Aromatic-Aromatic Interactions in Biological System: Structure Activity Relationships

International Nuclear Information System (INIS)

Rajagopal, Appavu; Deepa, Mohan; Govindaraju, Munisamy

2016-01-01

While, intramolecular hydrogen bonds have attracted the greatest attention in studies of peptide conformations, the recognition that several other weakly polar interactions may be important determinants of folded structure has been growing. Burley and Petsko provided a comprehensive overview of the importance of weakly polar interactions, in shaping protein structures. The interactions between aromatic rings, which are spatially approximate, have attracted special attention. A survey of the proximal aromatic residue pairs in proteins, allowed Burley and Petsko to suggest that, “phenyl ring centroids are separated by a preferential distance of between 4.5 and 7 Å, and dihedral angles approximately 90° are most common”

Aromatic-Aromatic Interactions in Biological System: Structure Activity Relationships

Energy Technology Data Exchange (ETDEWEB)

Rajagopal, Appavu; Deepa, Mohan [Molecular Biophysics Unit, Indian Institute of Sciences-Bangalore, Karnataka (India); Govindaraju, Munisamy [Bio-Spatial Technology Research Unit, Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu (India)

2016-02-26

While, intramolecular hydrogen bonds have attracted the greatest attention in studies of peptide conformations, the recognition that several other weakly polar interactions may be important determinants of folded structure has been growing. Burley and Petsko provided a comprehensive overview of the importance of weakly polar interactions, in shaping protein structures. The interactions between aromatic rings, which are spatially approximate, have attracted special attention. A survey of the proximal aromatic residue pairs in proteins, allowed Burley and Petsko to suggest that, “phenyl ring centroids are separated by a preferential distance of between 4.5 and 7 Å, and dihedral angles approximately 90° are most common”.

Novel short antibacterial and antifungal peptides with low cytotoxicity: Efficacy and action mechanisms

Energy Technology Data Exchange (ETDEWEB)

Qi, Xiaobao; Zhou, Chuncai; Li, Peng [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore (Singapore); Xu, Weixin [School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore (Singapore); Cao, Ye; Ling, Hua; Ning Chen, Wei; Ming Li, Chang; Xu, Rong [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore (Singapore); Lamrani, Mouad [Menicon Co., Ltd. Immeuble Espace Cordeliers, 2, rue President Carnot, 69002 Lyon (France); Mu, Yuguang, E-mail: ygmu@ntu.edu.sg [School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore (Singapore); Leong, Susanna Su Jan [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore (Singapore); Wook Chang, Matthew, E-mail: matthewchang@ntu.edu.sg [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore (Singapore); Chan-Park, Mary B., E-mail: mbechan@ntu.edu.sg [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore (Singapore)

2010-07-30

Research highlights: {yields} Short antimicrobial peptides with nine and eleven residues were developed. {yields} These peptides show strong bactericidal activity against clinically important bacterial and fungal pathogens. {yields} These peptides exhibit high stability in the presence of salts, and low cytotoxicity. {yields} These peptides exert their action by disrupting membrane lipids. -- Abstract: Short antimicrobial peptides with nine and eleven residues were developed against several clinically important bacterial and fungal pathogens (specifically Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Candida albicans, and Fusarium solani). Twelve analogues of previously reported peptides BP76 (KKLFKKILKFL) and Pac-525 (KWRRWVRWI) were designed, synthesized, and tested for their antimicrobial activities. Two of our eleven amino acid peptides, P11-5 (GKLFKKILKIL) and P11-6 (KKLIKKILKIL), have very low MICs of 3.1-12.5 {mu}g ml{sup -1} against all five pathogens. The MICs of these two peptides against S. aureus, C. albicans and F. solani are four to ten times lower than the corresponding MICs of the reference peptide BP76. P9-4 (KWRRWIRWL), our newly designed nine-amino acid analogue, also has particularly low MICs of 3.1-6.2 {mu}g ml{sup -1} against four of the tested pathogens; these MICs are two to eight times lower than those reported for Pac-525 (6.2-50 {mu}g ml{sup -1}).These new peptides (P11-5, P11-6 and P9-4) also exhibit improved stability in the presence of salts, and have low cytotoxicity as shown by the hemolysis and MTT assays. From the results of field-emission scanning electron microscopy, membrane depolarization and dye-leakage assays, we propose that these peptides exert their action by disrupting membrane lipids. Molecular dynamics simulation studies confirm that P11-6 peptide maintains relatively stable helical structure and exerts more perturbation action on the order of acyl tail of lipid bilayer.

Serum stabilities of short tryptophan- and arginine-rich antimicrobial peptide analogs.

Directory of Open Access Journals (Sweden)

Leonard T Nguyen

2010-09-01

Full Text Available Several short antimicrobial peptides that are rich in tryptophan and arginine residues were designed with a series of simple modifications such as end capping and cyclization. The two sets of hexapeptides are based on the Trp- and Arg-rich primary sequences from the "antimicrobial centre" of bovine lactoferricin as well as an antimicrobial sequence obtained through the screening of a hexapeptide combinatorial library.HPLC, mass spectrometry and antimicrobial assays were carried out to explore the consequences of the modifications on the serum stability and microbicidal activity of the peptides. The results show that C-terminal amidation increases the antimicrobial activity but that it makes little difference to its proteolytic degradation in human serum. On the other hand, N-terminal acetylation decreases the peptide activities but significantly increases their protease resistance. Peptide cyclization of the hexameric peptides was found to be highly effective for both serum stability and antimicrobial activity. However the two cyclization strategies employed have different effects, with disulfide cyclization resulting in more active peptides while backbone cyclization results in more proteolytically stable peptides. However, the benefit of backbone cyclization did not extend to longer 11-mer peptides derived from the same region of lactoferricin. Mass spectrometry data support the serum stability assay results and allowed us to determine preferred proteolysis sites in the peptides. Furthermore, isothermal titration calorimetry experiments showed that the peptides all had weak interactions with albumin, the most abundant protein in human serum.Taken together, the results provide insight into the behavior of the peptides in human serum and will therefore aid in advancing antimicrobial peptide design towards systemic applications.

Degradation of aromatic compounds in plants grown under aseptic conditions

Energy Technology Data Exchange (ETDEWEB)

Mithaishvili, T.; Ugrekhelidze, D.; Tsereteli, B.; Sadunishvili, T.; Kvesitadze, G. [Durmishidze Inst. of Biochemistry and Biotechnology, Academy of Sciences of Georgia, Tbilisi (Georgia); Scalla, R. [Lab. des Xenobiotiques, INRA, Toulouse (France)

2005-02-01

The aim of the work is to investigate the ability of higher plants to absorb and detoxify environmental pollutants - aromatic compounds via aromatic ring cleavage. Transformation of {sup 14}C specifically labelled benzene derivatives, [1-6-{sup 14}C]-nitrobenzene, [1-6-{sup 14}C]-aniline, [1-{sup 14}C]- and [7-{sup 14}C]-benzoic acid, in axenic seedlings of maize (Zea mays L.), kidney bean (Phaseolus vulgaris L.), pea (Pisum sativum L.) and pumpkin (Cucurbita pepo L.) were studied. After penetration in plants, the above xenobiotics are transformed by oxidative or reductive reactions, conjugation with cell endogenous compounds, and binding to biopolymers. The initial stage of oxidative degradation consists in hydroxylation reactions. The aromatic ring can then be cleaved and degraded into organic acids of the Krebs cycle. Ring cleavage is accompanied by {sup 14}CO{sub 2} evolution. Aromatic ring cleavage in plants has thus been demonstrated for different xenobiotics carrying different substitutions on their benzene ring. Conjugation with low molecular peptides is the main pathway of aromatic xenobiotics detoxification. Peptide conjugates are formed both by the initial xenobiotics (except nitrobenzene) and by intermediate transformation products. The chemical nature of the radioactive fragment and the amino acid composition of peptides participating in conjugation were identified. (orig.)

Short Anabolic Peptides for Bone Growth.

Science.gov (United States)

Amso, Zaid; Cornish, Jillian; Brimble, Margaret A

2016-07-01

Loss of bone occurs in the age-related skeletal disorder, osteoporosis, leading to bone fragility and increased incidence of fractures, which are associated with enormous costs and substantial morbidity and mortality. Recent data indicate that osteoporotic fractures are more common than other diseases, which usually attract public attention (e.g., heart attack and breast cancer). The prevention and treatment of this skeletal disorder are therefore of paramount importance. Majority of osteoporosis medications restore skeletal balance by reducing osteoclastic activity, thereby reducing bone resorption. These agents, however, do not regenerate damaged bone tissue, leaving limited options for patients once bone loss has occurred. Recently, attention has turned to bone-anabolic agents. Such agents have the ability to increase bone mass and strength, potentially reversing structural damage. To date, only one bone-anabolic drug is available in the market. The discovery of more novel, cost-effective bone anabolic agents is therefore a priority to treat those suffering from this disabling condition. Short peptides offer an important alternative for the development of novel bone-anabolic agents given their high target binding specificity, which translates into potent activity with limited side effects. This review summarizes attempts in the identification of bone-anabolic peptides, and their development for promoting bone growth. © 2016 Wiley Periodicals, Inc.

Serum Stabilities of Short Tryptophan-and Arginine-Rich Antimicrobial Peptide Analogs

NARCIS (Netherlands)

Nguyen, L.T.; Chau, J.K.; Perry, N.A.; de Boer, L.; Zaat, S.A.J.; Vogel, H.J.

2010-01-01

Background: Several short antimicrobial peptides that are rich in tryptophan and arginine residues were designed with a series of simple modifications such as end capping and cyclization. The two sets of hexapeptides are based on the Trp- and Arg-rich primary sequences from the "antimicrobial

Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters

Directory of Open Access Journals (Sweden)

Kenichi Dedachi

2013-01-01

Full Text Available Based on the observation that Ramachandran-type potential energy surfaces of single amino acid units in water are in good agreement with statistical structures of the corresponding amino acid residues in proteins, we recently developed a new all-atom force field called SAAP, in which the total energy function for a polypeptide is expressed basically as a sum of single amino acid potentials and electrostatic and Lennard-Jones potentials between the amino acid units. In this study, the SAAP force field (SAAPFF parameters were improved, and classical canonical Monte Carlo (MC simulation was carried out for short peptide models, that is, Met-enkephalin and chignolin, at 300 K in an implicit water model. Diverse structures were reasonably obtained for Met-enkephalin, while three folded structures, one of which corresponds to a native-like structure with three native hydrogen bonds, were obtained for chignolin. The results suggested that the SAAP-MC method is useful for conformational sampling for the short peptides. A protocol of SAAP-MC simulation followed by structural clustering and examination of the obtained structures by ab initio calculation or simply by the number of the hydrogen bonds (or the hardness was demonstrated to be an effective strategy toward structure prediction for short peptide molecules.

Designed β-Boomerang Antiendotoxic and Antimicrobial Peptides

Science.gov (United States)

Bhunia, Anirban; Mohanram, Harini; Domadia, Prerna N.; Torres, Jaume; Bhattacharjya, Surajit

2009-01-01

Lipopolysaccharide (LPS), an integral part of the outer membrane of Gram-negative bacteria, is involved in a variety of biological processes including inflammation, septic shock, and resistance to host-defense molecules. LPS also provides an environment for folding of outer membrane proteins. In this work, we describe the structure-activity correlation of a series of 12-residue peptides in LPS. NMR structures of the peptides derived in complex with LPS reveal boomerang-like β-strand conformations that are stabilized by intimate packing between the two aromatic residues located at the 4 and 9 positions. This structural feature renders these peptides with a high ability to neutralize endotoxicity, >80% at 10 nm concentration, of LPS. Replacements of these aromatic residues either with Ala or with Leu destabilizes the boomerang structure with the concomitant loss of antiendotoxic and antimicrobial activities. Furthermore, the aromatic packing stabilizing the β-boomerang structure in LPS is found to be maintained even in a truncated octapeptide, defining a structured LPS binding motif. The mode of action of the active designed peptides correlates well with their ability to perturb LPS micelle structures. Fourier transform infrared spectroscopy studies of the peptides delineate β-type conformations and immobilization of phosphate head groups of LPS. Trp fluorescence studies demonstrated selective interactions with LPS and the depth of insertion into the LPS bilayer. Our results demonstrate the requirement of LPS-specific structures of peptides for endotoxin neutralizations. In addition, we propose that structures of these peptides may be employed to design proteins for the outer membrane. PMID:19520860

Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns

DEFF Research Database (Denmark)

Larsen, Martin Røssel; Thingholm, Tine E; Jensen, Ole N

2005-01-01

based on TiO2microcolumns and peptide loading in 2,5-dihydroxybenzoic acid (DHB). The effect of DHB was a very efficient reduction in the binding of nonphosphorylated peptides to TiO2 while retaining its high binding affinity for phosphorylated peptides. Thus, inclusion of DHB dramatically increased...... the selectivity of the enrichment of phosphorylated peptides by TiO2. We demonstrated that this new procedure was more selective for binding phosphorylated peptides than IMAC using MALDI mass spectrometry. In addition, we showed that LC-ESI-MSMS was biased toward monophosphorylated peptides, whereas MALDI MS...... was not. Other substituted aromatic carboxylic acids were also capable of specifically reducing binding of nonphosphorylated peptides, whereas phosphoric acid reduced binding of both phosphorylated and nonphosphorylated peptides. A putative mechanism for this intriguing effect is presented....

Hypothesis driven development of new adjuvants: short peptides as immunomodulators.

Science.gov (United States)

Dong, Jessica C; Kobinger, Gary P

2013-04-01

To date, vaccinations have been one of the key strategies in the prevention and protection against infectious pathogens. Traditional vaccines have well-known limitations such as safety and efficacy issues, which consequently deems it inappropriate for particular populations and may not be an effective strategy against all pathogens. This evidence highlights the need to develop more efficacious vaccination regiments. Higher levels of protection can be achieved by the addition of immunostimulating adjuvants. Many adjuvants elicit strong, undefined inflammation, which produces increased immunogenicity but may also lead to undesirable effects. Hypothesis driven development of adjuvants is needed to achieve a more specific and directed immune response required for optimal and safe vaccine-induced immune protection. An example of such hypothesis driven development includes the use of short immunomodulating peptides as adjuvants. These peptides have the ability to influence the immune response and can be extrapolated for adjuvant use, but requires further investigation.

Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson-Crick base pairing.

Science.gov (United States)

Berger, Or; Adler-Abramovich, Lihi; Levy-Sakin, Michal; Grunwald, Assaf; Liebes-Peer, Yael; Bachar, Mor; Buzhansky, Ludmila; Mossou, Estelle; Forsyth, V Trevor; Schwartz, Tal; Ebenstein, Yuval; Frolow, Felix; Shimon, Linda J W; Patolsky, Fernando; Gazit, Ehud

2015-04-01

The two main branches of bionanotechnology involve the self-assembly of either peptides or DNA. Peptide scaffolds offer chemical versatility, architectural flexibility and structural complexity, but they lack the precise base pairing and molecular recognition available with nucleic acid assemblies. Here, inspired by the ability of aromatic dipeptides to form ordered nanostructures with unique physical properties, we explore the assembly of peptide nucleic acids (PNAs), which are short DNA mimics that have an amide backbone. All 16 combinations of the very short di-PNA building blocks were synthesized and assayed for their ability to self-associate. Only three guanine-containing di-PNAs-CG, GC and GG-could form ordered assemblies, as observed by electron microscopy, and these di-PNAs efficiently assembled into discrete architectures within a few minutes. The X-ray crystal structure of the GC di-PNA showed the occurrence of both stacking interactions and Watson-Crick base pairing. The assemblies were also found to exhibit optical properties including voltage-dependent electroluminescence and wide-range excitation-dependent fluorescence in the visible region.

Short, multiple-stranded β-hairpin peptides have antimicrobial potency with high selectivity and salt resistance.

Science.gov (United States)

Chou, Shuli; Shao, Changxuan; Wang, Jiajun; Shan, Anshan; Xu, Lin; Dong, Na; Li, Zhongyu

2016-01-01

The β-hairpin structure has been proposed to exhibit potent antimicrobial properties with low cytotoxicity, thus, multiple β-hairpin structures have been proved to be highly stable in structures containing tightly packed hydrophobic cores. The aim of this study was to develop peptide-based synthetic strategies for generating short, but effective AMPs as inexpensive antimicrobial agents. Multiple-stranded β-hairpin peptides with the same β-hairpin unit, (WRXxRW)n where n=1, 2, 3, or 4 and Xx represent the turn sequence, were synthesized, and their potential as antimicrobial agents was evaluated. Owning to the tightly packed hydrophobic core and paired Trp of this multiple-stranded β-hairpin structure, all the 12-residues peptides exhibited high cell selectivity towards bacterial cells over human red blood cells (hRBCs), and the peptide W2 exhibited stronger antimicrobial activities with the MIC values of 2-8μM against various tested bacteria. Not only that, but W2 also showed obvious synergy with streptomycin and chloramphenicol against Escherichia coli, and displayed synergy with ciprofloxacin against Staphylococcus aureus with the FICI values ⩽0.5. Fluorescence spectroscopy and electron microscopy analyses indicated that W2 kills microbial cells by permeabilizing the cell membrane and damaging membrane integrity. Collectively, based on the multiple β-hairpin peptides, the ability to develop libraries of short and effective peptides will be a powerful approach to the discovery of novel antimicrobial agents. We successfully screened a peptide W2 ((WRPGRW)2) from a series of multiple-stranded β-hairpin antimicrobial peptides based on the "S-shaped" motif that induced the formation of a globular structure, and Trp zipper was used to replace the disulfide bonds to reduce the cost of production. This novel structure applied to AMPs improved cell selectivity and salt stability. The findings of this study will promote the development of peptide

UV laser-induced cross-linking in peptides

Science.gov (United States)

Leo, Gabriella; Altucci, Carlo; Bourgoin-Voillard, Sandrine; Gravagnuolo, Alfredo M.; Esposito, Rosario; Marino, Gennaro; Costello, Catherine E.; Velotta, Raffaele; Birolo, Leila

2013-01-01

RATIONALE The aim of this study was to demonstrate, and to characterize by high resolution mass spectrometry, that it is possible to preferentially induce covalent cross-links in peptides by using high energy femtosecond UV laser pulses. The cross-link is readily formed only when aromatic amino acids are present in the peptide sequence. METHODS Three peptides, xenopsin, angiotensin I, interleukin, individually or in combination, were exposed to high energy femtosecond UV laser pulses, either alone or in the presence of spin trapping molecules, the reaction products being characterized by high resolution mass spectrometry. RESULTS High resolution mass spectrometry and spin trapping strategies showed that cross-linking occurs readily, proceeds via a radical mechanism, and is the highly dominant reaction, proceeding without causing significant photo-damage in the investigated range of experimental parameters. CONCLUSIONS High energy femtosecond UV laser pulses can be used to induce covalent cross-links between aromatic amino acids in peptides, overcoming photo-oxidation processes, that predominate as the mean laser pulse intensity approaches illumination conditions achievable with conventional UV light sources. PMID:23754800

Phosphorylation-induced conformational changes in short peptides probed by fluorescence resonance energy transfer in the 10A domain.

Science.gov (United States)

Sahoo, Harekrushna; Nau, Werner M

2007-03-26

Phosphorylation-induced conformational changes in short polypeptides were probed by a fluorescence resonance energy transfer (FRET) method by employing a short-distance FRET pair (R(0) approximately 10 A) based on tryptophan as natural donor and a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) as synthetic acceptor. Two substrates for kinases, LeuArgArgTrpSerLeuGly-Dbo (peptide I) and TrpLysArgThrLeuArgArg-Dbo (peptide II), were investigated, with serine and threonine, respectively, as phosphorylation sites. Steady-state and time-resolved fluorescence experiments in H(2)O revealed a decrease in FRET efficiency for peptide I and an increase for peptide II; this suggested that the effective distances between donor and acceptor increased and decreased, respectively. The same trends and similar absolute variations in effective donor-acceptor distances were observed in propylene glycol, a less polar and highly viscous solvent; this suggested that the variations are due to intrinsic structural preferences. Fitting of the time-resolved decay traces according to a distribution function model (Gaussian distribution) provided the mean donor-acceptor distances, which showed an increase upon phosphorylation for peptide I (from 9.7 to 10.5 A) and a decrease for peptide II (from 10.9 to 9.3 A) in H(2)O. The broadness (half-width) of the distributions, which provides a measure of the rigidity of the peptides, remained similar upon phosphorylation of peptide I (3.0 versus 3.1 A), but decreased for peptide II (from 3.1 to 0.73 A in H(2)O); this suggests a more compact, structured conformation upon phosphorylation of the latter peptide. The elongation of the peptide backbone (by ca. 0.7 A) for peptide I is attributed to an increase in steric demand upon phosphorylation, which favors an extended conformation. The contraction (by ca. 1.4 A) and structural rigidification of peptide II is attributed to attractive Coulombic interactions and hydrogen bonding between the

Dynamic stability of nano-fibers self-assembled from short amphiphilic A6D peptides.

Science.gov (United States)

Nikoofard, Narges; Maghsoodi, Fahimeh

2018-04-07

Self-assembly of A 6 D amphiphilic peptides in explicit water is studied by using coarse-grained molecular dynamics simulations. It is observed that the self-assembly of randomly distributed A 6 D peptides leads to the formation of a network of nano-fibers. Two other simulations with cylindrical nano-fibers as the initial configuration show the dynamic stability of the self-assembled nano-fibers. As a striking feature, notable fluctuations occur along the axes of the nano-fibers. Depending on the number of peptides per unit length of the nano-fiber, flat-shaped bulges or spiral shapes along the nano-fiber axis are observed at the fluctuations. Analysis of the particle distribution around the nano-fiber indicates that the hydrophobic core and the hydrophilic shell of the nano-structure are preserved in both simulations. The size of the deformations and their correlation times are different in the two simulations. This study gives new insights into the dynamics of the self-assembled nano-structures of short amphiphilic peptides.

Dynamic stability of nano-fibers self-assembled from short amphiphilic A6D peptides

Science.gov (United States)

Nikoofard, Narges; Maghsoodi, Fahimeh

2018-04-01

Self-assembly of A6D amphiphilic peptides in explicit water is studied by using coarse-grained molecular dynamics simulations. It is observed that the self-assembly of randomly distributed A6D peptides leads to the formation of a network of nano-fibers. Two other simulations with cylindrical nano-fibers as the initial configuration show the dynamic stability of the self-assembled nano-fibers. As a striking feature, notable fluctuations occur along the axes of the nano-fibers. Depending on the number of peptides per unit length of the nano-fiber, flat-shaped bulges or spiral shapes along the nano-fiber axis are observed at the fluctuations. Analysis of the particle distribution around the nano-fiber indicates that the hydrophobic core and the hydrophilic shell of the nano-structure are preserved in both simulations. The size of the deformations and their correlation times are different in the two simulations. This study gives new insights into the dynamics of the self-assembled nano-structures of short amphiphilic peptides.

Folding very short peptides using molecular dynamics.

Directory of Open Access Journals (Sweden)

Bosco K Ho

2006-04-01

Full Text Available Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides, the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.

Short-peptide-based molecular hydrogels: novel gelation strategies and applications for tissue engineering and drug delivery

Science.gov (United States)

Wang, Huaimin; Yang, Zhimou

2012-08-01

Molecular hydrogels hold big potential for tissue engineering and controlled drug delivery. Our lab focuses on short-peptide-based molecular hydrogels formed by biocompatible methods and their applications in tissue engineering (especially, 3D cell culture) and controlled drug delivery. This feature article firstly describes our recent progresses of the development of novel methods to form hydrogels, including the strategy of disulfide bond reduction and assistance with specific protein-peptide interactions. We then introduce the applications of our hydrogels in fields of controlled stem cell differentiation, cell culture, surface modifications of polyester materials by molecular self-assembly, and anti-degradation of recombinant complex proteins. A novel molecular hydrogel system of hydrophobic compounds that are only formed by hydrolysis processes was also included in this article. The hydrogels of hydrophobic compounds, especially those of hydrophobic therapeutic agents, may be developed into a carrier-free delivery system for long term delivery of therapeutic agents. With the efforts in this field, we believe that molecular hydrogels formed by short peptides and hydrophobic therapeutic agents can be practically applied for 3D cell culture and long term drug delivery in near future, respectively.

Designed beta-boomerang antiendotoxic and antimicrobial peptides: structures and activities in lipopolysaccharide.

Science.gov (United States)

Bhunia, Anirban; Mohanram, Harini; Domadia, Prerna N; Torres, Jaume; Bhattacharjya, Surajit

2009-08-14

Lipopolysaccharide (LPS), an integral part of the outer membrane of Gram-negative bacteria, is involved in a variety of biological processes including inflammation, septic shock, and resistance to host-defense molecules. LPS also provides an environment for folding of outer membrane proteins. In this work, we describe the structure-activity correlation of a series of 12-residue peptides in LPS. NMR structures of the peptides derived in complex with LPS reveal boomerang-like beta-strand conformations that are stabilized by intimate packing between the two aromatic residues located at the 4 and 9 positions. This structural feature renders these peptides with a high ability to neutralize endotoxicity, >80% at 10 nM concentration, of LPS. Replacements of these aromatic residues either with Ala or with Leu destabilizes the boomerang structure with the concomitant loss of antiendotoxic and antimicrobial activities. Furthermore, the aromatic packing stabilizing the beta-boomerang structure in LPS is found to be maintained even in a truncated octapeptide, defining a structured LPS binding motif. The mode of action of the active designed peptides correlates well with their ability to perturb LPS micelle structures. Fourier transform infrared spectroscopy studies of the peptides delineate beta-type conformations and immobilization of phosphate head groups of LPS. Trp fluorescence studies demonstrated selective interactions with LPS and the depth of insertion into the LPS bilayer. Our results demonstrate the requirement of LPS-specific structures of peptides for endotoxin neutralizations. In addition, we propose that structures of these peptides may be employed to design proteins for the outer membrane.

Temperature dependence of looping rates in a short peptide.

Science.gov (United States)

Roccatano, Danilo; Sahoo, Harekrushna; Zacharias, Martin; Nau, Werner M

2007-03-15

Knowledge of the influence of chain length and amino acid sequence on the structural and dynamic properties of small peptides in solution provides essential information on protein folding pathways. The combination of time-resolved optical spectroscopy and molecular dynamics (MD) simulation methods has become a powerful tool to investigate the kinetics of end-to-end collisions (looping rates) in short peptides, which are relevant in early protein folding events. We applied the combination of both techniques to study temperature-dependent (280-340 K) looping rates of the Dbo-AlaGlyGln-Trp-NH2 peptide, where Dbo represents a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine, which served as a fluorescent probe in the time-resolved spectroscopic experiments. The experimental looping rates increased from 4.8 x 10(7) s(-1) at 283 K to 2.0 x 10(8) s(-1) at 338 K in H2O. The corresponding Arrhenius plot provided as activation parameters Ea = 21.5 +/- 1.0 kJ mol(-1) and ln(A/s-1) = 26.8 +/- 0.2 in H2O. The results in D2O were consistent with a slight solvent viscosity effect, i.e., the looping rates were 10-20% slower. MD simulations were performed with the GROMOS96 force field in a water solvent model, which required first a parametrization of the synthetic amino acid Dbo. After corrections for solvent viscosity effects, the calculated looping rates varied from 1.5 x 10(8) s(-1) at 280 K to 8.2 x 10(8) s(-1) at 340 K in H2O, which was about four times larger than the experimental data. The calculated activation parameters were Ea = 24.7 +/- 1.5 kJ mol(-1) and ln(A/s(-1)) = 29.4 +/- 0.1 in H2O.

Critical point measurement of some polycyclic aromatic hydrocarbons

International Nuclear Information System (INIS)

Nikitin, Eugene D.; Popov, Alexander P.

2015-01-01

Highlights: • Critical properties of five polycyclic aromatic hydrocarbons were measured. • These hydrocarbons decompose at near-critical temperatures. • Pulse-heating method with short residence times was used. - Abstract: The critical temperatures and the critical pressures of five polycyclic aromatic compounds, namely, acenaphthene, fluorene, anthracene, phenanthrene, and pyrene have been measured. All the compounds studied decompose at near-critical temperatures. A pulse-heating technique applicable to measuring the critical properties of thermally unstable compounds has been used. The times from the beginning of a heating pulse to the moment of reaching the critical temperature were from (0.06 to 0.85) ms. The short residence times provide little degradation of the substances in the course of the experiments. The experimental critical parameters of the polycyclic aromatic compounds have been compared with those estimated by five predictive methods. The acentric factors of polycyclic aromatic compounds studied have been calculated

Acute effects of the Glucagon-Like Peptide 2 analogue, teduglutide, on intestinal adaptation in newborn pigs with short bowel syndrome

DEFF Research Database (Denmark)

Thymann, Thomas; Stoll, Barbara; Mecklenburg, Lars

2014-01-01

Neonatal short bowel syndrome following massive gut resection associates with malabsorption of nutrients. The intestinotrophic factor glucagon-like peptide 2 (GLP-2) improves gut function in adult short bowel patients, but its effect in pediatric patients remains unknown. Our objective was to test...

Enzymatic digestibility of peptides cross-linked by ionizing radiation

International Nuclear Information System (INIS)

Dizdaroglu, M.; Gajewski, E.; Simic, M.G.

1984-01-01

Digestibility by proteolytic enzymes of peptides cross-linked by ionizing radiation was investigated. Small peptides of alanine and phenylalanine were chosen as model compounds and aminopeptidases and carboxypeptidases were used as proteolytic enzymes. Peptides exposed to γ-radiation in aqueous solution were analysed by high-performance liquid chromatography before and after hydrolysis by aminopeptidase M, leucine aminopeptidase carboxypeptidase A and carboxypeptidase Y. The results obtained clearly demonstrate the different actions of these enzymes on cross-linked aliphatic and aromatic peptides. Peptide bonds of cross-linked dipeptides of alanine were completely resistant to enzymatic hydrolysis whereas the enzymes, except for carboxypeptidase Y, cleaved all peptide bonds of cross-linked peptides of phenylalanine. The actions of the enzymes on these particular compounds are discussed in detail. (author)

Structural Polymorphism in a Self-Assembled Tri-Aromatic Peptide System.

Science.gov (United States)

Brown, Noam; Lei, Jiangtao; Zhan, Chendi; Shimon, Linda J W; Adler-Abramovich, Lihi; Wei, Guanghong; Gazit, Ehud

2018-04-24

Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility, and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and interesting and varied characteristics. The larger triphenylalanine peptide (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures. Here, to understand the effect of triaromatic systems on the self-assembly process, we examined carboxybenzyl-protected diphenylalanine (z-FF) as a minimal model for such an arrangement. We explored different self-assembly conditions by changing solvent compositions and peptide concentrations, generating a phase diagram for the assemblies. We discovered that z-FF can form a variety of structures, including nanowires, fibers, nanospheres, and nanotoroids, the latter were previously observed only in considerably larger or co-assembly systems. Secondary structure analysis revealed that all assemblies possessed a β-sheet conformation. Additionally, in solvent combinations with high water ratios, z-FF formed rigid and self-healing hydrogels. X-ray crystallography revealed a "wishbone" structure, in which z-FF dimers are linked by hydrogen bonds mediated by methanol molecules, with a 2-fold screw symmetry along the c-axis. All-atom molecular dynamics (MD) simulations revealed conformations similar to the crystal structure. Coarse-grained MD simulated the assembly of the peptide into either fibers or spheres in different solvent systems, consistent with the experimental results. This work thus expands the building block library for the fabrication of nanostructures by peptide self-assembly.

Control of peptide nanotube diameter by chemical modifications of an aromatic residue involved in a single close contact

Science.gov (United States)

Tarabout, Christophe; Roux, Stéphane; Gobeaux, Frédéric; Fay, Nicolas; Pouget, Emilie; Meriadec, Cristelle; Ligeti, Melinda; Thomas, Daniel; IJsselstijn, Maarten; Besselievre, François; Buisson, David-Alexandre; Verbavatz, Jean-Marc; Petitjean, Michel; Valéry, Céline; Perrin, Lionel; Rousseau, Bernard; Artzner, Franck; Paternostre, Maité; Cintrat, Jean-Christophe

2011-01-01

Supramolecular self-assembly is an attractive pathway for bottom-up synthesis of novel nanomaterials. In particular, this approach allows the spontaneous formation of structures of well-defined shapes and monodisperse characteristic sizes. Because nanotechnology mainly relies on size-dependent physical phenomena, the control of monodispersity is required, but the possibility of tuning the size is also essential. For self-assembling systems, shape, size, and monodispersity are mainly settled by the chemical structure of the building block. Attempts to change the size notably by chemical modification usually end up with the loss of self-assembly. Here, we generated a library of 17 peptides forming nanotubes of monodisperse diameter ranging from 10 to 36 nm. A structural model taking into account close contacts explains how a modification of a few Å of a single aromatic residue induces a fourfold increase in nanotube diameter. The application of such a strategy is demonstrated by the formation of silica nanotubes of various diameters. PMID:21518895

Short-term administration of glucagon-like peptide-2. Effects on bone mineral density and markers of bone turnover in short-bowel patients with no colon

DEFF Research Database (Denmark)

Haderslev, K V; Jeppesen, P B; Hartmann, B

2002-01-01

Glucagon-like peptide 2 (GLP-2) is a newly discovered intestinotrophic hormone. We have recently reported that a 5-week GLP-2 treatment improved the intestinal absorptive capacity of short-bowel patients with no colon. Additionally, GLP-2 treatment was associated with changes in body composition ...

Short-term effects of beta-amyloid25-35 peptide aggregates on transmitter release in neuromuscular synapses.

Science.gov (United States)

Garcia, Neus; Santafé, Manel M; Tomàs, Marta; Lanuza, Maria A; Tomàs, Josep

2008-03-01

The beta-amyloid (AB) peptide25-35 contains the functional domain of the AB precursor protein that is both required for neurotrophic effects in normal neural tissues and is involved in the neurotoxic effects in Alzheimer disease. We demonstrated the presence of the amyloid precursor protein/AB peptide in intramuscular axons, presynaptic motor nerve terminals, terminal and myelinating Schwann cells, and the postsynaptic and subsarcolemmal region in the Levator auris longus muscle of adult rats by immunocytochemistry. Using intracellular recording, we investigated possible short-term functional effects of the AB fragment (0.1-10 micromol/L) on acetylcholine release in adult and newborn motor end plates. We found no change in evoked, spontaneous transmitter release or resting membrane potential of the muscle cells. A previous block of the presynaptic muscarinic receptor subtypes and a previous block or stimulation of protein kinase C revealed no masked effect of the peptide on the regulation of transmitter release. The aggregated form of AB peptide25-35, however, interfered acutely with acetylcholine release (quantal content reduction) when synaptic activity was maintained by electric stimulation. The possible relevance of this inhibition of neurotransmission by AB peptide25-35 to the pathogenesis of Alzheimer remains to be determined.

Increased electrical conductivity of peptides through annealing process

Directory of Open Access Journals (Sweden)

Seok Daniel Namgung

2017-08-01

Full Text Available Biocompatible biologically occurring polymer is suggested as a component of human implantable devices since conventional inorganic materials are apt to trigger inflammation and toxicity problem within human body. Peptides consisting of aromatic amino acid, tyrosine, are chosen, and enhancement on electrical conductivity is studied. Annealing process gives rise to the decrease on resistivity of the peptide films and the growth of the carrier concentration is a plausible reason for such a decrease on resistivity. The annealed peptides are further applied to an active layer of field effect transistor, in which low on/off current ratio (∼10 is obtained.

Design and evaluation of antimalarial peptides derived from prediction of short linear motifs in proteins related to erythrocyte invasion.

Directory of Open Access Journals (Sweden)

Alessandra Bianchin

Full Text Available The purpose of this study was to investigate the blood stage of the malaria causing parasite, Plasmodium falciparum, to predict potential protein interactions between the parasite merozoite and the host erythrocyte and design peptides that could interrupt these predicted interactions. We screened the P. falciparum and human proteomes for computationally predicted short linear motifs (SLiMs in cytoplasmic portions of transmembrane proteins that could play roles in the invasion of the erythrocyte by the merozoite, an essential step in malarial pathogenesis. We tested thirteen peptides predicted to contain SLiMs, twelve of them palmitoylated to enhance membrane targeting, and found three that blocked parasite growth in culture by inhibiting the initiation of new infections in erythrocytes. Scrambled peptides for two of the most promising peptides suggested that their activity may be reflective of amino acid properties, in particular, positive charge. However, one peptide showed effects which were stronger than those of scrambled peptides. This was derived from human red blood cell glycophorin-B. We concluded that proteome-wide computational screening of the intracellular regions of both host and pathogen adhesion proteins provides potential lead peptides for the development of anti-malarial compounds.

A cyclic peptidic serine protease inhibitor

DEFF Research Database (Denmark)

Zhao, Baoyu; Xu, Peng; Jiang, Longguang

2014-01-01

Peptides are attracting increasing interest as protease inhibitors. Here, we demonstrate a new inhibitory mechanism and a new type of exosite interactions for a phage-displayed peptide library-derived competitive inhibitor, mupain-1 (CPAYSRYLDC), of the serine protease murine urokinase...... pocket, its carbonyl group aligning improperly relative to Ser195 and the oxyanion hole, explaining why the peptide is an inhibitor rather than a substrate. Substitution of the P1 Arg with novel unnatural Arg analogues with aliphatic or aromatic ring structures led to an increased affinity, depending......, in spite of a less favorable binding entropy and loss of a polar interaction. We conclude that increased flexibility of the peptide allows more favorable exosite interactions, which, in combination with the use of novel Arg analogues as P1 residues, can be used to manipulate the affinity and specificity...

Transition metal ions mediated tyrosine based short peptide amphiphile nanostructures inhibit bacterial growth.

Science.gov (United States)

Joshi, Khashti Ballabh; Singh, Ramesh; Mishra, Narendra Kumar; Kumar, Vikas; Vinayak, Vandana

2018-05-17

We report the design and synthesis of biocompatible small peptide based molecule for the controlled and targeted delivery of the encapsulated bioactive metal ions via transforming their internal nanostructures. Tyrosine based short peptide amphiphile (sPA) was synthesized which self-assembled into β-sheet like secondary structures. The self assembly of the designed sPA was modulated by using different bioactive transition metal ions which is confirmed by spectroscopic and microscopic techniques. These bioactive metal ions conjugated sPA hybrid structures are further used to develop antibacterial materials. It is due to the excellent antibacterial activity of zinc ions that the growth of clinically relevant bacteria such as E. Coli was inhibited in the presence of zinc-sPA conjugate. The bacterial test demonstrated that owing to high biocompatibility with bacterial cell, the designed sPA worked as metal ions delivery agent and therefore it can show great potential in locally addressing bacterial infections. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of positively charged short peptides on stability of cubic phases of monoolein/dioleoylphosphatidic acid mixtures.

Science.gov (United States)

Masum, Shah Md; Li, Shu Jie; Awad, Tarek S; Yamazaki, Masahito

2005-06-07

To elucidate the stability and phase transition of cubic phases of biomembranes with infinite periodic minimal surface is indispensable from biological and physicochemical aspects. In this report, we investigated the effect of positively charged peptide-3K (LLKKK) and poly(L-lysine) on the phase stability of monoolein (MO) membranes containing negatively charged dioleoylphosphatidic acid (DOPA) (i.e., DOPA/MO membranes) using small-angle X-ray scattering. At first, the effect of peptide-3K on 10% DOPA/90% MO membrane in excess water, which is in the Q229 phase, was investigated. At 3.4 mM peptide-3K, a Q229 to Q230 phase transition occurred, and at >3.4 mM peptide-3K, the membrane was in the Q230 phase. Poly(L-lysine) (M(w) 1K-4K) also induced the Q230 phase, but peptide-2K (LLKK) could not induce it in the same membrane. We also investigated the effect of peptide-3K on the multilamellar vesicle (MLV) of 25% DOPA/75% MO membrane, which is in L(alpha) phase. In the absence of peptide, the spacing of MLV was very large (11.3 nm), but at > or = 8 mM peptide-3K, it greatly decreased to a constant value (5.2 nm), irrespective of the peptide concentration, indicating that peptide-3K and the membranes form an electrostatically stabilized aggregation with low water content. Poly(L-lysine) also decreased greatly the spacing of the 25% DOPA/75% MO MLV, indicating the formation of a similar aggregation. To compare the effects of peptide-3K and poly(L-lysine) with that of osmotic stress on stability of the cubic phase, we investigated the effect of poly(ethylene glycol) with molecular weight 7500 (PEG-6K) on the phase stability of 10% DOPA/90% MO membrane. With an increase in PEG-6K concentration, i.e., with an increase in osmotic stress, the most stable phase changed as follows; Q229 (Schwartz's P surface) --> Q224 (D) --> Q230 (G). On the basis of these results, we discuss the mechanism of the effects of the positively charged short peptides (peptide-3K) and poly

Characterization of model peptide adducts with reactive metabolites of naphthalene by mass spectrometry.

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Nathalie T Pham

Full Text Available Naphthalene is a volatile polycyclic aromatic hydrocarbon generated during combustion and is a ubiquitous chemical in the environment. Short term exposures of rodents to air concentrations less than the current OSHA standard yielded necrotic lesions in the airways and nasal epithelium of the mouse, and in the nasal epithelium of the rat. The cytotoxic effects of naphthalene have been correlated with the formation of covalent protein adducts after the generation of reactive metabolites, but there is little information about the specific sites of adduction or on the amino acid targets of these metabolites. To better understand the chemical species produced when naphthalene metabolites react with proteins and peptides, we studied the formation and structure of the resulting adducts from the incubation of model peptides with naphthalene epoxide, naphthalene diol epoxide, 1,2-naphthoquinone, and 1,4-naphthoquinone using high resolution mass spectrometry. Identification of the binding sites, relative rates of depletion of the unadducted peptide, and selectivity of binding to amino acid residues were determined. Adduction occurred on the cysteine, lysine, and histidine residues, and on the N-terminus. Monoadduct formation occurred in 39 of the 48 reactions. In reactions with the naphthoquinones, diadducts were observed, and in one case, a triadduct was detected. The results from this model peptide study will assist in data interpretation from ongoing work to detect peptide adducts in vivo as markers of biologic effect.

