soluble globulins, and the water-soluble

  14. Composition of amino acid using carbon monoxide. Amide carbonylation reaction

    Energy Technology Data Exchange (ETDEWEB)

    Izawa, Kunisuke (Ajinomoto Co., Inc., Tokyo (Japan))

    1989-02-01

    Amide carbonylation reaction is a method to compose N-acyl-{alpha}-amino acid from aldehyde, carboxylic acid amide, and carbon monoxide in a phase and with high yield. Unlike the conventional Strecker reaction, this method does not use HCN which is in question on public pollution and does not require hydrolysis. This amide carbonylation reaction was discovered by Wakamatsu and others of Ajinomoto Co.,Ltd. Present application examples of this method are the composition of N-acetyl amino acid from the aldehyde class, the composition of N-Acyl amino acid from olefin, the composition of N-acyl or acetyl amino acid from the raw material of alcohol and the halide class, the composition of N-acyl or acetyl amino acid via the isomerization of epoxide and allyl alcohol, the composition of amino dicarboxylic acid, applying deoxidation of ring acid anhydride, the composition of N-acyl amino acid from the raw material of the amine class, the stereoselective composition of -substitution ring-{alpha}-amino acid, and the composition of amino aldehyde. 24 refs., 2 figs., 2 tabs.

  15. Selective inhibition of Sarcocystis neurona calcium-dependent protein kinase 1 for equine protozoal myeloencephalitis therapy.

    Science.gov (United States)

    Ojo, Kayode K; Dangoudoubiyam, Sriveny; Verma, Shiv K; Scheele, Suzanne; DeRocher, Amy E; Yeargan, Michelle; Choi, Ryan; Smith, Tess R; Rivas, Kasey L; Hulverson, Matthew A; Barrett, Lynn K; Fan, Erkang; Maly, Dustin J; Parsons, Marilyn; Dubey, Jitender P; Howe, Daniel K; Van Voorhis, Wesley C

    2016-12-01

    Sarcocystis neurona is the most frequent cause of equine protozoal myeloencephalitis, a debilitating neurological disease of horses that can be difficult to treat. We identified SnCDPK1, the S. neurona homologue of calcium-dependent protein kinase 1 (CDPK1), a validated drug target in Toxoplasma gondii. SnCDPK1 shares the glycine "gatekeeper" residue of the well-characterized T. gondii enzyme, which allows the latter to be targeted by bumped kinase inhibitors. This study presents detailed molecular and phenotypic evidence that SnCDPK1 can be targeted for rational drug development. Recombinant SnCDPK1 was tested against four bumped kinase inhibitors shown to potently inhibit both T. gondii (Tg) CDPK1 and T. gondii tachyzoite growth. SnCDPK1 was inhibited by low nanomolar concentrations of these BKIs and S. neurona growth was inhibited at 40-120nM concentrations. Thermal shift assays confirmed these bumped kinase inhibitors bind CDPK1 in S. neurona cell lysates. Treatment with bumped kinase inhibitors before or after invasion suggests that bumped kinase inhibitors interfere with S. neurona mammalian host cell invasion in the 0.5-2.5μM range but interfere with intracellular division at 2.5μM. In vivo proof-of-concept experiments were performed in a murine model of S. neurona infection. The experimental infected groups treated for 30days with compound BKI-1553 (n=10 mice) had no signs of disease, while the infected control group had severe signs and symptoms of infection. Elevated antibody responses were found in 100% of control infected animals, but only 20% of BKI-1553 treated infected animals. Parasites were found in brain tissues of 100% of the control infected animals, but only in 10% of the BKI-1553 treated animals. The bumped kinase inhibitors used in these assays have been chemically optimized for potency, selectivity and pharmacokinetic properties, and hence are good candidates for treatment of equine protozoal myeloencephalitis. Copyright © 2016

  16. Selectable high-yield recombinant protein production in human cells using a GFP/YFP nanobody affinity support.

    Science.gov (United States)

    Schellenberg, Matthew J; Petrovich, Robert M; Malone, Christine C; Williams, R Scott

    2018-03-25

    Recombinant protein expression systems that produce high yields of pure proteins and multi-protein complexes are essential to meet the needs of biologists, biochemists, and structural biologists using X-ray crystallography and cryo-electron microscopy. An ideal expression system for recombinant human proteins is cultured human cells where the correct translation and chaperone machinery are present. However, compared to bacterial expression systems, human cell cultures present several technical challenges to their use as an expression system. We developed a method that utilizes a YFP fusion-tag to generate recombinant proteins using suspension-cultured HEK293F cells. YFP is a dual-function tag that enables direct visualization and fluorescence-based selection of high expressing clones for and rapid purification using a high-stringency, high-affinity anti-GFP/YFP nanobody support. We demonstrate the utility of this system by expressing two large human proteins, TOP2α (340 KDa dimer) and a TOP2β catalytic core (260 KDa dimer). This robustly and reproducibly yields >10 mg/L liter of cell culture using transient expression or 2.5 mg/L using stable expression. Published 2018. This article is a US Government work and is in the public domain in the USA.

  17. Administration of growth hormone in selectively protein-deprived rats decreases BMD and bone strength.

    Science.gov (United States)

    Ammann, Patrick; Brennan, Tara C; Mekraldi, Samia; Aubert, Michel L; Rizzoli, René

    2010-06-01

    Isocaloric protein undernutrition is associated with decreased bone mass and decreased bone strength, together with lower IGF-I levels. It remains unclear whether administration of growth hormone (GH) corrects these alterations in bone metabolism. Six-month-old female rats were fed isocaloric diets containing either 2.5% or 15% casein for 2 weeks. Bovine growth hormone (bGH, 0.5 or 2.5mg/kg of body weight) or vehicle was then administered as subcutaneous injections, twice daily, to rats on either diet for 4 weeks. At the proximal tibia, analysis of bone mineral density (BMD), maximal load and histomorphometry were performed. In addition, urinary deoxypyridinoline, plasma osteocalcin and IGF-I concentrations were measured. Weight was monitored weekly. bGH caused a dose-dependent increase in plasma IGF-I regardless of the dietary protein content. However, bGH dose-dependently decreased BMD and bone strength in rats fed the low-protein diet. There was no significant effect of bGH on BMD in rats fed the normal protein diet within this short-term treatment period, however bone formation as detected by histomorphometry was improved in this group but not the low-protein group. Osteoclast surface was increased in the low-protein bGH-treated animals only. Changes in bone turnover markers were detectable under both normal and low-protein diets. These results emphasize the major importance of dietary protein intake in the bone response to short-term GH administration, and highlight the need for further investigation into the effects of GH treatment in patients with reduced protein intake. Copyright 2010 Elsevier Inc. All rights reserved.

  18. Selective {sup 2}H and {sup 13}C labeling in NMR analysis of solution protein structure and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    LeMaster, D.M. [Northwestern Univ., Evanston, IL (United States)

    1994-12-01

    Preparation of samples bearing combined isotope enrichment patterns has played a central role in the recent advances in NMR analysis of proteins in solution. In particular, uniform {sup 13}C, {sup 15}N enrichment has made it possible to apply heteronuclear multidimensional correlation experiments for the mainchain assignments of proteins larger than 30 KDa. In contrast, selective labeling approaches can offer advantages in terms of the directedness of the information provided, such as chirality and residue type assignments, as well as through enhancements in resolution and sensitivity that result from editing the spectral complexity, the relaxation pathways and the scalar coupling networks. In addition, the combination of selective {sup 13}C and {sup 2}H enrichment can greatly facilitate the determination of heteronuclear relaxation behavior.

  19. Positive Selection Drives the Evolution of rhino, a Member of the Heterochromatin Protein 1 Family in Drosophila.

    Directory of Open Access Journals (Sweden)

    2005-07-01

    Full Text Available Heterochromatin comprises a significant component of many eukaryotic genomes. In comparison to euchromatin, heterochromatin is gene poor, transposon rich, and late replicating. It serves many important biological roles, from gene silencing to accurate chromosome segregation, yet little is known about the evolutionary constraints that shape heterochromatin. A complementary approach to the traditional one of directly studying heterochromatic DNA sequence is to study the evolution of proteins that bind and define heterochromatin. One of the best markers for heterochromatin is the heterochromatin protein 1 (HP1, which is an essential, nonhistone chromosomal protein. Here we investigate the molecular evolution of five HP1 paralogs present in Drosophila melanogaster. Three of these paralogs have ubiquitous expression patterns in adult Drosophila tissues, whereas HP1D/rhino and HP1E are expressed predominantly in ovaries and testes respectively. The HP1 paralogs also have distinct localization preferences in Drosophila cells. Thus, Rhino localizes to the heterochromatic compartment in Drosophila tissue culture cells, but in a pattern distinct from HP1A and lysine-9 dimethylated H3. Using molecular evolution and population genetic analyses, we find that rhino has been subject to positive selection in all three domains of the protein: the N-terminal chromo domain, the C-terminal chromo-shadow domain, and the hinge region that connects these two modules. Maximum likelihood analysis of rhino sequences from 20 species of Drosophila reveals that a small number of residues of the chromo and shadow domains have been subject to repeated positive selection. The rapid and positive selection of rhino is highly unusual for a gene encoding a chromosomal protein and suggests that rhino is involved in a genetic conflict that affects the germline, belying the notion that heterochromatin is simply a passive recipient of "junk DNA" in eukaryotic genomes.

  20. Positive selection drives the evolution of rhino, a member of the heterochromatin protein 1 family in Drosophila.

    Directory of Open Access Journals (Sweden)

    Danielle Vermaak

    2005-07-01

    Full Text Available Heterochromatin comprises a significant component of many eukaryotic genomes. In comparison to euchromatin, heterochromatin is gene poor, transposon rich, and late replicating. It serves many important biological roles, from gene silencing to accurate chromosome segregation, yet little is known about the evolutionary constraints that shape heterochromatin. A complementary approach to the traditional one of directly studying heterochromatic DNA sequence is to study the evolution of proteins that bind and define heterochromatin. One of the best markers for heterochromatin is the heterochromatin protein 1 (HP1, which is an essential, nonhistone chromosomal protein. Here we investigate the molecular evolution of five HP1 paralogs present in Drosophila melanogaster. Three of these paralogs have ubiquitous expression patterns in adult Drosophila tissues, whereas HP1D/rhino and HP1E are expressed predominantly in ovaries and testes respectively. The HP1 paralogs also have distinct localization preferences in Drosophila cells. Thus, Rhino localizes to the heterochromatic compartment in Drosophila tissue culture cells, but in a pattern distinct from HP1A and lysine-9 dimethylated H3. Using molecular evolution and population genetic analyses, we find that rhino has been subject to positive selection in all three domains of the protein: the N-terminal chromo domain, the C-terminal chromo-shadow domain, and the hinge region that connects these two modules. Maximum likelihood analysis of rhino sequences from 20 species of Drosophila reveals that a small number of residues of the chromo and shadow domains have been subject to repeated positive selection. The rapid and positive selection of rhino is highly unusual for a gene encoding a chromosomal protein and suggests that rhino is involved in a genetic conflict that affects the germline, belying the notion that heterochromatin is simply a passive recipient of "junk DNA" in eukaryotic genomes.

  1. Formylbenzene diazonium hexafluorophosphate reagent for tyrosine-selective modification of proteins and the introduction of a bioorthogonal aldehyde

    OpenAIRE

    Gavrilyuk, Julia; Ban, Hitoshi; Nagano, Masanobu; Hakamata, Wataru; Barbas, Carlos F.

    2012-01-01

    4-Formylbenzene diazonium hexafluorophosphate (FBDP) is a novel bench-stable crystalline diazonium salt that reacts selectively with tyrosine to install a bioorthogonal aldehyde functionality. Model studies with N-acyl-tyrosine methylamide allowed us to identify conditions optimal for tyrosine ligation reactions with small peptides and proteins. FBDP-based conjugation was used for the facile introduction of small molecule tags, poly(ethylene) glycol chains (PEGylation), and functional small m...

  2. Selection of symptomatic patients with Crohn's disease for abdominopelvic computed tomography: role of serum C-reactive protein.

    LENUS (Irish Health Repository)

    Desmond, Alan N

    2012-11-01

    Results of previous studies have shown that repeated abdominopelvic computed tomography (CT) examinations can lead to substantial cumulative diagnostic radiation exposure in patients with Crohn\\'s disease (CD). Improved selection of patients referred for CT will reduce unnecessary radiation exposure. This study examines if serum C-reactive protein (CRP) concentration predicts which symptomatic patients with CD are likely to have significant disease activity or disease complications (such as abscess) detected on abdominopelvic CT.

  3. A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments

    International Nuclear Information System (INIS)

    Schubert, Mario; Labudde, Dirk; Leitner, Dietmar; Oschkinat, Hartmut; Schmieder, Peter

    2005-01-01

    The determination of the three-dimensional structure of a protein or the study of protein-ligand interactions requires the assignment of all relevant nuclei as an initial step. This is nowadays almost exclusively performed using triple-resonance experiments. The conventional strategy utilizes one or more pairs of three dimensional spectra to obtain redundant information and thus reliable assignments. Here, a modified strategy for obtaining sequence specific assignments based on two dimensional amino acid type selective triple-resonance experiments is proposed. These experiments can be recorded with good resolution in a relatively short time. They provide very specific and redundant information, in particular on sequential connectivities, that drastically increases the ease and reliability of the assignment procedure, done either manually or in an automated fashion. The new strategy is demonstrated with the protein domain PB1 from yeast CDC24p

  4. Selection shaped the evolution of mouse androgen-binding protein (ABP) function and promoted the duplication of Abp genes.