Modulation of intra- and inter-sheet interactions in short peptide self-assembly by acetonitrile in aqueous solution

International Nuclear Information System (INIS)

Deng Li; Zhao Yurong; Zhou Peng; Xu Hai; Wang Yanting

2016-01-01

Besides our previous experimental discovery (Zhao Y R, et al . 2015 Langmuir , 31, 12975) that acetonitrile (ACN) can tune the morphological features of nanostructures self-assembled by short peptides KIIIIK (KI4K) in aqueous solution, further experiments reported in this work demonstrate that ACN can also tune the mass of the self-assembled nanostructures. To understand the microscopic mechanism how ACN molecules interfere peptide self-assembly process, we conducted a series of molecular dynamics simulations on a monomer, a cross- β sheet structure, and a proto-fibril of KI4K in pure water, pure ACN, and ACN-water mixtures, respectively. The simulation results indicate that ACN enhances the intra-sheet interaction dominated by the hydrogen bonding (H-bonding) interactions between peptide backbones, but weakens the inter-sheet interaction dominated by the interactions between hydrophobic side chains. Through analyzing the correlations between different groups of solvent and peptides and the solvent behaviors around the proto-fibril, we have found that both the polar and nonpolar groups of ACN play significant roles in causing the opposite effects on intermolecular interactions among peptides. The weaker correlation of the polar group of ACN than water molecule with the peptide backbone enhances H-bonding interactions between peptides in the proto-fibril. The stronger correlation of the nonpolar group of ACN than water molecule with the peptide side chain leads to the accumulation of ACN molecules around the proto-fibril with their hydrophilic groups exposed to water, which in turn allows more water molecules close to the proto-fibril surface and weakens the inter-sheet interactions. The two opposite effects caused by ACN form a microscopic mechanism clearly explaining our experimental observations. (paper)

Structural Insights into the Mechanisms of Action of Short-Peptide HIV-1 Fusion Inhibitors Targeting the Gp41 Pocket

Directory of Open Access Journals (Sweden)

Xiujuan Zhang

2018-02-01

Full Text Available The deep hydrophobic pocket of HIV-1 gp41 has been considered a drug target, but short-peptides targeting this site usually lack potent antiviral activity. By applying the M-T hook structure, we previously generated highly potent short-peptide fusion inhibitors that specifically targeted the pocket site, such as MT-SC22EK, HP23L, and LP-11. Here, the crystal structures of HP23L and LP-11 bound to the target mimic peptide N36 demonstrated the critical intrahelical and interhelical interactions, especially verifying that the hook-like conformation was finely adopted while the methionine residue was replaced by the oxidation-less prone residue leucine, and that addition of an extra glutamic acid significantly enhanced the binding and inhibitory activities. The structure of HP23L bound to N36 with two mutations (E49K and L57R revealed the critical residues and motifs mediating drug resistance and provided new insights into the mechanism of action of inhibitors. Therefore, the present data help our understanding for the structure-activity relationship (SAR of HIV-1 fusion inhibitors and facilitate the development of novel antiviral drugs.

Mechanism of action and in vitro activity of short hybrid antimicrobial peptide PV3 against Pseudomonas aeruginosa

International Nuclear Information System (INIS)

Memariani, Hamed; Shahbazzadeh, Delavar; Sabatier, Jean-Marc; Memariani, Mojtaba; Karbalaeimahdi, Ali; Bagheri, Kamran Pooshang

2016-01-01

Antimicrobial peptides are attractive candidates for developing novel therapeutic agents, since they are lethal to a broad spectrum of pathogens and have a unique low tendency for resistance development. In this study, mechanism of action and in vitro anti-pseudomonal activity of previously designed short hybrid antimicrobial peptide PV3 were investigated. Compared to ceftazidime, PV3 had not only higher antibacterial activity but also faster bactericidal activity. PV3 reduced biofilm biomass and viability of biofilm embedded bacteria in a concentration-dependent manner. Although the antimicrobial activity of PV3 was reduced in Mueller-Hinton broth (MHB) containing human serum, it was still active enough to eradication of bacteria at low concentrations. Compared with standard condition (MHB only), there was no significant decrease in antibacterial activity of PV3 against P. aeruginosa strains under 150 mM NaCl (p = 0.615) and 1 mM MgCl 2 (p = 0.3466). Fluorescence microscopy and field emission scanning electron microscopy further indicated that PV3 killed bacteria by disrupting the cell membrane. Since PV3 has potent anti-pseudomonal activity and has little cytotoxicity in vitro, it seems plausible that the peptide should be further investigated with animal studies to support future pharmacological formulations and potential topical applications. - Highlights: • PV3 killed Pseudomonas aeruginosa by membrane-disrupting mechanism. • PV3 reduced biofilm biomass and viability of biofilm embedded bacteria in a concentration-dependent manner. • Short hybrid antimicrobial peptide PV3 exhibited higher and faster bactericidal activity comparing to ceftazidime.

Spin-trapping and ESR studies of the direct photolysis of aromatic amino acids, dipeptides, tripeptides and polypeptides in aqueous solutions-II. Tyrosine and related compounds

Energy Technology Data Exchange (ETDEWEB)

Lion, Y; Kuwabara, M; Riesz, P [National Cancer Inst., Bethesda, MD (USA)

1982-01-01

The UV-photolysis of peptides containing tyrosine (Tyr) was investigated in aqueous solutions at room temperature at 220 and 265 nm. The short-lived free radicals formed during photolysis were spin-trapped by t-nitrosobutane and identified by electron spin resonance. For N-acetyl-and N-formyl-L-Tyr and for peptides containing L-Tyr as the middle residue, photolysis at 265 nm under neutral conditions produced mainly spin-adducts due to the scission between the alpha carbon and the methylene group attached to the aromatic ring, while at 220 nm decarboxylation radicals were spin-trapped. Photolysis of di- and tripeptides at 275 nm in alkaline solutions predominantly generated deamination radicals. The radicals produced in the photolysis of the oxidized A chain of insulin were tentatively characterized by comparison with the results for di- and tripeptides.

Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences.

Science.gov (United States)

Walsh, Patrick S; Dean, Jacob C; McBurney, Carl; Kang, Hyuk; Gellman, Samuel H; Zwier, Timothy S

2016-04-28

The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase. This work seeks a bottom-up understanding of the role played by glutamine residues in directing peptide structures that lead to neurodegenerative diseases. Resonant ion-dip infrared (RIDIR) spectroscopy is used to record single-conformation infrared spectra in the NH stretch, amide I and amide II regions. Comparison of the experimental spectra with the predictions of calculations carried out at the DFT M05-2X/6-31+G(d) level of theory lead to firm assignments for the H-bonding architectures of a total of eight conformers of four molecules, including three in Z-Gln-OH, one in Z-Gln-NHMe, three in Ac-Gln-NHBn, and one in Ac-Ala-Gln-NHBn. The Gln side chain engages actively in forming H-bonds with nearest-neighbor amide groups, forming C8 H-bonds to the C-terminal side, C9 H-bonds to the N-terminal side, and an amide-stacked geometry, all with an extended (C5) peptide backbone about the Gln residue. The Gln side chain also stabilizes an inverse γ-turn in the peptide backbone by forming a pair of H-bonds that bridge the γ-turn and stabilize it. Finally, the entire conformer population of Ac-Ala-Gln-NHBn is funneled into a single structure that incorporates the peptide backbone in a type I β-turn, stabilized by the Gln side chain forming a C7 H-bond to the central amide group in the β-turn not otherwise involved in a hydrogen bond. This β-turn backbone structure is nearly identical to that observed in a series of X-(AQ)-Y β-turns in the protein data bank, demonstrating that the gas-phase structure is robust to perturbations imposed by the crystalline protein environment.

Inhibition of the myostatin/Smad signaling pathway by short decorin-derived peptides.

Science.gov (United States)

El Shafey, Nelly; Guesnon, Mickaël; Simon, Françoise; Deprez, Eric; Cosette, Jérémie; Stockholm, Daniel; Scherman, Daniel; Bigey, Pascal; Kichler, Antoine

2016-02-15

Myostatin, also known as growth differentiation factor 8, is a member of the transforming growth factor-beta superfamily that has been shown to play a key role in the regulation of the skeletal muscle mass. Indeed, while myostatin deletion or loss of function induces muscle hypertrophy, its overexpression or systemic administration causes muscle atrophy. Since myostatin blockade is effective in increasing skeletal muscle mass, myostatin inhibitors have been actively sought after. Decorin, a member of the small leucine-rich proteoglycan family is a metalloprotein that was previously shown to bind and inactivate myostatin in a zinc-dependent manner. Furthermore, the myostatin-binding site has been shown to be located in the decorin N-terminal domain. In the present study, we investigated the anti-myostatin activity of short and soluble fragments of decorin. Our results indicate that the murine decorin peptides DCN48-71 and 42-65 are sufficient for inactivating myostatin in vitro. Moreover, we show that the interaction of mDCN48-71 to myostatin is strictly zinc-dependent. Binding of myostatin to activin type II receptor results in the phosphorylation of Smad2/3. Addition of the decorin peptide 48-71 decreased in a dose-dependent manner the myostatin-induced phosphorylation of Smad2 demonstrating thereby that the peptide inhibits the activation of the Smad signaling pathway. Finally, we found that mDCN48-71 displays a specificity towards myostatin, since it does not inhibit other members of the transforming growth factor-beta family. Copyright © 2016 Elsevier Inc. All rights reserved.

A general strategy for synthesis of cyclophane-braced peptide macrocycles via palladium-catalysed intramolecular sp3 C-H arylation

Science.gov (United States)

Zhang, Xuekai; Lu, Gang; Sun, Meng; Mahankali, Madhu; Ma, Yanfei; Zhang, Mingming; Hua, Wangde; Hu, Yuting; Wang, Qingbing; Chen, Jinghuo; He, Gang; Qi, Xiangbing; Shen, Weijun; Liu, Peng; Chen, Gong

2018-05-01

New methods capable of effecting cyclization, and forming novel three-dimensional structures while maintaining favourable physicochemical properties are needed to facilitate the development of cyclic peptide-based drugs that can engage challenging biological targets, such as protein-protein interactions. Here, we report a highly efficient and generally applicable strategy for constructing new types of peptide macrocycles using palladium-catalysed intramolecular C(sp3)-H arylation reactions. Easily accessible linear peptide precursors of simple and versatile design can be selectively cyclized at the side chains of either aromatic or modified non-aromatic amino acid units to form various cyclophane-braced peptide cycles. This strategy provides a powerful tool to address the long-standing challenge of size- and composition-dependence in peptide macrocyclization, and generates novel peptide macrocycles with uniquely buttressed backbones and distinct loop-type three-dimensional structures. Preliminary cell proliferation screening of the pilot library revealed a potent lead compound with selective cytotoxicity toward proliferative Myc-dependent cancer cell lines.

Tuning peptide self-assembly by an in-tether chiral center

Science.gov (United States)

Hu, Kuan; Xiong, Wei; Li, Hu; Zhang, Pei-Yu; Yin, Feng; Zhang, Qianling; Jiang, Fan; Li, Zigang

2018-01-01

The self-assembly of peptides into ordered nanostructures is important for understanding both peptide molecular interactions and nanotechnological applications. However, because of the complexity and various self-assembling pathways of peptide molecules, design of self-assembling helical peptides with high controllability and tunability is challenging. We report a new self-assembling mode that uses in-tether chiral center-induced helical peptides as a platform for tunable peptide self-assembly with good controllability. It was found that self-assembling behavior was governed by in-tether substitutional groups, where chirality determined the formation of helical structures and aromaticity provided the driving force for self-assembly. Both factors were essential for peptide self-assembly to occur. Experiments and theoretical calculations indicate long-range crystal-like packing in the self-assembly, which was stabilized by a synergy of interpeptide π-π and π-sulfur interactions and hydrogen bond networks. In addition, the self-assembled peptide nanomaterials were demonstrated to be promising candidate materials for applications in biocompatible electrochemical supercapacitors.

Effective modification of cell death-inducing intracellular peptides by means of a photo-cleavable peptide array-based screening system.

Science.gov (United States)

Kozaki, Ikko; Shimizu, Kazunori; Honda, Hiroyuki

2017-08-01

Intracellular functional peptides that play a significant role inside cells have been receiving a lot of attention as regulators of cellular activity. Previously, we proposed a novel screening system for intracellular functional peptides; it combined a photo-cleavable peptide array system with cell-penetrating peptides (CPPs). Various peptides can be delivered into cells and intracellular functions of the peptides can be assayed by means of our system. The aim of the present study was to demonstrate that the proposed screening system can be used for assessing the intracellular activity of peptides. The cell death-inducing peptide (LNLISKLF) identified in a mitochondria-targeting domain (MTD) of the Noxa protein served as an original peptide sequence for screening of peptides with higher activity via modification of the peptide sequence. We obtained 4 peptides with higher activity, in which we substituted serine (S) at the fifth position with phenylalanine (F), valine (V), tryptophan (W), or tyrosine (Y). During analysis of the mechanism of action, the modified peptides induced an increase in intracellular calcium concentration, which was caused by the treatment with the original peptide. Higher capacity for cell death induction by the modified peptides may be caused by increased hydrophobicity or an increased number of aromatic residues. Thus, the present work suggests that the intracellular activity of peptides can be assessed using the proposed screening system. It could be used for identifying intracellular functional peptides with higher activity through comprehensive screening. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

N-terminal diproline and charge group effects on the stabilization of helical conformation in alanine-based short peptides: CD studies with water and methanol as solvent.

Science.gov (United States)

Goyal, Bhupesh; Srivastava, Kinshuk Raj; Durani, Susheel

2017-06-01

Protein folding problem remains a formidable challenge as main chain, side chain and solvent interactions remain entangled and have been difficult to resolve. Alanine-based short peptides are promising models to dissect protein folding initiation and propagation structurally as well as energetically. The effect of N-terminal diproline and charged side chains is assessed on the stabilization of helical conformation in alanine-based short peptides using circular dichroism (CD) with water and methanol as solvent. A1 (Ac-Pro-Pro-Ala-Lys-Ala-Lys-Ala-Lys-Ala-NH 2 ) is designed to assess the effect of N-terminal homochiral diproline and lysine side chains to induce helical conformation. A2 (Ac-Pro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH 2 ) and A3 (Ac-dPro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH 2 ) with N-terminal homochiral and heterochiral diproline, respectively, are designed to assess the effect of Glu...Lys (i, i + 4) salt bridge interactions on the stabilization of helical conformation. The CD spectra of A1, A2 and A3 in water manifest different amplitudes of the observed polyproline II (PPII) signals, which indicate different conformational distributions of the polypeptide structure. The strong effect of solvent substitution from water to methanol is observed for the peptides, and CD spectra in methanol evidence A2 and A3 as helical folds. Temperature-dependent CD spectra of A1 and A2 in water depict an isodichroic point reflecting coexistence of two conformations, PPII and β-strand conformation, which is consistent with the previous studies. The results illuminate the effect of N-terminal diproline and charged side chains in dictating the preferences for extended-β, semi-extended PPII and helical conformation in alanine-based short peptides. The results of the present study will enhance our understanding on stabilization of helical conformation in short peptides and hence aid in the design of novel peptides with helical structures. Copyright © 2017 European Peptide

Peptides extracted from Artemisia herba alba have antimicrobial ...

African Journals Online (AJOL)

Background: Artemisia herba alba, classified into the family of Asteraceae, is an aromatic herb that is traditionally used as a purgative and antipyretic folk medicine by rural people of south Tunisia. This study reports the first identification of antimicrobial peptides from this medicinal plant that inhibited the growth of several ...

Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide.

Science.gov (United States)

Yakimov, Alexander; Pobegalov, Georgii; Bakhlanova, Irina; Khodorkovskii, Mikhail; Petukhov, Michael; Baitin, Dmitry

2017-09-19

The RecX protein, a very active natural RecA protein inhibitor, can completely disassemble RecA filaments at nanomolar concentrations that are two to three orders of magnitude lower than that of RecA protein. Based on the structure of RecX protein complex with the presynaptic RecA filament, we designed a short first in class α-helical peptide that both inhibits RecA protein activities in vitro and blocks the bacterial SOS-response in vivo. The peptide was designed using SEQOPT, a novel method for global sequence optimization of protein α-helices. SEQOPT produces artificial peptide sequences containing only 20 natural amino acids with the maximum possible conformational stability at a given pH, ionic strength, temperature, peptide solubility. It also accounts for restrictions due to known amino acid residues involved in stabilization of protein complexes under consideration. The results indicate that a few key intermolecular interactions inside the RecA protein presynaptic complex are enough to reproduce the main features of the RecX protein mechanism of action. Since the SOS-response provides a major mechanism of bacterial adaptation to antibiotics, these results open new ways for the development of antibiotic co-therapy that would not cause bacterial resistance. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Effect of micelle interface on the binding of anticoccidial PW2 peptide

International Nuclear Information System (INIS)

Tinoco, Luzineide W.; Gomes-Neto, Francisco; Valente, Ana Paula; Almeida, Fabio C. L.

2007-01-01

PW2 is an anticoccidial peptide active against Eimeria acervulina and Eimeria tenella. We determined the structure of PW2 in dodecylphosphocholine micelles. The structure showed two distinct regions: an amphipathic N-terminal 3 10 helix and an aromatic region containing WWR interface-binding motif. The aromatic region acted as a scaffold of the protein in the interface and shared the same structure in both DPC and SDS micelles. N-terminal helix interacted with DPC but not with SDS interface. Chemical shift change was slow when SDS was added to PW2 in DPC and fast when DPC was added to PW2 in SDS, indicating that interaction with DPC micelles was kinetically more stable than with SDS micelles. Also, DPC interface was able to accommodate PW2, but it maintained the conformational arrangement in the aromatic region observed for SDS micelles. This behavior, which is different from that observed for other antimicrobial peptides with WWR motif, may be associated with the absence of PW2 antibacterial activity and its selectivity for Eimeria parasites

Effect of micelle interface on the binding of anticoccidial PW2 peptide

Energy Technology Data Exchange (ETDEWEB)

Tinoco, Luzineide W. [Universidade Federal do Rio de Janeiro, Nucleo de Pesquisas de Produtos Naturais (Brazil); Gomes-Neto, Francisco; Valente, Ana Paula; Almeida, Fabio C. L. [Universidade Federal do Rio de Janeiro, Centro Nacional de Ressonancia Magnetica Nuclear Jiri Jonas, Instituto de Bioquimica Medica, Programa de Biologia Estrutural (Brazil)], E-mail: falmeida@cnrmn.bioqmed.ufrj.br

2007-12-15

PW2 is an anticoccidial peptide active against Eimeria acervulina and Eimeria tenella. We determined the structure of PW2 in dodecylphosphocholine micelles. The structure showed two distinct regions: an amphipathic N-terminal 3{sub 10} helix and an aromatic region containing WWR interface-binding motif. The aromatic region acted as a scaffold of the protein in the interface and shared the same structure in both DPC and SDS micelles. N-terminal helix interacted with DPC but not with SDS interface. Chemical shift change was slow when SDS was added to PW2 in DPC and fast when DPC was added to PW2 in SDS, indicating that interaction with DPC micelles was kinetically more stable than with SDS micelles. Also, DPC interface was able to accommodate PW2, but it maintained the conformational arrangement in the aromatic region observed for SDS micelles. This behavior, which is different from that observed for other antimicrobial peptides with WWR motif, may be associated with the absence of PW2 antibacterial activity and its selectivity for Eimeria parasites.

Mechanism of interaction of the antileukemic drug cytosine arabinoside with aromatic peptides: role of sugar conformation and peptide backbone.

Science.gov (United States)

Datta, G; Hosur, R V; Verma, N C; Khetrapal, C L; Gurnani, S

1989-01-01

Interaction of the antileukemic drugs, cytosine-arabinoside (Ara-C) and adenosine-arabinoside (Ara-A) and a structural analogue, cytidine, with aromatic dipeptides has been studied by fluorescence and NMR spectroscopy. Ara-C and cytidine bind tryptophanyl and histidyl dipeptides but not tyrosyl dipeptides, while Ara-A does not bind to any of them. Both studies indicate association involving stacking of aromatic moieties. NMR spectra also indicate a protonation of the histidine moiety by Ara-C. In case of cytidine, the chemical shifts observed on binding to His-Phe imply that the backbone protons of the dipeptide participate in the binding. The conformation of the sugar and the base seem to play a very important role in the binding phenomenon as three similar molecules, Ara-C, Ara-A and cytidine bind in totally different ways.

How non-conventional feedstocks will affect aromatics technologies

Energy Technology Data Exchange (ETDEWEB)

Koehler, E. [Clariant Produkte (Deutschland) GmbH, Muenchen (Germany)

2013-11-01

The abundance of non-conventional feedstocks such as coal and shale gas has begun to affect the availability of traditional base chemicals such as propylene and BTX aromatics. Although this trend is primarily fueled by the fast growing shale gas economy in the US and the abundance of coal in China, it will cause the global supply and demand situation to equilibrate across the regions. Lower demand for gasoline and consequently less aromatics rich reformate from refineries will further tighten the aromatics markets that are expected to grow at healthy rates, however. Refiners can benefit from this trend by abandoning their traditional fuel-oriented business model and becoming producers of petrochemical intermediates, with special focus on paraxylene (PX). Cheap gas from coal (via gasification) or shale reserves is an advantaged feedstock that offers a great platform to make aromatics in a cost-competitive manner, especially in regions where naphtha is in short supply. Gas condensates (LPG and naphtha) are good feedstocks for paraffin aromatization, and methanol from coal or (shale) gas can be directly converted to BTX aromatics (MTA) or alkylated with benzene or toluene to make paraxylene. Most of today's technologies for the production and upgrading of BTX aromatics and their derivatives make use of the unique properties of zeolites. (orig.)

Systematic discovery of new recognition peptides mediating protein interaction networks

DEFF Research Database (Denmark)

Neduva, Victor; Linding, Rune; Su-Angrand, Isabelle

2005-01-01

Many aspects of cell signalling, trafficking, and targeting are governed by interactions between globular protein domains and short peptide segments. These domains often bind multiple peptides that share a common sequence pattern, or "linear motif" (e.g., SH3 binding to PxxP). Many domains...... by interactions between globular protein domains and short peptide segments. These domains often bind multiple peptides that share a common sequence pattern, or "linear motif" (e.g., SH3 binding to PxxP). Many domains are known, though comparatively few linear motifs have been discovered. Their short length...

Anti-Inflammatory and Antioxidant Properties of Peptides Released from β-Lactoglobulin by High Hydrostatic Pressure-Assisted Enzymatic Hydrolysis.

Science.gov (United States)

Bamdad, Fatemeh; Bark, Seonghee; Kwon, Chul Hee; Suh, Joo-Won; Sunwoo, Hoon

2017-06-07

β-lactoglobulin hydrolysates (BLGH) have shown antioxidant, antihypertensive, antimicrobial, and opioid activity. In the current study, an innovative combination of high hydrostatic pressure and enzymatic hydrolysis (HHP-EH) was used to increase the yield of short bioactive peptides, and evaluate the anti-inflammatory and antioxidant properties of the BLGH produced by the HHP-EH process. BLG was enzymatically hydrolyzed by different proteases at an enzyme-to-substrate ratio of 1:100 under HHP (100 MPa) and compared with hydrolysates obtained under atmospheric pressure (AP-EH at 0.1 MPa). The degree of hydrolysis (DH), molecular weight distribution, and the antioxidant and anti-inflammatory properties of hydrolysates in chemical and cellular models were evaluated. BLGH obtained under HHP-EH showed higher DH than the hydrolysates obtained under AP-EH. Free radical scavenging and the reducing capacity were also significantly stronger in HHP-BLGH compared to AP-BLGH. The BLGH produced by alcalase (Alc) (BLG-Alc) showed significantly higher antioxidant properties among the six enzymes examined in this study. The anti-inflammatory properties of BLG-HHP-Alc were observed in lipopolysaccharide-stimulated macrophage cells by a lower level of nitric oxide production and the suppression of the synthesis of pro-inflammatory cytokines. Peptide sequencing revealed that 38% of the amino acids in BLG-HHP-Alc are hydrophobic and aromatic residues, which contribute to its anti-inflammatory properties. Enzymatic hydrolysis of BLG under HHP produces a higher yield of short bioactive peptides with potential antioxidant and anti-inflammatory effects.

Next-generation ELISA diagnostic assay for Chagas Disease based on the combination of short peptidic epitopes.

Directory of Open Access Journals (Sweden)

Juan Mucci

2017-10-01

Full Text Available Chagas Disease, caused by the protozoan Trypanosoma cruzi, is a major health and economic problem in Latin America for which no vaccine or appropriate drugs for large-scale public health interventions are yet available. Accurate diagnosis is essential for the early identification and follow up of vector-borne cases and to prevent transmission of the disease by way of blood transfusions and organ transplantation. Diagnosis is routinely performed using serological methods, some of which require the production of parasite lysates, parasite antigenic fractions or purified recombinant antigens. Although available serological tests give satisfactory results, the production of reliable reagents remains laborious and expensive. Short peptides spanning linear B-cell epitopes have proven ideal serodiagnostic reagents in a wide range of diseases. Recently, we have conducted a large-scale screening of T. cruzi linear B-cell epitopes using high-density peptide chips, leading to the identification of several hundred novel sequence signatures associated to chronic Chagas Disease. Here, we performed a serological assessment of 27 selected epitopes and of their use in a novel multipeptide-based diagnostic method. A combination of 7 of these peptides were finally evaluated in ELISA format against a panel of 199 sera samples (Chagas-positive and negative, including sera from Leishmaniasis-positive subjects. The multipeptide formulation displayed a high diagnostic performance, with a sensitivity of 96.3% and a specificity of 99.15%. Therefore, the use of synthetic peptides as diagnostic tools are an attractive alternative in Chagas' disease diagnosis.

Virtual screening using combinatorial cyclic peptide libraries reveals protein interfaces readily targetable by cyclic peptides.

Science.gov (United States)

Duffy, Fergal J; O'Donovan, Darragh; Devocelle, Marc; Moran, Niamh; O'Connell, David J; Shields, Denis C

2015-03-23

Protein-protein and protein-peptide interactions are responsible for the vast majority of biological functions in vivo, but targeting these interactions with small molecules has historically been difficult. What is required are efficient combined computational and experimental screening methods to choose among a number of potential protein interfaces worthy of targeting lead macrocyclic compounds for further investigation. To achieve this, we have generated combinatorial 3D virtual libraries of short disulfide-bonded peptides and compared them to pharmacophore models of important protein-protein and protein-peptide structures, including short linear motifs (SLiMs), protein-binding peptides, and turn structures at protein-protein interfaces, built from 3D models available in the Protein Data Bank. We prepared a total of 372 reference pharmacophores, which were matched against 108,659 multiconformer cyclic peptides. After normalization to exclude nonspecific cyclic peptides, the top hits notably are enriched for mimetics of turn structures, including a turn at the interaction surface of human α thrombin, and also feature several protein-binding peptides. The top cyclic peptide hits also cover the critical "hot spot" interaction sites predicted from the interaction crystal structure. We have validated our method by testing cyclic peptides predicted to inhibit thrombin, a key protein in the blood coagulation pathway of important therapeutic interest, identifying a cyclic peptide inhibitor with lead-like activity. We conclude that protein interfaces most readily targetable by cyclic peptides and related macrocyclic drugs may be identified computationally among a set of candidate interfaces, accelerating the choice of interfaces against which lead compounds may be screened.

Gold-catalyzed direct alkynylation of tryptophan in peptides using TIPS-EBX

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Gergely L. Tolnai

2016-04-01

Full Text Available The selective functionalization of peptides containing only natural amino acids is important for the modification of biomolecules. In particular, the installation of an alkyne as a useful handle for bioconjugation is highly attractive, but the use of a carbon linker is usually required. Herein, we report the gold-catalyzed direct alkynylation of tryptophan in peptides using the hypervalent iodine reagent TIPS-EBX (1-[(triisopropylsilylethynyl]-1,2-benziodoxol-3(1H-one. The reaction proceeded in 50–78% yield under mild conditions and could be applied to peptides containing other nucleophilic and aromatic amino acids, such as serine, phenylalanine or tyrosine.

Evolving the use of peptides as biomaterials components

Science.gov (United States)

Collier, Joel H.; Segura, Tatiana

2012-01-01

This manuscript is part of a debate on the statement that “the use of short synthetic adhesion peptides, like RGD, is the best approach in the design of biomaterials that guide cell behavior for regenerative medicine and tissue engineering”. We take the position that although there are some acknowledged disadvantages of using short peptide ligands within biomaterials, it is not necessary to discard the notion of using peptides within biomaterials entirely, but rather to reinvent and evolve their use. Peptides possess advantageous chemical definition, access to non-native chemistries, amenability to de novo design, and applicability within parallel approaches. Biomaterials development programs that require such aspects may benefit from a peptide-based strategy. PMID:21515167

Dynamic peptide libraries for the discovery of supramolecular nanomaterials

Science.gov (United States)

Pappas, Charalampos G.; Shafi, Ramim; Sasselli, Ivan R.; Siccardi, Henry; Wang, Tong; Narang, Vishal; Abzalimov, Rinat; Wijerathne, Nadeesha; Ulijn, Rein V.

2016-11-01

Sequence-specific polymers, such as oligonucleotides and peptides, can be used as building blocks for functional supramolecular nanomaterials. The design and selection of suitable self-assembling sequences is, however, challenging because of the vast combinatorial space available. Here we report a methodology that allows the peptide sequence space to be searched for self-assembling structures. In this approach, unprotected homo- and heterodipeptides (including aromatic, aliphatic, polar and charged amino acids) are subjected to continuous enzymatic condensation, hydrolysis and sequence exchange to create a dynamic combinatorial peptide library. The free-energy change associated with the assembly process itself gives rise to selective amplification of self-assembling candidates. By changing the environmental conditions during the selection process, different sequences and consequent nanoscale morphologies are selected.

Short-term glucagon stimulation test of C-peptide effect on glucose utilization in patients with type 1 diabetes mellitus.

Science.gov (United States)

Mojto, Viliam; Rausova, Zuzana; Chrenova, Jana; Dedik, Ladislav

2015-12-01

This work aimed to evaluate the use of a four-point glucagon stimulation test of C-peptide effect on glucose utilization in type 1 diabetic patients using a new mathematical model. A group of 32 type 1 diabetic patients and a group of 10 healthy control subjects underwent a four-point glucagon stimulation test with blood sampling at 0, 6, 15 and 30 min after 1 mg glucagon bolus intravenous administration. Pharmacokinetic and pharmacokinetic/pharmacodynamic models of C-peptide effect on glucose utilization versus area under curve (AUC) were used. A two-sample t test and ANOVA with Bonferroni correction were used to test the significance of differences between parameters. A significant difference between control and patient groups regarding the coefficient of whole-body glucose utilization and AUC C-peptide/AUC glucose ratio (p ≪ 0.001 and p = 0.002, respectively) was observed. The high correlation (r = 0.97) between modeled coefficient of whole-body glucose utilization and numerically calculated AUC C-peptide/AUC glucose ratio related to entire cohort indicated the stability of used method. The short-term four-point glucagon stimulation test allows the numerically calculated AUC C-peptide/AUC glucose ratio and/or the coefficient of whole-body glucose utilization calculated from model to be used to diagnostically identify type 1 diabetic patients.

Evidence for a strong sulfur-aromatic interaction derived from crystallographic data.

Science.gov (United States)

Zauhar, R J; Colbert, C L; Morgan, R S; Welsh, W J

2000-03-01

We have uncovered new evidence for a significant interaction between divalent sulfur atoms and aromatic rings. Our study involves a statistical analysis of interatomic distances and other geometric descriptors derived from entries in the Cambridge Crystallographic Database (F. H. Allen and O. Kennard, Chem. Design Auto. News, 1993, Vol. 8, pp. 1 and 31-37). A set of descriptors was defined sufficient in number and type so as to elucidate completely the preferred geometry of interaction between six-membered aromatic carbon rings and divalent sulfurs for all crystal structures of nonmetal-bearing organic compounds present in the database. In order to test statistical significance, analogous probability distributions for the interaction of the moiety X-CH(2)-X with aromatic rings were computed, and taken a priori to correspond to the null hypothesis of no significant interaction. Tests of significance were carried our pairwise between probability distributions of sulfur-aromatic interaction descriptors and their CH(2)-aromatic analogues using the Smirnov-Kolmogorov nonparametric test (W. W. Daniel, Applied Nonparametric Statistics, Houghton-Mifflin: Boston, New York, 1978, pp. 276-286), and in all cases significance at the 99% confidence level or better was observed. Local maxima of the probability distributions were used to define a preferred geometry of interaction between the divalent sulfur moiety and the aromatic ring. Molecular mechanics studies were performed in an effort to better understand the physical basis of the interaction. This study confirms observations based on statistics of interaction of amino acids in protein crystal structures (R. S. Morgan, C. E. Tatsch, R. H. Gushard, J. M. McAdon, and P. K. Warme, International Journal of Peptide Protein Research, 1978, Vol. 11, pp. 209-217; R. S. Morgan and J. M. McAdon, International Journal of Peptide Protein Research, 1980, Vol. 15, pp. 177-180; K. S. C. Reid, P. F. Lindley, and J. M. Thornton, FEBS

Salt-bridging effects on short amphiphilic helical structure and introducing sequence-based short beta-turn motifs.

Science.gov (United States)

Guarracino, Danielle A; Gentile, Kayla; Grossman, Alec; Li, Evan; Refai, Nader; Mohnot, Joy; King, Daniel

2018-02-01

Determining the minimal sequence necessary to induce protein folding is beneficial in understanding the role of protein-protein interactions in biological systems, as their three-dimensional structures often dictate their activity. Proteins are generally comprised of discrete secondary structures, from α-helices to β-turns and larger β-sheets, each of which is influenced by its primary structure. Manipulating the sequence of short, moderately helical peptides can help elucidate the influences on folding. We created two new scaffolds based on a modestly helical eight-residue peptide, PT3, we previously published. Using circular dichroism (CD) spectroscopy and changing the possible salt-bridging residues to new combinations of Lys, Arg, Glu, and Asp, we found that our most helical improvements came from the Arg-Glu combination, whereas the Lys-Asp was not significantly different from the Lys-Glu of the parent scaffold, PT3. The marked 3 10 -helical contributions in PT3 were lessened in the Arg-Glu-containing peptide with the beginning of cooperative unfolding seen through a thermal denaturation. However, a unique and unexpected signature was seen for the denaturation of the Lys-Asp peptide which could help elucidate the stages of folding between the 3 10 and α-helix. In addition, we developed a short six-residue peptide with β-turn/sheet CD signature, again to help study minimal sequences needed for folding. Overall, the results indicate that improvements made to short peptide scaffolds by fine-tuning the salt-bridging residues can enhance scaffold structure. Likewise, with the results from the new, short β-turn motif, these can help impact future peptidomimetic designs in creating biologically useful, short, structured β-sheet-forming peptides.

Boron-Doped Diamond Electrodes for the Electrochemical Oxidation and Cleavage of Peptides

NARCIS (Netherlands)

Roeser, Julien; Alting, Niels F. A.; Permentier, Hjalmar P.; Bruins, Andries P.; Bischoff, Rainer

2013-01-01

Electrochemical oxidation of peptides and proteins is traditionally performed on carbon-based electrodes. Adsorption caused by the affinity of hydrophobic and aromatic amino acids toward these surfaces leads to electrode fouling. We compared the performance of boron-doped diamond (BDD) and glassy

Short peptide based nanotubes capable of effective curcumin delivery for treating drug resistant malaria.

Science.gov (United States)

Alam, Shadab; Panda, Jiban Jyoti; Mukherjee, Tapan Kumar; Chauhan, Virander Singh

2016-04-05

Curcumin (Ccm) has shown immense potential as an antimalarial agent; however its low solubility and less bioavailability attenuate the in vivo efficacy of this potent compound. In order to increase Ccm's bioavailability, a number of organic/inorganic polymer based nanoparticles have been investigated. However, most of the present day nano based delivery systems pose a conundrum with respect to their complex synthesis procedures, poor in vivo stability and toxicity issues. Peptides due to their high biocompatibility could act as excellent materials for the synthesis of nanoparticulate drug delivery systems. Here, we have investigated dehydrophenylalanine (ΔPhe) di-peptide based self-assembled nanoparticles for the efficient delivery of Ccm as an antimalarial agent. The self-assembly and curcumin loading capacity of different ΔPhe dipeptides, phenylalanine-α,β-dehydrophenylalanine (FΔF), arginine-α,β-dehydrophenylalanine (RΔF), valine-α,β-dehydrophenylalanine (VΔF) and methonine-α,β-dehydrophenylalanine (MΔF) were investigated for achieving enhanced and effective delivery of the compound for potential anti-malarial therapy. FΔF, RΔF, VΔF and MΔF peptides formed different types of nanoparticles like nanotubes and nanovesicles under similar assembling conditions. Out of these, F∆F nanotubes showed maximum curcumin loading capacity of almost 68 % W/W. Ccm loaded F∆F nanotubes (Ccm-F∆F) showed comparatively higher (IC50, 3.0 µM) inhibition of Plasmodium falciparum (Indo strain) as compared to free Ccm (IC50, 13 µM). Ccm-F∆F nano formulation further demonstrated higher inhibition of parasite growth in malaria infected mice as compared to free Ccm. The dipeptide nanoparticles were highly biocompatible and didn't show any toxic effect on mammalian cell lines and normal blood cells. This work provides a proof of principle of using highly biocompatible short peptide based nanoparticles for entrapment and in vivo delivery of Ccm leading to an

Carotamine, a Unique Aromatic Amide from Daucus Carota L. Var Biossieri (Apiaceae

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Mohamed M. El-Azizi

2002-06-01

Full Text Available The unique aromatic peptide 4-(p-aminobenzoylamino-2-aminobenzoic acid, carotamine, together with 2,4-diaminobenzoic acid, isolated for the first time from a plant source, were identified from the aqueous alcoholic extract of the aerial parts of Daucus carota L. var. boissieri (Apiaceae. The structures were determined through conventional methods of analysis and confirmed by LC-ESI/MS and NMR spectral analysis.

Co-assembly of Peptide Amphiphiles and Lipids into Supramolecular Nanostructures Driven by Anion-π Interactions

Energy Technology Data Exchange (ETDEWEB)

Yu, Zhilin; Erbas, Aykut; Tantakitti, Faifan; Palmer, Liam C.; Jackman, Joshua A.; Olvera de la Cruz, Monica; Cho, Nam-Joon; Stupp, Samuel I. (Nanyang); (NWU)

2017-06-01

Co-assembly of binary systems driven by specific non-covalent interactions can greatly expand the structural and functional space of supramolecular nanostructures. We report here on the self-assembly of peptide amphiphiles and fatty acids driven primarily by anion-π interactions. The peptide sequences investigated were functionalized with a perfluorinated phenylalanine residue to promote anion-π interactions with carboxylate headgroups in fatty acids. These interactions were verified here by NMR and circular dichroism experiments as well as investigated using atomistic simulations. Positioning the aromatic units close to the N-terminus of the peptide backbone near the hydrophobic core of cylindrical nanofibers leads to strong anion-π interactions between both components. With a low content of dodecanoic acid in this position, the cylindrical morphology is preserved. However, as the aromatic units are moved along the peptide backbone away from the hydrophobic core, the interactions with dodecanoic acid transform the cylindrical supramolecular morphology into ribbon-like structures. Increasing the ratio of dodecanoic acid to PA leads to either the formation of large vesicles in the binary systems where the anion-π interactions are strong, or a heterogeneous mixture of assemblies when the peptide amphiphiles associate weakly with dodecanoic acid. Our findings reveal how co-assembly involving designed specific interactions can drastically change supramolecular morphology and even cross from nano to micro scales.

Degradation of peptides by gamma-irradiation, 2

Energy Technology Data Exchange (ETDEWEB)

Oku, Tadatake; Yoshida, Shigeki; Kondo, Mitsumasa; Ishida, Tomoharu; Fukui, Manabu; Ito, Teiichiro (Nihon Univ., Tokyo (Japan). Coll. of Agriculture and Veterinary Medicine)

1990-10-01

The radiolytic products of two kinds of dipeptides containing aromatic amino acid, gly-L-tyr and L-tyr-gly in 1 mM aqueous solution in the presence of air were examined by gamma-irradiation at doses of about 6, 12 and 25 kGy. Peptide samples in aqueous solution were analyzed by HPLC and GC after gamma-irradiation. Amides which the amounts of formation was very small, were collected several times by an amino acid autoanalyzer and isolated by HPLC. The ninhydrin-positive products from gly-L-tyr were detected gly, tyr, dopa, asp, ammonia, methylamine, ethylamine and glycinamide. The products from L-tyr-gly were tyr, gly, dopa, asp, ammonia, methylamine and ethylamine, but tyrosinamide was not confirmed. The total amounts of ninhydrin-positive products formed were less than the decreasing amount of each peptide at every irradiation dose. Methanal and ethanal were detected in both peptides. A radiolytic pathway of gly-L-tyr and L-tyr-gly was estimated from these results. (author).

Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins

International Nuclear Information System (INIS)

Garrison, W.M.

1985-01-01

The purpose of this review is to bring together and to correlate the wide variety of experimental studies that provide information on the reaction products and reaction mechanisms involved in the radiolysis of peptides, polypeptides and proteins (including chromosomal proteins) in both aqueous and solid-state systems. The comparative radiation chemistry of these systems is developed in terms of specific reactions of the peptide main-chain and the aliphatic, aromatic-unsaturated and sulfur-containing side-chains. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis and ESR spectroscopy is included. 147 refs

Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins

Energy Technology Data Exchange (ETDEWEB)

Garrison, W.M.

1985-01-01

The purpose of this review is to bring together and to correlate the wide variety of experimental studies that provide information on the reaction products and reaction mechanisms involved in the radiolysis of peptides, polypeptides and proteins (including chromosomal proteins) in both aqueous and solid-state systems. The comparative radiation chemistry of these systems is developed in terms of specific reactions of the peptide main-chain and the aliphatic, aromatic-unsaturated and sulfur-containing side-chains. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis and ESR spectroscopy is included. 147 refs.

Beta-blockers influence the short-term and long-term prognostic information of natriuretic peptides and catecholamines in chronic heart failure independent from specific agents.

Science.gov (United States)

Frankenstein, Lutz; Nelles, Manfred; Slavutsky, Maxim; Schellberg, Dieter; Doesch, Andreas; Katus, Hugo; Remppis, Andrew; Zugck, Christian

2007-10-01

In chronic heart failure (CHF), the physiologic effects of natriuretic peptides and catecholamines are interdependent. Furthermore, reports state an agent-dependent effect of individual beta-blockers on biomarkers. Data on the short-term and long-term predictive power comparing these biomarkers as well as accounting for the influence of beta-blocker treatment both on the marker or the resultant prognostic information are scarce. We included 513 consecutive patients with systolic CHF, measured atrial natriuretic peptide (ANP), N-terminal prohormone brain natriuretic peptide (NTproBNP), noradrenaline, and adrenaline, and monitored them for 90 +/- 25 months. Death or the combination of death and cardiac transplantation at 1 year, 5 years, and overall follow-up were considered end points. Compared with patients not taking beta-blockers, patients taking beta-blockers had significantly lower levels of catecholamines but not natriuretic peptides. Only for adrenaline was the amount of this effect related to the specific beta-blocker chosen. Receiver operating characteristic curves demonstrated superior prognostic accuracy for NTproBNP both at the 1- and 5-year follow-up compared with ANP, noradrenaline, and adrenaline. In multivariate analysis including established risk markers (New York Heart Association functional class, left ventricular ejection fraction, peak oxygen uptake, and 6-minute walk test), of all neurohumoral parameters, only NTproBNP remained an independent predictor for both end points. Long-term beta-blocker therapy is associated with decreased levels of plasma catecholamines but not natriuretic peptides. This effect is independent from the actual beta-blocker chosen for natriuretic peptides and noradrenaline. In multivariate analysis, both for short-term and long-term prediction of mortality or the combined end point of death and cardiac transplantation, only NTproBNP remained independent from established clinical risk markers.

Peptide design using alpha,beta-dehydro amino acids: from beta-turns to helical hairpins.