    Science.gov (United States)

    Karn, Robert C; Laukaitis, Christina M

    2014-08-01

    In the present article, we summarize two aspects of our work on mouse ABP (androgen-binding protein): (i) the sexual selection function producing incipient reinforcement on the European house mouse hybrid zone, and (ii) the mechanism behind the dramatic expansion of the Abp gene region in the mouse genome. Selection unifies these two components, although the ways in which selection has acted differ. At the functional level, strong positive selection has acted on key sites on the surface of one face of the ABP dimer, possibly to influence binding to a receptor. A different kind of selection has apparently driven the recent and rapid expansion of the gene region, probably by increasing the amount of Abp transcript, in one or both of two ways. We have shown previously that groups of Abp genes behave as LCRs (low-copy repeats), duplicating as relatively large blocks of genes by NAHR (non-allelic homologous recombination). The second type of selection involves the close link between the accumulation of L1 elements and the expansion of the Abp gene family by NAHR. It is probably predicated on an initial selection for increased transcription of existing Abp genes and/or an increase in Abp gene number providing more transcriptional sites. Either or both could increase initial transcript production, a quantitative change similar to increasing the volume of a radio transmission. In closing, we also provide a note on Abp gene nomenclature.

  5. BET Bromodomain Proteins Brd2, Brd3 and Brd4 Selectively Regulate Metabolic Pathways in the Pancreatic β-Cell.

    Directory of Open Access Journals (Sweden)

    Jude T Deeney

    Full Text Available Displacement of Bromodomain and Extra-Terminal (BET proteins from chromatin has promise for cancer and inflammatory disease treatments, but roles of BET proteins in metabolic disease remain unexplored. Small molecule BET inhibitors, such as JQ1, block BET protein binding to acetylated lysines, but lack selectivity within the BET family (Brd2, Brd3, Brd4, Brdt, making it difficult to disentangle contributions of each family member to transcriptional and cellular outcomes. Here, we demonstrate multiple improvements in pancreatic β-cells upon BET inhibition with JQ1 or BET-specific siRNAs. JQ1 (50-400 nM increases insulin secretion from INS-1 cells in a concentration dependent manner. JQ1 increases insulin content in INS-1 cells, accounting for increased secretion, in both rat and human islets. Higher concentrations of JQ1 decrease intracellular triglyceride stores in INS-1 cells, a result of increased fatty acid oxidation. Specific inhibition of both Brd2 and Brd4 enhances insulin transcription, leading to increased insulin content. Inhibition of Brd2 alone increases fatty acid oxidation. Overlapping yet discrete roles for individual BET proteins in metabolic regulation suggest new isoform-selective BET inhibitors may be useful to treat insulin resistant/diabetic patients. Results imply that cancer and diseases of chronic inflammation or disordered metabolism are related through shared chromatin regulatory mechanisms.

  6. BET Bromodomain Proteins Brd2, Brd3 and Brd4 Selectively Regulate Metabolic Pathways in the Pancreatic β-Cell.

    Science.gov (United States)

    Deeney, Jude T; Belkina, Anna C; Shirihai, Orian S; Corkey, Barbara E; Denis, Gerald V

    2016-01-01

    Displacement of Bromodomain and Extra-Terminal (BET) proteins from chromatin has promise for cancer and inflammatory disease treatments, but roles of BET proteins in metabolic disease remain unexplored. Small molecule BET inhibitors, such as JQ1, block BET protein binding to acetylated lysines, but lack selectivity within the BET family (Brd2, Brd3, Brd4, Brdt), making it difficult to disentangle contributions of each family member to transcriptional and cellular outcomes. Here, we demonstrate multiple improvements in pancreatic β-cells upon BET inhibition with JQ1 or BET-specific siRNAs. JQ1 (50-400 nM) increases insulin secretion from INS-1 cells in a concentration dependent manner. JQ1 increases insulin content in INS-1 cells, accounting for increased secretion, in both rat and human islets. Higher concentrations of JQ1 decrease intracellular triglyceride stores in INS-1 cells, a result of increased fatty acid oxidation. Specific inhibition of both Brd2 and Brd4 enhances insulin transcription, leading to increased insulin content. Inhibition of Brd2 alone increases fatty acid oxidation. Overlapping yet discrete roles for individual BET proteins in metabolic regulation suggest new isoform-selective BET inhibitors may be useful to treat insulin resistant/diabetic patients. Results imply that cancer and diseases of chronic inflammation or disordered metabolism are related through shared chromatin regulatory mechanisms.

  7. Developing a NIR multispectral imaging for prediction and visualization of peanut protein content using variable selection algorithms

    Science.gov (United States)

    Cheng, Jun-Hu; Jin, Huali; Liu, Zhiwei

    2018-01-01

    The feasibility of developing a multispectral imaging method using important wavelengths from hyperspectral images selected by genetic algorithm (GA), successive projection algorithm (SPA) and regression coefficient (RC) methods for modeling and predicting protein content in peanut kernel was investigated for the first time. Partial least squares regression (PLSR) calibration model was established between the spectral data from the selected optimal wavelengths and the reference measured protein content ranged from 23.46% to 28.43%. The RC-PLSR model established using eight key wavelengths (1153, 1567, 1972, 2143, 2288, 2339, 2389 and 2446 nm) showed the best predictive results with the coefficient of determination of prediction (R2P) of 0.901, and root mean square error of prediction (RMSEP) of 0.108 and residual predictive deviation (RPD) of 2.32. Based on the obtained best model and image processing algorithms, the distribution maps of protein content were generated. The overall results of this study indicated that developing a rapid and online multispectral imaging system using the feature wavelengths and PLSR analysis is potential and feasible for determination of the protein content in peanut kernels.

  8. Selection on Coding and Regulatory Variation Maintains Individuality in Major Urinary Protein Scent Marks in Wild Mice.

    Directory of Open Access Journals (Sweden)

    Michael J Sheehan

    2016-03-01

    Full Text Available Recognition of individuals by scent is widespread across animal taxa. Though animals can often discriminate chemical blends based on many compounds, recent work shows that specific protein pheromones are necessary and sufficient for individual recognition via scent marks in mice. The genetic nature of individuality in scent marks (e.g. coding versus regulatory variation and the evolutionary processes that maintain diversity are poorly understood. The individual signatures in scent marks of house mice are the protein products of a group of highly similar paralogs in the major urinary protein (Mup gene family. Using the offspring of wild-caught mice, we examine individuality in the major urinary protein (MUP scent marks at the DNA, RNA and protein levels. We show that individuality arises through a combination of variation at amino acid coding sites and differential transcription of central Mup genes across individuals, and we identify eSNPs in promoters. There is no evidence of post-transcriptional processes influencing phenotypic diversity as transcripts accurately predict the relative abundance of proteins in urine samples. The match between transcripts and urine samples taken six months earlier also emphasizes that the proportional relationships across central MUP isoforms in urine is stable. Balancing selection maintains coding variants at moderate frequencies, though pheromone diversity appears limited by interactions with vomeronasal receptors. We find that differential transcription of the central Mup paralogs within and between individuals significantly increases the individuality of pheromone blends. Balancing selection on gene regulation allows for increased individuality via combinatorial diversity in a limited number of pheromones.

  9. Multi-Population Selective Genotyping to Identify Soybean [Glycine max (L.) Merr.] Seed Protein and Oil QTLs.

    Science.gov (United States)

    Phansak, Piyaporn; Soonsuwon, Watcharin; Hyten, David L; Song, Qijian; Cregan, Perry B; Graef, George L; Specht, James E

    2016-06-01

    Plant breeders continually generate ever-higher yielding cultivars, but also want to improve seed constituent value, which is mainly protein and oil, in soybean [Glycine max (L.) Merr.]. Identification of genetic loci governing those two traits would facilitate that effort. Though genome-wide association offers one such approach, selective genotyping of multiple biparental populations offers a complementary alternative, and was evaluated here, using 48 F2:3 populations (n = ∼224 plants) created by mating 48 high protein germplasm accessions to cultivars of similar maturity, but with normal seed protein content. All F2:3 progeny were phenotyped for seed protein and oil, but only 22 high and 22 low extreme progeny in each F2:3 phenotypic distribution were genotyped with a 1536-SNP chip (ca 450 bimorphic SNPs detected per mating). A significant quantitative trait locus (QTL) on one or more chromosomes was detected for protein in 35 (73%), and for oil in 25 (52%), of the 48 matings, and these QTL exhibited additive effects of ≥ 4 g kg(-1) and R(2) values of 0.07 or more. These results demonstrated that a multiple-population selective genotyping strategy, when focused on matings between parental phenotype extremes, can be used successfully to identify germplasm accessions possessing large-effect QTL alleles. Such accessions would be of interest to breeders to serve as parental donors of those alleles in cultivar development programs, though 17 of the 48 accessions were not unique in terms of SNP genotype, indicating that diversity among high protein accessions in the germplasm collection is less than what might ordinarily be assumed. Copyright © 2016 Phansak et al.

  10. Selective translational repression of truncated proteins from frameshift mutation-derived mRNAs in tumors.

    Directory of Open Access Journals (Sweden)

    Kwon Tae You

    2007-05-01

    Full Text Available Frameshift and nonsense mutations are common in tumors with microsatellite instability, and mRNAs from these mutated genes have premature termination codons (PTCs. Abnormal mRNAs containing PTCs are normally degraded by the nonsense-mediated mRNA decay (NMD system. However, PTCs located within 50-55 nucleotides of the last exon-exon junction are not recognized by NMD (NMD-irrelevant, and some PTC-containing mRNAs can escape from the NMD system (NMD-escape. We investigated protein expression from NMD-irrelevant and NMD-escape PTC-containing mRNAs by Western blotting and transfection assays. We demonstrated that transfection of NMD-irrelevant PTC-containing genomic DNA of MARCKS generates truncated protein. In contrast, NMD-escape PTC-containing versions of hMSH3 and TGFBR2 generate normal levels of mRNA, but do not generate detectable levels of protein. Transfection of NMD-escape mutant TGFBR2 genomic DNA failed to generate expression of truncated proteins, whereas transfection of wild-type TGFBR2 genomic DNA or mutant PTC-containing TGFBR2 cDNA generated expression of wild-type protein and truncated protein, respectively. Our findings suggest a novel mechanism of gene expression regulation for PTC-containing mRNAs in which the deleterious transcripts are regulated either by NMD or translational repression.

  11. Investigation of the utility of selective methyl protonation for determination of membrane protein structures

    International Nuclear Information System (INIS)

    Shih, Steve C. C.; Stoica, Ileana; Goto, Natalie K.

    2008-01-01

    Polytopic α-helical membrane proteins present one of the final frontiers for protein structural biology, with significant challenges causing severe under-representation in the protein structure databank. However, with the advent of hardware and methodology geared to the study of large molecular weight complexes, solution NMR is being increasingly considered as a tool for structural studies of these types of membrane proteins. One method that has the potential to facilitate these studies utilizes uniformly deuterated samples with protons reintroduced at one or two methyl groups of leucine, valine and isoleucine. In this work we demonstrate that in spite of the increased proportion of these amino acids in membrane proteins, the quality of structures that can be obtained from this strategy is similar to that obtained for all α-helical water soluble proteins. This is partly attributed to the observation that NOEs between residues within the transmembrane helix did not have an impact on structure quality. Instead the most important factors controlling structure accuracy were the strength of dihedral angle restraints imposed and the number of unique inter-helical pairs of residues constrained by NOEs. Overall these results suggest that the most accurate structures will arise from accurate identification of helical segments and utilization of inter-helical distance restraints from various sources to maximize the distribution of long-range restraints

  12. Elucidating the role of select cytoplasmic proteins in altering diffusion of integrin receptors.

    Science.gov (United States)

    Sander, Suzanne; Arora, Neha; Smith, Emily A

    2012-06-01

    Cytoplasmic proteins that affect integrin diffusion in the cell membrane are identified using a combination of fluorescence recovery after photobleaching (FRAP) and RNA interference. Integrin receptors are essential for many cellular events, and alterations in lateral diffusion are one mechanism for modulating their function. In cells expressing native cytoplasmic protein concentrations and spread on a slide containing integrin extracellular ligand, 45 ± 2% of the integrin is mobile with a time-dependent 5.2 ± 0.9 × 10(-9) cm(2)/s diffusion coefficient at 1 s. The time exponent is 0.90 ± 0.07, indicating integrin diffusion moderately slows at longer times. The role of a specific cytoplasmic protein in altering integrin diffusion is revealed through changes in the FRAP curve after reducing the cytoplasmic protein's expression. Decreased expression of cytoplasmic proteins rhea, focal adhesion kinase (FAK), or steamer duck decreases the integrin mobile fraction. For rhea and FAK, there is a concomitant shift to Brownian (i.e., time-independent) diffusion at reduced concentrations of these proteins. In contrast, when the expression of actin 42A, dreadlocks, paxillin, integrin-linked kinase (ILK), or vinculin is reduced, integrin diffusion generally becomes more constrained with an increase in the integrin mobile fraction. This same change in integrin diffusion is measured in the absence of integrin extracellular ligand. The results indicate breaking the extracellular ligand-integrin-cytoskeletal linkage alters integrin diffusion properties, and, in most cases, there is no correlation between integrin and lipid diffusion properties.

  13. Rh(I) -Catalyzed Intramolecular Carbonylative C-H/C-I Coupling of 2-Iodobiphenyls Using Furfural as a Carbonyl Source.

    Science.gov (United States)

    Furusawa, Takuma; Morimoto, Tsumoru; Nishiyama, Yasuhiro; Tanimoto, Hiroki; Kakiuchi, Kiyomi

    2016-08-19

    Synthesis of fluoren-9-ones by a Rh-catalyzed intramolecular C-H/C-I carbonylative coupling of 2-iodobiphenyls using furfural as a carbonyl source is presented. The findings indicate that the rate-determining step is not a C-H bond cleavage but, rather, the oxidative addition of the C-I bond to a Rh(I) center. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Preparation and microwave shielding property of silver-coated carbonyl iron powder

    International Nuclear Information System (INIS)

    Cao, Xiao Guo; Ren, Hao; Zhang, Hai Yan

    2015-01-01

    Highlights: • The silver-coated carbonyl iron powder is prepared by the electroless plating process. • The silver-coated carbonyl iron powder is a new kind of conductive filler. • The reflection and absorption dominate the shielding mechanism of the prepared powder. • Increasing the thickness of electroconductive adhesive will increase the SE. - Abstract: Electroless silver coating of carbonyl iron powder is demonstrated in the present investigation. The carbonyl iron powders are characterized by scanning electron microscope (SEM), energy dispersive X-ray spectroscopy (EDX), and X-ray diffraction analysis (XRD) before and after the coating process. The relatively uniform and continuous silver coating is obtained under the given coating conditions. In this paper, the electromagnetic interference (EMI) shielding mechanism of the silver-coated carbonyl iron powder is suggested. The reflection of silver coating and absorption of carbonyl iron powder dominate the shielding mechanism of the silver-coated carbonyl iron powder. The silver-coated carbonyl iron powders are used as conductive filler in electroconductive adhesive for electromagnetic interference shielding applications. The effect of the thickness of electroconductive adhesive on the shielding effectiveness (SE) is investigated. The results indicate that the SE increases obviously with the increase of the thickness of electroconductive adhesive. The SE of the electroconductive adhesive with 0.35 mm thickness is above 38 dB across the tested frequency range

  15. Reactions of ruthenium and osmium cluster carbonyls with heteroatom-substituted and functionalized alkynes

    International Nuclear Information System (INIS)

    Koridze, A.A.