Science.gov (United States)

Mathur, Puniti; Ramakumar, S; Chauhan, V S

2004-01-01

Incorporation of alpha,beta-dehydrophenylalanine (DeltaPhe) residue in peptides induces folded conformations: beta-turns in short peptides and 3(10)-helices in larger ones. A few exceptions-namely, alpha-helix or flat beta-bend ribbon structures-have also been reported in a few cases. The most favorable conformation of DeltaPhe residues are (phi,psi) approximately (-60 degrees, -30 degrees ), (-60 degrees, 150 degrees ), (80 degrees, 0 degrees ) or their enantiomers. DeltaPhe is an achiral and planar residue. These features have been exploited in designing DeltaPhe zippers and helix-turn-helix motifs. DeltaPhe can be incorporated in both right and left-handed helices. In fact, consecutive occurrence of three or more DeltaPhe amino acids induce left-handed screw sense in peptides containing L-amino acids. Weak interactions involving the DeltaPhe residue play an important role in molecular association. The C--H.O==C hydrogen bond between the DeltaPhe side-chain and backbone carboxyl moiety, pi-pi stacking interactions between DeltaPhe side chains belonging to enantiomeric helices have shown to stabilize folding. The unusual capability of a DeltaPhe ring to form the hub of multicentered interactions namely, a donor in aromatic C--H.pi and C--H.O==C and an acceptor in a CH(3).pi interaction suggests its exploitation in introducing long-range interactions in the folding of supersecondary structures. Copyright 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2004

RECENT ADVANCES TOWARDS THE RATIONAL DESIGN OF PEPTIDE DRUGS

OpenAIRE

YEŞİLADA, Akgül; ÖZKANLI, Fügen

2004-01-01

In this review, after a short introduction to definition and physiological roles of regulatory peptides, problems faced during the development of peptide drugs, studies directed to solve these problems and rational design of peptide drugs with special emphesis on peptidomimetics are mentioned

Anticancer activities of bovine and human lactoferricin-derived peptides.

Science.gov (United States)

Arias, Mauricio; Hilchie, Ashley L; Haney, Evan F; Bolscher, Jan G M; Hyndman, M Eric; Hancock, Robert E W; Vogel, Hans J

2017-02-01

Lactoferrin (LF) is a mammalian host defense glycoprotein with diverse biological activities. Peptides derived from the cationic region of LF possess cytotoxic activity against cancer cells in vitro and in vivo. Bovine lactoferricin (LFcinB), a peptide derived from bovine LF (bLF), exhibits broad-spectrum anticancer activity, while a similar peptide derived from human LF (hLF) is not as active. In this work, several peptides derived from the N-terminal regions of bLF and hLF were studied for their anticancer activities against leukemia and breast-cancer cells, as well as normal peripheral blood mononuclear cells. The cyclized LFcinB-CLICK peptide, which possesses a stable triazole linkage, showed improved anticancer activity, while short peptides hLF11 and bLF10 were not cytotoxic to cancer cells. Interestingly, hLF11 can act as a cell-penetrating peptide; when combined with the antimicrobial core sequence of LFcinB (RRWQWR) through either a Pro or Gly-Gly linker, toxicity to Jurkat cells increased. Together, our work extends the library of LF-derived peptides tested for anticancer activity, and identified new chimeric peptides with high cytotoxicity towards cancerous cells. Additionally, these results support the notion that short cell-penetrating peptides and antimicrobial peptides can be combined to create new adducts with increased potency.

Polarization switching and patterning in self-assembled peptide tubular structures

Science.gov (United States)

Bdikin, Igor; Bystrov, Vladimir; Delgadillo, Ivonne; Gracio, José; Kopyl, Svitlana; Wojtas, Maciej; Mishina, Elena; Sigov, Alexander; Kholkin, Andrei L.

2012-04-01

Self-assembled peptide nanotubes are unique nanoscale objects that have great potential for a multitude of applications, including biosensors, nanotemplates, tissue engineering, biosurfactants, etc. The discovery of strong piezoactivity and polar properties in aromatic dipeptides [A. Kholkin, N. Amdursky, I. Bdikin, E. Gazit, and G. Rosenman, ACS Nano 4, 610 (2010)] opened up a new perspective for their use as biocompatible nanoactuators, nanomotors, and molecular machines. Another, as yet unexplored functional property is the ability to switch polarization and create artificial polarization patterns useful in various electronic and optical applications. In this work, we demonstrate that diphenylalanine peptide nanotubes are indeed electrically switchable if annealed at a temperature of about 150 °C. The new orthorhombic antipolar structure that appears after annealing allows for the existence of a radial polarization component, which is directly probed by piezoresponse force microscopy (PFM) measurements. Observation of the relatively stable polarization patterns and hysteresis loops via PFM testifies to the local reorientation of molecular dipoles in the radial direction. The experimental results are complemented with rigorous molecular calculations and create a solid background of electric-field induced deformation of aromatic rings and corresponding polarization switching in this emergent material.

Photoperiod Regulates vgf-Derived Peptide Processing in Siberian Hamsters.

Directory of Open Access Journals (Sweden)

Barbara Noli

Full Text Available VGF mRNA is induced in specific hypothalamic areas of the Siberian hamster upon exposure to short photoperiods, which is associated with a seasonal decrease in appetite and weight loss. Processing of VGF generates multiple bioactive peptides, so the objective of this study was to determine the profile of the VGF-derived peptides in the brain, pituitary and plasma from Siberian hamsters, and to establish whether differential processing might occur in the short day lean state versus long day fat. Antisera against short sequences at the C- or N- termini of proVGF, as well as against NERP-1, TPGH and TLQP peptides, were used for analyses of tissues, and both immunohistochemistry and enzyme linked immunosorbent assay (ELISA coupled with high-performance liquid (HPLC or gel chromatography were carried out. VGF peptide immunoreactivity was found within cortex cholinergic perikarya, in multiple hypothalamic nuclei, including those containing vasopressin, and in pituitary gonadotrophs. ELISA revealed that exposure to short day photoperiod led to a down-regulation of VGF immunoreactivity in the cortex, and a less pronounced decrease in the hypothalamus and pituitary, while the plasma VGF levels were not affected by the photoperiod. HPLC and gel chromatography both confirmed the presence of multiple VGF-derived peptides in these tissues, while gel chromatography showed the presence of the VGF precursor in all tissues tested except for the cortex. These observations are consistent with the view that VGF-derived peptides have pleiotropic actions related to changing photoperiod, possibly by regulating cholinergic systems in the cortex, vasopressin hypothalamic pathways, and the reproductive axis.

Bioavailability of polycyclic aromatic hydrocarbons (PAHs) to short-neck clam (Paphia undulata) from sediment matrices in mudflat ecosystem of the west coast of Peninsular Malaysia.

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Keshavarzifard, Mehrzad; Zakaria, Mohamad Pauzi; Hwai, Tan Shau

2017-06-01

The bioaccumulation and bioavailability of polycyclic aromatic hydrocarbons (PAHs) were characterized in sediment and Paphia undulata (short-neck clam) from six mudflat areas in the west coasts of Peninsular Malaysia. The concentrations of total PAHs varied from 357.1 to 6257.1 and 179.9 ± 7.6 to 1657.5 ± 53.9 ng g -1 dry weight in sediment and short-neck clam samples, respectively. PAHs can be classified as moderate to very high level of pollution in sediments and moderate to high level of pollution in short-neck clams. The diagnostic ratios of individual PAHs and principal component analysis indicate both petrogenic and pyrogenic sources with significant dominance of pyrogenic source. The first PAHs biota-sediment accumulation factors and relative biota-sediment accumulation factors data for short-neck clam were obtained in this study, indicating a preferential accumulation of lower molecular weight PAHs. Evaluation of PAH levels in sediments and short-neck clams indicates that short-neck clam could be introduced as a good biomonitor in mudflats. The results also demonstrated that under environmental conditions, the sedimentary load of hydrocarbons appears to be one of the factors controlling their bioavailability to biota.

Bioprinting synthetic self-assembling peptide hydrogels for biomedical applications

International Nuclear Information System (INIS)

Loo, Yihua; Hauser, Charlotte A E

2016-01-01

Three-dimensional (3D) bioprinting is a disruptive technology for creating organotypic constructs for high-throughput screening and regenerative medicine. One major challenge is the lack of suitable bioinks. Short synthetic self-assembling peptides are ideal candidates. Several classes of peptides self-assemble into nanofibrous hydrogels resembling the native extracellular matrix. This is a conducive microenvironment for maintaining cell survival and physiological function. Many peptides also demonstrate stimuli-responsive gelation and tuneable mechanical properties, which facilitates extrusion before dispensing and maintains the shape fidelity of the printed construct in aqueous media. The inherent biocompatibility and biodegradability bodes well for in vivo applications as implantable tissues and drug delivery matrices, while their short length and ease of functionalization facilitates synthesis and customization. By applying self-assembling peptide inks to bioprinting, the dynamic complexity of biological tissue can be recreated, thereby advancing current biomedical applications of peptide hydrogel scaffolds. (paper)

Expanding the informational chemistries of life: peptide/RNA networks

Science.gov (United States)

Taran, Olga; Chen, Chenrui; Omosun, Tolulope O.; Hsieh, Ming-Chien; Rha, Allisandra; Goodwin, Jay T.; Mehta, Anil K.; Grover, Martha A.; Lynn, David G.

2017-11-01

The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA. Peptide conformational networks are known to be capable of evolution in disease states and of co-opting metal ions, aromatic heterocycles and lipids to extend their emergent behaviours. The coexistence and association of dynamic peptide and RNA networks appear to have driven the emergence of higher-order informational systems in biology that are not available to either scaffold independently, and such mutualistic interdependence poses critical questions regarding the search for life across our Solar System and beyond. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Aromatic hydrocarbons

International Nuclear Information System (INIS)

Roder, M.

1985-01-01

Papers dealing with radiolysis of aromatic hydrocarbons of different composition (from benzene to terphenyls and hydrocarbons with condensed rings) as well as their mixtures (with alkanes, alkenes, other aromatic hydrocarbons) are reviewed. High radiation stability of aromatic hydrocarbons in condensed phases associated with peculiarities of molecular structure of compounds is underlined. Mechanisms of radiolytic processes, vaues of product yields are considered

Comparison Review of Short-Acting and Long-Acting Glucagon-like Peptide-1 Receptor Agonists.

Science.gov (United States)

Uccellatore, Annachiara; Genovese, Stefano; Dicembrini, Ilaria; Mannucci, Edoardo; Ceriello, Antonio

2015-09-01

Glucagon-like peptide-1 (GLP-1) receptor agonists (GLP-1 RAs) are useful tools for treating type 2 diabetes mellitus. In their recent position statement, the American Diabetes Association and European Association for the Study of Diabetes recommend GLP1-RAs as add-on to metformin when therapeutic goals are not achieved with monotherapy, particularly for patients who wish to avoid weight gain or hypoglycemia. GLP1-RAs differ substantially in their duration of action, frequency of administration and clinical profile. Members of this class approved for clinical use include exenatide twice-daily, exenatide once-weekly, liraglutide and lixisenatide once-daily. Recently, two new once-weekly GLP1-RAs have been approved: dulaglutide and albiglutide. This article summarizes properties of short- and long-acting GLP-1 analogs, and provides useful information to help choose the most appropriate compound for individual patients.

Modern treatment of short bowel syndrome

DEFF Research Database (Denmark)

Jeppesen, Palle B

2013-01-01

Recently, the US Food and Drug Administration and the European Medicines Agency approved the glucagon-like peptide 2 analogue, teduglutide, for the treatment of short bowel syndrome (SBS), and this review describes the physiological basis for its clinical use.......Recently, the US Food and Drug Administration and the European Medicines Agency approved the glucagon-like peptide 2 analogue, teduglutide, for the treatment of short bowel syndrome (SBS), and this review describes the physiological basis for its clinical use....

Spectroscopic Diagnosis of Excited-State Aromaticity: Capturing Electronic Structures and Conformations upon Aromaticity Reversal.

Science.gov (United States)

Oh, Juwon; Sung, Young Mo; Hong, Yongseok; Kim, Dongho

2018-03-06

Aromaticity, the special energetic stability derived from cyclic [4 n + 2]π-conjugated electronic structures, has been the topic of intense interest in chemistry because it plays a critical role in rationalizing molecular stability, reactivity, and physical/chemical properties. Recently, the pioneering work by Colin Baird on aromaticity reversal, postulating that aromatic (antiaromatic) character in the ground state reverses to antiaromatic (aromatic) character in the lowest excited triplet state, has attracted much scientific attention. The completely reversed aromaticity in the excited state provides direct insight into understanding the photophysical/chemical properties of photoactive materials. In turn, the application of aromatic molecules to photoactive materials has led to numerous studies revealing this aromaticity reversal. However, most studies of excited-state aromaticity have been based on the theoretical point of view. The experimental evaluation of aromaticity in the excited state is still challenging and strenuous because the assessment of (anti)aromaticity with conventional magnetic, energetic, and geometric indices is difficult in the excited state, which practically restricts the extension and application of the concept of excited-state aromaticity. Time-resolved optical spectroscopies can provide a new and alternative avenue to evaluate excited-state aromaticity experimentally while observing changes in the molecular features in the excited states. Time-resolved optical spectroscopies take advantage of ultrafast laser pulses to achieve high time resolution, making them suitable for monitoring ultrafast changes in the excited states of molecular systems. This can provide valuable information for understanding the aromaticity reversal. This Account presents recent breakthroughs in the experimental assessment of excited-state aromaticity and the verification of aromaticity reversal with time-resolved optical spectroscopic measurements. To

Near infrared optical biosensor based on peptide functionalized single-walled carbon nanotubes hybrids for 2,4,6-trinitrotoluene (TNT) explosive detection.

Science.gov (United States)

Wang, Jin

2018-06-01

A near infrared (NIR) optical biosensor based on peptide functionalized single-walled carbon nanotubes (SWCNTs) hybrids for 2,4,6-trinitrotoluene (TNT) explosive detection was developed. The TNT binding peptide was directly anchored on the sidewall of the SWCNTs using the π-π interaction between the aromatic amino acids and SWCNTs, forming the peptide-SWCNTs hybrids for near infrared absorption spectra measurement. The evidence of the morphology of peptide-SWCNTs hybrids was obtained using atomic force microscopy (AFM). The results demonstrated that peptide-SWCNTs hybrids based NIR optical biosensor exhibited sensitive and highly selective for TNT explosive determination, addressing a promising optical biosensor for security application. Copyright © 2018. Published by Elsevier Inc.

Peptides in headlock ? a novel high-affinity and versatile peptide-binding nanobody for proteomics and microscopy

OpenAIRE

Braun, Michael B.; Traenkle, Bjoern; Koch, Philipp A.; Emele, Felix; Weiss, Frederik; Poetz, Oliver; Stehle, Thilo; Rothbauer, Ulrich

2016-01-01

Nanobodies are highly valuable tools for numerous bioanalytical and biotechnical applications. Here, we report the characterization of a nanobody that binds a short peptide epitope with extraordinary affinity. Structural analysis reveals an unusual binding mode where the extended peptide becomes part of a ?-sheet structure in the nanobody. This interaction relies on sequence-independent backbone interactions augmented by a small number of specificity-determining side chain contacts. Once boun...

Immunomodulatory and Anti-Inflammatory Activities of Chicken Cathelicidin-2 Derived Peptides

Science.gov (United States)

van Dijk, Albert; van Eldik, Mandy; Veldhuizen, Edwin J. A.; Tjeerdsma-van Bokhoven, Hanne L. M.; de Zoete, Marcel R.; Bikker, Floris J.; Haagsman, Henk P.

2016-01-01

Host Defence Peptides and derived peptides are promising classes of antimicrobial and immunomodulatory lead compounds. For this purpose we examined whether chicken cathelicidin-2 (CATH-2)-derived peptides modulate the function and inflammatory response of avian immune cells. Using a chicken macrophage cell line (HD11) we found that full-length CATH-2 dose-dependently induced transcription of chemokines CXCLi2/IL-8, MCP-3 and CCLi4/RANTES, but not of pro-inflammatory cytokine IL-1β. In addition, CATH-2 efficiently inhibited IL-1β and nitric oxide production by HD11 cells induced by different sources of lipopolysaccharides (LPS). N-terminal truncated CATH-2 derived peptides maintained the capacity to selectively induce chemokine transcription, but despite their high LPS affinity several analogs lacked LPS-neutralizing capacity. Substitution of phenylalanine residues by tryptophan introduced endotoxin neutralization capacity in inactive truncated CATH-2 derived peptides. In contrast, amino acid substitution of phenylalanine by tyrosine abrogated endotoxin neutralization activity of CATH-2 analogs. These findings support a pivotal role for aromatic residues in peptide-mediated endotoxin neutralization by CATH-2 analogs and were shown to be independent of LPS affinity. The capacity to modulate chemokine production and dampen endotoxin-induced pro-inflammatory responses in chicken immune cells implicates that small CATH-2 based peptides could serve as leads for the design of CATH-2 based immunomodulatory anti-infectives. PMID:26848845

Immunomodulatory and Anti-Inflammatory Activities of Chicken Cathelicidin-2 Derived Peptides.

Directory of Open Access Journals (Sweden)

Albert van Dijk

Full Text Available Host Defence Peptides and derived peptides are promising classes of antimicrobial and immunomodulatory lead compounds. For this purpose we examined whether chicken cathelicidin-2 (CATH-2-derived peptides modulate the function and inflammatory response of avian immune cells. Using a chicken macrophage cell line (HD11 we found that full-length CATH-2 dose-dependently induced transcription of chemokines CXCLi2/IL-8, MCP-3 and CCLi4/RANTES, but not of pro-inflammatory cytokine IL-1β. In addition, CATH-2 efficiently inhibited IL-1β and nitric oxide production by HD11 cells induced by different sources of lipopolysaccharides (LPS. N-terminal truncated CATH-2 derived peptides maintained the capacity to selectively induce chemokine transcription, but despite their high LPS affinity several analogs lacked LPS-neutralizing capacity. Substitution of phenylalanine residues by tryptophan introduced endotoxin neutralization capacity in inactive truncated CATH-2 derived peptides. In contrast, amino acid substitution of phenylalanine by tyrosine abrogated endotoxin neutralization activity of CATH-2 analogs. These findings support a pivotal role for aromatic residues in peptide-mediated endotoxin neutralization by CATH-2 analogs and were shown to be independent of LPS affinity. The capacity to modulate chemokine production and dampen endotoxin-induced pro-inflammatory responses in chicken immune cells implicates that small CATH-2 based peptides could serve as leads for the design of CATH-2 based immunomodulatory anti-infectives.

Ecotoxicological and Health Risk Assessment of Polycyclic Aromatic Hydrocarbons (PAHs) in Short-Neck Clam (Paphia undulata) and Contaminated Sediments in Malacca Strait, Malaysia.

Science.gov (United States)

Keshavarzifard, Mehrzad; Zakaria, Mohamad Pauzi; Sharifi, Reza

2017-10-01

The distribution, sources, and human health risk assessment of polycyclic aromatic hydrocarbons (PAHs) in surface sediment and the edible tissue of short-neck clam (Paphia undulata) from mudflat ecosystem in the west coast of Malaysia were investigated. The concentrations of ∑ 16 PAHs varied from 347.05 to 6207.5 and 179.32 to 1657.5 ng g -1 in sediment and short-neck clam samples, respectively. The calculations of mean PEL quotients (mean-PELQs) showed that the ecological risk of PAHs in the sediment samples was low to moderate-high level, whereas the total health risk through ingestion and dermal contact was considerably high. The PAHs biota sediment accumulation factors data for short-neck clam were obtained in this study, indicating a preferential accumulation of lower molecular weight PAHs. The source apportionment of PAHs in sediment using positive matrix factorization model indicated that the highest contribution to the PAHs was from diesel emissions (30.38%) followed by oil and oil derivate and incomplete coal combustion (23.06%), vehicular emissions (16.43%), wood combustion (15.93%), and natural gas combustion (14.2%). A preliminary evaluation of human health risk using chronic daily intake, hazard index, benzo[a]pyrene-equivalent (BaP eq ) concentration, and the incremental lifetime cancer risk indicated that PAHs in short-neck clam would induce potential carcinogenic effects in the consumers.

What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning?

Science.gov (United States)

Lee, Ernest Y; Lee, Michelle W; Fulan, Benjamin M; Ferguson, Andrew L; Wong, Gerard C L

2017-12-06

Antimicrobial peptides (AMPs) are a diverse class of well-studied membrane-permeating peptides with important functions in innate host defense. In this short review, we provide a historical overview of AMPs, summarize previous applications of machine learning to AMPs, and discuss the results of our studies in the context of the latest AMP literature. Much work has been recently done in leveraging computational tools to design new AMP candidates with high therapeutic efficacies for drug-resistant infections. We show that machine learning on AMPs can be used to identify essential physico-chemical determinants of AMP functionality, and identify and design peptide sequences to generate membrane curvature. In a broader scope, we discuss the implications of our findings for the discovery of membrane-active peptides in general, and uncovering membrane activity in new and existing peptide taxonomies.

Self-assembling peptide semiconductors

Science.gov (United States)

Tao, Kai; Makam, Pandeeswar; Aizen, Ruth; Gazit, Ehud

2017-01-01

Semiconductors are central to the modern electronics and optics industries. Conventional semiconductive materials bear inherent limitations, especially in emerging fields such as interfacing with biological systems and bottom-up fabrication. A promising candidate for bioinspired and durable nanoscale semiconductors is the family of self-assembled nanostructures comprising short peptides. The highly ordered and directional intermolecular π-π interactions and hydrogen-bonding network allow the formation of quantum confined structures within the peptide self-assemblies, thus decreasing the band gaps of the superstructures into semiconductor regions. As a result of the diverse architectures and ease of modification of peptide self-assemblies, their semiconductivity can be readily tuned, doped, and functionalized. Therefore, this family of electroactive supramolecular materials may bridge the gap between the inorganic semiconductor world and biological systems. PMID:29146781

Photoinduced electron transfer involving eosin-tryptophan conjugates. Long-lived radical pair states for systems incorporating aromatic amino acid side chains

Energy Technology Data Exchange (ETDEWEB)

Jones, G. II; Farahat, C.W.; Oh, C. (Boston Univ., MA (United States))

1994-07-14

The electron-transfer photochemistry of the covalent derivatives of the dye eosin, in which the xanthene dye is covalently attached to the amino acid L-tryptophan via the thiohydantoin derivative, the tryptophan dipeptide, and an ethyl ester derivative, has been investigated. The singlet excited state of the dye is significantly quenched on attachment of the aromatic amino acid residue. Dye triplet states are also intercepted through intramolecular interaction of excited dye and amino acid pendants. Flash photolysis experiments verify that this interaction involves electron transfer from the indole side chains of tryptophan. Rate constants for electron transfer are discussed in terms of the distance relationships for the eosin chromophore and aromatic redox sites on peptide derivatives, the pathway for [sigma]-[pi] through-bond interaction between redox sites, and the multiplicity and state of protonation for electron-transfer intermediates. Selected electron-transfer photoreactions were studied under conditions of binding of the peptide derivatives in a high molecular weight, water-soluble, globular polymer, poly(vinyl-2-pyrrolidinone). 28 refs., 4 figs., 1 tab.

Site-selective modification of peptides: From "customizable units" to novel α-aryl and α-alkyl glycine derivatives, and components of branched peptides.

Science.gov (United States)

Romero-Estudillo, Iván; Saavedra, Carlos; Boto, Alicia; Álvarez, Eleuterio

2015-09-01

The creation of peptide libraries by site-selective modification of a few peptide substrates would increase the efficiency of discovery processes, but still is a real synthetic challenge. The site-selective modification of small peptides at serine or threonine residues, by using a short scission-addition procedure, allows the preparation of peptides with unnatural α-aryl glycines. In a similar way, the scission of hydroxyproline residues is the key step in the production of optically pure α-alkyl glycines which are precursors or components of branched peptides. With these versatile processes, a single peptide can be transformed into a variety of peptide derivatives. The process takes place under mild conditions, and good global yields are obtained. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 650-662, 2015. © 2015 Wiley Periodicals, Inc.

Synthesis of Mikto-Arm Star Peptide Conjugates.

Science.gov (United States)

Koo, Jin Mo; Su, Hao; Lin, Yi-An; Cui, Honggang

2018-01-01

Mikto-arm star peptide conjugates are an emerging class of self-assembling peptide-based structural units that contain three or more auxiliary segments of different chemical compositions and/or functionalities. This group of molecules exhibit interesting self-assembly behavior in solution due to their chemically asymmetric topology. Here we describe the detailed procedure for synthesis of an ABC Mikto-arm star peptide conjugate in which two immiscible entities (a saturated hydrocarbon and a hydrophobic and lipophobic fluorocarbon) are conjugated onto a short β-sheet forming peptide sequence, GNNQQNY, derived from the Sup35 prion, through a lysine junction. Automated and manual Fmoc-solid phase synthesis techniques are used to synthesize the Mikto-arm star peptide conjugates, followed by HPLC purification. We envision that this set of protocols can afford a versatile platform to synthesize a new class of peptidic building units for diverse applications.

Peptide Vaccine: Progress and Challenges

Directory of Open Access Journals (Sweden)

Weidang Li

2014-07-01

Full Text Available Conventional vaccine strategies have been highly efficacious for several decades in reducing mortality and morbidity due to infectious diseases. The bane of conventional vaccines, such as those that include whole organisms or large proteins, appear to be the inclusion of unnecessary antigenic load that, not only contributes little to the protective immune response, but complicates the situation by inducing allergenic and/or reactogenic responses. Peptide vaccines are an attractive alternative strategy that relies on usage of short peptide fragments to engineer the induction of highly targeted immune responses, consequently avoiding allergenic and/or reactogenic sequences. Conversely, peptide vaccines used in isolation are often weakly immunogenic and require particulate carriers for delivery and adjuvanting. In this article, we discuss the specific advantages and considerations in targeted induction of immune responses by peptide vaccines and progresses in the development of such vaccines against various diseases. Additionally, we also discuss the development of particulate carrier strategies and the inherent challenges with regard to safety when combining such technologies with peptide vaccines.

Acylation of Therapeutic Peptides

DEFF Research Database (Denmark)

Trier, Sofie; Henriksen, Jonas Rosager; Jensen, Simon Bjerregaard

) , which promotes intestinal growth and is used to treat bowel disorders such as inflammatory bowel diseases and short bowel syndrome, and the 32 amino acid salmon calcitonin (sCT), which lowers blood calcium and is employed in the treatment of post-menopausal osteoporosis and hypercalcemia. The two...... peptides are similar in size and structure, but oppositely charged at physiological pH. Both peptides were acylated with linear acyl chains of systematically increasing length, where sCT was furthermore acylated at two different positions on the peptide backbone. For GLP-2, we found that increasing acyl...... remained optimal overall. The results indicate that rational acylation of GLP-2 can increase its in vitro intestinal absorption, alone or in combination with permeation enhancers, and are consistent with the initial project hypothesis. For sCT, an unpredicted effect of acylation largely superseded...

Peptide drugs to target G protein-coupled receptors.

Science.gov (United States)

Bellmann-Sickert, Kathrin; Beck-Sickinger, Annette G

2010-09-01

Major indications for use of peptide-based therapeutics include endocrine functions (especially diabetes mellitus and obesity), infectious diseases, and cancer. Whereas some peptide pharmaceuticals are drugs, acting as agonists or antagonists to directly treat cancer, others (including peptide diagnostics and tumour-targeting pharmaceuticals) use peptides to 'shuttle' a chemotherapeutic agent or a tracer to the tumour and allow sensitive imaging or targeted therapy. Significant progress has been made in the last few years to overcome disadvantages in peptide design such as short half-life, fast proteolytic cleavage, and low oral bioavailability. These advances include peptide PEGylation, lipidisation or multimerisation; the introduction of peptidomimetic elements into the sequences; and innovative uptake strategies such as liposomal, capsule or subcutaneous formulations. This review focuses on peptides targeting G protein-coupled receptors that are promising drug candidates or that have recently entered the pharmaceutical market. Copyright 2010 Elsevier Ltd. All rights reserved.

Aromatic chemical feedstocks from coal

Energy Technology Data Exchange (ETDEWEB)

Collin, G

1982-06-01

Liquid byproducts of coal carbonization meet some 25% of the world demand for aromatic chemicals, currently at approx. 30 million t/a, in particular 15% of the demand for benzene and over 95% of the demand for condensed aromatics and heteroaromatics. Industrial processing of the aromatic byproducts of coal pressure gasification is carried out to only a minor extent. Other methods that may be employed in future to obtain carbochemical aromatic compounds are solvolysis and supercritical gas extraction, the catalytic liquid-phase hydrogenation and hydropyrolysis of coal, which also permit recovery of benzene and homologues, phenols, and condensed and partially hydrogenated aromatics, and the synthesis of aromatics using methanol as the key compound. As with the present means of obtaining aromatic chemicals from coal, the processes that may in the future be applied on an industrial scale to obtain pure aromatics will only be economically feasible if linked with the manufacture of other mass products and combined with the present production of carbochemical aromatics.

Aromatic raw materials from coal

Energy Technology Data Exchange (ETDEWEB)

Collin, G

1982-06-01

Liquid byproducts of coal carbonization meet some 25% of the world demand for aromatic chemicals, currently at approx. 30 million t/a, in particular 15% of the demand for benzene and over 95% of the demand for condensed aromatics and heteroaromatics. Industrial processing of the aromatic byproducts of coal pressure gasification is carried out to only a minor extent. Other methods that may be employed in future to obtain carbochemical aromatic compounds are solvolysis and supercritical gas extraction, the catalytic liquid-phase hydrogenation and hydropyrolysis of coal, which also permit recovery of benzene and homologues, phenols, and condensed and partially hydrogenated aromatics, and the synthesis of aromatics using methanol as the key compound. As with the present means of obtaining aromatic chemicals from coal, the processes that may in future be applied on an industrial scale to obtain pure aromatics will only be economically feasible if linked with the manufacture of other mass products and combined with the present production of carbochemical aromatics. (In German)

On-resin N-formylation of peptides: a head-to-head comparison of reagents in solid-phase synthesis of ligands for formyl peptide receptors

DEFF Research Database (Denmark)

Christensen, Simon Bendt; Hansen, Anna Mette; Franzyk, Henrik

2017-01-01

General conditions for efficient on-resin N-formylation of peptides were identified by screening of a number of reagents comprising aliphatic formates (ethyl formate, 2,2,2-trifluoroethyl formate, and cyanomethyl formate), aromatic esters (phenyl formate and p-nitrophenyl formate), and N-formylim...... available activated ester p-nitrophenyl formate proved to be most convenient and versatile as high formylation degrees were obtained after 1–3 h at room temperature, while either conventional or microwave-assisted heating allowed reduction of the formylation time to 20 min....

Prenatal exposure to polycyclic aromatic hydrocarbons/aromatics, BDNF and child development

International Nuclear Information System (INIS)

Perera, Frederica; Phillips, David H.; Wang, Ya; Roen, Emily; Herbstman, Julie; Rauh, Virginia; Wang, Shuang; Tang, Deliang

2015-01-01

Objectives: Within a New York City (NYC) birth cohort, we assessed the associations between polycyclic aromatic hydrocarbon (PAH) and other aromatic DNA adducts and brain derived neurotrophic factor (BDNF) concentrations in umbilical cord blood, and neurodevelopment at age 2 years and whether BDNF is a mediator of the associations between PAH/aromatic-DNA adducts and neurodevelopment. Methods: PAH/aromatic-DNA adduct concentrations in cord blood were measured in 505 children born to nonsmoking African-American and Dominican women residing in NYC, and a subset was assessed for neurodevelopment at 2 years using the Bayley Scales of Infant Development Mental Development Index (MDI). A spectrum of PAH/aromatic-DNA adducts was measured using the 32 P-postlabeling assay; DNA adducts formed by benzo[a]pyrene (B[a]P), a representative PAH, were measured by High Performance Liquid Chromatography (HPLC)/fluorescence. BDNF mature protein in cord blood plasma was quantified by an ELISA. Multivariate regression analysis, adjusting for potential confounders, was conducted. Results: PAH/aromatic-DNA adduct concentration measured by postlabeling was inversely associated with BDNF concentration (p=0.02) and with MDI scores at 2 years (p=0.04). BDNF level was positively associated with MDI scores (p=0.003). Restricting to subjects having all three measures (PAH/aromatic-DNA adducts by postlabeling, MDI, and BDNF), results were similar but attenuated (p=0.13, p=0.05, p=0.01, respectively). Associations between B[a]P-DNA adducts and BDNF and B[a]P-DNA adducts and MDI at age 2 years were not significant. At age 3 years, the positive association of BDNF with MDI was not observed. Conclusions: The results at age 2 suggest that prenatal exposure to a spectrum of PAH/aromatic pollutants may adversely affect early neurodevelopment, in part by reducing BDNF levels during the fetal period. However, the same relationship was not seen at age 3. - Highlights: • Cord blood Polycyclic Aromatic

Prenatal exposure to polycyclic aromatic hydrocarbons/aromatics, BDNF and child development

Energy Technology Data Exchange (ETDEWEB)

Perera, Frederica, E-mail: fpp1@columbia.edu [Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 W. 168th St., New York, NY 10032 (United States); Columbia Center for Children' s Environmental Health, Columbia University, 722 W. 168th St., New York, NY 10032 (United States); Phillips, David H. [Analytical and Environmental Sciences Division, MRC-PHE Centre for Environment and Health, King' s College London, Franklin-Wilkins Building, London SE1 9NH (United Kingdom); Wang, Ya [Columbia Center for Children' s Environmental Health, Columbia University, 722 W. 168th St., New York, NY 10032 (United States); Department of Biostatistics, Mailman School of Public Health, Columbia University, 722 W. 168th St., New York, NY 10032 (United States); Roen, Emily; Herbstman, Julie [Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 W. 168th St., New York, NY 10032 (United States); Columbia Center for Children' s Environmental Health, Columbia University, 722 W. 168th St., New York, NY 10032 (United States); Rauh, Virginia [Columbia Center for Children' s Environmental Health, Columbia University, 722 W. 168th St., New York, NY 10032 (United States); The Heilbrunn Department of Population and Family Health, Columbia University, 60 Haven Avenue, New York, NY 10032 (United States); Wang, Shuang [Columbia Center for Children' s Environmental Health, Columbia University, 722 W. 168th St., New York, NY 10032 (United States); Department of Biostatistics, Mailman School of Public Health, Columbia University, 722 W. 168th St., New York, NY 10032 (United States); Tang, Deliang [Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 W. 168th St., New York, NY 10032 (United States); Columbia Center for Children' s Environmental Health, Columbia University, 722 W. 168th St., New York, NY 10032 (United States)

2015-10-15

Objectives: Within a New York City (NYC) birth cohort, we assessed the associations between polycyclic aromatic hydrocarbon (PAH) and other aromatic DNA adducts and brain derived neurotrophic factor (BDNF) concentrations in umbilical cord blood, and neurodevelopment at age 2 years and whether BDNF is a mediator of the associations between PAH/aromatic-DNA adducts and neurodevelopment. Methods: PAH/aromatic-DNA adduct concentrations in cord blood were measured in 505 children born to nonsmoking African-American and Dominican women residing in NYC, and a subset was assessed for neurodevelopment at 2 years using the Bayley Scales of Infant Development Mental Development Index (MDI). A spectrum of PAH/aromatic-DNA adducts was measured using the {sup 32}P-postlabeling assay; DNA adducts formed by benzo[a]pyrene (B[a]P), a representative PAH, were measured by High Performance Liquid Chromatography (HPLC)/fluorescence. BDNF mature protein in cord blood plasma was quantified by an ELISA. Multivariate regression analysis, adjusting for potential confounders, was conducted. Results: PAH/aromatic-DNA adduct concentration measured by postlabeling was inversely associated with BDNF concentration (p=0.02) and with MDI scores at 2 years (p=0.04). BDNF level was positively associated with MDI scores (p=0.003). Restricting to subjects having all three measures (PAH/aromatic-DNA adducts by postlabeling, MDI, and BDNF), results were similar but attenuated (p=0.13, p=0.05, p=0.01, respectively). Associations between B[a]P-DNA adducts and BDNF and B[a]P-DNA adducts and MDI at age 2 years were not significant. At age 3 years, the positive association of BDNF with MDI was not observed. Conclusions: The results at age 2 suggest that prenatal exposure to a spectrum of PAH/aromatic pollutants may adversely affect early neurodevelopment, in part by reducing BDNF levels during the fetal period. However, the same relationship was not seen at age 3. - Highlights: • Cord blood Polycyclic

Designing anticancer peptides by constructive machine learning.

Science.gov (United States)

Grisoni, Francesca; Neuhaus, Claudia; Gabernet, Gisela; Müller, Alex; Hiss, Jan; Schneider, Gisbert

2018-04-21

Constructive machine learning enables the automated generation of novel chemical structures without the need for explicit molecular design rules. This study presents the experimental application of such a generative model to design membranolytic anticancer peptides (ACPs) de novo. A recurrent neural network with long short-term memory cells was trained on alpha-helical cationic amphipathic peptide sequences and then fine-tuned with 26 known ACPs. This optimized model was used to generate unique and novel amino acid sequences. Twelve of the peptides were synthesized and tested for their activity on MCF7 human breast adenocarcinoma cells and selectivity against human erythrocytes. Ten of these peptides were active against cancer cells. Six of the active peptides killed MCF7 cancer cells without affecting human erythrocytes with at least threefold selectivity. These results advocate constructive machine learning for the automated design of peptides with desired biological activities. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Short bowel patients treated for two years with glucagon-like peptide 2 (GLP-2): compliance, safety, and effects on quality of life

DEFF Research Database (Denmark)

Jeppesen, P B; Lund, P; Gottschalck, I B

2009-01-01

BACKGROUND AND AIMS: Glucagon-like peptide 2 (GLP-2) has been shown to improve intestinal absorption in short bowel syndrome (SBS) patients in a short-term study. This study describes safety, compliance, and changes in quality of life in 11 SBS patients at baseline, week 13, 26, and 52 during two...... years of subcutaneous GLP-2 treatment, 400 microgram TID, intermitted by an 8-week washout period. METHODS: Safety and compliance was evaluated during the admissions. The Sickness Impact Profile (SIP), Short Form 36 (SF 36), and Inflammatory Bowel Disease Questionnaire (IBDQ) evaluated quality of life......-ascendo-anastomosis. The investigator excluded a patient due to unreliable feedback. Stoma nipple enlargement was seen in all 9 jejunostomy patients. Reported GLP-2 compliance was excellent (>93%). GLP-2 improved the overall quality of life VAS-score (4.1 +/- 2.8 cm versus 6.0 +/- 2.4 cm, P

Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide.

Science.gov (United States)

Iwaoka, Michio; Suzuki, Toshiki; Shoji, Yuya; Dedachi, Kenichi; Shimosato, Taku; Minezaki, Toshiya; Hojo, Hironobu; Onuki, Hiroyuki; Hirota, Hiroshi

2017-12-01

Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH 2 ). For chignolin, REMC/SAAP3D simulation correctly produced native β-turn structures, whose minimal all-atom root-mean-square deviation value measured from the native NMR structure (except for H) was 1.2 Å, at 300 K in implicit water, along with misfolded β-hairpin structures with unpacked aromatic side chains of Tyr2 and Trp9. Similar results were obtained for chignolin analog [G1Y,G10Y], which folded more tightly to the native β-turn structure than chignolin did. For C-peptide, on the other hand, the α-helix content was larger than the β content on average, suggesting a significant helix-forming propensity. When the imidazole side chain of His12 was protonated (i.e., [His12Hip]), the α content became larger. These observations as well as the representative structures obtained by clustering analysis were in reasonable agreement not only with the structures of C-peptide that were determined in this study by NMR in 30% CD 3 CD in H 2 O at 298 K but also with the experimental and theoretical behaviors having been reported for protonated C-peptide. Thus, accuracy of the SAAP force field was improved by applying three-dimensional main-chain parameters, supporting prominent importance of SAAP for peptide conformations.

Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide

Science.gov (United States)

Iwaoka, Michio; Suzuki, Toshiki; Shoji, Yuya; Dedachi, Kenichi; Shimosato, Taku; Minezaki, Toshiya; Hojo, Hironobu; Onuki, Hiroyuki; Hirota, Hiroshi

2017-12-01

Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH2). For chignolin, REMC/SAAP3D simulation correctly produced native β-turn structures, whose minimal all-atom root-mean-square deviation value measured from the native NMR structure (except for H) was 1.2 Å, at 300 K in implicit water, along with misfolded β-hairpin structures with unpacked aromatic side chains of Tyr2 and Trp9. Similar results were obtained for chignolin analog [G1Y,G10Y], which folded more tightly to the native β-turn structure than chignolin did. For C-peptide, on the other hand, the α-helix content was larger than the β content on average, suggesting a significant helix-forming propensity. When the imidazole side chain of His12 was protonated (i.e., [His12Hip]), the α content became larger. These observations as well as the representative structures obtained by clustering analysis were in reasonable agreement not only with the structures of C-peptide that were determined in this study by NMR in 30% CD3CD in H2O at 298 K but also with the experimental and theoretical behaviors having been reported for protonated C-peptide. Thus, accuracy of the SAAP force field was improved by applying three-dimensional main-chain parameters, supporting prominent importance of SAAP for peptide conformations.

Substrate specific hydrolysis of aromatic and aromatic-aliphatic esters in orchid tissue cultures

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Agnieszka Mironowicz

2014-01-01

Full Text Available We found that tissue cultures of higher plants were able, similarly as microorganisms, to transform low-molecular-weight chemical compounds. In tissue cultures of orchids (Cymbidium 'Saint Pierre' and Dendrobium phalaenopsis acetates of phenols and aromatic-aliphatic alcohols were hydrolyzed, whereas methyl esters of aromatic and aromatic-aliphatic acids did not undergo this reaction. Acetates of racemic aromatic-aliphatic alcohols were hydrolyzed with distinct enantiospecificity.

Nuclear and Chloroplast DNA Variation Provides Insights into Population Structure and Multiple Origin of Native Aromatic Rices of Odisha, India.

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Pritesh Sundar Roy

Full Text Available A large number of short grain aromatic rice suited to the agro-climatic conditions and local preferences are grown in niche areas of different parts of India and their diversity is evolved over centuries as a result of selection by traditional farmers. Systematic characterization of these specialty rices has not been attempted. An effort was made to characterize 126 aromatic short grain rice landraces, collected from 19 different districts in the State of Odisha, from eastern India. High level of variation for grain quality and agronomic traits among these aromatic rices was observed and genotypes having desirable phenotypic traits like erect flag leaf, thick culm, compact and dense panicles, short plant stature, early duration, superior yield and grain quality traits were identified. A total of 24 SSR markers corresponding to the hyper variable regions of rice chromosomes were used to understand the genetic diversity and to establish the genetic relationship among the aromatic short grain rice landraces at nuclear genome level. SSR analysis of 126 genotypes from Odisha and 10 genotypes from other states revealed 110 alleles with an average of 4.583 and the Nei's genetic diversity value (He was in the range of 0.034-0.880 revealing two sub-populations SP 1 (membership percentage-27.1% and SP 2 (72.9%. At the organelle genomic level for the C/A repeats in PS1D sequence of chloroplasts, eight different plastid sub types and 33 haplotypes were detected. The japonica (Nipponbare subtype (6C7A was detected in 100 genotypes followed by O. rufipogon (KF428978 subtype (6C6A in 13 genotypes while indica (93-11 sub type (8C8A was seen in 14 genotypes. The tree constructed based on haplotypes suggests that short grain aromatic landraces might have independent origin of these plastid subtypes. Notably a wide range of diversity was observed among these landraces cultivated in different parts confined to the State of Odisha.