    2000-01-01

    The results of studies of the reactions of ruthenium and osmium cluster carbonyls with metal (M = Re, Mn, Fe) alkynes, silylalkynes, propargyl alcohols and their derivatives, diynes, enynes, and ferrocenylacetylene are summarized. Intramolecular rearrangements in the cluster complexes including migrations of carbonyl, hydride, and hydrocarbon ligands and the metal core reorganization are considered [ru

  16. Comparison of carbonyl compounds emissions from diesel engine fueled with biodiesel and diesel

    Science.gov (United States)

    He, Chao; Ge, Yunshan; Tan, Jianwei; You, Kewei; Han, Xunkun; Wang, Junfang; You, Qiuwen; Shah, Asad Naeem

    The characteristics of carbonyl compounds emissions were investigated on a direct injection, turbocharged diesel engine fueled with pure biodiesel derived from soybean oil. The gas-phase carbonyls were collected by 2,4-dinitrophenylhydrazine (DNPH)-coated silica cartridges from diluted exhaust and analyzed by HPLC with UV detector. A commercial standard mixture including 14 carbonyl compounds was used for quantitative analysis. The experimental results indicate that biodiesel-fueled engine almost has triple carbonyls emissions of diesel-fueled engine. The weighted carbonyls emission of 8-mode test cycle of biodiesel is 90.8 mg (kW h) -1 and that of diesel is 30.7 mg (kW h) -1. The formaldehyde is the most abundant compound of carbonyls for both biodiesel and diesel, taking part for 46.2% and 62.7% respectively. The next most significant compounds are acetaldehyde, acrolein and acetone for both fuels. The engine fueled with biodiesel emits a comparatively high content of propionaldehyde and methacrolein. Biodiesel, as an alternative fuel, has lower specific reactivity (SR) caused by carbonyls compared with diesel. When fueled with biodiesel, carbonyl compounds make more contribution to total hydrocarbon emission.

  17. Design and fabrication of microfluidic mixer from carbonyl iron–PDMS composite membrane

    KAUST Repository

    Li, Jiaxing; Zhang, Mengying; Wang, Limu; Li, Weihua; Sheng, Ping; Wen, Weijia

    2010-01-01

    This paper introduces a carbonyl iron-PDMS (CI-PDMS) composite magnetic elastomer in which carbonyl iron (CI) particles are uniformly distributed in a PDMS matrix. The CI particles and the PDMS were mixed at different weight ratios and tested

  18. Metal-atom fluorescence from the quenching of metastable rare gases by metal carbonyls

    International Nuclear Information System (INIS)

    Hollingsworth, W.E.

    1982-11-01

    A flowing afterglow apparatus was used to study the metal fluorescence resulting from the quenching of metastable rare-gas states by metal carbonyls. The data from the quenching or argon, neon, and helium by iron and nickel carbonyl agreed well with a restricted degree of freedom model indicating a concerted bond-breaking dissociation

  19. Increase in skeletal muscle protein content by the ß-2 selective adrenergic agonist clenbuterol exacerbates hypoalbuminemia in rats fed a low-protein diet

    Directory of Open Access Journals (Sweden)

    A.L. Sawaya

    1998-06-01

    Full Text Available This investigation examined how the nutritional status of rats fed a low-protein diet was affected when the animals were treated with the ß-2 selective agonist clenbuterol (CL. Males (4 weeks old from an inbred, specific-pathogen-free strain of hooded rats maintained at the Dunn Nutritional Laboratory were used in the experiments (N = 6 rats per group. CL treatment (Ventipulmin, Boehringer-Ingelheim Ltd., 3.2 mg/kg diet for 2 weeks caused an exacerbation of the symptoms associated with protein deficiency in rats. Plasma albumin concentrations, already low in rats fed a low-protein diet (group A, were further reduced in CL rats (A = 25.05 ± 0.31 vs CL = 23.64 ± 0.30 g/l, P<0.05. Total liver protein decreased below the level seen in either pair-fed animals (group P or animals with free access to the low-protein diet (A = 736.56 ± 26 vs CL = 535.41 ± 54 mg, P<0.05, whereas gastrocnemius muscle protein was higher than the values normally described for control (C animals (C = 210.88 ± 3.2 vs CL = 227.14 ± 1.7 mg/g, P<0.05. Clenbuterol-treated rats also showed a reduction in growth when compared to P rats (P = 3.2 ± 1.1 vs CL = -10.2 ± 1.9 g, P<0.05. This was associated with a marked decrease in fat stores (P = 5.35 ± 0.81 vs CL = 2.02 ± 0.16 g, P<0.05. Brown adipose tissue (BAT cytochrome oxidase activity, although slightly lower than in P rats (P = 469.96 ± 16.20 vs CL = 414.48 ± 11.32 U/BAT x kg body weight, P<0.05, was still much higher than in control rats (C = 159.55 ± 11.54 vs CL = 414.48 ± 11.32 U/BAT x kg body weight, P<0.05. The present findings support the hypothesis that an increased muscle protein content due to clenbuterol stimulation worsened amino acid availability to the liver and further reduced albumin synthesis causing exacerbation of hypoalbuminemia in rats fed a low-protein diet.

  20. Combining metal oxide affinity chromatography (MOAC and selective mass spectrometry for robust identification of in vivo protein phosphorylation sites

    Directory of Open Access Journals (Sweden)

    Weckwerth Wolfram

    2005-11-01

    Full Text Available Abstract Background Protein phosphorylation is accepted as a major regulatory pathway in plants. More than 1000 protein kinases are predicted in the Arabidopsis proteome, however, only a few studies look systematically for in vivo protein phosphorylation sites. Owing to the low stoichiometry and low abundance of phosphorylated proteins, phosphorylation site identification using mass spectrometry imposes difficulties. Moreover, the often observed poor quality of mass spectra derived from phosphopeptides results frequently in uncertain database hits. Thus, several lines of evidence have to be combined for a precise phosphorylation site identification strategy. Results Here, a strategy is presented that combines enrichment of phosphoproteins using a technique termed metaloxide affinity chromatography (MOAC and selective ion trap mass spectrometry. The complete approach involves (i enrichment of proteins with low phosphorylation stoichiometry out of complex mixtures using MOAC, (ii gel separation and detection of phosphorylation using specific fluorescence staining (confirmation of enrichment, (iii identification of phosphoprotein candidates out of the SDS-PAGE using liquid chromatography coupled to mass spectrometry, and (iv identification of phosphorylation sites of these enriched proteins using automatic detection of H3PO4 neutral loss peaks and data-dependent MS3-fragmentation of the corresponding MS2-fragment. The utility of this approach is demonstrated by the identification of phosphorylation sites in Arabidopsis thaliana seed proteins. Regulatory importance of the identified sites is indicated by conservation of the detected sites in gene families such as ribosomal proteins and sterol dehydrogenases. To demonstrate further the wide applicability of MOAC, phosphoproteins were enriched from Chlamydomonas reinhardtii cell cultures. Conclusion A novel phosphoprotein enrichment procedure MOAC was applied to seed proteins of A. thaliana and to

  1. Reactions of rhodium(I) carbonyl chloride with olefins

    International Nuclear Information System (INIS)

    Varshavskii, Yu.S.; Kiseleva, N.V.; Cherkasova, T.G.; Buzina, N.A.; Bresler, L.S.

    1987-01-01

    The reactions of [Rh(CO) 2 Cl] 2 (Y 0 ) with cyclooctene and several other olefins (1-heptene, 1-hexene, ethylene, and cyclohexene) have been studied by IR and 13 C NMR spectroscopy. The main reaction products are the binuclear complexes Rh 2 L(CO) 3 Cl 2 (Y 1 ) and [RhL(CO)Cl] 2 (Y 2 ), where L denotes the olefin. The extent of replacement of the carbonyl groups depends on the nature of the olefin and the conditions under which the reaction is carried out (the L:Rh ratio and the removal of CO from the reaction sphere). The liquid olefins form the following series according to their ability to replace the carbonyl groups: C 8 H 14 > C 7 H 14 , C 6 H 12 > C 6 H 10 . In the presence of an excess of C 8 H 14 , Y 2 disproportionates with the formation of a dicarbonyl product, which presumably corresponds to the formula Rh(C 8 H 14 ) 2 (CO) 2 Cl (a pentacoordinate complex with a trigonal-bipyramidal structure). The 13 C signal in the NMR spectrum of a solution of Y 2 in C 8 H 14 is a singlet with σ( 13 C) 180.3 ppm, which is an indication of the rapid exchange of the carbonyl groups. Rapid exchange of the CO ligands is also observed in solutions of Y 0 in the olefins (with the exception of C 6 H 10 ). For example, the 13 C signal in the spectrum of a solution of Y 0 in C 8 H 14 is a singlet with σ( 13 C) 179.8 ppm. The spectrum of Y 0 in C 6 H 10 is a doublet with σ( 13 C) = 178.5 ppm and 1 J(CRh) = 76.3 Hz. A scheme for the interaction of Y 0 with olefins based on the conception of the trans antagonism of π-acceptor ligands has been proposed

  2. Tailoring of the Nanotexture of Mesoporous Silica Films and their Functionalized Derivatives for Selectively Harvesting Low Molecular Weight Protein

    Science.gov (United States)

    Hu, Ye; Bouamrani, Ali; Tasciotti, Ennio; Li, Li; Liu, Xuewu; Ferrari, Mauro

    2010-01-01

    We present a fast, efficient and reliable system based on mesoporous silica chips to specifically fractionate and enrich the low molecular weight proteome. Mesoporous silica thin films with tunable features at the nanoscale were fabricated using the triblock copolymer template pathway. Using different templates and concentrations in the precursor solution, various pore size distributions, pore structures and connectivity were obtained and applied for selective recovery of low mass proteins. In combination with mass spectrometry and statistic analysis, we demonstrated the correlation between the nanophase characteristics of the mesoporous silica thin films and the specificity and efficacy of low mass proteome harvesting. In addition, to overcome the limitations of the pre-functionalization method in polymer selection, plasma ashing was used for the first time for the treatment of the mesoporous silica surface prior to chemical modification. Surface charge modifications by different functional groups resulted in a selective capture of the low molecular weight proteins from serum sample. In conclusion our study demonstrates that the ability to tune the physico-chemical properties of mesoporous silica surfaces, for a selective enrichment of the low molecular weight proteome from complex biological fluids, has the potential to promote proteomic biomarker discovery. PMID:20014864

  3. LSM Proteins Provide Accurate Splicing and Decay of Selected Transcripts to Ensure Normal Arabidopsis Development[W

    Science.gov (United States)

    Perea-Resa, Carlos; Hernández-Verdeja, Tamara; López-Cobollo, Rosa; Castellano, María del Mar; Salinas, Julio

    2012-01-01

    In yeast and animals, SM-like (LSM) proteins typically exist as heptameric complexes and are involved in different aspects of RNA metabolism. Eight LSM proteins, LSM1 to 8, are highly conserved and form two distinct heteroheptameric complexes, LSM1-7 and LSM2-8,that function in mRNA decay and splicing, respectively. A search of the Arabidopsis thaliana genome identifies 11 genes encoding proteins related to the eight conserved LSMs, the genes encoding the putative LSM1, LSM3, and LSM6 proteins being duplicated. Here, we report the molecular and functional characterization of the Arabidopsis LSM gene family. Our results show that the 11 LSM genes are active and encode proteins that are also organized in two different heptameric complexes. The LSM1-7 complex is cytoplasmic and is involved in P-body formation and mRNA decay by promoting decapping. The LSM2-8 complex is nuclear and is required for precursor mRNA splicing through U6 small nuclear RNA stabilization. More importantly, our results also reveal that these complexes are essential for the correct turnover and splicing of selected development-related mRNAs and for the normal development of Arabidopsis. We propose that LSMs play a critical role in Arabidopsis development by ensuring the appropriate development-related gene expression through the regulation of mRNA splicing and decay. PMID:23221597

  4. Betulinic acid selectively increases protein degradation and enhances prostate cancer-specific apoptosis: possible role for inhibition of deubiquitinase activity.

    Directory of Open Access Journals (Sweden)

    Teresita Reiner

    Full Text Available Inhibition of the ubiquitin-proteasome system (UPS of protein degradation is a valid anti-cancer strategy and has led to the approval of bortezomib for the treatment of multiple myeloma. However, the alternative approach of enhancing the degradation of oncoproteins that are frequently overexpressed in cancers is less developed. Betulinic acid (BA is a plant-derived small molecule that can increase apoptosis specifically in cancer but not in normal cells, making it an attractive anti-cancer agent. Our results in prostate cancer suggested that BA inhibited multiple deubiquitinases (DUBs, which resulted in the accumulation of poly-ubiquitinated proteins, decreased levels of oncoproteins, and increased apoptotic cell death. In normal fibroblasts, however, BA did not inhibit DUB activity nor increased total poly-ubiquitinated proteins, which was associated with a lack of effect on cell death. In the TRAMP transgenic mouse model of prostate cancer, treatment with BA (10 mg/kg inhibited primary tumors, increased apoptosis, decreased angiogenesis and proliferation, and lowered androgen receptor and cyclin D1 protein. BA treatment also inhibited DUB activity and increased ubiquitinated proteins in TRAMP prostate cancer but had no effect on apoptosis or ubiquitination in normal mouse tissues. Overall, our data suggests that BA-mediated inhibition of DUBs and induction of apoptotic cell death specifically in prostate cancer but not in normal cells and tissues may provide an effective non-toxic and clinically selective agent for chemotherapy.

  5. The Putative HORMA Domain Protein Atg101 Dimerizes and Is Required for Starvation-Induced and Selective Autophagy in Drosophila

    Directory of Open Access Journals (Sweden)

    Krisztina Hegedűs

    2014-01-01

    Full Text Available The large-scale turnover of intracellular material including organelles is achieved by autophagy-mediated degradation in lysosomes. Initiation of autophagy is controlled by a protein kinase complex consisting of an Atg1-family kinase, Atg13, FIP200/Atg17, and the metazoan-specific subunit Atg101. Here we show that loss of Atg101 impairs both starvation-induced and basal autophagy in Drosophila. This leads to accumulation of protein aggregates containing the selective autophagy cargo ref(2P/p62. Mapping experiments suggest that Atg101 binds to the N-terminal HORMA domain of Atg13 and may also interact with two unstructured regions of Atg1. Another HORMA domain-containing protein, Mad2, forms a conformational homodimer. We show that Drosophila Atg101 also dimerizes, and it is predicted to fold into a HORMA domain. Atg101 interacts with ref(2P as well, similar to Atg13, Atg8a, Atg16, Atg18, Keap1, and RagC, a known regulator of Tor kinase which coordinates cell growth and autophagy. These results raise the possibility that the interactions and dimerization of the putative HORMA domain protein Atg101 play critical roles in starvation-induced autophagy and proteostasis, by promoting the formation of protein aggregate-containing autophagosomes.

  6. Role of protein and mRNA oxidation in seed dormancy and germination

    Directory of Open Access Journals (Sweden)

    hayat eel-maarouf-bouteau

    2013-04-01

    Full Text Available Reactive oxygen species (ROS are key players in the regulation of seed germination and dormancy. Although their regulated accumulation is a prerequisite for germination, the cellular basis of their action remains unknown, but very challenging to elucidate due to the lack of specificity of these compounds that can potentially react with all biomolecules. Among these, nucleic acids and proteins are very prone to oxidative damage. RNA is highly sensitive to oxidation because of its single-stranded structure and the absence of a repair system. Oxidation of mRNAs induces their decay through processing bodies or results in the synthesis of aberrant proteins through altered translation. Depending on the oxidized amino acid, ROS damage of proteins can be irreversible (i.e. carbonylation thus triggering the degradation of the oxidized proteins by the cytosolic 20S proteasome or can be reversed through the action of thioredoxins, peroxiredoxins or glutaredoxins (cysteine oxidation or by methionine sulfoxide reductase (methionine oxidation. Seed dormancy alleviation in the dry state, referred to as after-ripening, requires both selective mRNA oxidation and protein carbonylation. Similarly, seed imbibition of non-dormant seeds is associated with targeted oxidation of a subset of proteins. Altogether, these specific features testify that such oxidative modifications play important role in commitment of the cellular functioning toward germination completion.

  7. Development of an automatic sampling device for the continuous measurement of atmospheric carbonyls compounds

    International Nuclear Information System (INIS)

    Perraud, V.

    2007-12-01

    Two sampling strategies were studied to develop an automatic instrument for the continuous measurement of atmospheric carbonyl compounds. Because of its specificity towards carbonyls compounds, sampling by using a transfer of gaseous phase in a liquid phase associated with a simultaneous chemical derivatization of the trapped compounds was first studied. However, this method do not allow a quantitative sampling of all studied carbonyl compounds, nor a continuous measurement in the field. To overcome the difficulties, a second strategy was investigated: the cryogenic adsorption onto solid adsorbent followed by thermodesorption and a direct analysis by GC/MS. Collection efficiency using different solid adsorbents was found greater than 95% for carbonyl compounds consisting of 1 to 7 carbons. This work is a successful first step towards the realization of the automatic sampling device for a continuous measurement of atmospheric carbonyls compounds. (author)

  8. Impact of HVAC filter on indoor air quality in terms of ozone removal and carbonyls generation

    Science.gov (United States)

    Lin, Chi-Chi; Chen, Hsuan-Yu

    2014-06-01

    This study aims at detecting ozone removal rates and corresponding carbonyls generated by ozone reaction with HVAC filters from various building, i.e., shopping mall, school, and office building. Studies were conducted in a small-scale environmental chamber. By examining dust properties including organic carbon proportion and specific surface area of dusts adsorbed on filters along with ozone removal rates and carbonyls generation rate, the relationship among dust properties, ozone removal rates, and carbonyls generation was identified. The results indicate a well-defined positive correlation between ozone removal efficiency and carbonyls generation on filters, as well as a positive correlation among the mass of organic carbon on filters, ozone removal efficiency and carbonyls generations.

  9. The selective phosphorylation of a guanine nucleotide-binding regulatory protein

    International Nuclear Information System (INIS)

    Carlson, K.E.

    1989-01-01

    Receptor-activated signal transduction pathways regulate the responsiveness of cells to external stimuli. These transduction pathways themselves are subject to regulation, most commonly by phosphorylation. Guanine nucleotide-binding regulatory proteins (G Proteins), as requisite signal transducing elements for many plasma membrane receptors, are considered likely targets for regulation by phosphorylation. Protein kinase C (PKC) has been shown to phosphorylate the α subunit of G i and other G proteins in solution. However, the occurrence of the phosphorylation of G 1 within intact cells in response to activation of PKC has not been rigorously demonstrated. In this thesis, the extent to which the α subunits of G i undergo phosphorylation within human platelets in response to activation of PKC was examined by means of radiolabeling and immunoprecipitation. Incubation of platelets with phorbol-12-myristate-13-acetate (PMA), a potent activator of PKC, promoted the phosphorylation of several proteins within saponin-permeabilized and intact platelets incubated with [γ 32 P]ATP and [ 32 P]H 3 PO 4 , respectively. None of the phosphoproteins, however, were precipitated by either of two antisera containing antibodies differing in specificities for epitopes within G iα -despite precipitation of a substantial fraction of the subunit itself. In contrast, other antisera, containing antibodies specific for the recently describe G zα , or antibodies for both G zα and G iα , precipitated a 40-kDa phosphoprotein

  10. Mutagenesis Objective Search and Selection Tool (MOSST: an algorithm to predict structure-function related mutations in proteins

    Directory of Open Access Journals (Sweden)

    Asenjo Juan A

    2011-04-01

    's primary sequence into a group of functionally non-disruptive amino acids and a second group of functionally deleterious amino acids. Conclusions With this approach, not only conserved amino acid positions in a protein family can be labeled as functionally relevant, but also non-conserved amino acid positions can be identified to have a physicochemically meaningful functional effect. These results become a discriminative tool in the selection and elaboration of rational mutagenesis strategies for the protein. They can also be used to predict if a given nsSNP, identified, for instance, in a genomic-scale analysis, can have a functional implication for a particular protein and which nsSNPs are most likely to be functionally silent for a protein. This analytical tool could be used to rapidly and automatically discard any irrelevant nsSNP and guide the research focus toward functionally significant mutations. Based on preliminary results and applications, this technique shows promising performance as a valuable bioinformatics tool to aid in the development of new protein variants and in the understanding of function-structure relationships in proteins.

  11. Carbonylation of aryl bromides with palladium polyphthalocyanine/active carbon catalyst

    Energy Technology Data Exchange (ETDEWEB)

    Ohkatsu, Y.; Nakazawa, K.; Osa, T.

    1979-11-01

    The reaction of bromobenzene with carbon monoxide over carbon-supported 1.7Vertical Bar3< palladium polyphthalocyanine yielded carbonylated products in the presence of water or methanol and only benzene and dibromobenzene in their absence. At 300/sup 0/C and 1 sec contact time, e.g., the reaction of a 1:2.6:1 mole ratio feed of bromobenzene/methanol/carbon monoxide yielded benzoic acid with 61.7Vertical Bar3< selectivity at 83.2Vertical Bar3< conversion, a 1:0.8:3 feed gave benzoic acid with 84.4Vertical Bar3< selectivity at 40.7Vertical Bar3< conversion. The addition of water instead of methanol gave higher conversions, e.g., a feed of 1:3:1 bromobenzene/water/carbon monoxide yielded benzoic acid with 69.2Vertical Bar3< selectivity at 90.9Vertical Bar3< conversion. Analyses of product distributions obtained in these and autoclaved experiments at 10-50 kg/sq cm carbon monoxide pressure suggested a free radical mechanism.

  12. Selective Advantage of Recombination in Evolving Protein Populations:. a Lattice Model Study

    Science.gov (United States)

    Williams, Paul D.; Pollock, David D.; Goldstein, Richard A.

    Recent research has attempted to clarify the contributions of several mutational processes, such as substitutions or homologous recombination. Simplistic, tractable protein models, which determine the compact native structure phenotype from the sequence genotype, are well-suited to such studies. In this paper, we use a lattice-protein model to examine the effects of point mutation and homologous recombination on evolving populations of proteins. We find that while the majority of mutation and recombination events are neutral or deleterious, recombination is far more likely to be beneficial. This results in a faster increase in fitness during evolution, although the final fitness level is not significantly changed. This transient advantage provides an evolutionary advantage to subpopulations that undergo recombination, allowing fixation of recombination to occur in the population.

  13. Quantitative and Selective Analysis of Feline Growth Related Proteins Using Parallel Reaction Monitoring High Resolution Mass Spectrometry.

    Directory of Open Access Journals (Sweden)

    Mårten Sundberg

    Full Text Available Today immunoassays are widely used in veterinary medicine, but lack of species specific assays often necessitates the use of assays developed for human applications. Mass spectrometry (MS is an attractive alternative due to high specificity and versatility, allowing for species-independent analysis. Targeted MS-based quantification methods are valuable complements to large scale shotgun analysis. A method referred to as parallel reaction monitoring (PRM, implemented on Orbitrap MS, has lately been presented as an excellent alternative to more traditional selected reaction monitoring/multiple reaction monitoring (SRM/MRM methods. The insulin-like growth factor (IGF-system is not well described in the cat but there are indications of important differences between cats and humans. In feline medicine IGF-I is mainly analyzed for diagnosis of growth hormone disorders but also for research, while the other proteins in the IGF-system are not routinely analyzed within clinical practice. Here, a PRM method for quantification of IGF-I, IGF-II, IGF binding protein (BP -3 and IGFBP-5 in feline serum is presented. Selective quantification was supported by the use of a newly launched internal standard named QPrEST™. Homology searches demonstrated the possibility to use this standard of human origin for quantification of the targeted feline proteins. Excellent quantitative sensitivity at the attomol/μL (pM level and selectivity were obtained. As the presented approach is very generic we show that high resolution mass spectrometry in combination with PRM and QPrEST™ internal standards is a versatile tool for protein quantitation across multispecies.

  14. Activation of heterogenised rhodium carbonylation catalyst infrared spectroscopic study

    Energy Technology Data Exchange (ETDEWEB)

    Scurrell, M S

    1977-01-01

    In a study related to heterogeneous versions of homogeneous catalysts active in carbonylation of methanol to acetic acid, the catalyst consisted of 1Vertical Bar3< rhodium as rhodium trichloride supported on 13X zeolite and evacuated at 437/sup 0/K. Contacting the catalyst with carbon monoxide caused two bands, at 2025 and 2095 cm/sup -1/, to appear. Contact with a mixture of carbon monoxide and methyl iodide (the usual promoter) caused bands at 2085, 1710, 1440, and 1370 cm/sup -1/ to appear; the first two correspond to the bands at 2062 and 1711 cm/sup -1/ in homogeneous catalysts attributed to the formation of Rh(CH/sup 3/CO)(CO)X/sup 2/I/sup -/. Spectra.

  15. Ellipsometric studies of synthetic albumin-binding chitosan-derivatives and selected blood plasma proteins

    Science.gov (United States)

    Sarkar, Sabyasachi

    This dissertation summarizes work on the synthesis of chitosan-derivatives and the development of ellipsometric methods to characterize materials of biological origin. Albumin-binding chitosan-derivatives were synthesized via addition reactions that involve amine groups naturally present in chitosan. These surfaces were shown to have an affinity towards human serum albumin via ELISA, UV spectroscopy and SDS PAGE. Modified surfaces were characterized with IR ellipsometry at various stages of their synthesis using appropriate optical models. It was found that spin cast chitosan films were anisotropic in nature. All optical models used for characterizing chitosan-derivatives were thus anisotropic. Chemical signal dependence on molecular structure and composition was illustrated via IR spectroscopic ellipsometry (IRSE). An anisotropic optical model of an ensemble of Lorentz oscillators were used to approximate material behavior. The presence of acetic acid in spin-cast non-neutralized chitosan samples was thus shown. IRSE application to biomaterials was also demonstrated by performing a step-wise chemical characterizations during synthesis stages. Protein adsorbed from single protein solutions on these modified surfaces was monitored by visible in-situ variable wavelength ellipsometry. Based on adsorption profiles obtained from single protein adsorption onto silicon surfaces, lumped parameter kinetic models were developed. These models were used to fit experimental data of immunoglobulin-G of different concentrations and approximate conformational changes in fibrinogen adsorption. Biomaterial characterization by ellipsometry was further extended to include characterization of individual protein solutions in the IR range. Proteins in an aqueous environment were characterized by attenuated total internal reflection (ATR) IR ellipsometry using a ZnSe prism. Parameterized dielectric functions were created for individual proteins using Lorentz oscillators. These

  16. Screening for Selective Protein Inhibitors by Using the IANUS Peptide Array.

    Science.gov (United States)

    Erdmann, Frank; Prell, Erik; Jahreis, Günther; Fischer, Gunter; Malešević, Miroslav

    2018-04-16

    Finding new road blacks: A peptidic inhibitor of calcineurin (CaN)-mediated nuclear factor of activated T cells (NFAT) dephosphorylation, which is developed through a template-assisted IANUS (Induced orgANisation of strUcture by matrix-assisted togethernesS) peptide array, is cell permeable and able to block the translocation of green fluorescent protein-NFAT fusion protein (GFP-NFAT) into the nucleus after stimulation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. An oxidoreductase from 'Alphonso' mango catalyzing biosynthesis of furaneol and reduction of reactive carbonyls.