RESEARCH METHODOLOGY OF SUS SCROFA TISSUE EXTRACTS PROTEIN-PEPTIDE COMPONENTS

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Ekaterina R.. Vasilevskaya

2017-01-01

Full Text Available The article presents a comparative analysis of four methods for quantifying the protein-peptide complexes content in extracts obtained from animal raw materials, as well as the low- and highmolecular weight extract fractions: the direct spectrophotometric determination at wavelengths of 260 and 280 nm with subsequent calculation by the Kalckar formula; the biuret reaction by the Kingsley-Weichselbaum method; the method with Bradford reagent and the standard Lowry method. Experimental data analysis demonstrates that in case of the extract that contains protein-peptidic complexes in different molecular weights range, the Kingsley-Weichselbaum method shows the highest quality of protein concentration determination; while studying highmolecular weight fraction (more than 30 kDa, it is possible to obtain more information by combining the spectrophotometric method and the Kingsley-Weichselbaum method. Low-molecular weight fractions (less than 30 kD should be investigated by complex methods including the spectrophotometric method, Lowry and Bradford methods. These methods make it possible to presumably estimate protein molecules size ranges (by amount of peptide bonds, and also to determine hydrophobic and aromatic amino acids presence.

Tuning peptide amphiphile supramolecular structure for biomedical applications

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Pashuck, Eugene Thomas, III

The use of biomaterials in regenerative medicine has been an active area of research for more than a decade. Peptide amphiphiles, which are short peptide sequences coupled to alkyl tails, have been studied in the Stupp group since the beginning of the decade and been used for a variety of biomedical applications. Most of the work has focused on the bioactive epitopes places on the periphery of the PA molecules, but the interior amino acids, known as the beta-sheet region, give the PA nanofiber gel much of its mechanical strength. To study the important parameters in the beta-sheet region, six PA molecules were constructed to determine the influence of beta-sheet length and order of the amino acids in the beta-sheet. It was found that having beta-sheet forming amino acids near the center of the fiber improves PA gel stiffness, and that having extra amino acids that have preferences for other secondary structures, like alpha-helix decreased the gels stiffness. Using FTIR and circular dichroism it was found that the mechanical properties are influenced by the amount of twist in the beta-sheet, and PAs that have more twisted beta-sheets form weaker gels. The effect amino acid properties have on peptide amphiphile self-assembly where studied by synthesizining molecules with varying side group size and hydrophobicity. It was found that smaller amino acids lead to stiffer gels and when two amino acids had the same size the amino acid with the larger beta-sheet propensity lead to a stiffer gel. Furthermore, small changes in peptide structure were found to lead to big changes in nanostructure, as leucine and isoleucine, which have the same size but slightly different structures, form flat ribbons and cylindrical nanofibers, respectively. Phenylalanine and alanine were studied more indepth because they represent the effects of adding an aromatic group to amino acids in the beta-sheet regon. These phenylalanine PAs formed short, twisted ribbons when freshly dissolved in water

Photodissociative Cross-Linking of Non-covalent Peptide-Peptide Ion Complexes in the Gas Phase

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Nguyen, Huong T. H.; Andrikopoulos, Prokopis C.; Rulíšek, Lubomír; Shaffer, Christopher J.; Tureček, František

2018-05-01

We report a gas-phase UV photodissociation study investigating non-covalent interactions between neutral hydrophobic pentapeptides and peptide ions incorporating a diazirine-tagged photoleucine residue. Phenylalanine (Phe) and proline (Pro) were chosen as the conformation-affecting residues that were incorporated into a small library of neutral pentapeptides. Gas-phase ion-molecule complexes of these peptides with photo-labeled pentapeptides were subjected to photodissociation. Selective photocleavage of the diazirine ring at 355 nm formed short-lived carbene intermediates that underwent cross-linking by insertion into H-X bonds of the target peptide. The cross-link positions were established from collision-induced dissociation tandem mass spectra (CID-MS3) providing sequence information on the covalent adducts. Effects of the amino acid residue (Pro or Phe) and its position in the target peptide sequence were evaluated. For proline-containing peptides, interactions resulting in covalent cross-links in these complexes became more prominent as proline was moved towards the C-terminus of the target peptide sequence. The photocross-linking yields of phenylalanine-containing peptides depended on the position of both phenylalanine and photoleucine. Density functional theory calculations were used to assign structures of low-energy conformers of the (GLPMG + GLL*LK + H)+ complex. Born-Oppenheimer molecular dynamics trajectory calculations were used to capture the thermal motion in the complexes within 100 ps and determine close contacts between the incipient carbene and the H-X bonds in the target peptide. This provided atomic-level resolution of potential cross-links that aided spectra interpretation and was in agreement with experimental data. [Figure not available: see fulltext.

Parsing of the free energy of aromatic-aromatic stacking interactions in solution

Energy Technology Data Exchange (ETDEWEB)

Kostjukov, Viktor V.; Khomytova, Nina M. [Department of Physics, Sevastopol National Technical University, Sevastopol 99053, Crimea (Ukraine); Hernandez Santiago, Adrian A.; Tavera, Anna-Maria Cervantes; Alvarado, Julieta Salas [Faculty of Chemical Sciences, Autonomous University of Puebla, Puebla (Mexico); Evstigneev, Maxim P., E-mail: max_evstigneev@mail.ru [Department of Physics, Sevastopol National Technical University, Sevastopol 99053, Crimea (Ukraine)

2011-10-15

Graphical abstract: Highlights: > A protocol for decomposition of the free energy of aromatic stacking is developed. > The factors stabilizing/destabilizing stacking of aromatic molecules are defined. > Hydrophobic contribution is found to be dominant. - Abstract: We report an analysis of the energetics of aromatic-aromatic stacking interactions for 39 non-covalent reactions of self- and hetero-association of 12 aromatic molecules with different structures and charge states. A protocol for computation of the contributions to the total energy from various energetic terms has been developed and the results are consistent with experiment in 92% of all the systems studied. It is found that the contributions from hydrogen bonds and entropic factors are always unfavorable, whereas contributions from van-der-Waals, electrostatic and/or hydrophobic effects may lead to stabilizing or destabilizing factors depending on the system studied. The analysis carried out in this work provides an answer to the questions 'What forces stabilize/destabilize the stacking of aromatic molecules in aqueous-salt solution and what are their relative importance?'

Parsing of the free energy of aromatic-aromatic stacking interactions in solution

International Nuclear Information System (INIS)

Kostjukov, Viktor V.; Khomytova, Nina M.; Hernandez Santiago, Adrian A.; Tavera, Anna-Maria Cervantes; Alvarado, Julieta Salas; Evstigneev, Maxim P.

2011-01-01

Graphical abstract: Highlights: → A protocol for decomposition of the free energy of aromatic stacking is developed. → The factors stabilizing/destabilizing stacking of aromatic molecules are defined. → Hydrophobic contribution is found to be dominant. - Abstract: We report an analysis of the energetics of aromatic-aromatic stacking interactions for 39 non-covalent reactions of self- and hetero-association of 12 aromatic molecules with different structures and charge states. A protocol for computation of the contributions to the total energy from various energetic terms has been developed and the results are consistent with experiment in 92% of all the systems studied. It is found that the contributions from hydrogen bonds and entropic factors are always unfavorable, whereas contributions from van-der-Waals, electrostatic and/or hydrophobic effects may lead to stabilizing or destabilizing factors depending on the system studied. The analysis carried out in this work provides an answer to the questions 'What forces stabilize/destabilize the stacking of aromatic molecules in aqueous-salt solution and what are their relative importance?'

Phospholyl(borane) Amino Acids and Peptides: Stereoselective Synthesis and Fluorescent Properties with Large Stokes Shift.

Science.gov (United States)

Arribat, Mathieu; Rémond, Emmanuelle; Clément, Sébastien; Lee, Arie Van Der; Cavelier, Florine

2018-01-24

The synthesis of phospholyl(borane) amino acids was stereoselectively achieved by reaction of phospholide anion with iodo α-amino ester derived from l-aspartic acid or l-serine, followed by in situ complexation with borane. Phospholyl(borane) amino acids are easy to store and can be subjected to direct transformation into the corresponding free phospholyl, gold complex, oxide or sulfur derivatives as well as phospholinium salts, thus offering a variety of side chains. After selective deprotection of carboxylic function or amine, C- or N- peptide coupling with an alanine moiety proved the possible incorporation into peptides. Such phospholyl amino acid and peptide derivatives exhibit fluorescent properties with a large Stokes shift (160 nm) and fluorescence up to 535 nm, depending on the phosphole aromaticity and the chemical environment. These phospholyl(borane) amino acids constitute a new class of unnatural amino acids useful for structure-activities relationship studies and appear to be promising fluorophores for the development of labeled peptides.

Development of novel ligands for peptide GPCRs.

Science.gov (United States)

Moran, Brian M; McKillop, Aine M; O'Harte, Finbarr Pm

2016-12-01

Incretin based glucagon-like peptide-1 receptor (GLP-1R) agonists which target a G-protein coupled receptor (GPCR) are currently used in the treatment of type 2 diabetes. This review focuses on GPCRs from pancreatic β-cells, including GLP-1, glucose-dependent insulinotropic polypeptide (GIP), glucagon, somatostatin, pancreatic polypeptide (PP), cholecystokinin (CCK), peptide YY (PYY), oxyntomodulin (OXM) and ghrelin receptors. In addition, fatty acids GPCRs are thought to have an increasing role in regulating peptide secretions namely short fatty acids GPCR (GPR41, GPR43), medium chain fatty acid GPCR (GPR84), long chain fatty acid GPCR (GPR40, GPR120) and cannabinoid-like GPCR (GPR55, GPR119). Several pre-clinical and clinical trials are currently ongoing in peptide GPCR based therapies, including dual and triple agonist peptides which activate two or more GPCRs simultaneously. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biogelx: Cell Culture on Self-Assembling Peptide Gels.

Science.gov (United States)

Harper, Mhairi M; Connolly, Michael L; Goldie, Laura; Irvine, Eleanore J; Shaw, Joshua E; Jayawarna, Vineetha; Richardson, Stephen M; Dalby, Matthew J; Lightbody, David; Ulijn, Rein V

2018-01-01

Aromatic peptide amphiphiles can form self-supporting nanostructured hydrogels with tunable mechanical properties and chemical compositions. These hydrogels are increasingly applied in two-dimensional (2D) and three-dimensional (3D) cell culture, where there is a rapidly growing need to store, grow, proliferate, and manipulate naturally derived cells within a hydrated, 3D matrix. Biogelx Limited is a biomaterials company, created to commercialize these bio-inspired hydrogels to cell biologists for a range of cell culture applications. This chapter describes methods of various characterization and cell culture techniques specifically optimized for compatibility with Biogelx products.

Pro-aromatic and anti-aromatic π-conjugated molecules: an irresistible wish to be diradicals

KAUST Repository

Zeng, Zebing

2015-01-01

© 2015 The Royal Society of Chemistry. Aromaticity is an important concept to understand the stability and physical properties of π-conjugated molecules. Recent studies on pro-aromatic and anti-aromatic molecules revealed their irresistible tendency to become diradicals in the ground state. Diradical character thus becomes another very important concept and it is fundamentally correlated to the physical (optical, electronic and magnetic) properties and chemical reactivity of most of the organic optoelectronic materials. Molecules with distinctive diradical character show unique properties which are very different from those of traditional closed-shell π-conjugated systems, and thus they have many potential applications in organic electronics, spintronics, non-linear optics and energy storage. This critical review first introduces the fundamental electronic structure of Kekulé diradicals within the concepts of anti-aromaticity and pro-aromaticity in the context of Hückel aromaticity and diradical character. Then recent research studies on various stable/persistent diradicaloids based on pro-aromatic and anti-aromatic compounds are summarized and discussed with regard to their synthetic chemistry, physical properties, structure-property relationships and potential material applications. A summary and personal perspective is given at the end.

Peptides in headlock--a novel high-affinity and versatile peptide-binding nanobody for proteomics and microscopy.

Science.gov (United States)

Braun, Michael B; Traenkle, Bjoern; Koch, Philipp A; Emele, Felix; Weiss, Frederik; Poetz, Oliver; Stehle, Thilo; Rothbauer, Ulrich

2016-01-21

Nanobodies are highly valuable tools for numerous bioanalytical and biotechnical applications. Here, we report the characterization of a nanobody that binds a short peptide epitope with extraordinary affinity. Structural analysis reveals an unusual binding mode where the extended peptide becomes part of a β-sheet structure in the nanobody. This interaction relies on sequence-independent backbone interactions augmented by a small number of specificity-determining side chain contacts. Once bound, the peptide is fastened by two nanobody side chains that clamp it in a headlock fashion. Exploiting this unusual binding mode, we generated a novel nanobody-derived capture and detection system. Matrix-coupled nanobody enables the fast and efficient isolation of epitope-tagged proteins from prokaryotic and eukaryotic expression systems. Additionally, the fluorescently labeled nanobody visualizes subcellular structures in different cellular compartments. The high-affinity-binding and modifiable peptide tag of this system renders it a versatile and robust tool to combine biochemical analysis with microscopic studies.

An etiologic prediction model incorporating biomarkers to predict the bladder cancer risk associated with occupational exposure to aromatic amines: a pilot study.

Science.gov (United States)

Mastrangelo, Giuseppe; Carta, Angela; Arici, Cecilia; Pavanello, Sofia; Porru, Stefano

2017-01-01

No etiological prediction model incorporating biomarkers is available to predict bladder cancer risk associated with occupational exposure to aromatic amines. Cases were 199 bladder cancer patients. Clinical, laboratory and genetic data were predictors in logistic regression models (full and short) in which the dependent variable was 1 for 15 patients with aromatic amines related bladder cancer and 0 otherwise. The receiver operating characteristics approach was adopted; the area under the curve was used to evaluate discriminatory ability of models. Area under the curve was 0.93 for the full model (including age, smoking and coffee habits, DNA adducts, 12 genotypes) and 0.86 for the short model (including smoking, DNA adducts, 3 genotypes). Using the "best cut-off" of predicted probability of a positive outcome, percentage of cases correctly classified was 92% (full model) against 75% (short model). Cancers classified as "positive outcome" are those to be referred for evaluation by an occupational physician for etiological diagnosis; these patients were 28 (full model) or 60 (short model). Using 3 genotypes instead of 12 can double the number of patients with suspect of aromatic amine related cancer, thus increasing costs of etiologic appraisal. Integrating clinical, laboratory and genetic factors, we developed the first etiologic prediction model for aromatic amine related bladder cancer. Discriminatory ability was excellent, particularly for the full model, allowing individualized predictions. Validation of our model in external populations is essential for practical use in the clinical setting.

Optimization of antibacterial peptides by genetic algorithms and cheminformatics

DEFF Research Database (Denmark)

Fjell, Christopher D.; Jenssen, Håvard; Cheung, Warren A.

2011-01-01

Pathogens resistant to available drug therapies are a pressing global health problem. Short, cationic peptides represent a novel class of agents that have lower rates of drug resistance than derivatives of current antibiotics. Previously, we created a software system utilizing artificial neural...... 47 of the top rated 50 peptides chosen from an in silico library of nearly 100 000 sequences. Here, we report a method of generating candidate peptide sequences using the heuristic evolutionary programming method of genetic algorithms (GA), which provided a large (19-fold) improvement...

Anti-Mycobacterial Peptides: From Human to Phage

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Tieshan Teng

2015-01-01

Full Text Available Mycobacterium tuberculosis is the major pathogen of tuberculosis (TB. With the growing problem of M. tuberculosis resistant to conventional antibiotics, especially multi-drug resistant tuberculosis (MDR-TB and extensively-drug resistant tuberculosis (XDR-TB, the need for new TB drugs is now more prominent than ever. Among the promising candidates for anti-TB drugs, anti-mycobacterial peptides have a few advantages, such as low immunogenicity, selective affinity to prokaryotic negatively charged cell envelopes, and diverse modes of action. In this review, we summarize the recent progress in the anti-mycobacterial peptides, highlighting the sources, effectiveness and bactericidal mechanisms of these antimicrobial peptides. Most of the current anti-mycobacterial peptides are derived either from host immune cells, bacterial extraction, or mycobacteriophages. Besides trans-membrane pore formation, which is considered to be the common bactericidal mechanism, many of the anti-mycobacterial peptides have the second non-membrane targets within mycobacteria. Additionally, some antimicrobial peptides play critical roles in innate immunity. However, a few obstacles, such as short half-life in vivo and resistance to antimicrobial peptides, need overcoming before clinical applications. Nevertheless, the multiple functions of anti-mycobacterial peptides, especially direct killing of pathogens and immune-modulators in infectious and inflammatory conditions, indicate that they are promising candidates for future drug development.

Effect of stereochemistry, chain length and sequence pattern on antimicrobial properties of short synthetic β-sheet forming peptide amphiphiles.

Science.gov (United States)

Ong, Zhan Yuin; Cheng, Junchi; Huang, Yuan; Xu, Kaijin; Ji, Zhongkang; Fan, Weimin; Yang, Yi Yan

2014-01-01

In the face of mounting global antibiotics resistance, the identification and development of membrane-active antimicrobial peptides (AMPs) as an alternative class of antimicrobial agent have gained significant attention. The physical perturbation and disruption of microbial membranes by the AMPs have been proposed to be an effective means to overcome conventional mechanisms of drug resistance. Recently, we have reported the design of a series of short synthetic β-sheet folding peptide amphiphiles comprised of recurring (X1Y1X2Y2)n-NH2 sequences where X: hydrophobic amino acids, Y: cationic amino acids and n: number of repeat units. In efforts to investigate the effects of key parameters including stereochemistry, chain length and sequence pattern on antimicrobial effects, systematic d-amino acid substitutions of the lead peptides (IRIK)2-NH2 (IK8-all L) and (IRVK)3-NH2 (IK12-all L) were performed. It was found that the corresponding D-enantiomers exhibited stronger antimicrobial activities with minimal or no change in hemolytic activities, hence translating very high selectivity indices of 407.0 and >9.8 for IK8-all D and IK12-all D respectively. IK8-all D was also demonstrated to be stable to degradation by broad spectrum proteases trypsin and proteinase K. The membrane disrupting bactericidal properties of IK8-all D effectively prevented drug resistance development and inhibited the growth of various clinically isolated MRSA, VRE, Acinetobacter baumanni, Pseudomonas aeruginosa, Cryptococcus. neoformans and Mycobacterium tuberculosis. Significant reduction in intracellular bacteria counts was also observed following treatment with IK8-all D in the Staphylococcus. aureus infected mouse macrophage cell line RAW264.7 (P < 0.01). These results suggest that the d-amino acids substituted β-sheet forming peptide IK8-all D with its enhanced antimicrobial activities and improved protease stability, is a promising therapeutic candidate with potential to combat

Identities of P2 and P3 Residues of H-2Kb-Bound Peptides Determine Mouse Ly49C Recognition.

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Elsa A Marquez

Full Text Available Ly49 receptors can be peptide selective in their recognition of MHC-I-peptide complexes, affording them a level of discrimination beyond detecting the presence or absence of specific MHC-I allele products. Despite this ability, little is understood regarding the properties that enable some peptides, when bound to MHC-I molecules, to support Ly49 recognition, but not others. Using RMA-S target cells expressing MHC-I molecules loaded with individual peptides and effector cells expressing the ectodomain of the inhibitory Ly49C receptor, we found that two adjacent amino acid residues, P2 and P3, both buried in the peptide binding groove of H-2Kb, determine mouse Ly49C specificity. If both are aliphatic residues, this is supportive. Whereas, small amino acids at P2 and aromatic amino acids at the P3 auxiliary anchor residue are detrimental to Ly49C recognition. These results resemble those with a rat Ly49 where the identity of a peptide anchor residue determines recognition, suggesting that dependence on specific peptide residues buried in the MHC-I peptide-binding groove may be fundamental to Ly49 peptide selectivity and recognition.

Cycloaddition in peptides for high-capacity optical storage

DEFF Research Database (Denmark)

Lohse, Brian; Berg, Rolf Henrik; Hvilsted, Søren

2006-01-01

Photodimerization of chromophores attached to a short peptide chain is investigated for high-capacity optical digital storage with UV lasers. The length and rigidity of the peptide chain assure an optimal distance and orientation of the chromophores for effective photodimerization. Using a theory...... developed by Tomlinson, the absorption cross section for the dimerization process in a uracil-ornithine-based hexamer is determined to be 9 x 10(-20) cm(2). A large change in the transmission due to irradiation in the UV area may make it possible to realize multilevel storage in a thin film of the peptides....

Peptide chemistry toolbox - Transforming natural peptides into peptide therapeutics.

Science.gov (United States)

Erak, Miloš; Bellmann-Sickert, Kathrin; Els-Heindl, Sylvia; Beck-Sickinger, Annette G

2018-06-01

The development of solid phase peptide synthesis has released tremendous opportunities for using synthetic peptides in medicinal applications. In the last decades, peptide therapeutics became an emerging market in pharmaceutical industry. The need for synthetic strategies in order to improve peptidic properties, such as longer half-life, higher bioavailability, increased potency and efficiency is accordingly rising. In this mini-review, we present a toolbox of modifications in peptide chemistry for overcoming the main drawbacks during the transition from natural peptides to peptide therapeutics. Modifications at the level of the peptide backbone, amino acid side chains and higher orders of structures are described. Furthermore, we are discussing the future of peptide therapeutics development and their impact on the pharmaceutical market. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bacterial degradation of monocyclic aromatic amines

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Pankaj Kumar Arora

2015-08-01

Full Text Available Aromatic amines are an important group of industrial chemicals, which are widely used for manufacturing of dyes, pesticides, drugs, pigments, and other industrial products. These compounds have been considered highly toxic to human beings due to their carcinogenic nature. Three groups of aromatic amines have been recognized: monocyclic, polycyclic and heterocyclic aromatic amines. Bacterial degradation of several monocyclic aromatic compounds has been studied in a variety of bacteria, which utilizes monocyclic aromatic amines as their sole source of carbon and energy. Several degradation pathways have been proposed and the related enzymes and genes have also been characterized. Many reviews have been reviewed toxicity of monocyclic aromatic amines; however, there is lack of review on biodegradation of monocyclic aromatic amines. The aim of this review is to summarize bacterial degradation of monocyclic aromatic amines. This review will increase our current understanding of biochemical and molecular basis of bacterial degradation of monocyclic aromatic amines.

Optimizing the Production of Renewable Aromatics via Crop Oil Catalytic Cracking

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Clancy Kadrmas

2015-04-01

Full Text Available While HZSM-5 catalytic cracking of crop oil toward aromatics have been well documented, this work adds to this body of knowledge with a full acid byproduct analysis that provides improved mass balance closure along with a design of experiment optimization of reaction conditions. Fatty acids are an inevitable byproduct when converting any triglyceride oil, but are most often overlooked; despite the impact fatty acids have on downstream processing. Acid analysis verified that only short chain fatty acids, mainly acetic acid, were present in low quantities when all feed oil was reacted. When relatively high fatty acid amounts were present, these were mainly uncracked C16 and C18 fatty acids. Optimization is a balance of aromatics formation vs. unwanted gas products, coke and residual fatty acids. A design of experiments approach was used to provide insight into where the optimal reaction conditions reside for HZSM-5 facilitated reactions. These conditions can then form the basis for further development into a commercially viable process for the production of renewable aromatics and other byproducts.

Boron-doped diamond electrodes for the electrochemical oxidation and cleavage of peptides.

Science.gov (United States)

Roeser, Julien; Alting, Niels F A; Permentier, Hjalmar P; Bruins, Andries P; Bischoff, Rainer

2013-07-16

Electrochemical oxidation of peptides and proteins is traditionally performed on carbon-based electrodes. Adsorption caused by the affinity of hydrophobic and aromatic amino acids toward these surfaces leads to electrode fouling. We compared the performance of boron-doped diamond (BDD) and glassy carbon (GC) electrodes for the electrochemical oxidation and cleavage of peptides. An optimal working potential of 2000 mV was chosen to ensure oxidation of peptides on BDD by electron transfer processes only. Oxidation by electrogenerated OH radicals took place above 2500 mV on BDD, which is undesirable if cleavage of a peptide is to be achieved. BDD showed improved cleavage yield and reduced adsorption for a set of small peptides, some of which had been previously shown to undergo electrochemical cleavage C-terminal to tyrosine (Tyr) and tryptophan (Trp) on porous carbon electrodes. Repeated oxidation with BDD electrodes resulted in progressively lower conversion yields due to a change in surface termination. Cathodic pretreatment of BDD at a negative potential in an acidic environment successfully regenerated the electrode surface and allowed for repeatable reactions over extended periods of time. BDD electrodes are a promising alternative to GC electrodes in terms of reduced adsorption and fouling and the possibility to regenerate them for consistent high-yield electrochemical cleavage of peptides. The fact that OH-radicals can be produced by anodic oxidation of water at elevated positive potentials is an additional advantage as they allow another set of oxidative reactions in analogy to the Fenton reaction, thus widening the scope of electrochemistry in protein and peptide chemistry and analytics.

The fluorodediazonation - a method for n.c.a.-18F-labelling of aromatic substrates

International Nuclear Information System (INIS)

Zwernemann, O.

1991-06-01

For the positron emission tomography (PET) applications, radiopharmaceuticals are required that are labelled with short-lived positron emitters. Fluorine-18 has become the leading radionuclide used for PET, due to its favourable physical properties. However, the labelling of aromatic substances with fluorine-18 with the methods available presents problems not encountered with aliphatic compounds. The decomposition of aromatic diazonium salts opens up feasible ways of preparing a broad range of labelled compounds. The dissertation investigated the possibilities of labelling with fluorine-18 by way of dediazonation on the standard substrate p-Toluidyl diazonium ion. The results reported show that the method of fluorodediazonation is an interesting further method for F-18 labelling of aromatic substrates in addition to the hitherto applied techniques. It allows carrier-free labelling of a large group of substances which cannot be fluorinated via direct nucleophilicity. (BBR) [de

Peptides in headlock – a novel high-affinity and versatile peptide-binding nanobody for proteomics and microscopy

Science.gov (United States)

Braun, Michael B.; Traenkle, Bjoern; Koch, Philipp A.; Emele, Felix; Weiss, Frederik; Poetz, Oliver; Stehle, Thilo; Rothbauer, Ulrich

2016-01-01

Nanobodies are highly valuable tools for numerous bioanalytical and biotechnical applications. Here, we report the characterization of a nanobody that binds a short peptide epitope with extraordinary affinity. Structural analysis reveals an unusual binding mode where the extended peptide becomes part of a β-sheet structure in the nanobody. This interaction relies on sequence-independent backbone interactions augmented by a small number of specificity-determining side chain contacts. Once bound, the peptide is fastened by two nanobody side chains that clamp it in a headlock fashion. Exploiting this unusual binding mode, we generated a novel nanobody-derived capture and detection system. Matrix-coupled nanobody enables the fast and efficient isolation of epitope-tagged proteins from prokaryotic and eukaryotic expression systems. Additionally, the fluorescently labeled nanobody visualizes subcellular structures in different cellular compartments. The high-affinity-binding and modifiable peptide tag of this system renders it a versatile and robust tool to combine biochemical analysis with microscopic studies. PMID:26791954

Recent progress in fluorine-18 labelled peptide radiopharmaceuticals

Energy Technology Data Exchange (ETDEWEB)

Okarvi, S.M. [Cyclotron and Radiopharmaceuticals Department, King Faisal Specialist Hospital and Research Centre, Riyadh (Saudi Arabia)

2001-07-01

The application of biologically active peptides labelled with positron-emitting nuclides has emerged as a useful and interesting field in nuclear medicine. Small synthetic receptor-binding peptides are currently the preferred agents over proteins and antibodies for diagnostic imaging of various tumours. Due to the smaller size of peptides, both higher target-to-background ratios and rapid blood clearance can often be achieved with radiolabelled peptides. Hence, short-lived positron emission tomography (PET) isotopes are potential candidates for labelling peptides. Among a number of positron-emitting nuclides, fluorine-18 appears to be the best candidate for labelling bioactive peptides by virtue of its favourable physical and nuclear characteristics. The major disadvantage of labelling peptides with {sup 18}F is the laborious and time-consuming preparation of the {sup 18}F labelling agents. In recent years, various techniques have been developed which allow efficient labelling of peptides with {sup 18}F without affecting their receptor-binding properties. Moreover, the development of a variety of prosthetic groups has facilitated the efficient and site-specific labelling of peptides with {sup 18}F. The {sup 18}F-labelled peptides hold enormous clinical potential owing to their ability to quantitatively detect and characterise a wide variety of human diseases when using PET. Recently, a number of {sup 18}F-labelled bioactive peptides have shown great promise as diagnostic imaging agents. This review presents the recent developments in {sup 18}F-labelled biologically active peptides used in PET. (orig.)

Recent progress in fluorine-18 labelled peptide radiopharmaceuticals

International Nuclear Information System (INIS)

Okarvi, S.M.

2001-01-01

The application of biologically active peptides labelled with positron-emitting nuclides has emerged as a useful and interesting field in nuclear medicine. Small synthetic receptor-binding peptides are currently the preferred agents over proteins and antibodies for diagnostic imaging of various tumours. Due to the smaller size of peptides, both higher target-to-background ratios and rapid blood clearance can often be achieved with radiolabelled peptides. Hence, short-lived positron emission tomography (PET) isotopes are potential candidates for labelling peptides. Among a number of positron-emitting nuclides, fluorine-18 appears to be the best candidate for labelling bioactive peptides by virtue of its favourable physical and nuclear characteristics. The major disadvantage of labelling peptides with 18 F is the laborious and time-consuming preparation of the 18 F labelling agents. In recent years, various techniques have been developed which allow efficient labelling of peptides with 18 F without affecting their receptor-binding properties. Moreover, the development of a variety of prosthetic groups has facilitated the efficient and site-specific labelling of peptides with 18 F. The 18 F-labelled peptides hold enormous clinical potential owing to their ability to quantitatively detect and characterise a wide variety of human diseases when using PET. Recently, a number of 18 F-labelled bioactive peptides have shown great promise as diagnostic imaging agents. This review presents the recent developments in 18 F-labelled biologically active peptides used in PET. (orig.)

Vaccatides: Antifungal Glutamine-Rich Hevein-Like Peptides from Vaccaria hispanica

Directory of Open Access Journals (Sweden)

Ka H. Wong

2017-06-01

Full Text Available Hevein and hevein-like peptides are disulfide-constrained chitin-binding cysteine-rich peptides. They are divided into three subfamilies, 6C-, 8C-, and 10C-hevein-like peptides, based on the number of cysteine residues. In addition, hevein-like peptides can exist in two forms, short and long. The long C-terminal form found in hevein and 10C-hevein-like peptides contain a C-terminal protein cargo. In contrast, the short form without a protein cargo is found in all three subfamilies. Here, we report the discovery and characterization of two novel glutamine-rich and protein cargo-free 8C-hevein-like peptides, vaccatides vH1 and vH2, from Vaccaria hispanica of the Caryophyllaceae family. Proteomic analyses showed that the vaccatides are 40–41 amino acids in length and contain a chitin-binding domain. NMR determination revealed that vaccatide vH2 displays a highly compact structure with a N-terminal cystine knot and an addition C-terminal disulfide bond. Stability studies showed that this compact structure renders vaccatide vH2 resistant to thermal, chemical and proteolytic degradation. The chitin-binding vH2 was shown to inhibit the mycelium growth of four phyto-pathogenic fungal strains with IC50 values in the micromolar range. Our findings show that vaccatides represent a new family of 8C-hevein-like peptides, which are protein cargo-free and glutamine-rich, characteristics that differentiate them from the prototypic hevein and the 10C-hevein-like peptides. In summary, this study enriches the existing library of hevein-like peptides and provides insight into their molecular diversity in sequence, structure and biosynthesis. Additionally, their highly disulfide-constrained structure could be used as a scaffold for developing metabolically and orally active peptidyl therapeutics.

Theoretical studies of the structures and local aromaticity of conjugated polycyclic hydrocarbons using three aromatic indices

Science.gov (United States)

Sakai, Shogo; Kita, Yuki

2013-07-01

The structures and local aromaticity of some conjugated polycyclic hydrocarbons (from the butadienoid, acene, and phenylene series) are studied using ab initio MO and density functional methods. The aromaticities of the molecules are estimated using three indices: the nucleus-independent chemical shift (NICS), the harmonic oscillator model of aromaticity (HOMA), and the index of deviation from aromaticity (IDA). Assessment of the relationships between the structures and the aromatic indices shows that the IDA values correspond best to the characteristics of the conjugated polycyclic hydrocarbon structures.

A novel 13 residue acyclic peptide from the marine snail, Conus monile, targets potassium channels.

Science.gov (United States)

Sudarslal, Sadasivannair; Singaravadivelan, Govindaswamy; Ramasamy, Palanisamy; Ananda, Kuppanna; Sarma, Siddhartha P; Sikdar, Sujit K; Krishnan, K S; Balaram, Padmanabhan

2004-05-07

A novel 13-residue peptide Mo1659 has been isolated from the venom of a vermivorous cone snail, Conus monile. HPLC fractions of the venom extract yielded an intense UV absorbing fraction with a mass of 1659Da. De novo sequencing using both matrix assisted laser desorption and ionization and electrospray MS/MS methods together with analysis of proteolytic fragments successfully yielded the amino acid sequence, FHGGSWYRFPWGY-NH(2). This was further confirmed by comparison with the chemically synthesized peptide and by conventional Edman sequencing. Mo1659 has an unusual sequence with a preponderance of aromatic residues and the absence of apolar, aliphatic residues like Ala, Val, Leu, and Ile. Mo1659 has no disulfide bridges distinguishing it from the conotoxins and bears no sequence similarity with any of the acyclic peptides isolated thus far from the venom of cone snails. Electrophysiological studies on the effect of Mo1659 on measured currents in dorsal root ganglion neurons suggest that the peptide targets non-inactivating voltage-dependent potassium channels.

Cyano-containing ionic liquids for the extraction of aromatic hydrocarbons from an aromatic/aliphatic mixture

NARCIS (Netherlands)

Meindersma, G.W.; Haan, de A.B.

2012-01-01

Ionic liquids can replace conventional solvents in aromatic/aliphatic extractions, if they have higher aromatic distribution coefficients and higher or similar aromatic/aliphatic selectivities. Also physical properties, such as density and viscosity, must be taken into account if a solvent is

C-terminal peptide extension via gas-phase ion/ion reactions

Science.gov (United States)

Peng, Zhou; McLuckey, Scott A.

2015-01-01

The formation of peptide bonds is of great importance from both a biological standpoint and in routine organic synthesis. Recent work from our group demonstrated the synthesis of peptides in the gas-phase via ion/ion reactions with sulfo-NHS reagents, which resulted in conjugation of individual amino acids or small peptides to the N-terminus of an existing ‘anchor’ peptide. Here, we demonstrate a complementary approach resulting in the C-terminal extension of peptides. Individual amino acids or short peptides can be prepared as reagents by incorporating gas phase-labile protecting groups to the reactive C-terminus and then converting the N-terminal amino groups to the active ketenimine reagent. Gas-phase ion/ion reactions between the anionic reagents and doubly protonated “anchor” peptide cations results in extension of the “anchor” peptide with new amide bond formation at the C-terminus. We have demonstrated that ion/ion reactions can be used as a fast, controlled, and efficient means for C-terminal peptide extension in the gas phase. PMID:26640400

Antimicrobial Peptides for Therapeutic Applications: A Review

Directory of Open Access Journals (Sweden)

Tsogbadrakh Mishig-Ochir

2012-10-01

Full Text Available Antimicrobial peptides (AMPs have been considered as potential therapeutic sources of future antibiotics because of their broad-spectrum activities and different mechanisms of action compared to conventional antibiotics. Although AMPs possess considerable benefits as new generation antibiotics, their clinical and commercial development still have some limitations, such as potential toxicity, susceptibility to proteases, and high cost of peptide production. In order to overcome those obstacles, extensive efforts have been carried out. For instance, unusual amino acids or peptido-mimetics are introduced to avoid the proteolytic degradation and the design of short peptides retaining antimicrobial activities is proposed as a solution for the cost issue. In this review, we focus on small peptides, especially those with less than twelve amino acids, and provide an overview of the relationships between their three-dimensional structures and antimicrobial activities. The efforts to develop highly active AMPs with shorter sequences are also described.

Recurrent Neural Network Model for Constructive Peptide Design.

Science.gov (United States)

Müller, Alex T; Hiss, Jan A; Schneider, Gisbert

2018-02-26

We present a generative long short-term memory (LSTM) recurrent neural network (RNN) for combinatorial de novo peptide design. RNN models capture patterns in sequential data and generate new data instances from the learned context. Amino acid sequences represent a suitable input for these machine-learning models. Generative models trained on peptide sequences could therefore facilitate the design of bespoke peptide libraries. We trained RNNs with LSTM units on pattern recognition of helical antimicrobial peptides and used the resulting model for de novo sequence generation. Of these sequences, 82% were predicted to be active antimicrobial peptides compared to 65% of randomly sampled sequences with the same amino acid distribution as the training set. The generated sequences also lie closer to the training data than manually designed amphipathic helices. The results of this study showcase the ability of LSTM RNNs to construct new amino acid sequences within the applicability domain of the model and motivate their prospective application to peptide and protein design without the need for the exhaustive enumeration of sequence libraries.

Predicting Three-Dimensional Conformations of Peptides Constructed of Only Glycine, Alanine, Aspartic Acid, and Valine

Science.gov (United States)

Oda, Akifumi; Fukuyoshi, Shuichi

2015-06-01

The GADV hypothesis is a form of the protein world hypothesis, which suggests that life originated from proteins (Lacey et al. 1999; Ikehara 2002; Andras 2006). In the GADV hypothesis, life is thought to have originated from primitive proteins constructed of only glycine, alanine, aspartic acid, and valine ([GADV]-proteins). In this study, the three-dimensional (3D) conformations of randomly generated short [GADV]-peptides were computationally investigated using replica-exchange molecular dynamics (REMD) simulations (Sugita and Okamoto 1999). Because the peptides used in this study consisted of only 20 residues each, they could not form certain 3D structures. However, the conformational tendencies of the peptides were elucidated by analyzing the conformational ensembles generated by REMD simulations. The results indicate that secondary structures can be formed in several randomly generated [GADV]-peptides. A long helical structure was found in one of the hydrophobic peptides, supporting the conjecture of the GADV hypothesis that many peptides aggregated to form peptide multimers with enzymatic activity in the primordial soup. In addition, these results indicate that REMD simulations can be used for the structural investigation of short peptides.

Comprehensive computational design of ordered peptide macrocycles

Science.gov (United States)

Hosseinzadeh, Parisa; Bhardwaj, Gaurav; Mulligan, Vikram Khipple; Shortridge, Matthew D.; Craven, Timothy W.; Pardo-Avila, Fátima; Rettie, Stephen A.; Kim, David E.; Silva, Daniel-Adriano; Ibrahim, Yehia M.; Webb, Ian K.; Cort, John R.; Adkins, Joshua N.; Varani, Gabriele; Baker, David

2018-01-01

Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with L-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of L- and D-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods. PMID:29242347

Glyphosate has limited short-term effects on commensal bacterial community composition in the gut environment due to sufficient aromatic amino acid levels

DEFF Research Database (Denmark)

Nielsen, Lene Nørby; Roager, Henrik Munch; Casas, Mònica Escolà

2017-01-01

in acetic acid produced by the gut bacteria. We conclude that sufficient intestinal levels of aromatic amino acids provided by the diet alleviates the need for bacterial synthesis of aromatic amino acids and thus prevents an antimicrobial effect of glyphosate in vivo. It is however possible...

Bacterial Degradation of Aromatic Compounds

Directory of Open Access Journals (Sweden)

Qing X. Li

2009-01-01

Full Text Available Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.

Short-acting glucagon-like peptide-1 receptor agonists as add-on to insulin therapy in type 1 diabetes

DEFF Research Database (Denmark)

Albèr, Anders; Brønden, Andreas; Knop, Filip K

2017-01-01

emptying in patients with type 1 diabetes, which could translate into effective lowering of postprandial glucose excursions; however, these observations regarding short-acting GLP-1RAs are all derived from small open-label trials and should thus be interpreted with caution. In the present paper we review......A large proportion of patients with type 1 diabetes do not reach their glycaemic target of glycated hemoglobin (HbA1c) type 1 diabetes are overweight and obese. Treatment of type 1 diabetes is based on insulin therapy......, which is associated with well-described and unfortunate adverse effects such as hypoglycaemia and increased body weight. Glucagon-like peptide-1 (GLP-1) receptor agonists (RAs) are the focus of increasing interest as a possible adjunctive treatment to insulin in type 1 diabetes because...

Aromater i drikkevand

DEFF Research Database (Denmark)

Nyeland, B. A.; Hansen, A. B.

DMU har den 10. Juni 1997 afholdt en præstationsprøvning: Aromater i drikkevand. Der deltog 21 laboratorier i præstationsprøvningen. Prøvningen omfattede 6 vandige prøver og 6 ampuller indeholdende 6 aromater. Laboratorierne spikede de tilsendte vandprøver med indholdet fra ampullerne...

Optimization of protein and peptide drugs based on the mechanisms of kidney clearance.

Science.gov (United States)

Huang, Jiaguo; Wu, Huizi

2018-05-30

Development of proteins and peptides into drugs has been considered as a promising strategy to target certain diseases. However, only few proteins and peptides has been approved as new drugs into the market each year. One major problem is that proteins and peptides often exhibit short plasma half-life times, which limits the application for their clinical use. In most cases a short half-life time is not effective to deliver sufficient amount of drugs to the target organs and tissues, which is generally caused by fast renal clearance and low plasma stability due to proteolytic degradation during systemic circulation, because the most common clearance pathway of small proteins and peptides is through glomerular filtration by the kidneys. In this review, enzymatic degradation of proteins and peptides were discussed. Furthermore, several approaches to lengthen the half-life of peptides and proteins drugs based on the unique structures of glomerular capillary wall and the mechanisms of glomerular filtration were summarized, such as increasing the size and hydrodynamic diameter; increasing the negative charge to delay the filtration; increasing plasma protein binding to decrease plasma clearance. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Identification of Cyclin A Binders with a Fluorescent Peptide Sensor.

Science.gov (United States)

Pazos, Elena; Mascareñas, José L; Vázquez, M Eugenio

2016-01-01

A peptide sensor that integrates the 4-dimethylaminophthalimide (4-DMAP) fluorophore in a short cyclin A binding sequence displays a large fluorescence emission increase upon interacting with the cyclin A Binding Groove (CBG). Competitive displacement assays of this probe allow the straightforward identification of peptides that interact with the CBG, which could potentially block the recognition of CDK/cyclin A kinase substrates.

Polymeric peptide pigments with sequence-encoded properties

Energy Technology Data Exchange (ETDEWEB)

Lampel, Ayala; McPhee, Scott A.; Park, Hang-Ah; Scott, Gary G.; Humagain, Sunita; Hekstra, Doeke R.; Yoo, Barney; Frederix, Pim W. J. M.; Li, Tai-De; Abzalimov, Rinat R.; Greenbaum, Steven G.; Tuttle, Tell; Hu, Chunhua; Bettinger, Christopher J.; Ulijn, Rein V.