    Science.gov (United States)

    Kulkarni, Ram; Chidley, Hemangi; Deshpande, Ashish; Schmidt, Axel; Pujari, Keshav; Giri, Ashok; Gershenzon, Jonathan; Gupta, Vidya

    2013-01-01

    Two furanones, furaneol (4-hydroxy-2,5-dimethyl-3(2H)-furanone) and mesifuran (2,5-dimethyl-4-methoxy-3(2H)-furanone), are important constituents of flavor of the Alphonso cultivar of mango (Mangifera indica). To get insights into the biosynthesis of these furanones, we isolated an enone oxidoreductase gene from the Alphonso mango. It has high sequence similarity to an alkenal/one oxidoreductase from cucumber (79% identity) and enone oxidoreductases from tomato (73% identity) and strawberry (72% identity). The complete open reading frame was expressed in E. coli and the (his)6-tagged recombinant protein was purified by affinity chromatography. The purified protein assayed with NADH as a reducing agent converted D-fructose-1,6-diphosphate into furaneol, the immediate precursor of mesifuran. The enzyme was also able to convert two highly reactive carbonyls, 3-buten-2-one and 1-penten-3-one, produced by lipid peroxidation in plants, into their saturated derivatives. Expression profiling in various ripening stages of Alphonso fruits depicted an expression maxima at 10 days after harvest stage, shortly before the appearance of the maximum amount of furanones (completely ripe stage, 15 days after harvest). Although no furanones were detected at the 0 day after harvest stage, significant expression of this gene was detected in the fruits at this stage. Overall, the results suggest that this oxidoreductase plays important roles in Alphonso mango fruits.

  18. Genetic variability and natural selection at the ligand domain of the Duffy binding protein in brazilian Plasmodium vivax populations

    Directory of Open Access Journals (Sweden)

    Gil Luiz HS

    2010-11-01

    Full Text Available Abstract Background Plasmodium vivax malaria is a major public health challenge in Latin America, Asia and Oceania, with 130-435 million clinical cases per year worldwide. Invasion of host blood cells by P. vivax mainly depends on a type I membrane protein called Duffy binding protein (PvDBP. The erythrocyte-binding motif of PvDBP is a 170 amino-acid stretch located in its cysteine-rich region II (PvDBPII, which is the most variable segment of the protein. Methods To test whether diversifying natural selection has shaped the nucleotide diversity of PvDBPII in Brazilian populations, this region was sequenced in 122 isolates from six different geographic areas. A Bayesian method was applied to test for the action of natural selection under a population genetic model that incorporates recombination. The analysis was integrated with a structural model of PvDBPII, and T- and B-cell epitopes were localized on the 3-D structure. Results The results suggest that: (i recombination plays an important role in determining the haplotype structure of PvDBPII, and (ii PvDBPII appears to contain neutrally evolving codons as well as codons evolving under natural selection. Diversifying selection preferentially acts on sites identified as epitopes, particularly on amino acid residues 417, 419, and 424, which show strong linkage disequilibrium. Conclusions This study shows that some polymorphisms of PvDBPII are present near the erythrocyte-binding domain and might serve to elude antibodies that inhibit cell invasion. Therefore, these polymorphisms should be taken into account when designing vaccines aimed at eliciting antibodies to inhibit erythrocyte invasion.

  19. Natural selection on protein-coding genes in the human genome

    DEFF Research Database (Denmark)

    Bustamente, Carlos D.; Fledel-Alon, Adi; Williamson, Scott

    2005-01-01

    , showing an excess of deleterious variation within local populations 9, 10 . Here we contrast patterns of coding sequence polymorphism identified by direct sequencing of 39 humans for over 11,000 genes to divergence between humans and chimpanzees, and find strong evidence that natural selection has shaped......Comparisons of DNA polymorphism within species to divergence between species enables the discovery of molecular adaptation in evolutionarily constrained genes as well as the differentiation of weak from strong purifying selection 1, 2, 3, 4 . The extent to which weak negative and positive darwinian...... selection have driven the molecular evolution of different species varies greatly 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 , with some species, such as Drosophila melanogaster, showing strong evidence of pervasive positive selection 6, 7, 8, 9 , and others, such as the selfing weed Arabidopsis thaliana...

  20. Emerging roles of molecular chaperones and co-chaperones in selective autophagy : focus on BAG proteins

    NARCIS (Netherlands)

    Gamerdinger, Martin; Carra, Serena; Behl, Christian

    2011-01-01

    Macroautophagy is a catabolic process by which the cell degrades cytoplasmic components through the lysosomal machinery. While initially acknowledged as a rather unspecific bulk degradation process, growing lines of evidence indicate the selectivity of macroautophagy pathways in the removal of

  1. Selective separation and concentration of antihypertensive peptides from rapeseed protein hydrolysate by electrodialysis with ultrafiltration membranes.

    Science.gov (United States)

    He, Rong; Girgih, Abraham T; Rozoy, Elodie; Bazinet, Laurent; Ju, Xing-Rong; Aluko, Rotimi E

    2016-04-15

    Rapeseed protein isolate was subjected to alcalase digestion to obtain a protein hydrolysate that was separated into peptide fractions using electrodialysis with ultrafiltration membrane (EDUF) technology. The EDUF process (6h duration) led to isolation of three peptide fractions: anionic (recovered in KCl-1 compartment), cationic (recovered in KCl-2 compartment), and those that remained in the feed compartment, which was labeled final rapeseed protein hydrolysate (FRPH). As expected the KCl-1 peptides were enriched in negatively-charged (43.57%) while KCl-2 contained high contents of positively-charged (28.35%) amino acids. All the samples inhibited angiotensin converting enzyme (ACE) and renin activities in dose-dependent manner with original rapeseed protein hydrolysate having the least ACE-inhibitory IC50 value of 0.0932±0.0037 mg/mL while FRPH and KCl-2 had least renin-inhibitory IC50 values of 0.47±0.05 and 0.55±0.06 mg/mL, respectively. Six hours after oral administration (100 mg/kg body weight) to spontaneously hypertensive rats, the FRPH produced the maximum systolic blood pressure reduction of -51 mmHg. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Selective inhibition of Sarcocystis neurona calcium-dependent protein kinase 1 for equine protozoal myeloencephalitis therapy

    Science.gov (United States)

    Sarcocystis neurona is the most frequent cause of Equine Protozoal Myeloencephalitis (EPM), a debilitating neurologic disease of horses that can be difficult to treat. We identified SnCDPK1, the S. neurona homologue of calcium dependent protein kinase 1 (CDPK1), a validated drug target in Toxoplasma...

  3. Light scattering evidence of selective protein fouling on biocompatible block copolymer micelles

    Czech Academy of Sciences Publication Activity Database

    Giacomelli, F. C.; Štěpánek, Petr; Schmidt, V.; Jäger, Eliezer; Jäger, Alessandro; Giacomelli, C.

    2012-01-01

    Roč. 4, č. 15 (2012), s. 4504-4514 ISSN 2040-3364 R&D Projects: GA ČR GAP208/10/1600 Institutional research plan: CEZ:AV0Z40500505 Keywords : copolymer micelles * protein fouling * light scattering Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.233, year: 2012

  4. Proteins in seed and seedlings of selected Austrian pine (Pinus nigra Arnold trees as genetic markers tolerant to drought

    Directory of Open Access Journals (Sweden)

    Mataruga Milan

    2007-01-01

    Full Text Available A precondition necessary for creation and selection of genotypes tolerant of stress conditions is a study of physiological, biochemical and molecular bases of their adaptive reaction to stress. The study includes 40 lines of free pollination originating from 5 provenances: Sutjeska, Višegrad, Tara, Teslić and Durmitor (B&H, Serbia and Montenegro. Two populations were selected from each provenance, i.e.: 5 lines of free pollination represent the population growing on the cliffs and 3 lines of free pollination represent the population growing at the best site of Austrian pine. Specific characteristics of the studied provenances, populations, and free pollination lines were confirmed by the analyses in the salt-soluble proteins. The identical protein composition was proved in a small number of cases in the replicates of the same free pollination line, which indicates a high intra-line variability, which can be the result of the effect of father, as well as of heterozygosity of mother trees. The analyses of protein composition of seed showed considerable differences at provenance level. Inter-line, population and provenance differences, and also, the interaction between the origin and drought factor, were recorded for 9-day-old seedlings germinated in induced drought conditions and in normal conditions.

  5. Selection for a Zinc-Finger Protein Contributes to Seed Oil Increase during Soybean Domestication1[OPEN

    Science.gov (United States)

    Li, Qing-Tian; Lu, Xiang; Song, Qing-Xin; Chen, Hao-Wei; Wei, Wei; Tao, Jian-Jun; Ma, Biao; Bi, Ying-Dong; Li, Wei; Lai, Yong-Cai; Shui, Guang-Hou; Chen, Shou-Yi

    2017-01-01

    Seed oil is a momentous agronomical trait of soybean (Glycine max) targeted by domestication in breeding. Although multiple oil-related genes have been uncovered, knowledge of the regulatory mechanism of seed oil biosynthesis is currently limited. We demonstrate that the seed-preferred gene GmZF351, encoding a tandem CCCH zinc finger protein, is selected during domestication. Further analysis shows that GmZF351 facilitates oil accumulation by directly activating WRINKLED1, BIOTIN CARBOXYL CARRIER PROTEIN2, 3-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III, DIACYLGLYCEROL O-ACYLTRANSFERASE1, and OLEOSIN2 in transgenic Arabidopsis (Arabidopsis thaliana) seeds. Overexpression of GmZF351 in transgenic soybean also activates lipid biosynthesis genes, thereby accelerating seed oil accumulation. The ZF351 haplotype from the cultivated soybean group and the wild soybean (Glycine soja) subgroup III correlates well with high gene expression level, seed oil contents and promoter activity, suggesting that selection of GmZF351 expression leads to increased seed oil content in cultivated soybean. Our study provides novel insights into the regulatory mechanism for seed oil accumulation, and the manipulation of GmZF351 may have great potential in the improvement of oil production in soybean and other related crops. PMID:28184009

  6. Lrit1, a Retinal Transmembrane Protein, Regulates Selective Synapse Formation in Cone Photoreceptor Cells and Visual Acuity

    Directory of Open Access Journals (Sweden)

    Akiko Ueno

    2018-03-01

    Full Text Available Summary: In the vertebrate retina, cone photoreceptors play crucial roles in photopic vision by transmitting light-evoked signals to ON- and/or OFF-bipolar cells. However, the mechanisms underlying selective synapse formation in the cone photoreceptor pathway remain poorly understood. Here, we found that Lrit1, a leucine-rich transmembrane protein, localizes to the photoreceptor synaptic terminal and regulates the synaptic connection between cone photoreceptors and cone ON-bipolar cells. Lrit1-deficient retinas exhibit an aberrant morphology of cone photoreceptor pedicles, as well as an impairment of signal transmission from cone photoreceptors to cone ON-bipolar cells. Furthermore, we demonstrated that Lrit1 interacts with Frmpd2, a photoreceptor scaffold protein, and with mGluR6, an ON-bipolar cell-specific glutamate receptor. Additionally, Lrit1-null mice showed visual acuity impairments in their optokinetic responses. These results suggest that the Frmpd2-Lrit1-mGluR6 axis regulates selective synapse formation in cone photoreceptors and is essential for normal visual function. : Ueno et al. finds that Lrit1 plays an important role in regulating the synaptic connection between cone photoreceptors and cone ON-bipolar cells. The Frmpd2-Lrit1-mGluR6 axis is crucial for selective synapse formation in cone photoreceptors and for development of normal visual function. Keywords: retina, circuit, synapse formation, cone photoreceptor cell, ON-bipolar cell, visual acuity

  7. Nuclear substructure reorganization during late stageerythropoiesis is selective and does not involve caspase cleavage ofmajor nuclear substructural proteins

    Energy Technology Data Exchange (ETDEWEB)

    Krauss, Sharon Wald; Lo, Annie J.; Short, Sarah A.; Koury, MarkJ.; Mohandas, Narla; Chasis, Joel Anne

    2005-04-06

    Enucleation, a rare feature of mammalian differentiation, occurs in three cell types: erythroblasts, lens epithelium and keratinocytes. Previous investigations suggest that caspase activation functions in lens epithelial and keratinocyte enucleation, as well as in early erythropoiesis encompassing BFU-E differentiation to proerythroblast. To determine whether caspase activation contributes to later erythropoiesis and whether nuclear substructures other than chromatin reorganize, we analyzed distributions of nuclear subcompartment proteins and assayed for caspase-induced cleavage of subcompartmental target proteins in mouse erythroblasts. We found that patterns of lamin B in the filamentous network interacting with both the nuclear envelope and DNA, nuclear matrix protein NuMA, and splicing factors Sm and SC35 persisted during nuclear condensation, consistent with effective transcription of genes expressed late in differentiation. Thus nuclear reorganization prior to enucleation is selective, allowing maintenance of critical transcriptional processes independent of extensive chromosomal reorganization. Consistent with these data, we found no evidence for caspase-induced cleavage of major nuclear subcompartment proteins during late erythropoiesis, in contrast to what has been observed in early erythropoiesis and in lens epithelial and keratinocyte differentiation. These findings imply that nuclear condensation and extrusion during terminal erythroid differentiation involve novel mechanisms that do not entail major activation of apoptotic machinery.

  8. An engineered genetic selection for ternary protein complexes inspired by a natural three-component hitchhiker mechanism.

    Science.gov (United States)

    Lee, Hyeon-Cheol; Portnoff, Alyse D; Rocco, Mark A; DeLisa, Matthew P

    2014-12-22

    The bacterial twin-arginine translocation (Tat) pathway is well known to translocate correctly folded monomeric and dimeric proteins across the tightly sealed cytoplasmic membrane. We identified a naturally occurring heterotrimer, the Escherichia coli aldehyde oxidoreductase PaoABC, that is co-translocated by the Tat translocase according to a ternary "hitchhiker" mechanism. Specifically, the PaoB and PaoC subunits, each devoid of export signals, are escorted to the periplasm in a piggyback fashion by the Tat signal peptide-containing subunit PaoA. Moreover, export of PaoA was blocked when either PaoB or PaoC was absent, revealing a surprising interdependence for export that is not seen for classical secretory proteins. Inspired by this observation, we created a bacterial three-hybrid selection system that links the formation of ternary protein complexes with antibiotic resistance. As proof-of-concept, a bispecific antibody was employed as an adaptor that physically crosslinked one antigen fused to a Tat export signal with a second antigen fused to TEM-1 β-lactamase (Bla). The resulting non-covalent heterotrimer was exported in a Tat-dependent manner, delivering Bla to the periplasm where it hydrolyzed β-lactam antibiotics. Collectively, these results highlight the remarkable flexibility of the Tat system and its potential for studying and engineering ternary protein interactions in living bacteria.

  9. ORF-selector ESPRIT: a second generation library screen for soluble protein expression employing precise open reading frame selection.

    Science.gov (United States)

    An, Yingfeng; Yumerefendi, Hayretin; Mas, Philippe J; Chesneau, Alban; Hart, Darren J

    2011-08-01

    Here we present ORF-selector ESPRIT, a 9-fold enhanced version of our technology for screening incremental truncation libraries to identify soluble high yielding constructs of challenging proteins. Gene fragments are truncated at both termini to access internal domains and the resulting reading frame problem is addressed by an unbiased, intein-based open reading frame selection yielding only in-frame DNA inserts. This enriched library is then subcloned into a standard high-level expression plasmid where tens of thousands of constructs can be assayed in a two-step process using colony- and liquid-handling robots to isolate rare highly expressing clones useful for production of multi milligram quantities of purifiable proteins. The p85α protein was used to benchmark the system resulting in isolation of all known domains, either alone or in tandem. The human kinase IKK1 was then screened resulting in purification of a predicted internal domain. This strategy provides an integrated, facile route to produce soluble proteins from challenging and poorly understood target genes at quantities compatible with structural biology, screening applications and immunisation studies. The high genetic diversity that can be sampled opens the way to study more diverse systems including multisubunit complexes. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Selection and characterization of resistance to the Vip3Aa20 protein from Bacillus thuringiensis in Spodoptera frugiperda.

    Science.gov (United States)

    Bernardi, Oderlei; Bernardi, Daniel; Horikoshi, Renato J; Okuma, Daniela M; Miraldo, Leonardo L; Fatoretto, Julio; Medeiros, Fernanda Cl; Burd, Tony; Omoto, Celso

    2016-09-01

    Spodoptera frugiperda is one the main target pests of maize events expressing Vip3Aa20 protein from Bacillus thuringiensis (Bt) in Brazil. In this study, we selected a resistant strain of S. frugiperda on Bt maize expressing Vip3Aa20 protein and characterized the inheritance and fitness costs of the resistance. The resistance ratio of the Vip3Aa20-resistant strain of S. frugiperda was >3200-fold. Neonates of the Vip3Aa20-resistant strain were able to survive and emerge as fertile adults on Vip3Aa20 maize, while larvae from susceptible and heterozygous strains did not survive. The inheritance of Vip3Aa20 resistance was autosomal recessive and monogenic. Life history studies to investigate fitness cost revealed an 11% reduction in the survival rate until adult stage and a ∼50% lower reproductive rate of the Vip3Aa20-resistant strain compared with susceptible and heterozygous strains. This is the first characterization of S. frugiperda resistance to Vip3Aa protein. Our results provide useful information for resistance management programs designed to prevent or delay resistance evolution to Vip3Aa proteins in S. frugiperda. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  11. Accurate Quantification of Cardiovascular Biomarkers in Serum Using Protein Standard Absolute Quantification (PSAQ™) and Selected Reaction Monitoring*

    Science.gov (United States)

    Huillet, Céline; Adrait, Annie; Lebert, Dorothée; Picard, Guillaume; Trauchessec, Mathieu; Louwagie, Mathilde; Dupuis, Alain; Hittinger, Luc; Ghaleh, Bijan; Le Corvoisier, Philippe; Jaquinod, Michel; Garin, Jérôme; Bruley, Christophe; Brun, Virginie

    2012-01-01

    Development of new biomarkers needs to be significantly accelerated to improve diagnostic, prognostic, and toxicity monitoring as well as therapeutic follow-up. Biomarker evaluation is the main bottleneck in this development process. Selected Reaction Monitoring (SRM) combined with stable isotope dilution has emerged as a promising option to speed this step, particularly because of its multiplexing capacities. However, analytical variabilities because of upstream sample handling or incomplete trypsin digestion still need to be resolved. In 2007, we developed the PSAQ™ method (Protein Standard Absolute Quantification), which uses full-length isotope-labeled protein standards to quantify target proteins. In the present study we used clinically validated cardiovascular biomarkers (LDH-B, CKMB, myoglobin, and troponin I) to demonstrate that the combination of PSAQ and SRM (PSAQ-SRM) allows highly accurate biomarker quantification in serum samples. A multiplex PSAQ-SRM assay was used to quantify these biomarkers in clinical samples from myocardial infarction patients. Good correlation between PSAQ-SRM and ELISA assay results was found and demonstrated the consistency between these analytical approaches. Thus, PSAQ-SRM has the capacity to improve both accuracy and reproducibility in protein analysis. This will be a major contribution to efficient biomarker development strategies. PMID:22080464

  12. Affinity and selectivity of plant proteins for red wine components relevant to color and aroma traits.

    Science.gov (United States)

    Granato, Tiziana Mariarita; Ferranti, Pasquale; Iametti, Stefania; Bonomi, Francesco

    2018-08-01

    The effects of fining with various plant proteins were assessed on Aglianico red wine, using both the young wine and wine aged for twelve and twenty-four months, and including wine unfined or fined with gelatin as controls. Color traits and fining efficiency were considered, along with the content of various types of phenolics and of aroma-related compounds of either varietal or fermentative origin. All agents had comparable fining efficiency, although with distinct kinetics, and had similar effects on wine color. Individual plant proteins and enzymatic hydrolyzates differed in their ability to interact with some anthocyanins, with specific proanthocyanidins complexes, and with some aroma components of fermentative origin. Changes in varietal aroma components upon fining were very limited or absent. Effects of all the fining agents tested in this study on the anthocyanidin components were most noticeable in young red wine, and decreased markedly with increasing wine ageing. Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. Improved production of membrane proteins in Escherichia coli by selective codon substitutions

    DEFF Research Database (Denmark)

    Nørholm, Morten H.H.; Toddo, Stephen; Virkki, Minttu T.I.

    2013-01-01

    Membrane proteins are extremely challenging to produce in sufficient quantities for biochemical and structural analysis and there is a growing demand for solutions to this problem. In this study we attempted to improve expression of two difficult-to-express coding sequences (araH and narK) for me......Membrane proteins are extremely challenging to produce in sufficient quantities for biochemical and structural analysis and there is a growing demand for solutions to this problem. In this study we attempted to improve expression of two difficult-to-express coding sequences (araH and nar......K) for membrane transporters. For both coding sequences, synonymous codon substitutions in the region adjacent to the AUG start led to significant improvements in expression, whereas multi-parameter sequence optimization of codons throughout the coding sequence failed. We conclude that coding sequences can be re...

  14. Potent and Selective Peptide-based Inhibition of the G Protein Gαq*

    Science.gov (United States)

    Charpentier, Thomas H.; Waldo, Gary L.; Lowery-Gionta, Emily G.; Krajewski, Krzysztof; Strahl, Brian D.; Kash, Thomas L.; Harden, T. Kendall; Sondek, John

    2016-01-01

    In contrast to G protein-coupled receptors, for which chemical and peptidic inhibitors have been extensively explored, few compounds are available that directly modulate heterotrimeric G proteins. Active Gαq binds its two major classes of effectors, the phospholipase C (PLC)-β isozymes and Rho guanine nucleotide exchange factors (RhoGEFs) related to Trio, in a strikingly similar fashion: a continuous helix-turn-helix of the effectors engages Gαq within its canonical binding site consisting of a groove formed between switch II and helix α3. This information was exploited to synthesize peptides that bound active Gαq in vitro with affinities similar to full-length effectors and directly competed with effectors for engagement of Gαq. A representative peptide was specific for active Gαq because it did not bind inactive Gαq or other classes of active Gα subunits and did not inhibit the activation of PLC-β3 by Gβ1γ2. In contrast, the peptide robustly prevented activation of PLC-β3 or p63RhoGEF by Gαq; it also prevented G protein-coupled receptor-promoted neuronal depolarization downstream of Gαq in the mouse prefrontal cortex. Moreover, a genetically encoded form of this peptide flanked by fluorescent proteins inhibited Gαq-dependent activation of PLC-β3 at least as effectively as a dominant-negative form of full-length PLC-β3. These attributes suggest that related, cell-penetrating peptides should effectively inhibit active Gαq in cells and that these and genetically encoded sequences may find application as molecular probes, drug leads, and biosensors to monitor the spatiotemporal activation of Gαq in cells. PMID:27742837

  15. Potent and Selective Peptide-based Inhibition of the G Protein Gαq.

    Science.gov (United States)

    Charpentier, Thomas H; Waldo, Gary L; Lowery-Gionta, Emily G; Krajewski, Krzysztof; Strahl, Brian D; Kash, Thomas L; Harden, T Kendall; Sondek, John

    2016-12-02

    In contrast to G protein-coupled receptors, for which chemical and peptidic inhibitors have been extensively explored, few compounds are available that directly modulate heterotrimeric G proteins. Active Gα q binds its two major classes of effectors, the phospholipase C (PLC)-β isozymes and Rho guanine nucleotide exchange factors (RhoGEFs) related to Trio, in a strikingly similar fashion: a continuous helix-turn-helix of the effectors engages Gα q within its canonical binding site consisting of a groove formed between switch II and helix α3. This information was exploited to synthesize peptides that bound active Gα q in vitro with affinities similar to full-length effectors and directly competed with effectors for engagement of Gα q A representative peptide was specific for active Gα q because it did not bind inactive Gα q or other classes of active Gα subunits and did not inhibit the activation of PLC-β3 by Gβ 1 γ 2 In contrast, the peptide robustly prevented activation of PLC-β3 or p63RhoGEF by Gα q ; it also prevented G protein-coupled receptor-promoted neuronal depolarization downstream of Gα q in the mouse prefrontal cortex. Moreover, a genetically encoded form of this peptide flanked by fluorescent proteins inhibited Gα q -dependent activation of PLC-β3 at least as effectively as a dominant-negative form of full-length PLC-β3. These attributes suggest that related, cell-penetrating peptides should effectively inhibit active Gα q in cells and that these and genetically encoded sequences may find application as molecular probes, drug leads, and biosensors to monitor the spatiotemporal activation of Gα q in cells. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Iron Loading Selectively Increases Hippocampal Levels of Ubiquitinated Proteins and Impairs Hippocampus-Dependent Memory.

    Science.gov (United States)

    Figueiredo, Luciana Silva; de Freitas, Betânia Souza; Garcia, Vanessa Athaíde; Dargél, Vinícius Ayub; Köbe, Luiza Machado; Kist, Luiza Wilges; Bogo, Maurício Reis; Schröder, Nadja

    2016-11-01

    Alterations of brain iron levels have been observed in a number of neurodegenerative disorders. We have previously demonstrated that iron overload in the neonatal period results in severe and persistent memory deficits in the adulthood. Protein degradation mediated by the ubiquitin-proteasome system (UPS) plays a central regulatory role in several cellular processes. Impairment of the UPS has been implicated in the pathogenesis of neurodegenerative disorders. Here, we examined the effects of iron exposure in the neonatal period (12th-14th day of postnatal life) on the expression of proteasome β-1, β-2, and β-5 subunits, and ubiquitinated proteins in brains of 15-day-old rats, to evaluate the immediate effect of the treatment, and in adulthood to assess long-lasting effects. Two different memory types, emotionally motivated conditioning and object recognition were assessed in adult animals. We found that iron administered in the neonatal period impairs both emotionally motivated and recognition memory. Polyubiquitinated protein levels were increased in the hippocampus, but not in the cortex, of adult animals treated with iron. Gene expression of subunits β1 and β5 was affected by age, being higher in the early stages of development in the hippocampus, accompanied by an age-related increase in polyubiquitinated protein levels in adults. In the cortex, gene expression of the three proteasome subunits was significantly higher in adulthood than in the neonatal period. These findings suggest that expression of proteasome subunits and activity are age-dependently regulated. Iron exposure in the neonatal period produces long-lasting harmful effects on the UPS functioning, which may be related with iron-induced memory impairment.

  17. Polymorphism of proteins in selected slovak winter wheat genotypes using SDS-PAGE

    Directory of Open Access Journals (Sweden)

    Dana Miháliková

    2016-12-01

    Full Text Available Winter wheat is especially used for bread-making. The specific composition of the grain storage proteins and the representation of individual subunits determines the baking quality of wheat. The aim of this study was to analyze 15 slovak varieties of the winter wheat (Triticum aestivum L. based on protein polymorphism and to predict their technological quality. SDS-PAGE method by ISTA was used to separate glutenin protein subunits. Glutenins were separated into HMW-GS (15.13% and LMW-GS (65.89% on the basis of molecular weight in SDS-PAGE. At the locus Glu-A1 was found allele Null (53% of genotypes and allele 1 (47% of genotypes. The locus Glu-B1 was represented by the HMW-GS subunits 6+8 (33% of genotypes, 7+8 (27% of genotypes, 7+9 (40% of genotypes. At the locus Glu-D1 were detected two subunits, 2+12 (33% of genotypes and 5+10 (67% of genotypes which is correlated with good bread-making properties. The Glu – score was ranged from 4 (genotype Viglanka to 10 (genotypes Viola, Vladarka. According to the representation of individual glutenin subunits in samples, the dendrogram of genetic similarity was constructed. By the prediction of quality the results showed that the best technological quality was significant in the varieties Viola and Vladarka which are suitable for use in food processing.

  18. Selection of organisms for the co-evolution-based study of protein interactions.

    Science.gov (United States)

    Herman, Dorota; Ochoa, David; Juan, David; Lopez, Daniel; Valencia, Alfonso; Pazos, Florencio

    2011-09-12

    The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature. We show that the performance of three mirrortree-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions. In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest.