2017-06-08

Melanins are a family of heterogeneous polymeric pigments that provide ultraviolet (UV) light protection, structural support, coloration, and free radical scavenging. Formed by oxidative oligomerization of catecholic small molecules, the physical properties of melanins are influenced by covalent and noncovalent disorder. We report the use of tyrosine-containing tripeptides as tunable precursors for polymeric pigments. In these structures, phenols are presented in a (supra-)molecular context dictated by the positions of the amino acids in the peptide sequence. Oxidative polymerization can be tuned in a sequence-dependent manner, resulting in peptide sequence–encoded properties such as UV absorbance, morphology, coloration, and electrochemical properties over a considerable range. Short peptides have low barriers to application and can be easily scaled, suggesting near-term applications in cosmetics and biomedicine.

Fluorescence method for enzyme analysis which couples aromatic amines with aromatic aldehydes

Science.gov (United States)

Smith, R.E.; Dolbeare, F.A.

1980-10-21

Analysis of proteinases is accomplished using conventional amino acid containing aromatic amine substrates. Aromatic amines such as 4-methoxy-2-naphthylamine (4M2NA), 2-naphthylamine, aminoisophthalic acid dimethyl ester, p-nitroaniline, 4-methoxy-1-aminofluorene and coumarin derivatives resulting from enzymatic hydrolysis of the substrate couples with aromatic aldehydes such as 5-nitrosalicylaldehyde (5-NSA), benzaldehyde and p-nitrobenzaldehyde to produce Schiff-base complexes which are water insoluble. Certain Schiff-base complexes produce a shift from blue to orange-red (visible) fluorescence. Such complexes are useful in the assay of enzymes. No Drawings

Proinsulin C-peptide interferes with insulin fibril formation

International Nuclear Information System (INIS)

Landreh, Michael; Stukenborg, Jan-Bernd; Willander, Hanna; Söder, Olle; Johansson, Jan; Jörnvall, Hans

2012-01-01

Highlights: ► Insulin and C-peptide can interact under insulin fibril forming conditions. ► C-peptide is incorporated into insulin aggregates and alters aggregation lag time. ► C-peptide changes insulin fibril morphology and affects backbone accessibility. ► C-peptide may be a regulator of fibril formation by β-cell granule proteins. -- Abstract: Insulin aggregation can prevent rapid insulin uptake and cause localized amyloidosis in the treatment of type-1 diabetes. In this study, we investigated the effect of C-peptide, the 31-residue peptide cleaved from proinsulin, on insulin fibrillation at optimal conditions for fibrillation. This is at low pH and high concentration, when the fibrils formed are regular and extended. We report that C-peptide then modulates the insulin aggregation lag time and profoundly changes the fibril appearance, to rounded clumps of short fibrils, which, however, still are Thioflavine T-positive. Electrospray ionization mass spectrometry also indicates that C-peptide interacts with aggregating insulin and is incorporated into the aggregates. Hydrogen/deuterium exchange mass spectrometry further reveals reduced backbone accessibility in insulin aggregates formed in the presence of C-peptide. Combined, these effects are similar to those of C-peptide on islet amyloid polypeptide fibrillation and suggest that C-peptide has a general ability to interact with amyloidogenic proteins from pancreatic β-cell granules. Considering the concentrations, these peptide interactions should be relevant also during physiological secretion, and even so at special sites post-secretory or under insulin treatment conditions in vivo.

Proinsulin C-peptide interferes with insulin fibril formation

Energy Technology Data Exchange (ETDEWEB)

Landreh, Michael [Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm (Sweden); Stukenborg, Jan-Bernd [Department of Women' s and Children' s Health, Astrid Lindgren Children' s Hospital, Pediatric Endocrinology Unit, Karolinska Institutet and University Hospital, S-17176 Stockholm (Sweden); Willander, Hanna [KI-Alzheimer' s Disease Research Center, NVS Department, Karolinska Institutet, S-141 86 Stockholm (Sweden); Soeder, Olle [Department of Women' s and Children' s Health, Astrid Lindgren Children' s Hospital, Pediatric Endocrinology Unit, Karolinska Institutet and University Hospital, S-17176 Stockholm (Sweden); Johansson, Jan [KI-Alzheimer' s Disease Research Center, NVS Department, Karolinska Institutet, S-141 86 Stockholm (Sweden); Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, S-751 23 Uppsala (Sweden); Joernvall, Hans, E-mail: Hans.Jornvall@ki.se [Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm (Sweden)

2012-02-17

Highlights: Black-Right-Pointing-Pointer Insulin and C-peptide can interact under insulin fibril forming conditions. Black-Right-Pointing-Pointer C-peptide is incorporated into insulin aggregates and alters aggregation lag time. Black-Right-Pointing-Pointer C-peptide changes insulin fibril morphology and affects backbone accessibility. Black-Right-Pointing-Pointer C-peptide may be a regulator of fibril formation by {beta}-cell granule proteins. -- Abstract: Insulin aggregation can prevent rapid insulin uptake and cause localized amyloidosis in the treatment of type-1 diabetes. In this study, we investigated the effect of C-peptide, the 31-residue peptide cleaved from proinsulin, on insulin fibrillation at optimal conditions for fibrillation. This is at low pH and high concentration, when the fibrils formed are regular and extended. We report that C-peptide then modulates the insulin aggregation lag time and profoundly changes the fibril appearance, to rounded clumps of short fibrils, which, however, still are Thioflavine T-positive. Electrospray ionization mass spectrometry also indicates that C-peptide interacts with aggregating insulin and is incorporated into the aggregates. Hydrogen/deuterium exchange mass spectrometry further reveals reduced backbone accessibility in insulin aggregates formed in the presence of C-peptide. Combined, these effects are similar to those of C-peptide on islet amyloid polypeptide fibrillation and suggest that C-peptide has a general ability to interact with amyloidogenic proteins from pancreatic {beta}-cell granules. Considering the concentrations, these peptide interactions should be relevant also during physiological secretion, and even so at special sites post-secretory or under insulin treatment conditions in vivo.

Photochemical coupling of 5-bromouracil to tryptophan, tyrosine and histidine, peptide-like derivatives in aqueous fluid solution

International Nuclear Information System (INIS)

Dietz, T.M.; Koch, T.H.

1987-01-01

Direct irradiation of 5-bromouracil (BU) in aqueous fluid solution in the presence of tryptophan (trp), tyrosine (tyr) or histidine (his) derivatives using a XeCl excimer laser at 308 nm yielded photocoupling of BU to the aromatic ring of each amino acid. Irradiation of BU at 308 nm most likely results in excitation of the n-π* transition, intersystem crossing to the triplet manifold, and coupling via electron transfer from the aromatic amino acid. The coupling observed was regiospecific between the 5-position of uracil (U) and the 2-position of the indole and phenol rings and the 5-position of the imidazole ring of the respective amino acids. Quantum yields of photocoupling to BU ranged from 1 x 10 -3 to 7 x 10 -3 and paralleled known rates of electron transfer and ionization potentials of the aromatic rings. The photocoupling between BU and some of the aromatic amino acid peptide-like derivatives possibly mimics photocrosslinking of BU-DNA to associated proteins, a potentially useful photoreaction for studying nucleic acid-protein interactions. Formation of crosslinks of the type proposed here might be detected by the characteristic fluorescence emission of the uracil amino acid adducts. (author)

A dose-equivalent comparison of the effects of continuous subcutaneous glucagon-like peptide 2 (GLP-2) infusions versus meal related GLP-2 injections in the treatment of short bowel syndrome (SBS) patients

DEFF Research Database (Denmark)

Naimi, R M; Madsen, K B; Askov-Hansen, C

2013-01-01

Glucagon-like peptide 2 (GLP-2), secreted endogenously from L-cells in the distal bowel in relation to meals, modulates intestinal absorption by adjusting gastric emptying and secretion and intestinal growth. Short bowel syndrome (SBS) patients with distal intestinal resections have attenuated...

Glyphosate has limited short-term effects on commensal bacterial community composition in the gut environment due to sufficient aromatic amino acid levels.

Science.gov (United States)

Nielsen, Lene Nørby; Roager, Henrik M; Casas, Mònica Escolà; Frandsen, Henrik L; Gosewinkel, Ulrich; Bester, Kai; Licht, Tine Rask; Hendriksen, Niels Bohse; Bahl, Martin Iain

2018-02-01

Recently, concerns have been raised that residues of glyphosate-based herbicides may interfere with the homeostasis of the intestinal bacterial community and thereby affect the health of humans or animals. The biochemical pathway for aromatic amino acid synthesis (Shikimate pathway), which is specifically inhibited by glyphosate, is shared by plants and numerous bacterial species. Several in vitro studies have shown that various groups of intestinal bacteria may be differently affected by glyphosate. Here, we present results from an animal exposure trial combining deep 16S rRNA gene sequencing of the bacterial community with liquid chromatography mass spectrometry (LC-MS) based metabolic profiling of aromatic amino acids and their downstream metabolites. We found that glyphosate as well as the commercial formulation Glyfonova ® 450 PLUS administered at up to fifty times the established European Acceptable Daily Intake (ADI = 0.5 mg/kg body weight) had very limited effects on bacterial community composition in Sprague Dawley rats during a two-week exposure trial. The effect of glyphosate on prototrophic bacterial growth was highly dependent on the availability of aromatic amino acids, suggesting that the observed limited effect on bacterial composition was due to the presence of sufficient amounts of aromatic amino acids in the intestinal environment. A strong correlation was observed between intestinal concentrations of glyphosate and intestinal pH, which may partly be explained by an observed reduction in acetic acid produced by the gut bacteria. We conclude that sufficient intestinal levels of aromatic amino acids provided by the diet alleviates the need for bacterial synthesis of aromatic amino acids and thus prevents an antimicrobial effect of glyphosate in vivo. It is however possible that the situation is different in cases of human malnutrition or in production animals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Self-Assembly of Peptides at the Air/Water Interface

Science.gov (United States)

Sayar, Mehmet

2013-03-01

Peptides are commonly used as building blocks for design and development of novel materials with a variety of application areas ranging from drug design to biotechnology. The precise control of molecular architecture and specific nature of the nonbonded interactions among peptides enable aggregates with well defined structural and functional properties. The interaction of peptides with interfaces leads to dramatic changes in their conformational and aggregation behavior. In this talk, I will discuss our research on the interplay of intermolecular forces and influence of interfaces. In the first part the amphiphilic nature of short peptide oligomers and their behavior at the air/water interface will be discussed. The surface driving force and its decomposition will be analyzed. In the second part aggregation of peptides in bulk water and at an interface will be discussed. Different design features which can be tuned to control aggregation behavior will be analyzed.

Synergistic effect of supplemental enteral nutrients and exogenous glucagon-like peptide 2 on intestinal adaptation in a rat model of short bowel syndrome

DEFF Research Database (Denmark)

Liu, Xiaowen; Nelson, David W; Holst, Jens Juul

2006-01-01

BACKGROUND: Short bowel syndrome (SBS) can lead to intestinal failure and require total or supplemental parenteral nutrition (TPN or PN, respectively). Glucagon-like peptide 2 (GLP-2) is a nutrient-dependent, proglucagon-derived gut hormone that stimulates intestinal adaptation. OBJECTIVE: Our...... objective was to determine whether supplemental enteral nutrients (SEN) modulate the intestinotrophic response to a low dose of GLP-2 coinfused with PN in a rat model of SBS (60% jejunoileal resection plus cecectomy). DESIGN: Rats were randomly assigned to 8 treatments by using a 2 x 2 x 2 factorial design...

Noncomparative scaling of aromaticity through electron itinerancy

International Nuclear Information System (INIS)

Paul, Satadal; Goswami, Tamal; Misra, Anirban

2015-01-01

Aromaticity is a multidimensional concept and not a directly observable. These facts have always stood in the way of developing an appropriate theoretical framework for scaling of aromaticity. In the present work, a quantitative account of aromaticity is developed on the basis of cyclic delocalization of π-electrons, which is the phenomenon leading to unique features of aromatic molecules. The stabilization in molecular energy, caused by delocalization of π-electrons is obtained as a second order perturbation energy for archetypal aromatic systems. The final expression parameterizes the aromatic stabilization energy in terms of atom to atom charge transfer integral, onsite repulsion energy and the population of spin orbitals at each site in the delocalized π-electrons. An appropriate computational platform is framed to compute each and individual parameter in the derived equation. The numerical values of aromatic stabilization energies obtained for various aromatic molecules are found to be in close agreement with available theoretical and experimental reports. Thus the reliable estimate of aromaticity through the proposed formalism renders it as a useful tool for the direct assessment of aromaticity, which has been a long standing problem in chemistry

Three-dimensional aromatic networks.

Science.gov (United States)

Toyota, Shinji; Iwanaga, Tetsuo

2014-01-01

Three-dimensional (3D) networks consisting of aromatic units and linkers are reviewed from various aspects. To understand principles for the construction of such compounds, we generalize the roles of building units, the synthetic approaches, and the classification of networks. As fundamental compounds, cyclophanes with large aromatic units and aromatic macrocycles with linear acetylene linkers are highlighted in terms of transannular interactions between aromatic units, conformational preference, and resolution of chiral derivatives. Polycyclic cage compounds are constructed from building units by linkages via covalent bonds, metal-coordination bonds, or hydrogen bonds. Large cage networks often include a wide range of guest species in their cavity to afford novel inclusion compounds. Topological isomers consisting of two or more macrocycles are formed by cyclization of preorganized species. Some complicated topological networks are constructed by self-assembly of simple building units.

Recognition of GPCRs by peptide ligands and membrane compartments theory: structural studies of endogenous peptide hormones in membrane environment.

Science.gov (United States)

Sankararamakrishnan, Ramasubbu

2006-04-01

One of the largest family of cell surface proteins, G-protein coupled receptors (GPCRs) regulate virtually all known physiological processes in mammals. With seven transmembrane segments, they respond to diverse range of extracellular stimuli and represent a major class of drug targets. Peptidergic GPCRs use endogenous peptides as ligands. To understand the mechanism of GPCR activation and rational drug design, knowledge of three-dimensional structure of receptor-ligand complex is important. The endogenous peptide hormones are often short, flexible and completely disordered in aqueous solution. According to "Membrane Compartments Theory", the flexible peptide binds to the membrane in the first step before it recognizes its receptor and the membrane-induced conformation is postulated to bind to the receptor in the second step. Structures of several peptide hormones have been determined in membrane-mimetic medium. In these studies, micelles, reverse micelles and bicelles have been used to mimic the cell membrane environment. Recently, conformations of two peptide hormones have also been studied in receptor-bound form. Membrane environment induces stable secondary structures in flexible peptide ligands and membrane-induced peptide structures have been correlated with their bioactivity. Results of site-directed mutagenesis, spectroscopy and other experimental studies along with the conformations determined in membrane medium have been used to interpret the role of individual residues in the peptide ligand. Structural differences of membrane-bound peptides that belong to the same family but differ in selectivity are likely to explain the mechanism of receptor selectivity and specificity of the ligands. Knowledge of peptide 3D structures in membrane environment has potential applications in rational drug design.

Cationic antimicrobial peptides inactivate Shiga toxin-encoding bacteriophages

Science.gov (United States)

Del Cogliano, Manuel E.; Hollmann, Axel; Martinez, Melina; Semorile, Liliana; Ghiringhelli, Pablo D.; Maffía, Paulo C.; Bentancor, Leticia V.

2017-12-01

Shiga toxin (Stx) is the principal virulence factor during Shiga toxin-producing Escherichia coli (STEC) infections. We have previously reported the inactivation of bacteriophage encoding Stx after treatment with chitosan, a linear polysaccharide polymer with cationic properties. Cationic antimicrobial peptides (cAMPs) are short linear aminoacidic sequences, with a positive net charge, which display bactericidal or bacteriostatic activity against a wide range of bacterial species. They are promising novel antibiotics since they have shown bactericidal effects against multiresistant bacteria. To evaluate whether cationic properties are responsible for bacteriophage inactivation, we tested seven cationic peptides with proven antimicrobial activity as anti-bacteriophage agents, and one random sequence cationic peptide with no antimicrobial activity as a control. We observed bacteriophage inactivation after incubation with five cAMPs, but no inactivating activity was observed with the random sequence cationic peptide or with the non alpha helical cAMP Omiganan. Finally, to confirm peptide-bacteriophage interaction, zeta potential was analyzed by following changes on bacteriophage surface charges after peptide incubation. According to our results we could propose that: 1) direct interaction of peptides with phage is a necessary step for bacteriophage inactivation, 2) cationic properties are necessary but not sufficient for bacteriophage inactivation, and 3) inactivation by cationic peptides could be sequence (or structure) specific. Overall our data suggest that these peptides could be considered a new family of molecules potentially useful to decrease bacteriophage replication and Stx expression.

Cationic Antimicrobial Peptides Inactivate Shiga Toxin-Encoding Bacteriophages

Directory of Open Access Journals (Sweden)

Manuel E. Del Cogliano

2017-12-01

Full Text Available Shiga toxin (Stx is the principal virulence factor during Shiga toxin-producing Escherichia coli (STEC infections. We have previously reported the inactivation of bacteriophage encoding Stx after treatment with chitosan, a linear polysaccharide polymer with cationic properties. Cationic antimicrobial peptides (cAMPs are short linear aminoacidic sequences, with a positive net charge, which display bactericidal or bacteriostatic activity against a wide range of bacterial species. They are promising novel antibiotics since they have shown bactericidal effects against multiresistant bacteria. To evaluate whether cationic properties are responsible for bacteriophage inactivation, we tested seven cationic peptides with proven antimicrobial activity as anti-bacteriophage agents, and one random sequence cationic peptide with no antimicrobial activity as a control. We observed bacteriophage inactivation after incubation with five cAMPs, but no inactivating activity was observed with the random sequence cationic peptide or with the non-alpha helical cAMP Omiganan. Finally, to confirm peptide-bacteriophage interaction, zeta potential was analyzed by following changes on bacteriophage surface charges after peptide incubation. According to our results we could propose that: (1 direct interaction of peptides with phage is a necessary step for bacteriophage inactivation, (2 cationic properties are necessary but not sufficient for bacteriophage inactivation, and (3 inactivation by cationic peptides could be sequence (or structure specific. Overall our data suggest that these peptides could be considered a new family of molecules potentially useful to decrease bacteriophage replication and Stx expression.

Antimicrobial Peptides: An Emerging Category of Therapeutic Agents.

Science.gov (United States)

Mahlapuu, Margit; Håkansson, Joakim; Ringstad, Lovisa; Björn, Camilla

2016-01-01

Antimicrobial peptides (AMPs), also known as host defense peptides, are short and generally positively charged peptides found in a wide variety of life forms from microorganisms to humans. Most AMPs have the ability to kill microbial pathogens directly, whereas others act indirectly by modulating the host defense systems. Against a background of rapidly increasing resistance development to conventional antibiotics all over the world, efforts to bring AMPs into clinical use are accelerating. Several AMPs are currently being evaluated in clinical trials as novel anti-infectives, but also as new pharmacological agents to modulate the immune response, promote wound healing, and prevent post-surgical adhesions. In this review, we provide an overview of the biological role, classification, and mode of action of AMPs, discuss the opportunities and challenges to develop these peptides for clinical applications, and review the innovative formulation strategies for application of AMPs.

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach

DEFF Research Database (Denmark)

Andreatta, Massimo; Lund, Ole; Nielsen, Morten

2013-01-01

Motivation: Proteins recognizing short peptide fragments play a central role in cellular signaling. As a result of high-throughput technologies, peptide-binding protein specificities can be studied using large peptide libraries at dramatically lower cost and time. Interpretation of such large...... peptide datasets, however, is a complex task, especially when the data contain multiple receptor binding motifs, and/or the motifs are found at different locations within distinct peptides.Results: The algorithm presented in this article, based on Gibbs sampling, identifies multiple specificities...... of unaligned peptide datasets of variable length. Example applications described in this article include mixtures of binders to different MHC class I and class II alleles, distinct classes of ligands for SH3 domains and sub-specificities of the HLA-A*02:01 molecule.Availability: The Gibbs clustering method...

Compositional changes of aromatic steroid hydrocarbons in naturally weathered oil residues in the Egyptian western desert

International Nuclear Information System (INIS)

Barakat, A.O.; Qian, Y.; Kim, M.; Kennicutt, M.C. II

2002-01-01

Aromatic steranes are geochemical markers that can be used to study the maturation of organic matter of sediments and to correlate crude oils and source rocks. In this study, naturally weathered oil residues from an arid waste disposal site in Al-Alamein, Egypt, were analyzed for monoaromatic and triaromatic steranes to show the usefulness of biomarker compounds in assessing changes in chemical composition during the degradation of oil residues that have been released onto terrestrial environments. Gas chromatography and mass spectrometry were used to characterize the individual aromatic compounds. Results indicate that triaromatic sterane distributions are similar in oil residues with varying extents of weathering. The distribution correlated with a fresh crude oil sample from Western Desert-sourced oil. Molecular ratios of triaromatic sterane compounds were found to be suitable for source identification. The major changes in chemical compositions resulting from the weathering of the oil included the depletion of short chain mono- and tri-aromatic steranes in extremely weathered samples. The results of the triaromatic sterane distribution correspond with weathering classifications based on the analyses of saturated and aromatic hydrocarbons and the ratios of n-alkanes, polycyclic aromatic hydrocarbons, and saturate biomarker compounds. 15 refs., 3 tabs., 3 figs

Carbon–carbon bond cleavage for Cu-mediated aromatic trifluoromethylations and pentafluoroethylations

Directory of Open Access Journals (Sweden)

Tsuyuka Sugiishi

2015-12-01

Full Text Available This short review highlights the copper-mediated fluoroalkylation using perfluoroalkylated carboxylic acid derivatives. Carbon–carbon bond cleavage of perfluoroalkylated carboxylic acid derivatives takes place in fluoroalkylation reactions at high temperature (150–200 °C or under basic conditions to generate fluoroalkyl anion sources for the formation of fluoroalkylcopper species. The fluoroalkylation reactions, which proceed through decarboxylation or tetrahedral intermediates, are useful protocols for the synthesis of fluoroalkylated aromatics.

Four faces of the interaction between ions and aromatic rings.

Science.gov (United States)

Papp, Dóra; Rovó, Petra; Jákli, Imre; Császár, Attila G; Perczel, András

2017-07-15

Non-covalent interactions between ions and aromatic rings play an important role in the stabilization of macromolecular complexes; of particular interest are peptides and proteins containing aromatic side chains (Phe, Trp, and Tyr) interacting with negatively (Asp and Glu) and positively (Arg and Lys) charged amino acid residues. The structures of the ion-aromatic-ring complexes are the result of an interaction between the large quadrupole moment of the ring and the charge of the ion. Four attractive interaction types are proposed to be distinguished based on the position of the ion with respect to the plane of the ring: perpendicular cation-π (CP ⊥ ), co-planar cation-π (CP ∥ ), perpendicular anion-π (AP ⊥ ), and co-planar anion-π (AP ∥ ). To understand more than the basic features of these four interaction types, a systematic, high-level quantum chemical study is performed, using the X -  + C 6 H 6 , M +  + C 6 H 6 , X -  + C 6 F 6 , and M +  + C 6 F 6 model systems with X -  = H - , F - , Cl - , HCOO - , CH 3 COO - and M +  = H + , Li + , Na + , NH4+, CH 3 NH3+, whereby C 6 H 6 and C 6 F 6 represent an electron-rich and an electron-deficient π system, respectively. Benchmark-quality interaction energies with small uncertainties, obtained via the so-called focal-point analysis (FPA) technique, are reported for the four interaction types. The computations reveal that the interactions lead to significant stabilization, and that the interaction energy order, given in kcal mol -1 in parentheses, is CP ⊥ (23-37) > AP ⊥ (14-21) > CP ∥ (9-22) > AP ∥ (6-16). A natural bond orbital analysis performed leads to a deeper qualitative understanding of the four interaction types. To facilitate the future quantum chemical characterization of ion-aromatic-ring interactions in large biomolecules, the performance of three density functional theory methods, B3LYP, BHandHLYP, and M06-2X, is tested against the FPA benchmarks

Folding Topology of a Short Coiled-Coil Peptide Structure Templated by an Oligonucleotide Triplex

DEFF Research Database (Denmark)

Lou, Chenguang; Christensen, Niels Johan; Martos Maldonado, Manuel Cristo

2017-01-01

by oligonucleotide duplex and triplex formation. POC synthesis was achieved by copper-free alkyne-azide cycloaddition between three oligonucleotides and a 23-mer peptide, which by itself exhibited multiple oligomeric states in solution. The oligonucleotide domain was designed to furnish a stable parallel triplex......, small-angle X-ray scattering (SAXS), and molecular modeling. Stabilizing cooperativity was observed between the trimeric peptide and the oligonucleotide triplex domains, and the overall molecular size (ca. 12nm) in solution was revealed to be independent of concentration. The topological folding...

An etiologic prediction model incorporating biomarkers to predict the bladder cancer risk associated with occupational exposure to aromatic amines: a pilot study

OpenAIRE

Mastrangelo, Giuseppe; Carta, Angela; Arici, Cecilia; Pavanello, Sofia; Porru, Stefano

2017-01-01

Background No etiological prediction model incorporating biomarkers is available to predict bladder cancer risk associated with occupational exposure to aromatic amines. Methods Cases were 199 bladder cancer patients. Clinical, laboratory and genetic data were predictors in logistic regression models (full and short) in which the dependent variable was 1 for 15 patients with aromatic amines related bladder cancer and 0 otherwise. The receiver operating characteristics approach was adopted; th...

A novel peptide nanomedicine for treatment of pancreatogenic diabetes.

Science.gov (United States)

Banerjee, Amrita; Onyuksel, Hayat

2013-08-01

Pancreatogenic diabetes (PD) is a potentially fatal disease that occurs secondary to pancreatic disorders. The current anti-diabetic therapy for PD is fraught with adverse effects that can increase morbidity. Here we investigated the efficacy of novel peptide nanomedicine: pancreatic polypeptide (PP) in sterically stabilized micelles (SSM) for management of PD. PP exhibits significant anti-diabetic efficacy but its short plasma half-life curtails its therapeutic application. To prolong and improve activity of PP in vivo, we evaluated the delivery of PP in SSM. PP-SSM administered to rats with PD, significantly improved glucose tolerance, insulin sensitivity and hepatic glycogen content compared to peptide in buffer. The studies established the importance of micellar nanocarriers in protecting enzyme-labile peptides in vivo and delivering them to target site, thereby enhancing their therapeutic efficacy. In summary, this study demonstrated that PP-SSM is a promising novel anti-diabetic nanomedicine and therefore should be further developed for management of PD. Pancreatic peptide was earlier demonstrated to address pancreatogenic diabetes, but its short half-life represented major difficulties in further development for therapeutic use. PP-SSM (pancreatic polypeptide in sterically stabilized micelles) is a promising novel anti-diabetic nanomedicine that enables prolonged half-life and increased bioactivity of PP, as shown in this novel study, paving the way toward clinical studies in the near future. Copyright © 2013 Elsevier Inc. All rights reserved.

Strong CH/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size.

Science.gov (United States)

Veljković, Dušan Ž

2018-03-01

Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1.97 kcal/mol. These interactions are stronger than CH/O contacts in benzene/water complex (-1.44 kcal/mol) while CH/O contacts in tetracene/water complex are even stronger than CH/O contacts in pyridine/water complexes (-2.21 kcal/mol). Electrostatic potential maps for different polycyclic aromatic hydrocarbons were calculated and used to explain trends in the energies of interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Chimeric mitochondrial peptides from contiguous regular and swinger RNA.

Science.gov (United States)

Seligmann, Hervé

2016-01-01

Previous mass spectrometry analyses described human mitochondrial peptides entirely translated from swinger RNAs, RNAs where polymerization systematically exchanged nucleotides. Exchanges follow one among 23 bijective transformation rules, nine symmetric exchanges (X ↔ Y, e.g. A ↔ C) and fourteen asymmetric exchanges (X → Y → Z → X, e.g. A → C → G → A), multiplying by 24 DNA's protein coding potential. Abrupt switches from regular to swinger polymerization produce chimeric RNAs. Here, human mitochondrial proteomic analyses assuming abrupt switches between regular and swinger transcriptions, detect chimeric peptides, encoded by part regular, part swinger RNA. Contiguous regular- and swinger-encoded residues within single peptides are stronger evidence for translation of swinger RNA than previously detected, entirely swinger-encoded peptides: regular parts are positive controls matched with contiguous swinger parts, increasing confidence in results. Chimeric peptides are 200 × rarer than swinger peptides (3/100,000 versus 6/1000). Among 186 peptides with > 8 residues for each regular and swinger parts, regular parts of eleven chimeric peptides correspond to six among the thirteen recognized, mitochondrial protein-coding genes. Chimeric peptides matching partly regular proteins are rarer and less expressed than chimeric peptides matching non-coding sequences, suggesting targeted degradation of misfolded proteins. Present results strengthen hypotheses that the short mitogenome encodes far more proteins than hitherto assumed. Entirely swinger-encoded proteins could exist.

A novel adipokinetic peptide from the corpus cardiacum of the primitive caeliferan pygmy grasshopper Tetrix subulata (Caelifera, Tetrigidae).

Science.gov (United States)

Gäde, Gerd; Šimek, Petr; Marco, Heather G

2015-06-01

The basal caeliferan family Tetrigidae is investigated to identify neuropeptides belonging to the adipokinetic hormone (AKH) family. The pygmy grasshopper Tetrix subulata contains in its corpus cardiacum two octapeptides as revealed by liquid chromatography coupled to electrospray ionization mass spectrometry. The less abundant peptide is the well-known Schgr-AKH-II (pELNFSTGW amide) which is suggested to be the ancestral AKH of Caelifera and Ensifera. The second peptide, Tetsu-AKH (pEFNFTPGW amide), is novel and quite unusual with its third aromatic residue at position 2. It is thought to be autapomorphic for Caelifera. Tetsu-AKH has hyperlipemic activity in T. subulata and in Schistocerca gregaria. Copyright © 2015 Elsevier Inc. All rights reserved.

Petroleum geochemistry of the Potwar Basin, Pakistan: II – Oil classification based on heterocyclic and polycyclic aromatic hydrocarbons

International Nuclear Information System (INIS)

Asif, Muhammad; Fazeelat, Tahira

2012-01-01

In a previous study, oils in the Potwar Basin (Upper Indus) of Pakistan were correlated based on the dissimilarity of source and depositional environment of organic matter (OM) using biomarkers and bulk stable isotopes. This study is aimed at supporting the classification of Potwar Basin oils into three groups (A, B and C) using the distribution of alkylnaphthalenes, alkylphenanthrenes, alkyldibenzothiophenes, alkyldibenzofurans, alkylfluorenes, alkylbiphenyls, triaromatic steroids, methyl triaromatic steroids, retene, methyl retenes and cadalene. The higher relative abundance of specific methyl isomers of naphthalene and phenanthrene and the presence of diagnostic aromatic biomarkers clearly indicate the terrigenous and oxic depositional environment of OM for group A oil. Group B and C oils are of marine origin and the aforementioned heterocyclic and polycyclic aromatic hydrocarbons (HCs) differentiate them clearly into two different groups. The relative percentages of heterocyclic aromatic HCs reveal that the distribution of these compounds is controlled by the depositional environment of the OM. Sulfur-containing heterocyclic aromatic HCs are higher in crude oils generated from source rocks deposited in suboxic depositional environments, while oxygen-containing heterocyclic aromatic HCs in combination with alkylfluorenes are higher in marine oxic and deltaic oils. Biomarker and aromatic HC parameters do not indicate significant differences in the thermal maturity of Potwar Basin oils. Triaromatic and methyl triaromatic steroids support the division of Potwar Basin oils into the three groups and their relative abundances are related to source OM rather than thermal maturity. Significantly higher amounts of C 20 and C 21 triaromtic steroids and the presence or absence of long chain triaromatic steroids (C 25 , C 26 , C 27 , and C 28 ) indicates that these compounds are probably formed from different biological precursors in each group. Different isomers of methyl

Utilizing the σ-complex stability for quantifying reactivity in nucleophilic substitution of aromatic fluorides

Directory of Open Access Journals (Sweden)

Magnus Liljenberg

2013-04-01

Full Text Available A computational approach using density functional theory to compute the energies of the possible σ-complex reaction intermediates, the “σ-complex approach”, has been shown to be very useful in predicting regioselectivity, in electrophilic as well as nucleophilic aromatic substitution. In this article we give a short overview of the background for these investigations and the general requirements for predictive reactivity models for the pharmaceutical industry. We also present new results regarding the reaction rates and regioselectivities in nucleophilic substitution of fluorinated aromatics. They were rationalized by investigating linear correlations between experimental rate constants (k from the literature with a theoretical quantity, which we call the sigma stability (SS. The SS is the energy change associated with formation of the intermediate σ-complex by attachment of the nucleophile to the aromatic ring. The correlations, which include both neutral (NH3 and anionic (MeO− nucleophiles are quite satisfactory (r = 0.93 to r = 0.99, and SS is thus useful for quantifying both global (substrate and local (positional reactivity in SNAr reactions of fluorinated aromatic substrates. A mechanistic analysis shows that the geometric structure of the σ-complex resembles the rate-limiting transition state and that this provides a rationale for the observed correlations between the SS and the reaction rate.

pH-dependent and pH-independent self-assembling behavior of surfactant-like peptides

DEFF Research Database (Denmark)

Gurevich, Leonid; Fojan, Peter

2012-01-01

formation of ordered aggregates with well-defined secondary structure from short unstructured peptides and provide a simple system where factors responsible for self-assembly can be singled out and studied one by one. The ability to control the shape and structure of peptide aggregates can provide basis...

Coulomb repulsion in short polypeptides.

Science.gov (United States)

Norouzy, Amir; Assaf, Khaleel I; Zhang, Shuai; Jacob, Maik H; Nau, Werner M

2015-01-08

Coulomb repulsion between like-charged side chains is presently viewed as a major force that impacts the biological activity of intrinsically disordered polypeptides (IDPs) by determining their spatial dimensions. We investigated short synthetic models of IDPs, purely composed of ionizable amino acid residues and therefore expected to display an extreme structural and dynamic response to pH variation. Two synergistic, custom-made, time-resolved fluorescence methods were applied in tandem to study the structure and dynamics of the acidic and basic hexapeptides Asp6, Glu6, Arg6, Lys6, and His6 between pH 1 and 12. (i) End-to-end distances were obtained from the short-distance Förster resonance energy transfer (sdFRET) from N-terminal 5-fluoro-l-tryptophan (FTrp) to C-terminal Dbo. (ii) End-to-end collision rates were obtained for the same peptides from the collision-induced fluorescence quenching (CIFQ) of Dbo by FTrp. Unexpectedly, the very high increase of charge density at elevated pH had no dynamical or conformational consequence in the anionic chains, neither in the absence nor in the presence of salt, in conflict with the common view and in partial conflict with accompanying molecular dynamics simulations. In contrast, the cationic peptides responded to ionization but with surprising patterns that mirrored the rich individual characteristics of each side chain type. The contrasting results had to be interpreted, by considering salt screening experiments, N-terminal acetylation, and simulations, in terms of an interplay of local dielectric constant and peptide-length dependent side chain charge-charge repulsion, side chain functional group solvation, N-terminal and side chain charge-charge repulsion, and side chain-side chain as well as side chain-backbone interactions. The common picture that emerged is that Coulomb repulsion between water-solvated side chains is efficiently quenched in short peptides as long as side chains are not in direct contact with each

Pulse shape discrimination in non-aromatic plastics

Energy Technology Data Exchange (ETDEWEB)

Paul Martinez, H.; Pawelczak, Iwona; Glenn, Andrew M.; Leslie Carman, M.; Zaitseva, Natalia; Payne, Stephen

2015-01-21

Recently it has been demonstrated that plastic scintillators have the ability to distinguish neutrons from gamma rays by way of pulse shape discrimination (PSD). This discovery has lead to new materials and new capabilities. Here we report our work with the effects of aromatic, non-aromatic, and mixed aromatic/non-aromatic matrices have on the performance of PSD plastic scintillators.

Synthesis and Pharmacology of Halogenated δ-Opioid-Selective [D-Ala2]Deltorphin II Peptide Analogues

Science.gov (United States)

Pescatore, Robyn; Marrone, Gina F.; Sedberry, Seth; Vinton, Daniel; Finkelstein, Netanel; Katlowitz, Yitzchak E.; Pasternak, Gavril W.; Wilson, Krista R.; Majumdar, Susruta

2015-01-01

Deltorphins are naturally occurring peptides produced by the skin of the giant monkey frog (Phyllomedusa bicolor). They are δ-opioid receptor-selective agonists. Herein, we report the design and synthesis of a peptide, Tyr-D-Ala-(pI)Phe-Glu-Ile-Ile-Gly-NH2 3 (GATE3-8), based on the [D-Ala2]deltorphin II template, which is δ-selective in in vitro radioligand binding assays over the μ- and κ-opioid receptors. It is a full agonist in [35S]GTPγS functional assays and analgesic when administered supraspinally to mice. Analgesia of 3 (GATE3-8) is blocked by the selective δ receptor antagonist naltrindole, indicating that the analgesic action of 3 is mediated by the δ-opioid receptor. We have established a radioligand in which 125I isincorporated into 3 (GATE3-8). The radioligand has a KD of 0.1 nM in Chinese hamster ovary (CHO) cells expressing the δ receptor. Additionally, a series of peptides based on 3 (GATE3-8) was synthesized by incorporating various halogens in the para position on the aromatic ring of Phe3. The peptides were characterized for binding affinity at the μ-, δ-, and κ-opioid receptors, which showed a linear correlation between binding affinity and the size of the halogen substituent. These peptides may be interesting tools for probing δ-opioid receptor pharmacology. PMID:25844930

Synthesis and pharmacology of halogenated δ-opioid-selective [d-Ala(2)]deltorphin II peptide analogues.

Science.gov (United States)

Pescatore, Robyn; Marrone, Gina F; Sedberry, Seth; Vinton, Daniel; Finkelstein, Netanel; Katlowitz, Yitzchak E; Pasternak, Gavril W; Wilson, Krista R; Majumdar, Susruta

2015-06-17

Deltorphins are naturally occurring peptides produced by the skin of the giant monkey frog (Phyllomedusa bicolor). They are δ-opioid receptor-selective agonists. Herein, we report the design and synthesis of a peptide, Tyr-d-Ala-(pI)Phe-Glu-Ile-Ile-Gly-NH2 3 (GATE3-8), based on the [d-Ala(2)]deltorphin II template, which is δ-selective in in vitro radioligand binding assays over the μ- and κ-opioid receptors. It is a full agonist in [(35)S]GTPγS functional assays and analgesic when administered supraspinally to mice. Analgesia of 3 (GATE3-8) is blocked by the selective δ receptor antagonist naltrindole, indicating that the analgesic action of 3 is mediated by the δ-opioid receptor. We have established a radioligand in which (125)I is incorporated into 3 (GATE3-8). The radioligand has a KD of 0.1 nM in Chinese hamster ovary (CHO) cells expressing the δ receptor. Additionally, a series of peptides based on 3 (GATE3-8) was synthesized by incorporating various halogens in the para position on the aromatic ring of Phe(3). The peptides were characterized for binding affinity at the μ-, δ-, and κ-opioid receptors, which showed a linear correlation between binding affinity and the size of the halogen substituent. These peptides may be interesting tools for probing δ-opioid receptor pharmacology.

pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning.

Science.gov (United States)

Zhou, Xie-Xuan; Zeng, Wen-Feng; Chi, Hao; Luo, Chunjie; Liu, Chao; Zhan, Jianfeng; He, Si-Min; Zhang, Zhifei

2017-12-05

In tandem mass spectrometry (MS/MS)-based proteomics, search engines rely on comparison between an experimental MS/MS spectrum and the theoretical spectra of the candidate peptides. Hence, accurate prediction of the theoretical spectra of peptides appears to be particularly important. Here, we present pDeep, a deep neural network-based model for the spectrum prediction of peptides. Using the bidirectional long short-term memory (BiLSTM), pDeep can predict higher-energy collisional dissociation, electron-transfer dissociation, and electron-transfer and higher-energy collision dissociation MS/MS spectra of peptides with >0.9 median Pearson correlation coefficients. Further, we showed that intermediate layer of the neural network could reveal physicochemical properties of amino acids, for example the similarities of fragmentation behaviors between amino acids. We also showed the potential of pDeep to distinguish extremely similar peptides (peptides that contain isobaric amino acids, for example, GG = N, AG = Q, or even I = L), which were very difficult to distinguish using traditional search engines.

Administration of a dipeptidyl peptidase IV inhibitor enhances the intestinal adaptation in a mouse model of short bowel syndrome

DEFF Research Database (Denmark)

Okawada, Manabu; Holst, Jens Juul; Teitelbaum, Daniel H

2011-01-01

Glucagon-like peptide-2 induces small intestine mucosal epithelial cell proliferation and may have benefit for patients who suffer from short bowel syndrome. However, glucagon-like peptide-2 is inactivated rapidly in vivo by dipeptidyl peptidase IV. Therefore, we hypothesized that selectively inh...... inhibiting dipeptidyl peptidase IV would prolong the circulating life of glucagon-like peptide-2 and lead to increased intestinal adaptation after development of short bowel syndrome....

Monitoring peptide-surface interaction by means of molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Nonella, Marco, E-mail: mnonella@pci.uzh.ch [Physikalisch-Chemisches Institut, Universitaet Zuerich, Winterthurerstrasse 190, CH-8057 Zuerich (Switzerland); Seeger, Stefan, E-mail: sseeger@pci.uzh.ch [Physikalisch-Chemisches Institut, Universitaet Zuerich, Winterthurerstrasse 190, CH-8057 Zuerich (Switzerland)

2010-12-09

Graphical abstract: Protein-surface interactions play a crucial role in a wide field of research areas like biology, biotechnology, or pharmacology. Only recently, it has been shown that not only peptide adsorption represents an important process but also spreading and clustering of adsorbed proteins. By means of classical molecular dynamics, peptide adsorption as well as the dynamics of adsorbed peptides have been investigated in order to gain deeper insight into such processes. The picture shows a snapshot of an adsorbed peptide on a silica surface showing strong direct hydrogen bonding. Research highlights: {yields} Simulation of peptide surface interaction. {yields} Dynamics of hydrogen bond formation and destruction. {yields} Internal flexibility of adsorbed peptides. - Abstract: Protein adsorption and protein surface interactions have become an important research topic in recent years. Very recently, for example, it has been shown that protein clusters can undergo a surface-induced spreading after adsorption. Such phenomena emphasize the need of a more detailed insight into protein-silica interaction at an atomic level. Therefore, we have studied a model system consisting of a short peptide, a silica slab, and water molecules by means of classical molecular dynamics simulations. The study reveals that, besides of electrostatic interactions caused by the chosen charge distribution, the peptide interacts with the silica surface through formation of direct peptide-surface hydrogen bonds as well as indirect peptide-water-surface hydrogen bonds. The number of created hydrogen bonds varies considerably among the simulated structures. The strength of hydrogen bonding determines the mobility of the peptide on the surface and the internal flexibility of the adsorbed peptide.