  19. Optimized localization of bacterial infections with technetium-99m labelled human immunoglobulin after protein charge selection

    International Nuclear Information System (INIS)

    Welling, M.; Feitsma, H.I.J.; Calame, W.; Ensing, G.J.; Goedemans, W.; Pauwels, E.K.J.

    1994-01-01

    To improve the scintigraphic detection of bacterial infections a protein charge-purified fraction of polyclonal human immunoglobulin was applied as a radiopharmaceutical. This purification was achieved by attaching the immunoglobulin to an anion-exchanger column and by obtaining the column-bound fraction with buffer. The binding to bacteria in vitro and the target to non-target ratios of an experimental thigh infection with Staphylococcus aureus or Klebsiella pneumoniae in mice were evaluated to compare the purified and the unpurified immunoglobulin. The percentage of binding to all gram-positive and gram-negative bacteria used in this study was significantly (P 99m Tc-labelled protein charge-purified polyclonal human immunoglobulin was administered intravenously. At all time intervals the target (infected thighs) to non-target (non-infected thighs) ratios for both infections were significantly higher (P 99m Tc-labelled protein charge-purified immunoglobulin localizes both a gram-positive and a gram-negative thigh infection more intensely and faster than 99m Tc-labelled unpurified immunoglobulin. (orig.)

  20. Simultaneous detection of low and high molecular weight carbonylated compounds derived from lipid peroxidation by electrospray ionization-tandem mass spectrometry.

    Science.gov (United States)

    Milic, Ivana; Hoffmann, Ralf; Fedorova, Maria

    2013-01-02

    Reactive oxygen species (ROS) and other oxidative agents such as free radicals can oxidize polyunsaturated fatty acids (PUFA) as well as PUFA in lipids. The oxidation products can undergo consecutive reactions including oxidative cleavages to yield a chemically diverse group of products, such as lipid peroxidation products (LPP). Among them are aldehydes and ketones ("reactive carbonyls") that are strong electrophiles and thus can readily react with nucleophilic side chains of proteins, which can alter the protein structure, function, cellular distribution, and antigenicity. Here, we report a novel technique to specifically derivatize both low molecular and high molecular weight carbonylated LPP with 7-(diethylamino)coumarin-3-carbohydrazide (CHH) and analyze all compounds by electrospray ionization-mass spectrometry (ESI-MS) in positive ion mode. CHH-derivatized compounds were identified by specific neutral losses or fragment ions. The fragment ion spectra displayed additional signals that allowed unambiguous identification of the lipid, fatty acids, cleavage sites, and oxidative modifications. Oxidation of docosahexaenoic (DHA, 22:6), arachidonic (AA, 20:4), linoleic (LA, 18:2), and oleic acids (OA, 18:1) yielded 69 aliphatic carbonyls, whose structures were all deduced from the tandem mass spectra. When four phosphatidylcholine (PC) vesicles containing the aforementioned unsaturated fatty acids were oxidized, we were able to deduce the structures of 122 carbonylated compounds from the tandem mass spectra of a single shotgun analysis acquired within 15 min. The high sensitivity (LOD ∼ 1 nmol/L for 4-hydroxy-2-nonenal, HNE) and a linear range of more than 3 orders of magnitude (10 nmol/L to 10 μmol/L for HNE) will allow further studies on complex biological samples including plasma.

  1. Driving Calmodulin Protein towards Conformational Shift by Changing Ionization States of Select Residues

    International Nuclear Information System (INIS)

    Negi, Sunita; Atilgan, Ali Rana; Atilgan, Canan

    2012-01-01

    Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca +2 ion between the two lobes.

  2. Driving Calmodulin Protein towards Conformational Shift by Changing Ionization States of Select Residues

    Science.gov (United States)

    Negi, Sunita; Rana Atilgan, Ali; Atilgan, Canan

    2012-12-01

    Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca+2 ion between the two lobes.

  3. Wet SiO2 As a Suitable Media for Fast and Efficient Reduction of Carbonyl Compounds with NaBH3CN under Solvent-Free and Acid-Free Conditions

    International Nuclear Information System (INIS)

    Kouhkan, Mehri; Zeynizadeh, Behzad

    2010-01-01

    Reduction of carbonyl compounds such as aldehydes, ketones, α,β-unsaturated enals and enones, α-diketones and acyloins was carried out readily with NaBH 3 CN in the presence of wet SiO 2 as a neutral media. The reactions were performed at solvent-free conditions in oil bath (70 - 80 .deg. C) or under microwave irradiation (240 W) to give the product alcohols in high to excellent yields. Regioselective 1,2-reduction of conjugated carbonyl compounds took place in a perfect selectivity without any side product formation

  4. Wet SiO{sub 2} As a Suitable Media for Fast and Efficient Reduction of Carbonyl Compounds with NaBH{sub 3}CN under Solvent-Free and Acid-Free Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Kouhkan, Mehri; Zeynizadeh, Behzad [Urmia University, Urmia (Iran, Islamic Republic of)

    2010-10-15

    Reduction of carbonyl compounds such as aldehydes, ketones, α,β-unsaturated enals and enones, α-diketones and acyloins was carried out readily with NaBH{sub 3}CN in the presence of wet SiO{sub 2} as a neutral media. The reactions were performed at solvent-free conditions in oil bath (70 - 80 .deg. C) or under microwave irradiation (240 W) to give the product alcohols in high to excellent yields. Regioselective 1,2-reduction of conjugated carbonyl compounds took place in a perfect selectivity without any side product formation.

  5. The influence of selection for protein stability on dN/dS estimations

    DEFF Research Database (Denmark)

    Dasmeh, Pouria; Serohijos, Adrian W. R.; Kepp, Kasper Planeta

    2014-01-01

    Understanding the relative contributions of various evolutionary processes-purifying selection, neutral drift, and adaptation-is fundamental to evolutionary biology. A common metric to distinguish these processes is the ratio of nonsynonymous to synonymous substitutions (i.e., dN/dS) interpreted ...

  6. LiCABEDS II. Modeling of ligand selectivity for G-protein-coupled cannabinoid receptors.

    Science.gov (United States)

    Ma, Chao; Wang, Lirong; Yang, Peng; Myint, Kyaw Z; Xie, Xiang-Qun

    2013-01-28

    The cannabinoid receptor subtype 2 (CB2) is a promising therapeutic target for blood cancer, pain relief, osteoporosis, and immune system disease. The recent withdrawal of Rimonabant, which targets another closely related cannabinoid receptor (CB1), accentuates the importance of selectivity for the development of CB2 ligands in order to minimize their effects on the CB1 receptor. In our previous study, LiCABEDS (Ligand Classifier of Adaptively Boosting Ensemble Decision Stumps) was reported as a generic ligand classification algorithm for the prediction of categorical molecular properties. Here, we report extension of the application of LiCABEDS to the modeling of cannabinoid ligand selectivity with molecular fingerprints as descriptors. The performance of LiCABEDS was systematically compared with another popular classification algorithm, support vector machine (SVM), according to prediction precision and recall rate. In addition, the examination of LiCABEDS models revealed the difference in structure diversity of CB1 and CB2 selective ligands. The structure determination from data mining could be useful for the design of novel cannabinoid lead compounds. More importantly, the potential of LiCABEDS was demonstrated through successful identification of newly synthesized CB2 selective compounds.

  7. Plant protein and secondary metabolites influence diet selection in a mammalian specialist herbivore

    Science.gov (United States)

    Amy C. Ulappa; Rick G. Kelsey; Graham G. Frye; Janet L. Rachlow; LIsa A. Shipley; Laura Bond; Xinzhu Pu; Jennifer Sorensen. Forbey

    2014-01-01

    For herbivores, nutrient intake is limited by the relatively low nutritional quality of plants and high concentrations of potentially toxic defensive compounds (plant secondary metabolites [PSMs]) produced by many plants. In response to phytochemical challenges, some herbivores selectively forage on plants with higher nutrient and lower PSM concentrations relative to...

  8. Improvement of operational stability of Ogataea minuta carbonyl reductase for chiral alcohol production.

    Science.gov (United States)

    Honda, Kohsuke; Inoue, Mizuha; Ono, Tomohiro; Okano, Kenji; Dekishima, Yasumasa; Kawabata, Hiroshi

    2017-06-01

    Directed evolution of enantio-selective carbonyl reductase from Ogataea minuta was conducted to improve the operational stability of the enzyme. A mutant library was constructed by an error-prone PCR and screened using a newly developed colorimetric assay. The stability of a mutant with two amino acid substitutions was significantly higher than that of the wild type at 50°C in the presence of dimethyl sulfoxide. Site-directed mutagenesis analysis showed that the improved stability of the enzyme can be attributed to the amino acid substitution of V166A. The half-lives of the V166A mutant were 11- and 6.1-times longer than those of the wild type at 50°C in the presence and absence, respectively, of 20% (v/v) dimethyl sulfoxide. No significant differences in the substrate specificity and enantio-selectivity of the enzyme were observed. The mutant enzyme converted 60 mM 2,2,2-trifluoroacetophenone to (R)-(-)-α-(trifluoromethyl)benzyl alcohol in a molar yield of 71% whereas the conversion yield with an equivalent concentration of the wild-type enzyme was 27%. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  9. The Emergence of Manganese-Based Carbonyl Hydrosilylation Catalysts.

    Science.gov (United States)

    Trovitch, Ryan J

    2017-11-21

    In recent years, interest in homogeneous manganese catalyst development has intensified because of the earth-abundant and nontoxic nature of this metal. Although compounds of Mn have largely been utilized for epoxidation reactions, recent efforts have revealed that Mn catalysts can mediate a broad range of reductive transformations. Low-valent Mn compounds have proven to be particularly effective for the hydrosilylation of carbonyl- and carboxylate-containing substrates, and this Account aims to highlight my research group's contributions to this field. In our initial 2014 communication, we reported that the bis(imino)pyridine-supported compound ( Ph2PPr PDI)Mn mediates ketone hydrosilylation with exceptional activity under solvent-free conditions. Silanes including Ph 2 SiH 2 , (EtO) 3 SiH, (EtO) 2 MeSiH, and (EtO)Me 2 SiH were found to partially reduce cyclohexanone in the presence of ( Ph2PPr PDI)Mn, while turnover frequencies of up to 1280 min -1 were observed using PhSiH 3 . This led us to evaluate the hydrosilylation of 11 additional ketones and allowed for the atom-efficient preparation of tertiary and quaternary silanes. At that time, it was also discovered that ( Ph2PPr PDI)Mn catalyzes the dihydrosilylation of esters (by way of acyl C-O bond hydrosilylation) to yield a mixture of silyl ethers with modest activity. Earlier this year, the scope of these transformations was extended to aldehydes and formates, and the observed hydrosilylation activities are among the highest obtained for any transition-metal catalyst. The effectiveness of three related catalysts has also been evaluated: ( Ph2PPr PDI)MnH, ( PyEt PDEA)Mn, and [( Ph2PEt PDI)Mn] 2 . To our surprise, ( Ph2PPr PDI)MnH was found to exhibit higher carboxylate dihydrosilylation activity than ( Ph2PPr PDI)Mn, while ( PyEt PDEA)Mn demonstrated remarkable carbonyl hydrosilylation activity considering that it lacks a redox-active supporting ligand. The evaluation of [( Ph2PEt PDI)Mn] 2 revealed

  10. Low pressure carbonylation of benzyl chloride = Die carbonylierung von benzylchlorid bei niedrigen drücken

    OpenAIRE

    Luggenhorst, H.J.; Westerterp, K.R.

    1986-01-01

    For carbonylations, metal carbonyls, particularly cobalt and iron carbonyls, are often used as catalysts. These reactions take place under rather drastic reaction conditions, e.g. 200–300 °C and 60–100 MPa. In some patents it is stated that similar reactions using the same catalysts can also be carried out under rather mild reaction conditions, such as 0–100 °C and 0–2.5 MPa. We studied the conversion of benzyl chloride to phenyl acetic methyl ester in a semi-batch reactor in which one of the...

  11. Formation of neutral and charged gold carbonyls on highly facetted gold nanostructures

    Science.gov (United States)

    Chau, Thoi-Dai; Visart de Bocarmé, Thierry; Kruse, Norbert; Wang, Richard L. C.; Kreuzer, Hans Jürgen

    2003-12-01

    We show that gold mono- and di-carbonyls are formed on gold field emitter tips during interaction with carbon monoxide gas at room temperature and in the presence of high electrostatic fields. The experiments are done in a time-of-flight atom probe to obtain mass spectra. The yield of monocarbonyl cations is about twice that of di-carbonyl ions. Density functional theory calculations are reported that explain the field stabilization of adsorbed carbonyls and the desorption yield of their cations.

  12. Carbonylation of 1-hexene in the presence of palladium-anion-exchange resin catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, A.L.; Pirozhkov, S.D.; Buiya, M.A.; Lunin, A.F.; Karapetyan, L.P.; Saldadze, K.M.

    1986-06-20

    Activated charcoal, silica gel, and zeolites containing palladium are active in the carbonylation of lower olefins by carbon monoxide. In the present work, they studied the carbonylation of 1-hexene in the presence of a series of palladium catalysts containing An-221, An-251, and AN-511 anion-exchange catalysts produced in the USSR as the supports. A catalyst obtained by the deposition of palladium(II) on weakly basic anion-exchange resins displays high efficiency in the carbonylation of 1-hexene with the formation of a nixture of enanthoic and 2-methylcaproic acids.

  13. Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.

    Directory of Open Access Journals (Sweden)

    Roshan Mascarenhas

    Full Text Available mRNA translation into proteins is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs, and genetic variants remains poorly understood. mRNA levels on polysomes have been shown to correlate well with expressed protein levels, pointing to polysomal loading as a critical factor. To study regulation and genetic factors of protein translation we measured levels and allelic ratios of mRNAs and ncRNAs (including microRNAs in lymphoblast cell lines (LCL and in polysomal fractions. We first used targeted assays to measure polysomal loading of mRNA alleles, confirming reported genetic effects on translation of OPRM1 and NAT1, and detecting no effect of rs1045642 (3435C>T in ABCB1 (MDR1 on polysomal loading while supporting previous results showing increased mRNA turnover of the 3435T allele. Use of high-throughput sequencing of complete transcript profiles (RNA-Seq in three LCLs revealed significant differences in polysomal loading of individual RNA classes and isoforms. Correlated polysomal distribution between protein-coding and non-coding RNAs suggests interactions between them. Allele-selective polysome recruitment revealed strong genetic influence for multiple RNAs, attributable either to differential expression of RNA isoforms or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Genes identified by different allelic RNA ratios between cytosol and polysomes were enriched with published expression quantitative trait loci (eQTLs affecting RNA functions, and associations with clinical phenotypes. Polysomal RNA-Seq combined with allelic ratio analysis provides a powerful approach to study polysomal RNA recruitment and regulatory variants affecting protein translation.