Advances towards aromatic oligoamide foldamers

DEFF Research Database (Denmark)

Hjelmgaard, Thomas; Plesner, Malene; Dissing, Mette Marie

2014-01-01

We have efficiently synthesized 36 arylopeptoid dimers with ortho-, meta-, and para-substituted aromatic backbones and tert-butyl or phenyl side chains. The dimers were synthesized by using a "submonomer method" on solid phase, by applying a simplified common set of reaction conditions. X......-ray crystallographic analysis of two of these dimers disclosed that the tert-butyl side chain invokes a cis amide conformation with a comparatively more closely packed structure of the surrounding aromatic backbone while the phenyl side chain results in a trans amide conformation with a more open, extended structure...... of the surrounding aromatic backbone. Investigation of the X-ray structures of two arylopeptoid dimers disclosed that the tert-butyl side chain invokes a cis amide conformation with a closely packed structure of the surrounding aromatic backbone while the phenyl side chain results in a trans amide conformation...

Comprehensive computational design of ordered peptide macrocycles

Energy Technology Data Exchange (ETDEWEB)

Hosseinzadeh, Parisa; Bhardwaj, Gaurav; Mulligan, Vikram K.; Shortridge, Matthew D.; Craven, Timothy W.; Pardo-Avila, Fatima; Rettie, Stephan A.; Kim, David E.; Silva, Daniel A.; Ibrahim, Yehia M.; Webb, Ian K.; Cort, John R.; Adkins, Joshua N.; Varani, Gabriele; Baker, David

2017-12-14

Mixed chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to-date, but there is currently no way to systematically search through the structural space spanned by such compounds for new drug candidates. Natural proteins do not provide a useful guide: peptide macrocycles lack regular secondary structures and hydrophobic cores and have different backbone torsional constraints. Hence the development of new peptide macrocycles has been approached by modifying natural products or using library selection methods; the former is limited by the small number of known structures, and the latter by the limited size and diversity accessible through library-based methods. To overcome these limitations, here we enumerate the stable structures that can be adopted by macrocyclic peptides composed of L and D amino acids. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. We synthesize and characterize by NMR twelve 7-10 residue macrocycles, 9 of which have structures very close to the design models in solution. NMR structures of three 11-14 residue bicyclic designs are also very close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide based macrocycles unparalleled for other molecular systems, and vastly increase the available starting scaffolds for both rational drug design and library selection methods.

A metabolomics strategy to assess the combined toxicity of polycyclic aromatic hydrocarbons (PAHs) and short-chain chlorinated paraffins (SCCPs).

Science.gov (United States)

Wang, Feidi; Zhang, Haijun; Geng, Ningbo; Ren, Xiaoqian; Zhang, Baoqin; Gong, Yufeng; Chen, Jiping

2018-03-01

The combined toxicity of mixed chemicals is usually evaluated according to several specific endpoints, and other potentially toxic effects are disregarded. In this study, we provided a metabolomics strategy to achieve a comprehensive understanding of toxicological interactions between mixed chemicals on metabolism. The metabolic changes were quantified by a pseudotargeted analysis, and the types of combined effects were quantitatively discriminated according to the calculation of metabolic effect level index (MELI). The metabolomics strategy was used to assess the combined effects of polycyclic aromatic hydrocarbons (PAHs) and short-chain chlorinated paraffins (SCCPs) on the metabolism of human hepatoma HepG2 cells. Our data suggested that exposure to a combination of PAHs and SCCPs at human internal exposure levels could result in an additive effect on the overall metabolism, whereas diverse joint effects were observed on various metabolic pathways. The combined exposure could induce a synergistic up-regulation of phospholipid metabolism, an additive up-regulation of fatty acid metabolism, an additive down-regulation of tricarboxylic acid cycle and glycolysis, and an antagonistic effect on purine metabolism. SCCPs in the mixture acted as the primary driver for the acceleration of phospholipid and fatty acid metabolism. Lipid metabolism disorder caused by exposure to a combination of PAHs and SCCPs should be an important concern for human health. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparative mode of action of novel hybrid peptide CS-1a and its rearranged amphipathic analogue CS-2a.

Science.gov (United States)

Joshi, Seema; Bisht, Gopal S; Rawat, Diwan S; Maiti, Souvik; Pasha, Santosh

2012-10-01

Cell selective, naturally occurring, host defence cationic peptides present a good template for the design of novel peptides with the aim of achieving a short length with improved antimicrobial potency and selectivity. A novel, short peptide CS-1a (14 residues) was derived using a sequence hybridization approach on sarcotoxin I (39 residues) and cecropin B (35 residues). The sequence of CS-1a was rearranged to enhance amphipathicity with the help of a Schiffer-Edmundson diagram to obtain CS-2a. Both peptides showed good antibacterial activity in the concentration range 4-16 μg·mL(-1) against susceptible as well as drug-resistant bacterial strains, including the clinically relevant pathogens Acenatobacter sp. and methicillin-resistant Staphylococcus aureus. The major thrust of these peptides is their nonhaemolytic activity against human red blood cells up to a high concentration of 512 μg·mL(-1). Compared to CS-1a, amphipathic peptide CS-2a showed a more pronounced α-helical conformation, along with a better membrane insertion depth in bacterial mimic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) small unilamellar vesicles. With equivalent lipid-binding affinity, the two peptides assumed different pathways of membrane disruption, as demonstrated by calcein leakage and the results of transmission electron microscopy on model bacterial mimic large unilamellar vesicles. Extending the work from model membranes to intact Escherichia coli cells, differences in membrane perturbation were visible in microscopic images of peptide-treated E. coli. The present study describes two novel short peptides with potent activity, cell selectivity and divergent modes of action that will aid in the future design of peptides with better therapeutic potential. © 2012 The Authors Journal compilation © 2012 FEBS.

A Short Peptide That Mimics the Binding Domain of TGF-β1 Presents Potent Anti-Inflammatory Activity.

Directory of Open Access Journals (Sweden)

Emília R Vaz

Full Text Available The transforming growth factor beta 1 (TGF-β1 is a pleiotropic cytokine with multiple roles in development, wound healing, and immune regulation. TGF-β1-mediated immune dysfunction may lead to pathological conditions, such as inflammation. Chronic inflammatory process is characterized by a continuous release of pro-inflammatory cytokines, and the inhibition or the blockage of these cytokines signaling pathways are considered a target treatment. In this context, despite the high numbers of TGF-β-targeted pathways, the inducible regulatory T cells (iTreg to control inflammation seems to be a promising approach. Our aim was to develop novel peptides through phage display (PhD technology that could mimic TGF-β1 function with higher potency. Specific mimetic peptides were obtained through a PhD subtraction strategy from whole cell binding using TGF-β1 recombinant as a competitor during elution step. We have selected a peptide that seems to play an important role on cellular differentiation and modulation of TNF-α and IL-10 cytokines. The synthetic pm26TGF-β1 peptide tested in PBMC significantly down-modulated TNF-α and up-regulated IL-10 responses, leading to regulatory T cells (Treg phenotype differentiation. Furthermore, the synthetic peptide was able to decrease leukocytes rolling in BALB/C mice and neutrophils migration during inflammatory process in C57BL/6 mice. These data suggest that this peptide may be useful for the treatment of inflammatory diseases, especially because it displays potent anti-inflammatory properties and do not exhibit neutrophils' chemoattraction.

Interpretation of Tandem Mass Spectrometry (MSMS) Spectra for Peptide Analysis

DEFF Research Database (Denmark)

Hjernø, Karin; Højrup, Peter

2015-01-01

The aim of this chapter is to give a short introduction to peptide analysis by mass spectrometry (MS) and interpretation of fragment mass spectra. Through examples and guidelines we demonstrate how to understand and validate search results and how to perform de novo sequencing based on the often...... very complex fragmentation pattern obtained by tandem mass spectrometry (also referred to as MSMS). The focus is on simple rules for interpretation of MSMS spectra of tryptic as well as non-tryptic peptides....

Biopharmaceuticals: From peptide to drug

Science.gov (United States)

Hannappel, Margarete

2017-08-01

Biologics are therapeutic proteins or peptides that are produced by means of biological processes within living organisms and cells. They are highly specific molecules and play a crucial role as therapeutics for the treatment of severe and chronic diseases (e.g. cancer, rheumatoid arthritis, diabetes, autoimmune disorders). The development of new biologics and biologics-based drugs gains more and more importance in the fight against various diseases. A short overview on biotherapeutical drug development is given. Cone snails are a large group of poisonous, predatory sea snails with more than 700 species. They use a very powerful venom which rapidly inactivates and paralyzes their prey. Most bioactive venom components are small peptides (conotoxins, conopeptides) which are precisely directed towards a specific target (e.g. ion channel, receptors). Due to their small size, their precision and speed of action, naturally occurring cone snail venom peptides represent an attractive source for the identification and design of novel biological drug entities. The Jagna cone snail project is an encouraging initiative to map the ecological variety of cone snails around the island of Bohol (Philippines) and to conserve the biological information for potential future application.

Selected-ion storage GC-MS analysis of polycyclic aromatic hydrocarbons in palm dates and tuna fish

Energy Technology Data Exchange (ETDEWEB)

Al-Omair, A.; Helaleh, M.I.H. [Kuwait Inst. for Scientific Research (KISR), Central Analytical Lab. (CAL), Safat (Kuwait)

2004-06-01

A rapid analytical method based on Soxhlet extraction has been developed for determination of polycyclic aromatic hydrocarbons (PAH) in palm dates and tuna fish. The method is based on selected ion-storage gas chromatography-mass spectrometry. In the work discussed we were interested in the analysis of 16 polycyclic aromatic hydrocarbons (PAH) regarded by the EPA as priority pollutants. Soxhlet extraction of real, fortified, and blank samples, with hexane as solvent, was used to extract the analytes of interest. An excellent detection limit and good relative standard deviations (RSD) were obtained and analysis time was short. The linearity and sensitivity of the method for measurement of these analytes at trace levels are discussed. (orig.)

Morintides: cargo-free chitin-binding peptides from Moringa oleifera.

Science.gov (United States)

Kini, Shruthi G; Wong, Ka H; Tan, Wei Liang; Xiao, Tianshu; Tam, James P

2017-03-31

Hevein-like peptides are a family of cysteine-rich and chitin-binding peptides consisting of 29-45 amino acids. Their chitin-binding property is essential for plant defense against fungi. Based on the number of cysteine residues in their sequences, they are divided into three sub-families: 6C-, 8C- and 10C-hevein-like peptides. All three subfamilies contain a three-domain precursor comprising a signal peptide, a mature hevein-like peptide and a C-terminal domain comprising a hinge region with protein cargo in 8C- and 10C-hevein-like peptides. Here we report the isolation and characterization of two novel 8C-hevein-like peptides, designated morintides (mO1 and mO2), from the drumstick tree Moringa oleifera, a drought-resistant tree belonging to the Moringaceae family. Proteomic analysis revealed that morintides comprise 44 amino acid residues and are rich in cysteine, glycine and hydrophilic amino acid residues such as asparagine and glutamine. Morintides are resistant to thermal and enzymatic degradation, able to bind to chitin and inhibit the growth of phyto-pathogenic fungi. Transcriptomic analysis showed that they contain a three-domain precursor comprising an endoplasmic reticulum (ER) signal sequence, a mature peptide domain and a C-terminal domain. A striking feature distinguishing morintides from other 8C-hevein-like peptides is a short and protein-cargo-free C-terminal domain. Previously, a similar protein-cargo-free C-terminal domain has been observed only in ginkgotides, the 8C-hevein-like peptides from a gymnosperm Ginkgo biloba. Thus, morintides, with a cargo-free C-terminal domain, are a stand-alone class of 8C-hevein-like peptides from angiosperms. Our results expand the existing library of hevein-like peptides and shed light on molecular diversity within the hevein-like peptide family. Our work also sheds light on the anti-fungal activity and stability of 8C-hevein-like peptides.

Converting lignin to aromatics: step by step

NARCIS (Netherlands)

Strassberger, Z.I.

2014-01-01

Lignin, the glue that holds trees together, is the most abundant natural resource of aromatics. In that respect, it is a far more advanced resource than crude oil. This is because lignin already contains the aromatic functional groups. Thus, catalytic conversion of lignin to high-value aromatics is

Photoinduced electron transfer through peptide-based self-assembled monolayers chemisorbed on gold electrodes: directing the flow-in and flow-out of electrons through peptide helices.

Science.gov (United States)

Venanzi, Mariano; Gatto, Emanuela; Caruso, Mario; Porchetta, Alessandro; Formaggio, Fernando; Toniolo, Claudio

2014-08-21

Photoinduced electron transfer (PET) experiments have been carried out on peptide self-assembled monolayers (SAM) chemisorbed on a gold substrate. The oligopeptide building block was exclusively formed by C(α)-tetrasubstituted α-aminoisobutyric residues to attain a helical conformation despite the shortness of the peptide chain. Furthermore, it was functionalized at the C-terminus by a pyrene choromophore to enhance the UV photon capture cross-section of the compound and by a lipoic group at the N-terminus for linking to gold substrates. Electron transfer across the peptide SAM has been studied by photocurrent generation experiments in an electrochemical cell employing a gold substrate modified by chemisorption of a peptide SAM as a working electrode and by steady-state and time-resolved fluorescence experiments in solution and on a gold-coated glass. The results show that the electronic flow through the peptide bridge is strongly asymmetric; i.e., PET from the C-terminus to gold is highly favored with respect to PET in the opposite direction. This effect arises from the polarity of the Au-S linkage (Au(δ+)-S(δ-), junction effect) and from the electrostatic field generated by the peptide helix.

Driving forces for adsorption of amphiphilic peptides to the air-water interface.

Science.gov (United States)

Engin, Ozge; Villa, Alessandra; Sayar, Mehmet; Hess, Berk

2010-09-02

We have studied the partitioning of amphiphilic peptides at the air-water interface. The free energy of adsorption from bulk to interface was calculated by determining the potential of mean force via atomistic molecular dynamics simulations. To this end a method is introduced to restrain or constrain the center of mass of a group of molecules in a periodic system. The model amphiphilic peptides are composed of alternating valine and asparagine residues. The decomposition of the free energy difference between the bulk and interface is studied for different peptide block lengths. Our analysis revealed that for short amphiphilic peptides the surface driving force dominantly stems from the dehydration of hydrophobic side chains. The only opposing force is associated with the loss of orientational freedom of the peptide at the interface. For the peptides studied, the free energy difference scales linearly with the size of the molecule, since the peptides mainly adopt extended conformations both in bulk and at the interface. The free energy difference depends strongly on the water model, which can be rationalized through the hydration thermodynamics of hydrophobic solutes. Finally, we measured the reduction of the surface tension associated with complete coverage of the interface with peptides.

Predicting binding within disordered protein regions to structurally characterised peptide-binding domains.

Directory of Open Access Journals (Sweden)

Waqasuddin Khan

Full Text Available Disordered regions of proteins often bind to structured domains, mediating interactions within and between proteins. However, it is difficult to identify a priori the short disordered regions involved in binding. We set out to determine if docking such peptide regions to peptide binding domains would assist in these predictions.We assembled a redundancy reduced dataset of SLiM (Short Linear Motif containing proteins from the ELM database. We selected 84 sequences which had an associated PDB structures showing the SLiM bound to a protein receptor, where the SLiM was found within a 50 residue region of the protein sequence which was predicted to be disordered. First, we investigated the Vina docking scores of overlapping tripeptides from the 50 residue SLiM containing disordered regions of the protein sequence to the corresponding PDB domain. We found only weak discrimination of docking scores between peptides involved in binding and adjacent non-binding peptides in this context (AUC 0.58.Next, we trained a bidirectional recurrent neural network (BRNN using as input the protein sequence, predicted secondary structure, Vina docking score and predicted disorder score. The results were very promising (AUC 0.72 showing that multiple sources of information can be combined to produce results which are clearly superior to any single source.We conclude that the Vina docking score alone has only modest power to define the location of a peptide within a larger protein region known to contain it. However, combining this information with other knowledge (using machine learning methods clearly improves the identification of peptide binding regions within a protein sequence. This approach combining docking with machine learning is primarily a predictor of binding to peptide-binding sites, and is not intended as a predictor of specificity of binding to particular receptors.

Lactoferricin Peptides Increase Macrophages' Capacity To Kill Mycobacterium avium.

Science.gov (United States)

Silva, Tânia; Moreira, Ana C; Nazmi, Kamran; Moniz, Tânia; Vale, Nuno; Rangel, Maria; Gomes, Paula; Bolscher, Jan G M; Rodrigues, Pedro N; Bastos, Margarida; Gomes, Maria Salomé

2017-01-01

Mycobacterial infections cause a significant burden of disease and death worldwide. Their treatment is long, toxic, costly, and increasingly prone to failure due to bacterial resistance to currently available antibiotics. New therapeutic options are thus clearly needed. Antimicrobial peptides represent an important source of new antimicrobial molecules, both for their direct activity and for their immunomodulatory potential. We have previously reported that a short version of the bovine antimicrobial peptide lactoferricin with amino acids 17 to 30 (LFcin17-30), along with its variants obtained by specific amino acid substitutions, killed Mycobacterium avium in broth culture. In the present work, those peptides were tested against M. avium living inside its natural host cell, the macrophage. We found that the peptides increased the antimicrobial action of the conventional antibiotic ethambutol inside macrophages. Moreover, the d-enantiomer of the lactoferricin peptide (d-LFcin17-30) was more stable and induced significant killing of intracellular mycobacteria by itself. Interestingly, d-LFcin17-30 did not localize to M. avium -harboring phagosomes but induced the production of proinflammatory cytokines and increased the formation of lysosomes and autophagosome-like vesicles. These results lead us to conclude that d-LFcin17-30 primes macrophages for intracellular microbial digestion through phagosomal maturation and/or autophagy, culminating in mycobacterial killing. IMPORTANCE The genus Mycobacterium comprises several pathogenic species, including M. tuberculosis , M. leprae , M. avium , etc. Infections caused by these bacteria are particularly difficult to treat due to their intrinsic impermeability, low growth rate, and intracellular localization. Antimicrobial peptides are increasingly acknowledged as potential treatment tools, as they have a high spectrum of activity, low tendency to induce bacterial resistance, and immunomodulatory properties. In this study, we

ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana.

Science.gov (United States)

Hazarika, Rashmi R; De Coninck, Barbara; Yamamoto, Lidia R; Martin, Laura R; Cammue, Bruno P A; van Noort, Vera

2017-01-17

Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism Arabidopsis thaliana. To aid the functional annotation of these peptides, we have developed ARA-PEPs (available at http://www.biw.kuleuven.be/CSB/ARA-PEPs ), a repository of putative peptides encoded by sORFs in the A. thaliana genome starting from in-house Tiling arrays, RNA-seq data and other publicly available datasets. ARA-PEPs currently lists 13,748 sORF-encoded peptides with transcriptional evidence. In addition to existing data, we have identified 100 novel transcriptionally active regions (TARs) that might encode 341 novel stress-induced peptides (SIPs). To aid in identification of bioactivity, we add functional annotation and sequence conservation to predicted peptides. To our knowledge, this is the largest repository of plant peptides encoded by sORFs with transcript evidence, publicly available and this resource will help scientists to effortlessly navigate the list of experimentally studied peptides, the experimental and computational evidence supporting the activity of these peptides and gain new perspectives for peptide discovery.

High atmosphere–ocean exchange of semivolatile aromatic hydrocarbons

KAUST Repository

González-Gaya, Belén

2016-05-16

Polycyclic aromatic hydrocarbons, and other semivolatile aromatic-like compounds, are an important and ubiquitous fraction of organic matter in the environment. The occurrence of semivolatile aromatic hydrocarbons is due to anthropogenic sources such as incomplete combustion of fossil fuels or oil spills, and other biogenic sources. However, their global transport, fate and relevance for the carbon cycle have been poorly assessed, especially in terms of fluxes. Here we report a global assessment of the occurrence and atmosphere-ocean fluxes of 64 polycyclic aromatic hydrocarbons analysed in paired atmospheric and seawater samples from the tropical and subtropical Atlantic, Pacific and Indian oceans. The global atmospheric input of polycyclic aromatic hydrocarbons to the global ocean is estimated at 0.09 Tg per month, four times greater than the input from the Deepwater Horizon spill. Moreover, the environmental concentrations of total semivolatile aromatic-like compounds were 10 2 -10 3 times higher than those of the targeted polycyclic aromatic hydrocarbons, with a relevant contribution of an aromatic unresolved complex mixture. These concentrations drive a large global deposition of carbon, estimated at 400 Tg C yr -1, around 15% of the oceanic CO2 uptake. © 2016 Macmillan Publishers Limited.

Peptide catalysed prebiotic polymerization of RNA

DEFF Research Database (Denmark)

Wieczorek, Rafal; Luisi, Pier Luigi; Monnard, Pierre-Alain

A short peptide composed of only two amino acid residues, serine and histidine, is here reported to enable oligomerization of RNA monomers. SerHis dipeptide was previously reported to catalyse formation of peptide bonds (Gorlero et al. 2009) as well as possessing broad hydrolytic activities...... – in such environment hydrolysis is thermodynamically favoured over condensation. However, the thermodynamic equilibrium towards condensation can be shifted even in this environment. In this poster we describe a prebiotically plausible system in which the SerHis dipeptide acts as catalyst for the formation of RNA...... oligomers from imidazole derivatives of mononucleotides. The thermodynamic shift towards condensation was achieved using water/ice eutectic phase environment (Monnard and Ziock 2008). To obtain such an environment, a reaction solution is cooled below its freezing point, but above the eutectic point. Under...

Meat and fermented meat products as a source of bioactive peptides.

Science.gov (United States)

Stadnik, Joanna; Kęska, Paulina

2015-01-01

Bioactive peptides are short amino acid sequences, that upon release from the parent protein may play different physiological roles, including antioxidant, antihypertensive, antimicrobial, and other bioactivities. They have been identified from a range of foods, including those of animal origin, e.g., milk and muscle sources (with pork, beef, or chicken and various species of fish and marine organism). Bioactive peptides are encrypted within the sequence of the parent protein molecule and latent until released and activated by enzymatic proteolysis, e.g. during gastrointestinal digestion or food processing. Bioactive peptides derived from food sources have the potential for incorporation into functional foods and nutraceuticals. The aim of this paper is to present an overview of the muscle-derived bioactive peptides, especially those of fermented meats and the potential benefits of these bioactive compounds to human health.

[Effects of introduction of short peptides before carotid artery occlusion on behaviour and caspase-3 activity in the brain of old rats].

Science.gov (United States)

Mendzheritskiĭ, A M; Karantysh, G V; Ivonina, K O

2011-01-01

The comparative research of effect of Pinealon and Cortexin on behavior and activity of caspase-3 in a brain of old rats in a model of carotid arteries occlusion was conducted. It is shown that introduction of short peptides promotes a survival rate of the animals that have modeled occlusion of carotid arteries. Under Pinealon before occlusion of carotid arteries, behavioral dream has been increased and a position-finding behavior, a motivational behavior and a motor performance have been reduced. The rats that were introduced Cortexin before carotid arteries occlusion demonstrated the raise of behavioral dream time. At introduction of Pinealon activity of caspase-3 moderately raises in false-operated animals and in a model of occlusion of carotid arteries.

Benzo-thia-fused [n]Thienoacenequinodimethanes with Small to Moderate Diradical Characters: The Role of Pro-aromaticity versus Anti-aromaticity

KAUST Repository

Shi, Xueliang

2016-01-19

Open-shell singlet diradicaloids recently have received much attention due to their unique optical, electronic and magnetic properties and promising applications in materials science. Among various diradicaloids, quinoidal π-conjugated molecules have become the prevailing designs. However, there still lacks fundamental understanding on how the fusion mode and pro-aromaticity/anti-aromaticity affect their diradical character and physical properties. In this work, a series of pro-aromatic benzo-thia-fused [n]thienoacenequinodimethanes (Thn-TIPS (n=1-3) and BDTh-TIPS) were synthesized and compared with the previously reported anti-aromatic bisindeno-[n]thienoacenes (Sn-TIPS, n=1-4). The ground-state geometric and electronic structures of these new quinoidal molecules were systematically investigated by X-ray crystallographic analysis, variable temperature NMR, ESR, SQUID, Raman, and electronic absorption spectroscopy, assisted by DFT calculations. It was found that the diradical character index (y0) increased from nearly zero for Th1-TIPS to 2.4% for Th2-TIPS, 18.2% for Th3-TIPS, and 38.2% for BDTh-TIPS, due to the enhanced aromatic stabilization. Consequently, with the extension of molecular size, the one-photon absorption spectra are gradually red-shifted, the two-photon absorption (TPA) cross section values increase, and the singlet excited state lifetimes decrease. By comparison with the corresponding anti-aromatic analogues Sn-TIPS (n=1-3), the pro-aromatic Thn-TIPS (n=1-3) exhibit larger diradical character, longer singlet excited state lifetime and larger TPA cross section value. At the same time, they display distinctively different electronic absorption spectra and improved electrochemical amphotericity. Spectroelectrochemical studies revealed a good linear relationship between the optical energy gaps and the molecular length in the neutral, radical cationic and dicationic forms. Our research work disclosed the significant difference between the pro-aromatic

Benzo-thia-fused [n]Thienoacenequinodimethanes with Small to Moderate Diradical Characters: The Role of Pro-aromaticity versus Anti-aromaticity

KAUST Repository

Shi, Xueliang; Quintero, EstefanÍ a; Lee, Sangsu; Jing, Linzhi; Herng, Tun Seng; Zheng, Bin; Huang, Kuo-Wei; Ló pez Navarrete, Juan T.; Ding, Jun; Kim, Dongho; Casado, Juan; Chi, Chunyan

2016-01-01

Open-shell singlet diradicaloids recently have received much attention due to their unique optical, electronic and magnetic properties and promising applications in materials science. Among various diradicaloids, quinoidal π-conjugated molecules have become the prevailing designs. However, there still lacks fundamental understanding on how the fusion mode and pro-aromaticity/anti-aromaticity affect their diradical character and physical properties. In this work, a series of pro-aromatic benzo-thia-fused [n]thienoacenequinodimethanes (Thn-TIPS (n=1-3) and BDTh-TIPS) were synthesized and compared with the previously reported anti-aromatic bisindeno-[n]thienoacenes (Sn-TIPS, n=1-4). The ground-state geometric and electronic structures of these new quinoidal molecules were systematically investigated by X-ray crystallographic analysis, variable temperature NMR, ESR, SQUID, Raman, and electronic absorption spectroscopy, assisted by DFT calculations. It was found that the diradical character index (y0) increased from nearly zero for Th1-TIPS to 2.4% for Th2-TIPS, 18.2% for Th3-TIPS, and 38.2% for BDTh-TIPS, due to the enhanced aromatic stabilization. Consequently, with the extension of molecular size, the one-photon absorption spectra are gradually red-shifted, the two-photon absorption (TPA) cross section values increase, and the singlet excited state lifetimes decrease. By comparison with the corresponding anti-aromatic analogues Sn-TIPS (n=1-3), the pro-aromatic Thn-TIPS (n=1-3) exhibit larger diradical character, longer singlet excited state lifetime and larger TPA cross section value. At the same time, they display distinctively different electronic absorption spectra and improved electrochemical amphotericity. Spectroelectrochemical studies revealed a good linear relationship between the optical energy gaps and the molecular length in the neutral, radical cationic and dicationic forms. Our research work disclosed the significant difference between the pro-aromatic

Small surfactant-like peptides can drive soluble proteins into active aggregates

Directory of Open Access Journals (Sweden)

Zhou Bihong

2012-01-01

Full Text Available Abstract Background Inactive protein inclusion bodies occur commonly in Escherichia coli (E. coli cells expressing heterologous proteins. Previously several independent groups have found that active protein aggregates or pseudo inclusion bodies can be induced by a fusion partner such as a cellulose binding domain from Clostridium cellulovorans (CBDclos when expressed in E. coli. More recently we further showed that a short amphipathic helical octadecapeptide 18A (EWLKAFYEKVLEKLKELF and a short beta structure peptide ELK16 (LELELKLKLELELKLK have a similar property. Results In this work, we explored a third type of peptides, surfactant-like peptides, for performing such a "pulling-down" function. One or more of three such peptides (L6KD, L6K2, DKL6 were fused to the carboxyl termini of model proteins including Aspergillus fumigatus amadoriase II (AMA, all three peptides were used, Bacillus subtilis lipase A (LipA, only L6KD was used, hereinafter the same, Bacillus pumilus xylosidase (XynB, and green fluorescent protein (GFP, and expressed in E. coli. All fusions were found to predominantly accumulate in the insoluble fractions, with specific activities ranging from 25% to 92% of the native counterparts. Transmission electron microscopic (TEM and confocal fluorescence microscopic analyses confirmed the formation of protein aggregates in the cell. Furthermore, binding assays with amyloid-specific dyes (thioflavin T and Cong red to the AMA-L6KD aggregate and the TEM analysis of the aggregate following digestion with protease K suggested that the AMA-L6KD aggregate may contain structures reminiscent of amyloids, including a fibril-like structure core. Conclusions This study shows that the surfactant-like peptides L6KD and it derivatives can act as a pull-down handler for converting soluble proteins into active aggregates, much like 18A and ELK16. These peptide-mediated protein aggregations might have important implications for protein aggregation in

A 10-A spectroscopic ruler applied to short polyprolines.

Science.gov (United States)

Sahoo, Harekrushna; Roccatano, Danilo; Hennig, Andreas; Nau, Werner M

2007-08-08

Fluorescence resonance energy transfer (FRET) from the amino acid tryptophan (Trp) as donor and a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) as acceptor in peptides of the general structure Trp-(Pro)n-Dbo-NH2 (n = 1-6) was investigated by steady-state and time-resolved fluorescence, CD, and NMR spectroscopy as well as by molecular dynamics (MD) simulations (GROMOS96 force field). The Trp/Dbo FRET pair is characterized by a very short Förster radius (R0 ca. 9 A), which allowed distance determinations in such short peptides. Water and propylene glycol were investigated as solvents. The peptides were designed to show an early nucleation of the poly(Pro)II (PPII) secondary helix structure for n > or = 2, which was confirmed by their CD spectra. The shortest peptide (n = 1) adopts preferentially the trans conformation about the Trp-Pro bond, as confirmed by NMR spectra. The FRET efficiencies ranged 2-72% and were found to depend sensitively on the peptide length, i.e., the number of intervening proline residues. The analysis of the FRET data at different levels of theory (assuming either a fixed distance or distance distributions according to a wormlike chain or Gaussian model) afforded donor-acceptor distances between ca. 8 A (n = 1) and ca. 16 A (n = 6) in water, which were found to be similar or slightly higher in propylene glycol. The distances afforded by the Trp/Dbo FRET pair were found to be reasonable in comparison to literature data, expectations from the PPII helix structure, and the results from MD simulations. The persistence lengths for the longer peptides were found to lie at 30-70 A in water and 220 +/- 40 A in propylene glycol, suggesting a more rigid PPII helical structure in propylene glycol. A detailed comparison with literature data on FRET in polyprolines demonstrates that the donor-acceptor distances extracted by FRET are correlated with the Förster radii of the employed FRET pairs. This demonstrates the limitations of using FRET

Greener Friedel-Crafts Acylation using Microwave-enhanced reactivity of Bismuth Triflate in the Friedel-Crafts Benzoylation of Aromatic Compounds with Benzoic Anhydride

DEFF Research Database (Denmark)

Tran, Phuong Hoang; Nguyen, Hai Truong; Hansen, Poul Erik

2017-01-01

An efficient and facile bismuth trifluoromethanesulfonate-catalyzed benzoylation of aromatic compounds using benzoic anhydride under solvent-free microwave irradiation has been developed. The microwave-assisted Friedel-Crafts benzoylation results in good yields within short reaction times. Bismuth...

Pharmacological characterization of lipidized analogs of prolactin-releasing peptide with a modified C-terminal aromatic ring

Czech Academy of Sciences Publication Activity Database

Pražienková, Veronika; Tichá, Anežka; Blechová, Miroslava; Špolcová, Andrea; Železná, Blanka; Maletínská, Lenka

2016-01-01

Roč. 67, č. 1 (2016), s. 121-128 ISSN 0867-5910 R&D Projects: GA ČR(CZ) GA15-08679S Institutional support: RVO:61388963 Keywords : prolactin-releasing peptide * blood-brain barrier * food intake * lipidization * phenylalanine derivatives Subject RIV: FB - Endocrinology, Diabetology, Metabolism, Nutrition Impact factor: 2.883, year: 2016 http://www.jpp.krakow.pl/journal/archive/02_16/articles/11_article.html

Exploring the role of peptides in polymer-based gene delivery.

Science.gov (United States)

Sun, Yanping; Yang, Zhen; Wang, Chunxi; Yang, Tianzhi; Cai, Cuifang; Zhao, Xiaoyun; Yang, Li; Ding, Pingtian

2017-09-15

Polymers are widely studied as non-viral gene vectors because of their strong DNA binding ability, capacity to carry large payload, flexibility of chemical modifications, low immunogenicity, and facile processes for manufacturing. However, high cytotoxicity and low transfection efficiency substantially restrict their application in clinical trials. Incorporating functional peptides is a promising approach to address these issues. Peptides demonstrate various functions in polymer-based gene delivery systems, such as targeting to specific cells, breaching membrane barriers, facilitating DNA condensation and release, and lowering cytotoxicity. In this review, we systematically summarize the role of peptides in polymer-based gene delivery, and elaborate how to rationally design polymer-peptide based gene delivery vectors. Polymers are widely studied as non-viral gene vectors, but suffer from high cytotoxicity and low transfection efficiency. Incorporating short, bioactive peptides into polymer-based gene delivery systems can address this issue. Peptides demonstrate various functions in polymer-based gene delivery systems, such as targeting to specific cells, breaching membrane barriers, facilitating DNA condensation and release, and lowering cytotoxicity. In this review, we highlight the peptides' roles in polymer-based gene delivery, and elaborate how to utilize various functional peptides to enhance the transfection efficiency of polymers. The optimized peptide-polymer vectors should be able to alter their structures and functions according to biological microenvironments and utilize inherent intracellular pathways of cells, and consequently overcome the barriers during gene delivery to enhance transfection efficiency. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Peptides and Anti-peptide Antibodies for Small and Medium Scale Peptide and Anti-peptide Affinity Microarrays: Antigenic Peptide Selection, Immobilization, and Processing.

Science.gov (United States)

Zhang, Fan; Briones, Andrea; Soloviev, Mikhail

2016-01-01

This chapter describes the principles of selection of antigenic peptides for the development of anti-peptide antibodies for use in microarray-based multiplex affinity assays and also with mass-spectrometry detection. The methods described here are mostly applicable to small to medium scale arrays. Although the same principles of peptide selection would be suitable for larger scale arrays (with 100+ features) the actual informatics software and printing methods may well be different. Because of the sheer number of proteins/peptides to be processed and analyzed dedicated software capable of processing all the proteins and an enterprise level array robotics may be necessary for larger scale efforts. This report aims to provide practical advice to those who develop or use arrays with up to ~100 different peptide or protein features.

A non-covalent peptide-based carrier for in vivo delivery of DNA mimics

OpenAIRE

Morris, May C.; Gros, Edwige; Aldrian-Herrada, Gudrun; Choob, Michael; Archdeacon, John; Heitz, Frederic; Divita, Gilles

2007-01-01

The dramatic acceleration in identification of new nucleic-acid-based therapeutic molecules has provided new perspectives in pharmaceutical research. However, their development is limited by their poor cellular uptake and inefficient trafficking. Here we describe a short amphipathic peptide, Pep-3, that combines a tryptophan/phenylalanine domain with a lysine/arginine-rich hydrophilic motif. Pep-3 forms stable nano-size complexes with peptide-nucleic acid analogues and promotes their efficien...

Therapeutic peptides for cancer therapy. Part II - cell cycle inhibitory peptides and apoptosis-inducing peptides.

Science.gov (United States)

Raucher, Drazen; Moktan, Shama; Massodi, Iqbal; Bidwell, Gene L

2009-10-01

Therapeutic peptides have great potential as anticancer agents owing to their ease of rational design and target specificity. However, their utility in vivo is limited by low stability and poor tumor penetration. The authors review the development of peptide inhibitors with potential for cancer therapy. Peptides that arrest the cell cycle by mimicking CDK inhibitors or induce apoptosis directly are discussed. The authors searched Medline for articles concerning the development of therapeutic peptides and their delivery. Inhibition of cancer cell proliferation directly using peptides that arrest the cell cycle or induce apoptosis is a promising strategy. Peptides can be designed that interact very specifically with cyclins and/or cyclin-dependent kinases and with members of apoptotic cascades. Use of these peptides is not limited by their design, as a rational approach to peptide design is much less challenging than the design of small molecule inhibitors of specific protein-protein interactions. However, the limitations of peptide therapy lie in the poor pharmacokinetic properties of these large, often charged molecules. Therefore, overcoming the drug delivery hurdles could open the door for effective peptide therapy, thus making an entirely new class of molecules useful as anticancer drugs.

Survey of benzene and aromatics in Canadian Gasoline - 1994

International Nuclear Information System (INIS)

Tushingham, M.

1996-01-01

A comprehensive database of the benzene and aromatics levels of gasoline produced in or imported into Canada during 1994, was presented. Environment Canada conducted a survey that requested refineries and importers to report quarterly on benzene and aromatics levels in gasoline. Benzene, which has been declared toxic by the Canadian Environmental Protection Act, is found in gasoline and is formed during the combustion of the aromatic components of gasoline. It was shown that benzene and aromatics levels differ regionally and seasonally. There are also variations in benzene levels between batches of gasoline produced at any one refinery. This report listed the responses to the benzene/aromatics survey. It also described the analytical procedures used to measure benzene and aromatics levels in gasoline, and provided guidelines for reporting gasoline benzene and total aromatics data. 7 tabs., 21 figs

Ultrashort peptide nanogels release in situ generated silver manoparticles to combat emerging antimicrobial resistance strains

KAUST Repository

Seferji, Kholoud; Susapto, Hepi Hari; Arab, Wafaa Talat Abdullah; Sharip, Ainur; Sundaramurthi, Dhakshinamoorthy; Rauf, Sakandar; Hauser, Charlotte

2017-01-01

Nanogels made from self-assembling ultrashort peptides (3-6 amino acids in size) are promising biomaterials for various biomedical applications such as tissue engineering, drug delivery, regenerative medicine, microbiology and biosensing.We have developed silver-releasing peptide nanogels with promising wound care applications. The peptide nanogels allow a precise control of in situ syntesized silver nanoparticles (AgNPs), using soley short UV radiation and no other chemical reducing agent. We propose these silver-releasing nanogels as excellent biomaterial to combat emerging antimicrobial resistant strains.

Ultrashort peptide nanogels release in situ generated silver manoparticles to combat emerging antimicrobial resistance strains

KAUST Repository

Seferji, Kholoud

2017-01-08

Nanogels made from self-assembling ultrashort peptides (3-6 amino acids in size) are promising biomaterials for various biomedical applications such as tissue engineering, drug delivery, regenerative medicine, microbiology and biosensing.We have developed silver-releasing peptide nanogels with promising wound care applications. The peptide nanogels allow a precise control of in situ syntesized silver nanoparticles (AgNPs), using soley short UV radiation and no other chemical reducing agent. We propose these silver-releasing nanogels as excellent biomaterial to combat emerging antimicrobial resistant strains.

Peptides, polypeptides and peptide-polymer hybrids as nucleic acid carriers.

Science.gov (United States)

Ahmed, Marya

2017-10-24

Cell penetrating peptides (CPPs), and protein transduction domains (PTDs) of viruses and other natural proteins serve as a template for the development of efficient peptide based gene delivery vectors. PTDs are sequences of acidic or basic amphipathic amino acids, with superior membrane trespassing efficacies. Gene delivery vectors derived from these natural, cationic and cationic amphipathic peptides, however, offer little flexibility in tailoring the physicochemical properties of single chain peptide based systems. Owing to significant advances in the field of peptide chemistry, synthetic mimics of natural peptides are often prepared and have been evaluated for their gene expression, as a function of amino acid functionalities, architecture and net cationic content of peptide chains. Moreover, chimeric single polypeptide chains are prepared by a combination of multiple small natural or synthetic peptides, which imparts distinct physiological properties to peptide based gene delivery therapeutics. In order to obtain multivalency and improve the gene delivery efficacies of low molecular weight cationic peptides, bioactive peptides are often incorporated into a polymeric architecture to obtain novel 'polymer-peptide hybrids' with improved gene delivery efficacies. Peptide modified polymers prepared by physical or chemical modifications exhibit enhanced endosomal escape, stimuli responsive degradation and targeting efficacies, as a function of physicochemical and biological activities of peptides attached onto a polymeric scaffold. The focus of this review is to provide comprehensive and step-wise progress in major natural and synthetic peptides, chimeric polypeptides, and peptide-polymer hybrids for nucleic acid delivery applications.

Bicyclic Baird-type aromaticity

Science.gov (United States)

Cha, Won-Young; Kim, Taeyeon; Ghosh, Arindam; Zhang, Zhan; Ke, Xian-Sheng; Ali, Rashid; Lynch, Vincent M.; Jung, Jieun; Kim, Woojae; Lee, Sangsu; Fukuzumi, Shunichi; Park, Jung Su; Sessler, Jonathan L.; Chandrashekar, Tavarekere K.; Kim, Dongho

2017-12-01

Classic formulations of aromaticity have long been associated with topologically planar conjugated macrocyclic systems. The theoretical possibility of so-called bicycloaromaticity was noted early on. However, it has yet to be demonstrated by experiment in a simple synthetic organic molecule. Conjugated organic systems are attractive for studying the effect of structure on electronic features. This is because, in principle, they can be modified readily through dedicated synthesis. As such, they can provide useful frameworks for testing by experiment with fundamental insights provided by theory. Here we detail the synthesis and characterization of two purely organic non-planar dithienothiophene-bridged [34]octaphyrins that permit access to two different aromatic forms as a function of the oxidation state. In their neutral forms, these congeneric systems contain competing 26 and 34 π-electronic circuits. When subject to two-electron oxidation, electronically mixed [4n+1]/[4n+1] triplet biradical species in the ground state are obtained that display global aromaticity in accord with Baird's rule.

β-Boomerang Antimicrobial and Antiendotoxic Peptides: Lipidation and Disulfide Bond Effects on Activity and Structure.

Science.gov (United States)

Mohanram, Harini; Bhattacharjya, Surajit

2014-04-21

Drug-resistant Gram-negative bacterial pathogens and endotoxin- or lipopolysaccharide (LPS)-mediated inflammations are among some of the most  prominent health issues globally. Antimicrobial peptides (AMPs) are eminent molecules that can kill drug-resistant strains and neutralize LPS toxicity. LPS, the outer layer of the outer membrane of Gram-negative bacteria safeguards cell integrity against hydrophobic compounds, including antibiotics and AMPs. Apart from maintaining structural integrity, LPS, when released into the blood stream, also induces inflammatory pathways leading to septic shock. In previous works, we have reported the de novo design of a set of 12-amino acid long cationic/hydrophobic peptides for LPS binding and activity. These peptides adopt β-boomerang like conformations in complex with LPS. Structure-activity studies demonstrated some critical features of the β-boomerang scaffold that may be utilized for the further development of potent analogs. In this work, β-boomerang lipopeptides were designed and structure-activity correlation studies were carried out. These lipopeptides were homo-dimerized through a disulfide bridge to stabilize conformations and for improved activity. The designed peptides exhibited potent antibacterial activity and efficiently neutralized LPS toxicity under in vitro assays. NMR structure of C4YI13C in aqueous solution demonstrated the conserved folding of the lipopeptide with a boomerang aromatic lock stabilized with disulfide bond at the C-terminus and acylation at the N-terminus. These lipo-peptides displaying bacterial sterilization and low hemolytic activity may be useful for future applications as antimicrobial and antiendotoxin molecules.

β-Boomerang Antimicrobial and Antiendotoxic Peptides: Lipidation and Disulfide Bond Effects on Activity and Structure

Directory of Open Access Journals (Sweden)

Harini Mohanram

2014-04-01

Full Text Available Drug-resistant Gram-negative bacterial pathogens and endotoxin- or lipopolysaccharide (LPS-mediated inflammations are among some of the most  prominent health issues globally. Antimicrobial peptides (AMPs are eminent molecules that can kill drug-resistant strains and neutralize LPS toxicity. LPS, the outer layer of the outer membrane of Gram-negative bacteria safeguards cell integrity against hydrophobic compounds, including antibiotics and AMPs. Apart from maintaining structural integrity, LPS, when released into the blood stream, also induces inflammatory pathways leading to septic shock. In previous works, we have reported the de novo design of a set of 12-amino acid long cationic/hydrophobic peptides for LPS binding and activity. These peptides adopt β-boomerang like conformations in complex with LPS. Structure-activity studies demonstrated some critical features of the β-boomerang scaffold that may be utilized for the further development of potent analogs. In this work, β-boomerang lipopeptides were designed and structure-activity correlation studies were carried out. These lipopeptides were homo-dimerized through a disulfide bridge to stabilize conformations and for improved activity. The designed peptides exhibited potent antibacterial activity and efficiently neutralized LPS toxicity under in vitro assays. NMR structure of C4YI13C in aqueous solution demonstrated the conserved folding of the lipopeptide with a boomerang aromatic lock stabilized with disulfide bond at the C-terminus and acylation at the N-terminus. These lipo-peptides displaying bacterial sterilization and low hemolytic activity may be useful for future applications as antimicrobial and antiendotoxin molecules.

Fabrication of Nanostructures Using Self-Assembled Peptides as Templates

DEFF Research Database (Denmark)

Castillo, Jaime

2015-01-01

the advantages of diphenylalanine are explained step by step offering new alternatives to fabricate nanostructures in a simple and rapid way. The chapter is complemented with techniques to manipulate the self-assembled diphenylalanine nanostructures without changing its properties during the manipulation process.......This chapter evaluates the use of a short-aromatic dipeptide, diphenylalanine, as a template in the fabrication of new nanostructures (nanowires, coaxial nanocables, nanochannels) using materials such as silicon, conducting and non-conducting polymers. Diphenylalanine self...

Efficient Cargo Delivery into Adult Brain Tissue Using Short Cell-Penetrating Peptides.

Directory of Open Access Journals (Sweden)

Caghan Kizil

Full Text Available Zebrafish brains can regenerate lost neurons upon neurogenic activity of the radial glial progenitor cells (RGCs that reside at the ventricular region. Understanding the molecular events underlying this ability is of great interest for translational studies of regenerative medicine. Therefore, functional analyses of gene function in RGCs and neurons are essential. Using cerebroventricular microinjection (CVMI, RGCs can be targeted efficiently but the penetration capacity of the injected molecules reduces dramatically in deeper parts of the brain tissue, such as the parenchymal regions that contain the neurons. In this report, we tested the penetration efficiency of five known cell-penetrating peptides (CPPs and identified two- polyR and Trans - that efficiently penetrate the brain tissue without overt toxicity in a dose-dependent manner as determined by TUNEL staining and L-Plastin immunohistochemistry. We also found that polyR peptide can help carry plasmid DNA several cell diameters into the brain tissue after a series of coupling reactions using DBCO-PEG4-maleimide-based Michael's addition and azide-mediated copper-free click reaction. Combined with the advantages of CVMI, such as rapidness, reproducibility, and ability to be used in adult animals, CPPs improve the applicability of the CVMI technique to deeper parts of the central nervous system tissues.

Temperature-sensitive elastin-mimetic dendrimers: Effect of peptide length and dendrimer generation to temperature sensitivity.

Science.gov (United States)

Kojima, Chie; Irie, Kotaro; Tada, Tomoko; Tanaka, Naoki

2014-06-01

Dendrimers are synthetic macromolecules with unique structure, which are a potential scaffold for peptides. Elastin is one of the main components of extracellular matrix and a temperature-sensitive biomacromolecule. Previously, Val-Pro-Gly-Val-Gly peptides have been conjugated to a dendrimer for designing an elastin-mimetic dendrimer. In this study, various elastin-mimetic dendrimers using different length peptides and different dendrimer generations were synthesized to control the temperature dependency. The elastin-mimetic dendrimers formed β-turn structure by heating, which was similar to the elastin-like peptides. The elastin-mimetic dendrimers exhibited an inverse phase transition, largely depending on the peptide length and slightly depending on the dendrimer generation. The elastin-mimetic dendrimers formed aggregates after the phase transition. The endothermal peak was observed in elastin-mimetic dendrimers with long peptides, but not with short ones. The peptide length and the dendrimer generation are important factors to tune the temperature dependency on the elastin-mimetic dendrimer. Copyright © 2013 Wiley Periodicals, Inc.

Volatilisation of aromatic hydrocarbons from soil

DEFF Research Database (Denmark)

Lindhardt, B.; Christensen, T.H.

1996-01-01

The non-steady-state fluxes of aromatic hydrocarbons were measured in the laboratory from the surface of soils contaminated with coal tar Four soil samples from a former gasworks site were used for the experiments. The fluxes were quantified for 11 selected compounds, 4 mono- and 7 polycyclic...... aromatic hydrocarbons, for a period of up to 8 or 16 days. The concentrations of the selected compounds in the soils were between 0.2 and 3,100 mu g/g. The study included the experimental determination of the distribution coefficient of the aromatic hydrocarbons between the sorbed phase and the water under...... saturated conditions. The determined distribution coefficients showed that the aromatic hydrocarbons were more strongly sorbed to the total organic carbon including the coal tar pitch - by a factor of 8 to 25 - than expected for natural organic matter. The fluxes were also estimated using an analytical...

Can Natural Proteins Designed with ‘Inverted’ Peptide Sequences Adopt Native-Like Protein Folds?

Science.gov (United States)

Sridhar, Settu; Guruprasad, Kunchur

2014-01-01

We have carried out a systematic computational analysis on a representative dataset of proteins of known three-dimensional structure, in order to evaluate whether it would possible to ‘swap’ certain short peptide sequences in naturally occurring proteins with their corresponding ‘inverted’ peptides and generate ‘artificial’ proteins that are predicted to retain native-like protein fold. The analysis of 3,967 representative proteins from the Protein Data Bank revealed 102,677 unique identical inverted peptide sequence pairs that vary in sequence length between 5–12 and 18 amino acid residues. Our analysis illustrates with examples that such ‘artificial’ proteins may be generated by identifying peptides with ‘similar structural environment’ and by using comparative protein modeling and validation studies. Our analysis suggests that natural proteins may be tolerant to accommodating such peptides. PMID:25210740

Teduglutide for the treatment of short bowel syndrome

DEFF Research Database (Denmark)

Jeppesen, P B

2013-01-01

Glucagon-like peptide 2 (GLP-2) decreases gastric and intestinal motility, reduces gastric secretions, promotes intestinal growth and improves post-resection structural and functional adaptation in short bowel syndrome (SBS). Teduglutide, an analogue of GLP-2, has a prolonged half-life and provides...

Bioassay of polycyclic aromatic hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

Van Kirk, E.A.

1980-08-01

A positive relationship was found between the photodynamic activity of 24 polycyclic aromatic hydrocarbons versus published results on the mutagenicity, carcinogenicity, and initiation of unscheduled DNA synthesis. Metabolic activation of benzo(a)pyrene resulted in detection of increased mutagenesis in Paramecium tetraurelia as found also in the Ames Salmonella assay. The utility of P. tetraurelia as a biological detector of hazardous polycyclic aromatic hydrocarbons is discussed.

Peptide-based biosensors: From self-assembled interfaces to molecular probes in electrochemical assays.

Science.gov (United States)

Puiu, Mihaela; Bala, Camelia

2018-04-01

Redox-tagged peptides have emerged as functional materials with multiple applications in the area of sensing and biosensing applications due to their high stability, excellent redox properties and versatility of biomolecular interactions. They allow direct observation of molecular interactions in a wide range of affinity and enzymatic assays and act as electron mediators. Short helical peptides possess the ability to self-assemble in specific configurations with the possibility to develop in highly-ordered, stable 1D, 2D and 3D architectures in a hierarchical controlled manner. We provide here a brief overview of the electrochemical techniques available to study the electron transfer in peptide films with particular interest in developing biosensors with immobilized peptide motifs, for biological and clinical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Antibacterial activity of novel cationic peptides against clinical isolates of multi-drug resistant Staphylococcus pseudintermedius from infected dogs.

Directory of Open Access Journals (Sweden)

Mohamed F Mohamed

Full Text Available Staphylococcus pseudintermedius is a major cause of skin and soft tissue infections in companion animals and has zoonotic potential. Additionally, methicillin-resistant S. pseudintermedius (MRSP has emerged with resistance to virtually all classes of antimicrobials. Thus, novel treatment options with new modes of action are required. Here, we investigated the antimicrobial activity of six synthetic short peptides against clinical isolates of methicillin-susceptible and MRSP isolated from infected dogs. All six peptides demonstrated potent anti-staphylococcal activity regardless of existing resistance phenotype. The most effective peptides were RRIKA (with modified C terminus to increase amphipathicity and hydrophobicity and WR-12 (α-helical peptide consisting exclusively of arginine and tryptophan with minimum inhibitory concentration50 (MIC50 of 1 µM and MIC90 of 2 µM. RR (short anti-inflammatory peptide and IK8 "D isoform" demonstrated good antimicrobial activity with MIC50 of 4 µM and MIC90 of 8 µM. Penetratin and (KFF3K (two cell penetrating peptides were the least effective with MIC50 of 8 µM and MIC90 of 16 µM. Killing kinetics revealed a major advantage of peptides over conventional antibiotics, demonstrating potent bactericidal activity within minutes. Studies with propidium iodide and transmission electron microscopy revealed that peptides damaged the bacterial membrane leading to leakage of cytoplasmic contents and consequently, cell death. A potent synergistic increase in the antibacterial effect of the cell penetrating peptide (KFF3K was noticed when combined with other peptides and with antibiotics. In addition, all peptides displayed synergistic interactions when combined together. Furthermore, peptides demonstrated good therapeutic indices with minimal toxicity toward mammalian cells. Resistance to peptides did not evolve after 10 passages of S. pseudintermedius at sub-inhibitory concentration. However, the MICs of amikacin

Erbium trifluoromethanesulfonate-catalyzed Friedel–Crafts acylation using aromatic carboxylic acids as acylating agents under monomode-microwave irradiation

DEFF Research Database (Denmark)

Tran, Phuong Hoang; Hansen, Poul Erik; Nguyen, Hai Truong

2015-01-01

Erbium trifluoromethanesulfonate is found to be a good catalyst for the Friedel–Crafts acylation of arenes containing electron-donating substituents using aromatic carboxylic acids as the acylating agents under microwave irradiation. An effective, rapid and waste-free method allows the preparation...... of a wide range of aryl ketones in good yields and in short reaction times with minimum amounts of waste...

Protein interaction networks by proteome peptide scanning.

Directory of Open Access Journals (Sweden)

Christiane Landgraf

2004-01-01

Full Text Available A substantial proportion of protein interactions relies on small domains binding to short peptides in the partner proteins. Many of these interactions are relatively low affinity and transient, and they impact on signal transduction. However, neither the number of potential interactions mediated by each domain nor the degree of promiscuity at a whole proteome level has been investigated. We have used a combination of phage display and SPOT synthesis to discover all the peptides in the yeast proteome that have the potential to bind to eight SH3 domains. We first identified the peptides that match a relaxed consensus, as deduced from peptides selected by phage display experiments. Next, we synthesized all the matching peptides at high density on a cellulose membrane, and we probed them directly with the SH3 domains. The domains that we have studied were grouped by this approach into five classes with partially overlapping specificity. Within the classes, however, the domains display a high promiscuity and bind to a large number of common targets with comparable affinity. We estimate that the yeast proteome contains as few as six peptides that bind to the Abp1 SH3 domain with a dissociation constant lower than 100 microM, while it contains as many as 50-80 peptides with corresponding affinity for the SH3 domain of Yfr024c. All the targets of the Abp1 SH3 domain, identified by this approach, bind to the native protein in vivo, as shown by coimmunoprecipitation experiments. Finally, we demonstrate that this strategy can be extended to the analysis of the entire human proteome. We have developed an approach, named WISE (whole interactome scanning experiment, that permits rapid and reliable identification of the partners of any peptide recognition module by peptide scanning of a proteome. Since the SPOT synthesis approach is semiquantitative and provides an approximation of the dissociation constants of the several thousands of interactions that are

Metabolism and Biomarkers of Heterocyclic Aromatic Amines in Molecular Epidemiology Studies: Lessons Learned from Aromatic Amines

Science.gov (United States)

2011-01-01

Aromatic amines and heterocyclic aromatic amines (HAAs) are structurally related classes of carcinogens that are formed during the combustion of tobacco or during the high-temperature cooking of meats. Both classes of procarcinogens undergo metabolic activation by N-hydroxylation of the exocyclic amine group, to produce a common proposed intermediate, the arylnitrenium ion, which is the critical metabolite implicated in toxicity and DNA damage. However, the biochemistry and chemical properties of these compounds are distinct and different biomarkers of aromatic amines and HAAs have been developed for human biomonitoring studies. Hemoglobin adducts have been extensively used as biomarkers to monitor occupational and environmental exposures to a number of aromatic amines; however, HAAs do not form hemoglobin adducts at appreciable levels and other biomarkers have been sought. A number of epidemiologic studies that have investigated dietary consumption of well-done meat in relation to various tumor sites reported a positive association between cancer risk and well-done meat consumption, although some studies have shown no associations between well-done meat and cancer risk. A major limiting factor in most epidemiological studies is the uncertainty in quantitative estimates of chronic exposure to HAAs and, thus, the association of HAAs formed in cooked meat and cancer risk has been difficult to establish. There is a critical need to establish long-term biomarkers of HAAs that can be implemented in molecular epidemioIogy studies. In this review article, we highlight and contrast the biochemistry of several prototypical carcinogenic aromatic amines and HAAs to which humans are chronically exposed. The biochemical properties and the impact of polymorphisms of the major xenobiotic-metabolizing enzymes on the biological effects of these chemicals are examined. Lastly, the analytical approaches that have been successfully employed to biomonitor aromatic amines and HAAs, and

Cathepsin-Mediated Cleavage of Peptides from Peptide Amphiphiles Leads to Enhanced Intracellular Peptide Accumulation

Energy Technology Data Exchange (ETDEWEB)

Acar, Handan [Institute; Department; Samaeekia, Ravand [Institute; Department; Schnorenberg, Mathew R. [Institute; Department; Medical; Sasmal, Dibyendu K. [Institute; Huang, Jun [Institute; Tirrell, Matthew V. [Institute; Institute; LaBelle, James L. [Department

2017-08-24

Peptides synthesized in the likeness of their native interaction domain(s) are natural choices to target protein protein interactions (PPIs) due to their fidelity of orthostatic contact points between binding partners. Despite therapeutic promise, intracellular delivery of biofunctional peptides at concentrations necessary for efficacy remains a formidable challenge. Peptide amphiphiles (PAs) provide a facile method of intracellular delivery and stabilization of bioactive peptides. PAs consisting of biofunctional peptide headgroups linked to hydrophobic alkyl lipid-like tails prevent peptide hydrolysis and proteolysis in circulation, and PA monomers are internalized via endocytosis. However, endocytotic sequestration and steric hindrance from the lipid tail are two major mechanisms that limit PA efficacy to target intracellular PPIs. To address these problems, we have constructed a PA platform consisting of cathepsin-B cleavable PAs in which a selective p53-based inhibitory peptide is cleaved from its lipid tail within endosomes, allowing for intracellular peptide accumulation and extracellular recycling of the lipid moiety. We monitor for cleavage and follow individual PA components in real time using a resonance energy transfer (FRET)-based tracking system. Using this platform, components in real time using a Forster we provide a better understanding and quantification of cellular internalization, trafficking, and endosomal cleavage of PAs and of the ultimate fates of each component.

Aromatization of n-octane over Pd/C catalysts

KAUST Repository

Yin, Mengchen; Natelson, Robert H.; Campos, Andrew A.; Kolar, Praveen; Roberts, William L.

2013-01-01

Gas-phase aromatization of n-octane was investigated using Pd/C catalyst. The objectives were to: (1) determine the effects of temperature (400-600 °C), weight hourly space velocity (WHSV) (0.8-∞), and hydrogen to hydrocarbon molar ratio (MR) (0-6) on conversion, selectivity, and yield (2) compare the activity of Pd/C with Pt/C and Pt/KL catalysts and (3) test the suitability of Pd/C for aromatization of different alkanes including n-hexane, n-heptane, and n-octane. Pd/C exhibited the best aromatization performance, including 54.4% conversion and 31.5% aromatics yield at 500 °C, WHSV = 2 h-1, and a MR of 2. The Pd/C catalyst had higher selectivity towards the preferred aromatics including ethylbenzene and xylenes, whereas Pt/KL had higher selectivity towards benzene and toluene. The results were somewhat consistent with adsorbed n-octane cyclization proceeding mainly through the six-membered ring closure mechanism. In addition, Pd/C was also capable of catalyzing aromatization of n-hexane and n-heptane. © 2012 Elsevier Ltd. All rights reserved.

Proximate Composition, Mineral Content and Fatty Acids Analyses of Aromatic and Non-Aromatic Indian Rice

Directory of Open Access Journals (Sweden)

Deepak Kumar Verma

2017-01-01

Full Text Available Awareness on nutritive value and health benefits of rice is of vital importance in order to increase the consumption of rice in daily diet of the human beings. In this study, a total of six aromatic and two non-aromatic rice accessions grown in India were analysed for their nutritional quality attributes including proximate composition, mineral contents and fatty acids. Data with three replications were used to measure Pearson's simple correlation co-efficient in order to establish the relationship among various nutritional quality attributes. The result on proximate composition showed that Govind Bhog had the highest moisture (13.57% and fat (0.92% content, which signifies its tasty attribute. Badshah Bhog exhibited the highest fibre content (0.85%, carbohydrate content (82.70% and food energy (365.23 kCal per 100 g. Among the minerals, the higher Ca (98.75 mg/kg, Zn (17.00 mg/kg and Fe (31.50 mg/kg were in Gopal Bhog, whereas the highest Na (68.85 mg/kg was in Badshah Bhog, the highest K (500.00 mg/kg was in Swetganga, Khushboo and Sarbati. The highest contents of unsaturated fatty acids viz. oleic acid (49.14%, linoleic acid (46.99% and linolenic acid (1.27% were found in Sarbati, whereas the highest content of saturated fatty acids viz. myristic acid (4.60% and palmitic acid (31.91% were found in Govind Bhog and stearic acid (6.47% in Todal. The identified aromatic rice accessions Gopal Bhog, Govind Bhog and Badshah Bhog and non-aromatic rice accession Sarbati were found nutritionally superior among all eight tested accessions. The nutritional quality oriented attributes in this study were competent with recognized prominent aromatic and non-aromatic rice accessions as an index of their nutritional worth and recommend to farmers and consumers which may be graded as export quality rice with good unique nutritional values in international market.

Fall in C-Peptide During First 2 Years From Diagnosis

Science.gov (United States)

Greenbaum, Carla J.; Beam, Craig A.; Boulware, David; Gitelman, Stephen E.; Gottlieb, Peter A.; Herold, Kevan C.; Lachin, John M.; McGee, Paula; Palmer, Jerry P.; Pescovitz, Mark D.; Krause-Steinrauf, Heidi; Skyler, Jay S.; Sosenko, Jay M.

2012-01-01

Interpretation of clinical trials to alter the decline in β-cell function after diagnosis of type 1 diabetes depends on a robust understanding of the natural history of disease. Combining data from the Type 1 Diabetes TrialNet studies, we describe the natural history of β-cell function from shortly after diagnosis through 2 years post study randomization, assess the degree of variability between patients, and investigate factors that may be related to C-peptide preservation or loss. We found that 93% of individuals have detectable C-peptide 2 years from diagnosis. In 11% of subjects, there was no significant fall from baseline by 2 years. There was a biphasic decline in C-peptide; the C-peptide slope was −0.0245 pmol/mL/month (95% CI −0.0271 to −0.0215) through the first 12 months and −0.0079 (−0.0113 to −0.0050) from 12 to 24 months (P < 0.001). This pattern of fall in C-peptide over time has implications for understanding trial results in which effects of therapy are most pronounced early and raises the possibility that there are time-dependent differences in pathophysiology. The robust data on the C-peptide obtained under clinical trial conditions should be used in planning and interpretation of clinical trials. PMID:22688329

Assessment of the bioavailability and phytotoxicity of sediment spiked with polycyclic aromatic hydrocarbons.

Science.gov (United States)

Rončević, Srđan; Spasojević, Jelena; Maletić, Snežana; Jazić, Jelena Molnar; Isakovski, Marijana Kragulj; Agbaba, Jasmina; Grgić, Marko; Dalmacija, Božo

2016-02-01

Large amounts of sediment are dredged globally every year. This sediment is often contaminated with low concentrations of metals, polycyclic aromatic hydrocarbons, pesticides and other organic pollutants. Some of this sediment is disposed of on land, creating a need for risk assessment of the sediment disposal method, to minimize the degradation of environmental quality and prevent risks to human health. Evaluating the available fractions of certain polycyclic aromatic hydrocarbons is very important, as in the presence of various organisms, they are believed to be easily subject to the processes of bioaccumulation, biosorption and transformation. In order to determine the applicability of applying these methods for the evaluation of pollutant bioavailability in sediments, the desorption kinetics from the sediment of various polycyclic aromatic hydrocarbons in the presence of Tenax and XAD4 were examined over the course of 216 h. Changes in the PAH concentrations in dredged sediments using five different seed plants during a short time of period (10 days) were also followed. Using chemical extraction techniques with Tenax and XAD4, a time of around 24 h is enough to achieve equilibrium for all four PAHs. Results showed good agreement between the seed accumulation and PAH extraction methods with both agents. If we compare the two extraction techniques, XAD4 gave better results for phenanthrene, pyrene and benzo(a)pyrene, and Tenax gave better results for chrysene.

Molding a peptide into an RNA site by in vivo peptide evolution

OpenAIRE

Harada, Kazuo; Martin, Shelley S.; Tan, Ruoying; Frankel, Alan D.

1997-01-01

Short peptides corresponding to the arginine-rich domains of several RNA-binding proteins are able to bind to their specific RNA sites with high affinities and specificities. In the case of the HIV-1 Rev-Rev response element (RRE) complex, the peptide forms a single α-helix that binds deeply in a widened, distorted RNA major groove and makes a substantial set of base-specific and backbone contacts. Using a reporter system based on antitermination by the bacteriophage λ N protein, it has been ...

AN AROMATIC INVENTORY OF THE LOCAL VOLUME

International Nuclear Information System (INIS)

Marble, A. R.; Engelbracht, C. W.; Block, M.; Van Zee, L.; Dale, D. A.; Cohen, S. A.; Schuster, M. D.; Smith, J. D. T.; Gordon, K. D.; Wu, Y.; Lee, J. C.; Kennicutt, R. C.; Skillman, E. D.; Johnson, L. C.; Calzetti, D.; Lee, H.

2010-01-01

Using infrared photometry from the Spitzer Space Telescope, we perform the first inventory of aromatic feature emission (also commonly referred to as polycyclic aromatic hydrocarbon emission) for a statistically complete sample of star-forming galaxies in the local volume. The photometric methodology involved is calibrated and demonstrated to recover the aromatic fraction of the Infrared Array Camera 8 μm flux with a standard deviation of 6% for a training set of 40 SINGS galaxies (ranging from stellar to dust dominated) with both suitable mid-infrared Spitzer Infrared Spectrograph spectra and equivalent photometry. A potential factor of 2 improvement could be realized with suitable 5.5 μm and 10 μm photometry, such as what may be provided in the future by the James Webb Space Telescope. The resulting technique is then applied to mid-infrared photometry for the 258 galaxies from the Local Volume Legacy (LVL) survey, a large sample dominated in number by low-luminosity dwarf galaxies for which obtaining comparable mid-infrared spectroscopy is not feasible. We find the total LVL luminosity due to five strong aromatic features in the 8 μm complex to be 2.47 x 10 10 L sun with a mean volume density of 8.8 x 10 6 L sun Mpc -3 . Twenty-four of the LVL galaxies, corresponding to a luminosity cut at M B = -18.22, account for 90% of the aromatic luminosity. Using oxygen abundances compiled from the literature for 129 of the 258 LVL galaxies, we find a correlation between metallicity and the aromatic-to-total infrared emission ratio but not the aromatic-to-total 8 μm dust emission ratio. A possible explanation is that metallicity plays a role in the abundance of aromatic molecules relative to the total dust content, but other factors, such as star formation and/or the local radiation field, affect the excitation of those molecules.

Binding stability of peptides on major histocompatibility complex class I proteins: role of entropy and dynamics

Science.gov (United States)

Gul, Ahmet; Erman, Burak

2018-03-01

Prediction of peptide binding on specific human leukocyte antigens (HLA) has long been studied with successful results. We herein describe the effects of entropy and dynamics by investigating the binding stabilities of 10 nanopeptides on various HLA Class I alleles using a theoretical model based on molecular dynamics simulations. The fluctuational entropies of the peptides are estimated over a temperature range of 310-460 K. The estimated entropies correlate well with experimental binding affinities of the peptides: peptides that have higher binding affinities have lower entropies compared to non-binders, which have significantly larger entropies. The computation of the entropies is based on a simple model that requires short molecular dynamics trajectories and allows for approximate but rapid determination. The paper draws attention to the long neglected dynamic aspects of peptide binding, and provides a fast computation scheme that allows for rapid scanning of large numbers of peptides on selected HLA antigens, which may be useful in defining the right peptides for personal immunotherapy.

Self-assembling peptide nanofiber hydrogels in tissue engineering and regenerative medicine: Progress, design guidelines, and applications.

Science.gov (United States)

Koutsopoulos, Sotirios

2016-04-01

Until the mid-1980s, mainly biologists were conducting peptide research. This changed with discoveries that opened new paths of research involving the use of peptides in bioengineering, biotechnology, biomedicine, nanotechnology, and bioelectronics. Peptide engineering and rational design of novel peptide sequences with unique and tailor-made properties further expanded the field. The discovery of short self-assembling peptides, which upon association form well-defined supramolecular architectures, created new and exciting areas of research. Depending on the amino acid sequence, the pH, and the type of the electrolyte in the medium, peptide self-assembly leads to the formation of nanofibers, which are further organized to form a hydrogel. In this review, the application of ionic complementary peptides which self-assemble to form nanofiber hydrogels for tissue engineering and regenerative medicine will be discussed through a selective presentation of the most important work performed during the last 25 years. © 2016 Wiley Periodicals, Inc.

Applicability of the black slug Arion ater for monitoring exposure to polycyclic aromatic hydrocarbons and their subsequent bioactivation into DNA binding metabolites

NARCIS (Netherlands)

Hamers, T.; Kalis, E.J.J.; Berg, van den J.H.J.; Maas, L.M.; Schooten, van F.J.; Murk, A.J.

2004-01-01

The applicability of terrestrial black slugs Arion ater (Mollusca, Gastropoda) was studied for biomonitoring environmental exposure to polycyclic aromatic hydrocarbons (PAHs). In laboratory experiments, slugs were orally exposed to benzo[a]pyrene (BaP) for a short term (3 days) or a long term (119

Self-assembly of fibronectin mimetic peptide-amphiphile nanofibers

Science.gov (United States)

Rexeisen, Emilie Lynn

Many therapeutic strategies incorporate peptides into their designs to mimic the natural protein ligands found in vivo. A few examples are the short peptide sequences RGD and PHSRN that mimic the primary and synergy-binding domains of the extracellular matrix protein, fibronectin, which is recognized by the cell surface receptor, alpha5beta 1 integrin. Even though scaffold modification with biomimetic peptides remains one of the most promising approaches for tissue engineering, the use of these peptides in therapeutic tissue-engineered products and drug delivery systems available on the commercial market is limited because the peptides are not easily able to mimic the natural protein. The design of a peptide that can effectively target the alpha5beta1 integrin would greatly increase biomimetic scaffold therapeutic potential. A novel peptide containing both the RGD primary binding domain and PHSRN synergy-binding domain for fibronectin joined with the appropriate linker should bind alpha 5beta1 integrin more efficiently and lead to greater cell adhesion over RGD alone. Several fibronectin mimetic peptides were designed and coupled to dialkyl hydrocarbon tails to make peptide-amphiphiles. The peptides contained different linkers connecting the two binding domains and different spacers separating the hydrophobic tails from the hydrophilic headgroups. The peptide-amphiphiles were deposited on mica substrates using the Langmuir-Blodgett technique. Langmuir isotherms indicated that the peptide-amphiphiles that contained higher numbers of serine residues formed a more tightly packed monolayer, but the increased number of serines also made transferring the amphiphiles to the mica substrate more difficult. Atomic force microscopy (AFM) images of the bilayers showed that the headgroups might be bent, forming small divots in the surface. These divots may help expose the PHSRN synergy-binding domain. Parallel studies undertaken by fellow group members showed that human

Fused aromatic thienopyrazines: structure, properties and function

KAUST Repository

Mondal, Rajib; Ko, Sangwon; Bao, Zhenan

2010-01-01

Recent development of a fused aromatic thieno[3.4-b]pyrazine system and their application in optoelectronic devices are reviewed. Introduction of a fused aromatic unit followed by side chain engineering, dramatically enhanced the charge carrier

Sensing lymphoma cells based on a cell-penetrating/apoptosis-inducing/electron-transfer peptide probe

International Nuclear Information System (INIS)

Sugawara, Kazuharu; Shinohara, Hiroki; Kadoya, Toshihiko; Kuramitz, Hideki

2016-01-01

To electrochemically sense lymphoma cells (U937), we fabricated a multifunctional peptide probe that consists of cell-penetrating/apoptosis-inducing/electron-transfer peptides. Electron-transfer peptides derive from cysteine residue combined with the C-terminals of four tyrosine residues (Y_4). A peptide whereby Y_4C is bound to the C-terminals of protegrin 1 (RGGRLCYCRRRFCVCVGR-NH_2) is known to be an apoptosis-inducing agent against U937 cells, and is referred to as a peptide-1 probe. An oxidation response of the peptide-1 probe has been observed due to a phenolic hydroxyl group, and this response is decreased by the uptake of the peptide probe into the cells. To improve the cell membrane permeability against U937 cells, the RGGR at the N-terminals of the peptide-1 probe was replaced by RRRR (peptide-2 probe). In contrast, RNRCKGTDVQAWY_4C (peptide-3 probe), which recognizes ovalbumin, was constructed as a control. Compared with the other probes, the change in the peak current of the peptide-2 probe was the greatest at low concentrations and occurred in a short amount of time. Therefore, the cell membrane permeability of the peptide-2 probe was increased based on the arginine residues and the apoptosis-inducing peptides. The peak current was linear and ranged from 100 to 1000 cells/ml. The relative standard deviation of 600 cells/ml was 5.0% (n = 5). Furthermore, the membrane permeability of the peptide probes was confirmed using fluorescent dye. - Highlights: • We constructed a multifunctional peptide probe for the electrochemical sensing of lymphoma cells. • The peptide probe consists of cell-penetrating/apoptosis-inducing/electron-transfer peptides. • The electrode response of the peptide probe changes due to selective uptake into the cells.

Sensing lymphoma cells based on a cell-penetrating/apoptosis-inducing/electron-transfer peptide probe

Energy Technology Data Exchange (ETDEWEB)

Sugawara, Kazuharu, E-mail: kzsuga@maebashi-it.ac.jp [Maebashi Institute of Technology, Gunma 371-0816 (Japan); Shinohara, Hiroki; Kadoya, Toshihiko [Maebashi Institute of Technology, Gunma 371-0816 (Japan); Kuramitz, Hideki [Department of Environmental Biology and Chemistry, Graduate School of Science and Engineering for Research, University of Toyama, Toyama 930-8555 (Japan)

2016-06-14

To electrochemically sense lymphoma cells (U937), we fabricated a multifunctional peptide probe that consists of cell-penetrating/apoptosis-inducing/electron-transfer peptides. Electron-transfer peptides derive from cysteine residue combined with the C-terminals of four tyrosine residues (Y{sub 4}). A peptide whereby Y{sub 4}C is bound to the C-terminals of protegrin 1 (RGGRLCYCRRRFCVCVGR-NH{sub 2}) is known to be an apoptosis-inducing agent against U937 cells, and is referred to as a peptide-1 probe. An oxidation response of the peptide-1 probe has been observed due to a phenolic hydroxyl group, and this response is decreased by the uptake of the peptide probe into the cells. To improve the cell membrane permeability against U937 cells, the RGGR at the N-terminals of the peptide-1 probe was replaced by RRRR (peptide-2 probe). In contrast, RNRCKGTDVQAWY{sub 4}C (peptide-3 probe), which recognizes ovalbumin, was constructed as a control. Compared with the other probes, the change in the peak current of the peptide-2 probe was the greatest at low concentrations and occurred in a short amount of time. Therefore, the cell membrane permeability of the peptide-2 probe was increased based on the arginine residues and the apoptosis-inducing peptides. The peak current was linear and ranged from 100 to 1000 cells/ml. The relative standard deviation of 600 cells/ml was 5.0% (n = 5). Furthermore, the membrane permeability of the peptide probes was confirmed using fluorescent dye. - Highlights: • We constructed a multifunctional peptide probe for the electrochemical sensing of lymphoma cells. • The peptide probe consists of cell-penetrating/apoptosis-inducing/electron-transfer peptides. • The electrode response of the peptide probe changes due to selective uptake into the cells.

Affinity Purification and Comparative Biosensor Analysis of Citrulline-Peptide-Specific Antibodies in Rheumatoid Arthritis

Directory of Open Access Journals (Sweden)

Eszter Szarka

2018-01-01

Full Text Available Background: In rheumatoid arthritis (RA, anti-citrullinated protein/peptide antibodies (ACPAs are responsible for disease onset and progression, however, our knowledge is limited on ligand binding affinities of autoantibodies with different citrulline-peptide specificity. Methods: Citrulline-peptide-specific ACPA IgGs were affinity purified and tested by ELISA. Binding affinities of ACPA IgGs and serum antibodies were compared by surface plasmon resonance (SPR analysis. Bifunctional nanoparticles harboring a multi-epitope citrulline-peptide and a complement-activating peptide were used to induce selective depletion of ACPA-producing B cells. Results: KD values of affinity-purified ACPA IgGs varied between 10−6 and 10−8 M and inversely correlated with disease activity. Based on their cross-reaction with citrulline-peptides, we designed a novel multi-epitope peptide, containing Cit-Gly and Ala-Cit motifs in two–two copies, separated with a short, neutral spacer. This peptide detected antibodies in RA sera with 66% sensitivity and 98% specificity in ELISA and was recognized by 90% of RA sera, while none of the healthy samples in SPR. When coupled to nanoparticles, the multi-epitope peptide specifically targeted and depleted ACPA-producing B cells ex vivo. Conclusions: The unique multi-epitope peptide designed based on ACPA cross-reactivity might be suitable to develop better diagnostics and novel therapies for RA.

Two functional motifs define the interaction, internalization and toxicity of the cell-penetrating antifungal peptide PAF26 on fungal cells.

Directory of Open Access Journals (Sweden)

Alberto Muñoz

Full Text Available The synthetic, cell penetrating hexapeptide PAF26 (RKKWFW is antifungal at low micromolar concentrations and has been proposed as a model for cationic, cell-penetrating antifungal peptides. Its short amino acid sequence facilitates the analysis of its structure-activity relationships using the fungal models Neurospora crassa and Saccharomyces cerevisiae, and human and plant pathogens Aspergillus fumigatus and Penicillium digitatum, respectively. Previously, PAF26 at low fungicidal concentrations was shown to be endocytically internalized, accumulated in vacuoles and then actively transported into the cytoplasm where it exerts its antifungal activity. In the present study, two PAF26 derivatives, PAF95 (AAAWFW and PAF96 (RKKAAA, were designed to characterize the roles of the N-terminal cationic and the C-terminal hydrophobic motifs in PAF26's mode-of-action. PAF95 and PAF96 exhibited substantially reduced antifungal activity against all the fungi analyzed. PAF96 localized to fungal cell envelopes and was not internalized by the fungi. In contrast, PAF95 was taken up into vacuoles of N. crassa, wherein it accumulated and was trapped without toxic effects. Also, the PAF26 resistant Δarg1 strain of S. cerevisiae exhibited increased PAF26 accumulation in vacuoles. Live-cell imaging of GFP-labelled nuclei in A. fumigatus showed that transport of PAF26 from the vacuole to the cytoplasm was followed by nuclear breakdown and dissolution. This work demonstrates that the amphipathic PAF26 possesses two distinct motifs that allow three stages in its antifungal action to be defined: (i its interaction with the cell envelope; (ii its internalization and transport to vacuoles mediated by the aromatic hydrophobic domain; and (iii its transport from vacuoles to the cytoplasm. Significantly, cationic residues in PAF26 are important not only for the electrostatic attraction and interaction with the fungal cell but also for transport from the vacuole to the

Recent advances in protein and Peptide drug delivery: a special emphasis on polymeric nanoparticles.

Science.gov (United States)

Patel, Ashaben; Patel, Mitesh; Yang, Xiaoyan; Mitra, Ashim K

2014-01-01

Proteins and peptides are widely indicated in many diseased states. Parenteral route is the most commonly em- ployed method of administration for therapeutic proteins and peptides. However, requirement of frequent injections due to short in vivo half-life results in poor patient compliance. Non-invasive drug delivery routes such as nasal, transdermal, pulmonary, and oral offer several advantages over parenteral administration. Intrinsic physicochemical properties and low permeability across biological membrane limit protein delivery via non-invasive routes. One of the strategies to improve protein and peptide absorption is by delivering through nanostructured delivery carriers. Among nanocarriers, polymeric nanoparticles (NPs) have demonstrated significant advantages over other delivery systems. This article summarizes the application of polymeric NPs for protein and peptide drug delivery following oral, nasal, pulmonary, parenteral, transder mal, and ocular administrations.

A method of refining aromatic hydrocarbons from coal chemical production

Energy Technology Data Exchange (ETDEWEB)

Zieborak, K.; Koprowski, A.; Ratajczak, W.

1979-10-01

A method is disclosed for refining aromatic hydrocarbons of coal chemical production by contact of liquid aromatic hydrocarbons and their mixtures with a strongly acid macroporous sulfocationite in the H-form at atmospheric pressure and high temperature. The method is distinguished in that the aromatic hydrocarbons and their mixtures, from which alkali compounds have already been removed, are supplied for refinement with the sulfocationite with simultaneous addition of olefin derivatives of aromatic hydrocarbons, followed by separation of pure hydrocarbons by rectification. Styrene or alpha-methylstyrene is used as the olefin derivatives of the aromatic hydrocarbons. The method is performed in several stages with addition of olefin derivatives of aromatic hydrocarbons at each stage.

PinaColada: peptide-inhibitor ant colony ad-hoc design algorithm.

Science.gov (United States)

Zaidman, Daniel; Wolfson, Haim J

2016-08-01

Design of protein-protein interaction (PPI) inhibitors is a major challenge in Structural Bioinformatics. Peptides, especially short ones (5-15 amino acid long), are natural candidates for inhibition of protein-protein complexes due to several attractive features such as high structural compatibility with the protein binding site (mimicking the surface of one of the proteins), small size and the ability to form strong hotspot binding connections with the protein surface. Efficient rational peptide design is still a major challenge in computer aided drug design, due to the huge space of possible sequences, which is exponential in the length of the peptide, and the high flexibility of peptide conformations. In this article we present PinaColada, a novel computational method for the design of peptide inhibitors for protein-protein interactions. We employ a version of the ant colony optimization heuristic, which is used to explore the exponential space ([Formula: see text]) of length n peptide sequences, in combination with our fast robotics motivated PepCrawler algorithm, which explores the conformational space for each candidate sequence. PinaColada is being run in parallel, on a DELL PowerEdge 2.8 GHZ computer with 20 cores and 256 GB memory, and takes up to 24 h to design a peptide of 5-15 amino acids length. An online server available at: http://bioinfo3d.cs.tau.ac.il/PinaColada/. danielza@post.tau.ac.il; wolfson@tau.ac.il. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

International congress on aromatic and medicinal plants

International Nuclear Information System (INIS)

2009-01-01

Full Text : In Morocco, medicinal and aromatic plants occupy an important place in the traditional care system of a large number of local people. They are also economically strong potential, but unfortunately they are not valued enough. Indeed, Morocco by its privileged geographical position in the Mediterranean basin and its floristic diversity (with a total of over 4,200 species and subspecies of which over 500 are recognized as medicinal and aromatic plants), is a leading provider of traditional global market. In this context and given the back label of the natural global, group research and studies on Aromatic and Medicinal Plants (GREPAM), the Faculty of Semlalia and University Cadi Ayyad, organize: the International Congress on Medicinal and Aromatic Plants CIPAM 2009. The organization of this conference is part of scientific research developed by the GREPAM. [fr

A novel monoclonal antibody to a defined peptide epitope in MUC16

DEFF Research Database (Denmark)

Marcos-Silva, Lara; Ricardo, Sara; Chen, Kowa

2015-01-01

with the tandem-repeat region, their epitopes appear to be conformational dependent and not definable by a short peptide. Aberrant glycoforms of MUC16 may constitute promising targets for diagnostic and immunotherapeutic intervention, and it is important to develop well-defined immunogens for induction of potent...... immunodominant linear peptide epitopes within the tandem repeat. We developed one monoclonal antibody, 5E11, reactive with a minimum epitope with the sequence FNTTER. This sequence contains potential N- and O-glycosylation sites and, interestingly, glycosylation blocked binding of 5E11. In immunochemistry...

Hexacoordinate bonding and aromaticity in silicon phthalocyanine.

Science.gov (United States)

Yang, Yang

2010-12-23

Si-E bondings in hexacoordinate silicon phthalocyanine were analyzed using bond order (BO), energy partition, atoms in molecules (AIM), electron localization function (ELF), and localized orbital locator (LOL). Bond models were proposed to explain differences between hexacoordinate and tetracoordinate Si-E bondings. Aromaticity of silicon phthalocyanine was investigated using nucleus-independent chemical shift (NICS), harmonic oscillator model of aromaticity (HOMA), conceptual density functional theory (DFT), ring critical point (RCP) descriptors, and delocalization index (DI). Structure, energy, bonding, and aromaticity of tetracoordinate silicon phthalocyanine were studied and compared with hexacoordinate one.

40 CFR 721.5762 - Aromatic aldehyde phenolic resin (generic).

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Aromatic aldehyde phenolic resin... Specific Chemical Substances § 721.5762 Aromatic aldehyde phenolic resin (generic). (a) Chemical substance... aromatic aldehyde phenolic resin (PMN P-01-573) is subject to reporting under this section for the...

Peptide array-based interaction assay of solid-bound peptides and anchorage-dependant cells and its effectiveness in cell-adhesive peptide design.