  14. Genetic Diversity, Natural Selection and Haplotype Grouping of Plasmodium knowlesi Gamma Protein Region II (PkγRII): Comparison with the Duffy Binding Protein (PkDBPαRII).

    Science.gov (United States)

    Fong, Mun Yik; Rashdi, Sarah A A; Yusof, Ruhani; Lau, Yee Ling

    2016-01-01

    Plasmodium knowlesi is a simian malaria parasite that has been reported to cause malaria in humans in Southeast Asia. This parasite invades the erythrocytes of humans and of its natural host, the macaque Macaca fascicularis, via interaction between the Duffy binding protein region II (PkDBPαRII) and the Duffy antigen receptor on the host erythrocytes. In contrast, the P. knowlesi gamma protein region II (PkγRII) is not involved in the invasion of P. knowlesi into humans. PkγRII, however, mediates the invasion of P. knowlesi into the erythrocytes of M. mulata, a non-natural host of P. knowlesi via a hitherto unknown receptor. The haplotypes of PkDBPαRII in P. knowlesi isolates from Peninsular Malaysia and North Borneo have been shown to be genetically distinct and geographically clustered. Also, the PkDBPαRII was observed to be undergoing purifying (negative) selection. The present study aimed to determine whether similar phenomena occur in PkγRII. Blood samples from 78 knowlesi malaria patients were used. Forty-eight of the samples were from Peninsular Malaysia, and 30 were from Malaysia Borneo. The genomic DNA of the samples was extracted and used as template for the PCR amplification of the PkγRII. The PCR product was cloned and sequenced. The sequences obtained were analysed for genetic diversity and natural selection using MEGA6 and DnaSP (version 5.10.00) programmes. Genetic differentiation between the PkγRII of Peninsular Malaysia and North Borneo isolates was estimated using the Wright's FST fixation index in DnaSP (version 5.10.00). Haplotype analysis was carried out using the Median-Joining approach in NETWORK (version 4.6.1.3). A total of 78 PkγRII sequences was obtained. Comparative analysis showed that the PkγRII have similar range of haplotype (Hd) and nucleotide diversity (π) with that of PkDBPαRII. Other similarities between PkγRII and PkDBPαRII include undergoing purifying (negative) selection, geographical clustering of haplotypes

  15. Genetic Diversity, Natural Selection and Haplotype Grouping of Plasmodium knowlesi Gamma Protein Region II (PkγRII: Comparison with the Duffy Binding Protein (PkDBPαRII.

    Directory of Open Access Journals (Sweden)

    Mun Yik Fong

    Full Text Available Plasmodium knowlesi is a simian malaria parasite that has been reported to cause malaria in humans in Southeast Asia. This parasite invades the erythrocytes of humans and of its natural host, the macaque Macaca fascicularis, via interaction between the Duffy binding protein region II (PkDBPαRII and the Duffy antigen receptor on the host erythrocytes. In contrast, the P. knowlesi gamma protein region II (PkγRII is not involved in the invasion of P. knowlesi into humans. PkγRII, however, mediates the invasion of P. knowlesi into the erythrocytes of M. mulata, a non-natural host of P. knowlesi via a hitherto unknown receptor. The haplotypes of PkDBPαRII in P. knowlesi isolates from Peninsular Malaysia and North Borneo have been shown to be genetically distinct and geographically clustered. Also, the PkDBPαRII was observed to be undergoing purifying (negative selection. The present study aimed to determine whether similar phenomena occur in PkγRII.Blood samples from 78 knowlesi malaria patients were used. Forty-eight of the samples were from Peninsular Malaysia, and 30 were from Malaysia Borneo. The genomic DNA of the samples was extracted and used as template for the PCR amplification of the PkγRII. The PCR product was cloned and sequenced. The sequences obtained were analysed for genetic diversity and natural selection using MEGA6 and DnaSP (version 5.10.00 programmes. Genetic differentiation between the PkγRII of Peninsular Malaysia and North Borneo isolates was estimated using the Wright's FST fixation index in DnaSP (version 5.10.00. Haplotype analysis was carried out using the Median-Joining approach in NETWORK (version 4.6.1.3.A total of 78 PkγRII sequences was obtained. Comparative analysis showed that the PkγRII have similar range of haplotype (Hd and nucleotide diversity (π with that of PkDBPαRII. Other similarities between PkγRII and PkDBPαRII include undergoing purifying (negative selection, geographical clustering of

  16. Selective renal vasoconstriction, exaggerated natriuresis and excretion rates of exosomic proteins in essential hypertension

    DEFF Research Database (Denmark)

    Damkjaer, M.; Jensen, Pia Hønnerup; Schwämmle, Veit

    2014-01-01

    AimIn essential hypertension (EH), the regulation of renal sodium excretion is aberrant. We hypothesized that in mild EH, (i) abnormal dynamics of plasma renin concentration (PRC) and atrial natriuretic peptide (ANP) are responsible for the exaggerated natriuresis, and (ii) exosomic protein...... patterns reflect the renal tubular abnormality involved in the dysregulation of sodium excretion. MethodsAfter 2-week drug washout and 4-day diet, systemic and renal hemodynamics, cardio-renal hormones, glomerular filtration and renal excretion were studied in male patients during saline loading (SL...

  17. Estimation of Selected Milk Protein Genetic Variants by Multi-Component Analysis of Amino Acid Profiles

    OpenAIRE

    Hollar, Carol M.

    1992-01-01

    Cation-exchange fast protein liquid chromatography separated whole casein into β-casein A2, A1, and B, K-casein, αs1-casein, and αs2-casein fractions as well as γ-caseins and several unidentified peaks using a urea-acetate buffer at pH 5 and a NaCl gradient. The whole casein fractions eluted in the following order: breakdown products of β-casein and unidentified peaks; β-casein A2, Al, and B; additional breakdown products of β-casein and unidentified peaks; K-casein; αs1-casein; and αs2-casei...

  18. Application of Cavity Enhanced Absorption Spectroscopy to the Detection of Nitric Oxide, Carbonyl Sulphide, and Ethane--Breath Biomarkers of Serious Diseases.

    Science.gov (United States)

    Wojtas, Jacek

    2015-06-17

    The paper presents one of the laser absorption spectroscopy techniques as an effective tool for sensitive analysis of trace gas species in human breath. Characterization of nitric oxide, carbonyl sulphide and ethane, and the selection of their absorption lines are described. Experiments with some biomarkers showed that detection of pathogenic changes at the molecular level is possible using this technique. Thanks to cavity enhanced spectroscopy application, detection limits at the ppb-level and short measurements time (laser and a tunable laser system consisting of an optical parametric oscillator and difference frequency generator. Setup using the first source provided a detection limit of 30 ppb for nitric oxide and 250 ppb for carbonyl sulphide. During experiments employing a second laser, detection limits of 0.9 ppb and 0.3 ppb were obtained for carbonyl sulphide and ethane, respectively. The conducted experiments show that this type of diagnosis would significantly increase chances for effective therapy of some diseases. Additionally, it offers non-invasive and real time measurements, high sensitivity and selectivity as well as minimizing discomfort for patients. For that reason, such sensors can be used in screening for early detection of serious diseases.

  19. Selection and characterization of specific nanobody against bovine virus diarrhea virus (BVDV E2 protein.

    Directory of Open Access Journals (Sweden)

    Tiansen Li

    Full Text Available Bovine viral diarrhea-mucosal disease (BVD-MD is caused by bovine viral diarrhea virus (BVDV, and results in abortion, stillbirth, and fetal malformation in cows. Here, we constructed the phage display vector pCANTAB 5E-VHH and then transformed it into Escherichia coli TG1-competent cells, to construct an initial anti-BVDV nanobody gene library. We obtained a BVDV-E2 antigen epitope bait protein by prokaryotic expression using the nucleotide sequence of the E2 gene of the BVDV-NADL strain published in GenBank. Phage display was used to screen the anti-BVDV nanobody gene library. We successfully constructed a high quality phage display nanobody library, with an initial library capacity of 4.32×105. After the rescue of helper phage, the titer of the phage display nanobody library was 1.3×1011. The BVDV-E2 protein was then expressed in Escherichia coli (DE3, and a 49.5 kDa band was observed with SDS-PAGE analysis that was consistent with the expected nanobody size. Thus, we were able to isolate one nanobody that exhibits high affinity and specificity against BVDV using phage display techniques. This isolated nanobody was then used in Enzyme Linked Immunosorbent Assay and qRT-PCR, and ELISA analyses of BVDV infection of MDBK cells indicated that the nanobodies exhibited good antiviral effect.

  20. Selection and characterization of specific nanobody against bovine virus diarrhea virus (BVDV) E2 protein.

    Science.gov (United States)

    Li, Tiansen; Huang, Meiling; Xiao, Hongran; Zhang, Guoqi; Ding, Jinhua; Wu, Peng; Zhang, Hui; Sheng, Jinliang; Chen, Chuangfu

    2017-01-01

    Bovine viral diarrhea-mucosal disease (BVD-MD) is caused by bovine viral diarrhea virus (BVDV), and results in abortion, stillbirth, and fetal malformation in cows. Here, we constructed the phage display vector pCANTAB 5E-VHH and then transformed it into Escherichia coli TG1-competent cells, to construct an initial anti-BVDV nanobody gene library. We obtained a BVDV-E2 antigen epitope bait protein by prokaryotic expression using the nucleotide sequence of the E2 gene of the BVDV-NADL strain published in GenBank. Phage display was used to screen the anti-BVDV nanobody gene library. We successfully constructed a high quality phage display nanobody library, with an initial library capacity of 4.32×105. After the rescue of helper phage, the titer of the phage display nanobody library was 1.3×1011. The BVDV-E2 protein was then expressed in Escherichia coli (DE3), and a 49.5 kDa band was observed with SDS-PAGE analysis that was consistent with the expected nanobody size. Thus, we were able to isolate one nanobody that exhibits high affinity and specificity against BVDV using phage display techniques. This isolated nanobody was then used in Enzyme Linked Immunosorbent Assay and qRT-PCR, and ELISA analyses of BVDV infection of MDBK cells indicated that the nanobodies exhibited good antiviral effect.

  1. Protein structural model selection by combining consensus and single scoring methods.

    Directory of Open Access Journals (Sweden)

    Zhiquan He

    Full Text Available Quality assessment (QA for predicted protein structural models is an important and challenging research problem in protein structure prediction. Consensus Global Distance Test (CGDT methods assess each decoy (predicted structural model based on its structural similarity to all others in a decoy set and has been proved to work well when good decoys are in a majority cluster. Scoring functions evaluate each single decoy based on its structural properties. Both methods have their merits and limitations. In this paper, we present a novel method called PWCom, which consists of two neural networks sequentially to combine CGDT and single model scoring methods such as RW, DDFire and OPUS-Ca. Specifically, for every pair of decoys, the difference of the corresponding feature vectors is input to the first neural network which enables one to predict whether the decoy-pair are significantly different in terms of their GDT scores to the native. If yes, the second neural network is used to decide which one of the two is closer to the native structure. The quality score for each decoy in the pool is based on the number of winning times during the pairwise comparisons. Test results on three benchmark datasets from different model generation methods showed that PWCom significantly improves over consensus GDT and single scoring methods. The QA server (MUFOLD-Server applying this method in CASP 10 QA category was ranked the second place in terms of Pearson and Spearman correlation performance.

  2. Halloysite-based dopamine-imprinted polymer for selective protein capture.

    Science.gov (United States)

    Zhu, Xiaohong; Li, Hui; Liu, Hui; Peng, Wei; Zhong, Shian; Wang, Yan

    2016-06-01

    We describe a facile, general, and highly efficient approach to obtain polydopamine-coated molecularly imprinted polymer based on halloysite nanotubes for bovine serum albumin. The method combined surface molecular imprinting and one-step immobilized template technique. Hierarchically structured polymer was prepared in physiological conditions adopting dopamine as functional monomer. A thin layer of polydopamine can be coated on the surface of amino-modified halloysite nanotubes by self-polymerization, and the thickness of the imprinted shells can be controlled by the mass ratio of matrix and dopamine. The polymer was characterized by Fourier transform infrared spectrometry, transmission electron microscopy, and thermogravimetric analysis. The prepared material showed high binding capacity (45.4 mg/g) and specific recognition behavior toward the template protein. In addition, stability and regeneration analyses indicated that the imprinted polymer exhibited excellent reusability (relative standard deviation < 9% for batch-to-batch evaluation). Therefore, the developed polymer is effective for protein recognition and separation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Selective translation of the measles virus nucleocapsid mRNA by La protein

    Directory of Open Access Journals (Sweden)

    Yoshihisa eInoue

    2011-08-01

    Full Text Available Measles, caused by measles virus (MeV infection, is the leading cause of death in children because of secondary infections attributable to MeV-induced immune suppression. Recently, we have shown that wild-type MeVs induce the suppression of protein synthesis in host cells (referred to as "shutoff" and that viral mRNAs are preferentially translated under shutoff conditions in infected cells. To determine the mechanism behind the preferential translation of viral mRNA, we focused on the 5 untranslated region (UTR of nucleocapsid (N mRNA. The La/SSB autoantigen (La was found to specifically bind to an N-5UTR probe. Recombinant La enhanced the translation of luciferase mRNA containing the N-5UTR (N-fLuc, and RNA interference of La suppressed N-fLuc translation. Furthermore, recombinant MeV lacking the La-binding motif in the N-5UTR displayed delayed viral protein synthesis and growth kinetics at an early phase of infection. These results suggest that La induced predominant translation of N mRNA via binding to i