Science.gov (United States)

Kato, Ryuji; Kaga, Chiaki; Kunimatsu, Mitoshi; Kobayashi, Takeshi; Honda, Hiroyuki

2006-06-01

Peptide array, the designable peptide library covalently synthesized on cellulose support, was applied to assay peptide-cell interaction, between solid-bound peptides and anchorage-dependant cells, to study objective peptide design. As a model case, cell-adhesive peptides that could enhance cell growth as tissue engineering scaffold material, was studied. On the peptide array, the relative cell-adhesion ratio of NIH/3T3 cells was 2.5-fold higher on the RGDS (Arg-Gly-Asp-Ser) peptide spot as compared to the spot with no peptide, thus indicating integrin-mediated peptide-cell interaction. Such strong cell adhesion mediated by the RGDS peptide was easily disrupted by single residue substitution on the peptide array, thus indicating that the sequence recognition accuracy of cells was strictly conserved in our optimized scheme. The observed cellular morphological extension with active actin stress-fiber on the RGD motif-containing peptide supported our strategy that peptide array-based interaction assay of solid-bound peptide and anchorage-dependant cells (PIASPAC) could provide quantitative data on biological peptide-cell interaction. The analysis of 180 peptides obtained from fibronectin type III domain (no. 1447-1629) yielded 18 novel cell-adhesive peptides without the RGD motif. Taken together with the novel candidates, representative rules of ineffective amino acid usage were obtained from non-effective candidate sequences for the effective designing of cell-adhesive peptides. On comparing the amino acid usage of the top 20 and last 20 peptides from the 180 peptides, the following four brief design rules were indicated: (i) Arg or Lys of positively charged amino acids (except His) could enhance cell adhesion, (ii) small hydrophilic amino acids are favored in cell-adhesion peptides, (iii) negatively charged amino acids and small amino acids (except Gly) could reduce cell adhesion, and (iv) Cys and Met could be excluded from the sequence combination since they have

Gene introduction into the mitochondria of Arabidopsis thaliana via peptide-based carriers

Science.gov (United States)

Chuah, Jo-Ann; Yoshizumi, Takeshi; Kodama, Yutaka; Numata, Keiji

2015-01-01

Available methods in plant genetic transformation are nuclear and plastid transformations because similar procedures have not yet been established for the mitochondria. The double membrane and small size of the organelle, in addition to its large population in cells, are major obstacles in mitochondrial transfection. Here we report the intracellular delivery of exogenous DNA localized to the mitochondria of Arabidopsis thaliana using a combination of mitochondria-targeting peptide and cell-penetrating peptide. Low concentrations of peptides were sufficient to deliver DNA into the mitochondria and expression of imported DNA reached detectable levels within a short incubation period (12 h). We found that electrostatic interaction with the cell membrane is not a critical factor for complex internalization, instead, improved intracellular penetration of mitochondria-targeted complexes significantly enhanced gene transfer efficiency. Our results delineate a simple and effective peptide-based method, as a starting point for the development of more sophisticated plant mitochondrial transfection strategies.

A non-covalent peptide-based strategy for ex vivo and in vivo oligonucleotide delivery.

Science.gov (United States)

Crombez, Laurence; Morris, May C; Heitz, Frederic; Divita, Gilles

2011-01-01

The dramatic acceleration in identification of new nucleic acid-based therapeutic molecules such as short interfering RNA (siRNA) and peptide-nucleic acid (PNA) analogues has provided new perspectives for therapeutic targeting of specific genes responsible for pathological disorders. However, the poor cellular uptake of nucleic acids together with the low permeability of the cell membrane to negatively charged molecules remain major obstacles to their clinical development. Several non-viral strategies have been proposed to improve the delivery of synthetic short oligonucleotides both in cultured cells and in vivo. Cell-penetrating peptides constitute very promising tools for non-invasive cellular import of oligonucleotides and analogs. We recently described a non-covalent strategy based on short amphiphatic peptides (MPG8/PEP3) that have been successfully applied ex vivo and in vivo for the delivery of therapeutic siRNA and PNA molecules. PEP3 and MPG8 form stable nanoparticles with PNA analogues and siRNA, respectively, and promote their efficient cellular uptake, independently of the endosomal pathway, into a wide variety of cell lines, including primary and suspension lines, without any associated cytotoxicity. This chapter describes easy-to-handle protocols for the use of MPG-8 or PEP-3-nanoparticle technologies for PNA and siRNA delivery into adherent and suspension cell lines as well as in vivo into cancer mouse models.

Aromatic VOCs global influence in the ozone production

Science.gov (United States)

Cabrera-Perez, David; Pozzer, Andrea

2016-04-01

Aromatic hydrocarbons are a subgroup of Volatile Organic Compounds (VOCs) of special interest in the atmosphere of urban and semi-urban areas. Aromatics form a high fraction of VOCs, are highly reactive and upon oxidation they are an important source of ozone. These group of VOCs are released to the atmosphere by processes related to biomass burning and fossil fuel consumption, while they are removed from the atmosphere primarily by OH reaction and by dry deposition. In addition, a branch of aromatics (ortho-nitrophenols) produce HONO upon photolysis, which is responsible of certain amount of the OH recycling. Despite their importance in the atmosphere in anthropogenic polluted areas, the influence of aromatics in the ozone production remains largely unknown. This is of particular relevance, being ozone a pollutant with severe side effects on air quality, health and climate. In this work the atmospheric impacts at global scale of the most emitted aromatic VOCs in the gas phase (benzene, toluene, xylenes, ethylbenzene, styrene, phenol, benzaldehyde and trimethylbenzenes) are analysed and assessed. Specifically, the impact on ozone due to aromatic oxidation is estimated, as this is of great interest in large urban areas and can be helpful for developing air pollution control strategies. Further targets are the quantification of the NOx loss and the OH recycling due to aromatic oxidation. In order to investigate these processes, two simulations were performed with the numerical chemistry and climate simulation ECHAM/MESSy Atmospheric Chemistry (EMAC) model. The simulations compare two cases, one with ozone concentrations when aromatics are present or the second one when they are missing. Finally, model simulated ozone is compared against a global set of observations in order to better constrain the model accuracy.

Recent Advances in Microbial Production of Aromatic Chemicals and Derivatives.

Science.gov (United States)

Noda, Shuhei; Kondo, Akihiko

2017-08-01

Along with the development of metabolic engineering and synthetic biology tools, various microbes are being used to produce aromatic chemicals. In microbes, aromatics are mainly produced via a common important precursor, chorismate, in the shikimate pathway. Natural or non-natural aromatics have been produced by engineering metabolic pathways involving chorismate. In the past decade, novel approaches have appeared to produce various aromatics or to increase their productivity, whereas previously, the targets were mainly aromatic amino acids and the strategy was deregulating feedback inhibition. In this review, we summarize recent studies of microbial production of aromatics based on metabolic engineering approaches. In addition, future perspectives and challenges in this research area are discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Exploring the nature of the H-bonds between the human class II MHC protein, HLA-DR1 (DRB*0101) and the influenza virus hemagglutinin peptide, HA306-318, using the quantum theory of atoms in molecules.

Science.gov (United States)

Aray, Yosslen; Aguilera-García, Ricardo; Izquierdo, Daniel R

2018-01-02

The nature of the H-bonds between the human protein HLA-DR1 (DRB*0101) and the hemagglutinin peptide HA306-318 has been studied using the Quantum Theory of Atoms in Molecules for the first time. We have found four H-bond groups: one conventional CO··HN bond group and three nonconventional CO··HC, π··HC involving aromatic rings and HN··HC aliphatic groups. The calculated electron density at the determined H-bond critical points suggests the follow protein pocket binding trend: P1 (2,311) > P9 (1.109) > P4 (0.950) > P6 (0.553) > P7 (0.213) which agrees and reveal the nature of experimental findings, showing that P1 produces by a long way the strongest binding of the HLA-DR1 human protein molecule with the peptide backbone as consequence of the vast number of H-bonds in the P1 area and at the same time the largest specific binding of the peptide Tyr308 residue with aromatic residues located at the binding groove floor. The present results suggest the topological analysis of the electronic density as a valuable tool that allows a non-arbitrary partition of the pockets binding energy via the calculated electron density at the determined critical points.

Albumin-derived peptides efficiently reduce renal uptake of radiolabelled peptides

International Nuclear Information System (INIS)

Vegt, Erik; Eek, Annemarie; Oyen, Wim J.G.; Gotthardt, Martin; Boerman, Otto C.; Jong, Marion de

2010-01-01

In peptide-receptor radionuclide therapy (PRRT), the maximum activity dose that can safely be administered is limited by high renal uptake and retention of radiolabelled peptides. The kidney radiation dose can be reduced by coinfusion of agents that competitively inhibit the reabsorption of radiolabelled peptides, such as positively charged amino acids, Gelofusine, or trypsinised albumin. The aim of this study was to identify more specific and potent inhibitors of the kidney reabsorption of radiolabelled peptides, based on albumin. Albumin was fragmented using cyanogen bromide and six albumin-derived peptides with different numbers of electric charges were selected and synthesised. The effect of albumin fragments (FRALB-C) and selected albumin-derived peptides on the internalisation of 111 In-albumin, 111 In-minigastrin, 111 In-exendin and 111 In-octreotide by megalin-expressing cells was assessed. In rats, the effect of Gelofusine and albumin-derived peptides on the renal uptake and biodistribution of 111 In-minigastrin, 111 In-exendin and 111 In-octreotide was determined. FRALB-C significantly reduced the uptake of all radiolabelled peptides in vitro. The albumin-derived peptides showed different potencies in reducing the uptake of 111 In-albumin, 111 In-exendin and 111 In-minigastrin in vitro. The most efficient albumin-derived peptide (peptide 6), was selected for in vivo testing. In rats, 5 mg of peptide 6 very efficiently inhibited the renal uptake of 111 In-minigastrin, by 88%. Uptake of 111 In-exendin and 111 In-octreotide was reduced by 26 and 33%, respectively. The albumin-derived peptide 6 efficiently inhibited the renal reabsorption of 111 In-minigastrin, 111 In-exendin and 111 In-octreotide and is a promising candidate for kidney protection in PRRT. (orig.)

Hormone-like peptides in the venoms of marine cone snails

Science.gov (United States)

Robinson, Samuel D.; Li, Qing; Bandyopadhyay, Pradip K.; Gajewiak, Joanna; Yandell, Mark; Papenfuss, Anthony T.; Purcell, Anthony W.; Norton, Raymond S.; Safavi-Hemami, Helena

2015-01-01

The venoms of cone snails (genus Conus) are remarkably complex, consisting of hundreds of typically short, disulfide-rich peptides termed conotoxins. These peptides have diverse pharmacological targets, with injection of venom eliciting a range of physiological responses, including sedation, paralysis and sensory overload. Most conotoxins target the prey’s nervous system but evidence of venom peptides targeting neuroendocrine processes is emerging. Examples include vasopressin, RFamide neuropeptides and recently also insulin. To investigate the diversity of hormone/neuropeptide-like molecules in the venoms of cone snails we systematically mined the venom gland transcriptomes of several cone snail species and examined secreted venom peptides in dissected and injected venom of the Australian cone snail Conus victoriae. Using this approach we identified several novel hormone/neuropeptide-like toxins, including peptides similar to the bee brain hormone prohormone-4, the mollusc ganglia neuropeptide elevenin, and thyrostimulin, a member of the glycoprotein hormone family, and confirmed the presence of insulin. We confirmed that at least two of these peptides are not only expressed in the venom gland but also form part of the injected venom cocktail, unambiguously demonstrating their role in envenomation. Our findings suggest that hormone/neuropeptide-like toxins are a diverse and integral part of the complex envenomation strategy of Conus. Exploration of this group of venom components offers an exciting new avenue for the discovery of novel pharmacological tools and drug candidates, complementary to conotoxins. PMID:26301480

Hormone-like peptides in the venoms of marine cone snails.

Science.gov (United States)

Robinson, Samuel D; Li, Qing; Bandyopadhyay, Pradip K; Gajewiak, Joanna; Yandell, Mark; Papenfuss, Anthony T; Purcell, Anthony W; Norton, Raymond S; Safavi-Hemami, Helena

2017-04-01

The venoms of cone snails (genus Conus) are remarkably complex, consisting of hundreds of typically short, disulfide-rich peptides termed conotoxins. These peptides have diverse pharmacological targets, with injection of venom eliciting a range of physiological responses, including sedation, paralysis and sensory overload. Most conotoxins target the prey's nervous system but evidence of venom peptides targeting neuroendocrine processes is emerging. Examples include vasopressin, RFamide neuropeptides and recently also insulin. To investigate the diversity of hormone/neuropeptide-like molecules in the venoms of cone snails we systematically mined the venom gland transcriptomes of several cone snail species and examined secreted venom peptides in dissected and injected venom of the Australian cone snail Conus victoriae. Using this approach we identified several novel hormone/neuropeptide-like toxins, including peptides similar to the bee brain hormone prohormone-4, the mollusc ganglia neuropeptide elevenin, and thyrostimulin, a member of the glycoprotein hormone family, and confirmed the presence of insulin. We confirmed that at least two of these peptides are not only expressed in the venom gland but also form part of the injected venom cocktail, unambiguously demonstrating their role in envenomation. Our findings suggest that hormone/neuropeptide-like toxins are a diverse and integral part of the complex envenomation strategy of Conus. Exploration of this group of venom components offers an exciting new avenue for the discovery of novel pharmacological tools and drug candidates, complementary to conotoxins. Copyright © 2015 Elsevier Inc. All rights reserved.

Analogs of solid nanoparticles as precursors of aromatic hydrocarbons

Science.gov (United States)

Gadallah, K. A. K.; Mutschke, H.; Jäger, C.

2013-06-01

Context. Aromatic =CH and C=C vibrational bands have been observed within shocked interstellar regions, indicating the presence of aromatic emission carriers such as PAHs, which may have been created from adjacent molecular cloud material by interaction with a shock front. Aims: We investigate the evolution of the aromatic =CH and C=C vibrational modes at 3.3 and 6.2 μm wavelength in heated HAC materials, PAHs and mixed PAHs and HACs, respectively, aiming at an explanation of the evolution of carbonaceous dust grains in the shocked regions. Methods: Materials used in these analogs (HAC and PAH materials) were prepared by the laser ablation and the laser pyrolysis methods, respectively. The transmission electron microscopy (TEM) in high-resolution mode was used as an analytical technique to characterize the aromatic layers in HACs. Spectroscopic analysis was prformed in the mid-IR range. Results: A remarkable destruction of aliphatic structures in HACs has been observed with the thermal processing, while aromatic structures become dominating by increasing the diameters of the graphene layers. The aromatic bands at 3.3 and 6.2 μm, observed in the laboratory spectra of PAHs and of the combination of the PAHs and HAC materials, are also clearly observed in the spectrum of the heated HACs. These bands agree with those of aromatic bands observed in astronomical observations. Conclusions: Aromatization of HACs could be a pre-stage in the decomposition process of hydrocarbons that form PAH-clusters in such hot interstellar medium.

Solvent-free functionalization of fullerene C{sub 60} and pristine multi-walled carbon nanotubes with aromatic amines

Energy Technology Data Exchange (ETDEWEB)

Ramírez-Calera, Itzel J. [Centro de Ciencias Aplicadas y Desarrollo Tecnológico, Universidad Nacional Autónoma de México, Circuito Exterior C. U., 04510, México, D.F. (Mexico); Meza-Laguna, Victor [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito Exterior C. U., 04510 México, D.F. (Mexico); Gromovoy, Taras Yu. [O.O. Chuiko Institute of Surface Chemistry, National Academy of Sciences of the Ukraine, Gen. Naumova 17, 03164 Kiev (Ukraine); Chávez-Uribe, Ma. Isabel [Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior C. U., 04510 México, D.F. (Mexico); Basiuk, Vladimir A., E-mail: basiuk@nucleares.unam.mx [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito Exterior C. U., 04510 México, D.F. (Mexico); Basiuk, Elena V., E-mail: elbg1111@gmail.com [Centro de Ciencias Aplicadas y Desarrollo Tecnológico, Universidad Nacional Autónoma de México, Circuito Exterior C. U., 04510, México, D.F. (Mexico)

2015-02-15

Highlights: • Pristine multi-walled carbon nanotubes were functionalized with aromatic amines. • The amines add onto nanotube defects, likewise they add onto fullerene C{sub 60}. • The addition takes place at elevated temperature and without organic solvents. • Functionalized nanotubes were characterized by a number of instrumental techniques. - Abstract: We employed a direct one-step solvent-free covalent functionalization of solid fullerene C{sub 60} and pristine multi-walled carbon nanotubes (MWCNTs) with aromatic amines 1-aminopyrene (AP), 2-aminofluorene (AF) and 1,5-diaminonaphthalene (DAN). The reactions were carried out under moderate vacuum, in a wide temperature range of 180–250 °C, during relatively short time of about 2 h. To confirm successful amine attachment, a large number of analytical techniques were used (depending on the nanomaterial functionalized) such as Fourier transform infrared, Raman, X-ray photoelectron, {sup 13}C cross-polarization magic angle spinning NMR spectroscopy, thermogravimetric analysis, laser-desorption ionization time-of-flight mass spectrometry, temperature-programmed desorption with mass spectrometric detection, as well as scanning and transmission electron microscopy. The nucleophilic addition of the aromatic amines to C{sub 60} molecule was studied theoretically by using density functional theory (PBE GGA functional with Grimme dispersion correction in conjunction with the DNP basis set). In the case of crystalline C{sub 60}, the solvent-free technique has a limited applicability due to poor diffusion of vaporous aromatic amines into the bulk. Nevertheless, the approach proposed allows for a facile preparation of aromatic amine-functionalized pristine MWCNTs without contamination with other chemical reagents, detergents and solvents, which is especially important for a vast variety of nanotube applications spanning from nanoelectronics to nanomedicine.

Artificially synthesized helper/killer-hybrid epitope long peptide (H/K-HELP): preparation and immunological analysis of vaccine efficacy.

Science.gov (United States)

Masuko, Kazutaka; Wakita, Daiko; Togashi, Yuji; Kita, Toshiyuki; Kitamura, Hidemitsu; Nishimura, Takashi

2015-01-01

To elucidate the immunologic mechanisms of artificially synthesized helper/killer-hybrid epitope long peptide (H/K-HELP), which indicated a great vaccine efficacy in human cancers, we prepared ovalbumin (OVA)-H/K-HELP by conjugating killer and helper epitopes of OVA-model tumor antigen via a glycine-linker. Vaccination of C57BL/6 mice with OVA-H/K-HELP (30 amino acids) but not with short peptides mixture of class I-binding peptide (8 amino-acids) and class II-binding peptide (17 amino-acids) combined with adjuvant CpG-ODN (cytosine-phosphorothioate-guanine oligodeoxynucleotides), induced higher numbers of OVA-tetramer-positive CTL with concomitant activation of IFN-γ-producing CD4(+) Th1 cells. However, replacement of glycine-linker of OVA-H/K-HELP with other peptide-linker caused a significant decrease of vaccine efficacy of OVA-H/K-HELP. In combination with adjuvant CpG-ODN, OVA-H/KHELP exhibited greater vaccine efficacy compared with short peptides vaccine, in both preventive and therapeutic vaccine models against OVA-expressing EG-7 tumor. The elevated vaccine efficacy of OVAH/K-HELP might be derived from the following mechanisms: (i) selective presentation by only professional dendritic cells (DC) in vaccinated draining lymph node (dLN); (ii) a long-term sustained antigen presentation exerted by DC to stimulate both CTL and Th1 cells; (iii) formation of three cells interaction among DC, Th and CTL. In comparative study, H/K-HELP indicated stronger therapeutic vaccine efficacy compared with that of extended class I synthetic long peptide, indicating that both the length of peptide and the presence of Th epitope peptide were crucial aspects for preparing artificially synthesized H/K-HELP vaccine. Copyright © 2014 European Federation of Immunological Societies. Published by Elsevier B.V. All rights reserved.

Antimicrobial Peptides: a promising class of antimicrobial compounds against BWA and multi-drug resistant bacteria: in the spotlight: the lactoferrin chimera

NARCIS (Netherlands)

Bikker, F.J.; Sijbrandij, T.; Nazmi, K.; Bolscher, J.G.M.; Veerman, E.C.I.; Jansen, H-J.

2014-01-01

Anti-Microbial Peptides (AMPs) are part of the innate immune defense system and considered as promising lead compounds for the development of novel anti-bacterial agents. In general, AMPs are simple, short peptides with broad-spectrum activity against Gram-negative and Gram-positive bacteria, fungi,

Residual DNA-bound proteins are a source of in vitro transcription inhibitor peptides

International Nuclear Information System (INIS)

Venanzi, F.M.

1989-01-01

Enzymatic breakdown of residual proteins occurs at mild alkaline pH (pH optimum 8.5) as monitored by using radioiodinated, purified genomic DNA from calf thymus. These DNA fibers also possess a differential ability to hydrolyze added exogenous small and linker histones. The results described argue strongly that a putative protease activity, co-purified with DNA, is the source of short chain peptides which inhibit transcription in vitro. Therefore, we propose that RNA repressor peptides must be of higher molecular weight than previously reported

Interactions of Bio-Inspired Membranes with Peptides and Peptide-Mimetic Nanoparticles

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Michael Sebastiano

2015-08-01

Full Text Available Via Dissipative Particle Dynamics (DPD and implicit solvent coarse-grained (CG Molecular Dynamics (MD we examine the interaction of an amphiphilic cell-penetrating peptide PMLKE and its synthetic counterpart with a bio-inspired membrane. We use the DPD technique to investigate the interaction of peptide-mimetic nanoparticles, or nanopins, with a three-component membrane. The CG MD approach is used to investigate the interaction of a cell-penetrating peptide PMLKE with single-component membrane. We observe the spontaneous binding and subsequent insertion of peptide and nanopin in the membrane by using CG MD and DPD approaches, respectively. In addition, we find that the insertion of peptide and nanopins is mainly driven by the favorable enthalpic interactions between the hydrophobic components of the peptide, or nanopin, and the membrane. Our study provides insights into the mechanism underlying the interactions of amphiphilic peptide and peptide-mimetic nanoparticles with a membrane. The result of this study can be used to guide the functional integration of peptide and peptide-mimetic nanoparticles with a cell membrane.

Detection of chlorinated aromatic compounds

Science.gov (United States)

Ekechukwu, A.A.

1996-02-06

A method for making a composition for measuring the concentration of chlorinated aromatic compounds in aqueous fluids, and an optical probe for use with the method are disclosed. The composition comprises a hydrophobic polymer matrix, preferably polyamide, with a fluorescent indicator uniformly dispersed therein. The indicator fluoresces in the presence of the chlorinated aromatic compounds with an intensity dependent on the concentration of these compounds in the fluid of interest, such as 8-amino-2-naphthalene sulfonate. The probe includes a hollow cylindrical housing that contains the composition in its distal end. The probe admits an aqueous fluid to the probe interior for exposure to the composition. An optical fiber transmits excitation light from a remote source to the composition while the indicator reacts with chlorinated aromatic compounds present in the fluid. The resulting fluorescence light signal is reflected to a second optical fiber that transmits the light to a spectrophotometer for analysis. 5 figs.

[Plant signaling peptides. Cysteine-rich peptides].

Science.gov (United States)

Ostrowski, Maciej; Kowalczyk, Stanisław

2015-01-01

Recent bioinformatic and genetic analyses of several model plant genomes have revealed the existence of a highly abundant group of signaling peptides that are defined as cysteine-rich peptides (CRPs). CRPs are usually in size between 50 and 90 amino acid residues, they are positively charged, and they contain 4-16 cysteine residues that are important for the correct conformational folding. Despite the structural differences among CRP classes, members from each class have striking similarities in their molecular properties and function. The present review presents the recent progress in research on signaling peptides from several families including: EPF/EPFL, SP11/SCR, PrsS, RALF, LURE, and some other peptides belonging to CRP group. There is convincing evidence indicating multiple roles for these CRPs as signaling molecules during the plant life cycle, ranging from stomata development and patterning, self-incompatibility, pollen tube growth and guidance, reproductive processes, and nodule formation.

Sequence dependent aggregation of peptides and fibril formation

Science.gov (United States)

Hung, Nguyen Ba; Le, Duy-Manh; Hoang, Trinh X.

2017-09-01

Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides. Fibril-like ordered aggregates are found for several sequences that contain the common HPH pattern, while other sequences may form helix bundles or disordered aggregates. A wide variation of the aggregation transition temperatures among sequences, even among those of the same hydrophobic fraction, indicates that not all sequences undergo aggregation at a presumable physiological temperature. The transition is found to be the most cooperative for sequences forming fibril-like structures. For a fibril-prone sequence, it is shown that fibril formation follows the nucleation and growth mechanism. Interestingly, a binary mixture of peptides of an aggregation-prone and a non-aggregation-prone sequence shows the association and conversion of the latter to the fibrillar structure. Our study highlights the role of a sequence in selecting fibril-like aggregates and also the impact of a structural template on fibril formation by peptides of unrelated sequences.

Protonation sites of aromatic compounds in (+) atmospheric pressure photoionization

Energy Technology Data Exchange (ETDEWEB)

Kim, Sung Hwan; Ahmed, Arif [Dept. of Chemistry, Kyungpoo k National University, Daegu (Korea, Republic of)

2017-02-15

Reaction enthalpy of hydrogen transfer reactions of aromatic compounds has been observed to be greatly affected by the exact location of the protonation site. Therefore, to clearly identify the protonation location, each candidate protonation site for 43 aromatic compounds were theoretically determined and their location was compared with that determined based on experimental MS data. Only the basic nitrogen atom is favorable as a protonation site for pyridine-type aromatic compounds, whereas carbon atoms are preferable for the protonation of pyrrole-type compounds. The most favorable protonation sites for aniline or methylated aniline-type aromatic compounds are either the nitrogen atom in the amine group or the carbon atom at the para-position to the amine group. Like pyrrole-type compounds, aromatic compounds with amine groups also favor protonation at the carbon atom instead of at the nitrogen atom. In addition, hydrocarbons having an anthracene structural motif without heteroatoms produced higher or equal percentages of protonated ions compared to that achieved with molecular ions. The results of this study can be used to improve the analyses of aromatic compounds.

Glucagon-like peptide-1 analogues: An overview

Directory of Open Access Journals (Sweden)

Vishal Gupta

2013-01-01

Full Text Available Abnormalities of the incretin axis have been implicated in the pathogenesis of type 2 diabetes mellitus. Glucagon-like peptide-1 (GLP-1 and gastroinhibitory intestinal peptide constitutes >90% of all the incretin function. Augmentation of GLP-1 results in improvement of beta cell health in a glucose-dependant manner (post-prandial hyperglycemia and suppression of glucagon (fasting hyperglycemia, amongst other beneficial pleiotropic effects. Native GLP-1 has a very short plasma half-life and novel methods have been developed to augment its half life, such that its anti-hyperglycemic effects can be exploited. They can be broadly classified as exendin-based therapies (exenatide, exenatide once weekly, DPP-4-resistant analogues (lixisenatide, albiglutide, and analogues of human GLP-1 (liraglutide, taspoglutide. Currently, commercially available analogues are exenatide, exenatide once weekly, and liraglutide. This review aims to provide an overview of most GLP-1 analogues.

The mutagenic potential of high flash aromatic naphtha.

Science.gov (United States)

Schreiner, C A; Edwards, D A; McKee, R H; Swanson, M; Wong, Z A; Schmitt, S; Beatty, P

1989-06-01

Catalytic reforming is a refining process that converts naphthenes to aromatics by dehydrogenation to make higher octane gasoline blending components. A portion of this wide boiling range hydrocarbon stream can be separated by distillation and used for other purposes. One such application is a mixture of predominantly 9-carbon aromatic molecules (C9 aromatics, primarily isomers of ethyltoluene and trimethylbenzene), which is removed and used as a solvent--high-flash aromatic naphtha. A program was initiated to assess the toxicological properties of high-flash aromatic naphtha since there may be human exposure through inhalation or external body contact. The current study was conducted partly to assess the potential for mutagenic activity and also to assist in an assessment of carcinogenic potential. The specific tests utilized included the Salmonella/mammalian microsome mutagenicity assay, the hypoxanthine-guanine phosphoribosyl transferase (HGPRT) forward mutation assay in CHO cells, in vitro chromosome aberration and sister chromatid exchange (SCE) assays in CHO cells, and an in vivo chromosome aberration assay in rat bone marrow.

Effects of halogenated aromatics/aliphatics and nitrogen(N)-heterocyclic aromatics on estimating the persistence of future pharmaceutical compounds using a modified QSAR model.

Science.gov (United States)

Lim, Seung Joo; Fox, Peter

2014-02-01

The effects of halogenated aromatics/aliphatics and nitrogen(N)-heterocyclic aromatics on estimating the persistence of future pharmaceutical compounds were investigated using a modified half life equation. The potential future pharmaceutical compounds investigated were approximately 2000 pharmaceutical drugs currently undergoing the United States Food and Drug Administration (US FDA) testing. EPI Suite (BIOWIN) model estimates the fates of compounds based on the biodegradability under aerobic conditions. While BIOWIN considered the biodegradability of a compound only, the half life equation used in this study was modified by biodegradability, sorption and cometabolic oxidation. It was possible that the potential future pharmaceutical compounds were more accurately estimated using the modified half life equation. The modified half life equation considered sorption and cometabolic oxidation of halogenated aromatic/aliphatics and nitrogen(N)-heterocyclic aromatics in the sub-surface, while EPI Suite (BIOWIN) did not. Halogenated aliphatics in chemicals were more persistent than halogenated aromatics in the sub-surface. In addition, in the sub-surface environment, the fates of organic chemicals were much more affected by halogenation in chemicals than by nitrogen(N)-heterocyclic aromatics. © 2013.

Human peptide transporters

DEFF Research Database (Denmark)

Nielsen, Carsten Uhd; Brodin, Birger; Jørgensen, Flemming Steen

2002-01-01

Peptide transporters are epithelial solute carriers. Their functional role has been characterised in the small intestine and proximal tubules, where they are involved in absorption of dietary peptides and peptide reabsorption, respectively. Currently, two peptide transporters, PepT1 and PepT2, wh...

Peptide dendrimers

Czech Academy of Sciences Publication Activity Database

Niederhafner, Petr; Šebestík, Jaroslav; Ježek, Jan

2005-01-01

Roč. 11, - (2005), 757-788 ISSN 1075-2617 R&D Projects: GA ČR(CZ) GA203/03/1362 Institutional research plan: CEZ:AV0Z40550506 Keywords : multiple antigen peptides * peptide dendrimers * synthetic vaccine * multipleantigenic peptides Subject RIV: CC - Organic Chemistry Impact factor: 1.803, year: 2005

Bio-Based Aromatic Epoxy Monomers for Thermoset Materials

Directory of Open Access Journals (Sweden)

Feifei Ng

2017-01-01

Full Text Available The synthesis of polymers from renewable resources is a burning issue that is actively investigated. Polyepoxide networks constitute a major class of thermosetting polymers and are extensively used as coatings, electronic materials, adhesives. Owing to their outstanding mechanical and electrical properties, chemical resistance, adhesion, and minimal shrinkage after curing, they are used in structural applications as well. Most of these thermosets are industrially manufactured from bisphenol A (BPA, a substance that was initially synthesized as a chemical estrogen. The awareness on BPA toxicity combined with the limited availability and volatile cost of fossil resources and the non-recyclability of thermosets implies necessary changes in the field of epoxy networks. Thus, substitution of BPA has witnessed an increasing number of studies both from the academic and industrial sides. This review proposes to give an overview of the reported aromatic multifunctional epoxide building blocks synthesized from biomass or from molecules that could be obtained from transformed biomass. After a reminder of the main glycidylation routes and mechanisms and the recent knowledge on BPA toxicity and legal issues, this review will provide a brief description of the main natural sources of aromatic molecules. The different epoxy prepolymers will then be organized from simple, mono-aromatic di-epoxy, to mono-aromatic poly-epoxy, to di-aromatic di-epoxy compounds, and finally to derivatives possessing numerous aromatic rings and epoxy groups.

Development and use of engineered peptide deformylase in chemoenzymatic peptide synthesis

NARCIS (Netherlands)

Di Toma, Claudia

2012-01-01

Deze thesis beschrijft het onderzoek naar potentieel van het gebruik van het peptide deformylase (PDF) in chemo enzymatische peptide synthese. PDF is geschikt voor selective N terminale deformylatie van bepaalde N-formyl-peptides zonder gelijktijdige hydrolyse van de peptide binding. Door de

A Tetrameric Peptide Derived from Bovine Lactoferricin Exhibits Specific Cytotoxic Effects against Oral Squamous-Cell Carcinoma Cell Lines.

Science.gov (United States)

Solarte, Víctor A; Rosas, Jaiver E; Rivera, Zuly J; Arango-Rodríguez, Martha L; García, Javier E; Vernot, Jean-Paul

2015-01-01

Several short linear peptides derived from cyclic bovine lactoferricin were synthesized and tested for their cytotoxic effect against the oral cavity squamous-cell carcinoma (OSCC) cell lines CAL27 and SCC15. As a control, an immortalized and nontumorigenic cell line, Het-1A, was used. Linear peptides based on the RRWQWR core sequence showed a moderate cytotoxic effect and specificity towards tumorigenic cells. A tetrameric peptide, LfcinB(20-25)4, containing the RRWQWR motif, exhibited greater cytotoxic activity (>90%) in both OSCC cell lines compared to the linear lactoferricin peptide or the lactoferrin protein. Additionally, this tetrameric peptide showed the highest specificity towards tumorigenic cells among the tested peptides. Interestingly, this effect was very fast, with cell shrinkage, severe damage to cell membrane permeability, and lysis within one hour of treatment. Our results are consistent with a necrotic effect rather than an apoptotic one and suggest that this tetrameric peptide could be considered as a new candidate for the therapeutic treatment of OSCC.

Aromatic Plants as a Source of Bioactive Compounds

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Panagiota Florou-Paneri

2012-09-01

Full Text Available Aromatic plants, also known as herbs and spices, have been used since antiquity as folk medicine and as preservatives in foods. The best known aromatic plants, such as oregano, rosemary, sage, anise, basil, etc., originate from the Mediterranean area. They contain many biologically active compounds, mainly polyphenolics, which have been found to possess antimicrobial, antioxidant, antiparasitic, antiprotozoal, antifungal, and anti-inflammatory properties. Currently, the demand for these plants and their derivatives has increased because they are natural, eco-friendly and generally recognized as safe products. Therefore, aromatic plants and their extracts have the potential to become new generation substances for human and animal nutrition and health. The purpose of this review is to provide an overview of the literature surrounding the in vivo and in vitro use of aromatic plants.

Clicked bis-PEG-peptide conjugates for studying calmodulin-Kv7.2 channel binding.

Science.gov (United States)

Bonache, M Angeles; Alaimo, Alessandro; Malo, Covadonga; Millet, Oscar; Villarroel, Alvaro; González-Muñiz, Rosario

2014-11-28

The recombinant Kv7.2 calmodulin (CaM) binding site (Q2AB CaMBD) shows a high tendency to aggregate, thus complicating biochemical and structural studies. To facilitate these studies we have conceived bis-PEG-peptide CaMBD-mimetics linking helices A and B in single, easy to handle molecules. Short PEG chains were selected as spacers between the two peptide molecules, and a Cu(i)-catalyzed cycloaddition (CuAAC) protocol was used to assemble the final bis-PEG-peptide conjugate, by the convenient functionalization of PEG arms with azide and alkyne groups. The resulting conjugates, with a certain helical character in TFE solutions (CD), showed nanomolar affinity in a fluorescence CaM binding in vitro assay, higher than just the sum of the precursor PEG-peptide affinities, thus validating our design. The approach to these first described examples of Kv7.2 CaMBD-mimetics could pave the way to chimeric conjugates merging helices A and B from different Kv7 subunits.

The formation of aromatics and PAH's in laminar flames

International Nuclear Information System (INIS)

Marinov, N M; Pitz, W J; Westbrook, C K

1999-01-01

The formation of aromatics and PAH's is an important problem in combustion. These compounds are believed to contribute to the formation of soot whose emission from diesel engines is regulated widely throughout the industrial world. Additionally, the United States Environmental Protection Agency regulates the emission of many aromatics and PAH species from stationary industrial burners, under the 1990 Clean Air Act Amendments. The above emission regulations have created much interest in understanding how these species are formed in combustion systems. Much previous work has been done on aromatics and PAH's. The work is too extensive to review here, but is reviewed in Reference 1. A few recent developments are highlighted here. McEnally, Pfefferle and coworkers have studied aromatic, PAH and soot formation in a variety of non-premixed flames with hydrocarbon additives[2-4]. They found additives that contain a C5 ring increase the concentration of aromatics and soot[4]. Howard and coworkers have studied the formation of aromatic and PAH's in low pressure, premixed, laminar hydrocarbon flames. They found the cyclopentadienyl radical to be a key species in naphthalene formation in a fuel-rich, benzene/Ar/O2 flame[5

The conjugation of nonsteroidal anti-inflammatory drugs (NSAID to small peptides for generating multifunctional supramolecular nanofibers/hydrogels

Directory of Open Access Journals (Sweden)

Jiayang Li

2013-05-01

Full Text Available Here we report supramolecular hydrogelators made of nonsteroidal anti-inflammatory drugs (NSAID and small peptides. The covalent linkage of Phe–Phe and NSAIDs results in conjugates that self-assemble in water to form molecular nanofibers as the matrices of hydrogels. When the NSAID is naproxen (1, the resultant hydrogelator 1a forms a hydrogel at a critical concentration (cgc of 0.2 wt % at pH 7.0. Hydrogelator 1a, also acting as a general motif, enables enzymatic hydrogelation in which the precursor turns into a hydrogelator upon hydrolysis catalyzed by a phosphatase at physiological conditions. The conjugates of Phe–Phe with other NSAIDs, such as (R-flurbiprofen (2, racemic flurbiprofen (3, and racemic ibuprofen (4, are able to form molecular hydrogels, except in the case of aspirin (5. After the conjugation with the small peptides, NSAIDs exhibit improved selectivity to their targets. In addition, the peptides made of D-amino acids help preserve the activities of NSAIDs. Besides demonstrating that common NSAIDs are excellent candidates to promote aromatic–aromatic interaction in water to form hydrogels, this work contributes to the development of functional molecules that have dual or multiple roles and ultimately may lead to new molecular hydrogels of therapeutic agents for topical use.

Peptides reproducibly released by in vivo digestion of beef meat and trout flesh in pigs.

Science.gov (United States)

Bauchart, Caroline; Morzel, Martine; Chambon, Christophe; Mirand, Philippe Patureau; Reynès, Christelle; Buffière, Caroline; Rémond, Didier

2007-12-01

Characterisation and identification of peptides (800 to 5000 Da) generated by intestinal digestion of fish or meat were performed using MS analyses (matrix-assisted laser desorption ionisation time of flight and nano-liquid chromatography electrospray-ionisation ion trap MS/MS). Four pigs fitted with cannulas at the duodenum and jejunum received a meal exclusively made of cooked Pectoralis profundus beef meat or cooked trout fillets. A protein-free meal, made of free amino acids, starch and fat, was used to identify peptides of endogenous origin. Peptides reproducibly detected in digesta (i.e. from at least three pigs) were evidenced predominantly in the first 3 h after the meal. In the duodenum, most of the fish- and meat-derived peptides were characteristic of a peptic digestion. In the jejunum, the majority of peptides appeared to result from digestion by chymotrypsin and trypsin. Despite slight differences in gastric emptying kinetics and overall peptide production, possibly in relation to food structure and texture, six and four similar peptides were released after ingestion of fish or meat in the duodenum and jejunum. A total of twenty-six different peptides were identified in digesta. All were fragments of major structural (actin, myosin) or sarcoplasmic (creatine kinase, glyceraldehyde-3-phosphate dehydrogenase and myoglobin) muscle proteins. Peptides were short ( digestion, some of them can be reproducibly observed in intestinal digesta.

Rapid discovery of peptide capture candidates with demonstrated specificity for structurally similar toxins

Science.gov (United States)

Sarkes, Deborah A.; Hurley, Margaret M.; Coppock, Matthew B.; Farrell, Mikella E.; Pellegrino, Paul M.; Stratis-Cullum, Dimitra N.

2016-05-01

Peptides have emerged as viable alternatives to antibodies for molecular-based sensing due to their similarity in recognition ability despite their relative structural simplicity. Various methods for peptide capture reagent discovery exist, including phage display, yeast display, and bacterial display. One of the primary advantages of peptide discovery by bacterial display technology is the speed to candidate peptide capture agent, due to both rapid growth of bacteria and direct utilization of the sorted cells displaying each individual peptide for the subsequent round of biopanning. We have previously isolated peptide affinity reagents towards protective antigen of Bacillus anthracis using a commercially available automated magnetic sorting platform with improved enrichment as compared to manual magnetic sorting. In this work, we focus on adapting our automated biopanning method to a more challenging sort, to demonstrate the specificity possible with peptide capture agents. This was achieved using non-toxic, recombinant variants of ricin and abrin, RiVax and abrax, respectively, which are structurally similar Type II ribosomal inactivating proteins with significant sequence homology. After only two rounds of biopanning, enrichment of peptide capture candidates binding abrax but not RiVax was achieved as demonstrated by Fluorescence Activated Cell Sorting (FACS) studies. Further sorting optimization included negative sorting against RiVax, proper selection of autoMACS programs for specific sorting rounds, and using freshly made buffer and freshly thawed protein target for each round of biopanning for continued enrichment over all four rounds. Most of the resulting candidates from biopanning for abrax binding peptides were able to bind abrax but not RiVax, demonstrating that short peptide sequences can be highly specific even at this early discovery stage.

New dendrimer - Peptide host - Guest complexes: Towards dendrimers as peptide carriers

DEFF Research Database (Denmark)

Boas, Ulrik; Sontjens, S.H.M.; Jensen, Knud Jørgen

2002-01-01

Adamantyl urea and adamantyl thiourea modified poly(propylene imine) dendrimers act as hosts for N-terminal tert-butoxycarbonyl (Boc)-protected peptides and form chloroform-soluble complexes. investigations with NMR spectroscopy show that the peptide is bound to the dendrimer by ionic interactions...... between the dendrimer outer shell tertiary amines and the C-terminal carboxylic acid of the peptide, and also through host-urea to peptide-amide hydrogen bonding. The hydrogen-bonding nature of the peptide dendrimer interactions was further confirmed by using Fourier transform IR spectroscopy, for which...... the NH- and CO-stretch signals of the peptide amide moieties shift towards lower wave-numbers upon complexation with the dendrimer. Spatial analysis of the complexes with NOESY spectroscopy generally shows close proximity of the N-terminal Boc group of the peptide to the peripheral adamantyl groups...

Human Antimicrobial Peptides and Proteins

Directory of Open Access Journals (Sweden)

Guangshun Wang

2014-05-01

medicine to combat drug-resistant superbugs, fungi, viruses, parasites, or cancer. Alternatively, multiple factors (e.g., albumin, arginine, butyrate, calcium, cyclic AMP, isoleucine, short-chain fatty acids, UV B light, vitamin D, and zinc are able to induce the expression of antimicrobial peptides, opening new avenues to the development of anti-infectious drugs.

Peptide aptamers: The versatile role of specific protein function inhibitors in plant biotechnology.

Science.gov (United States)

Colombo, Monica; Mizzotti, Chiara; Masiero, Simona; Kater, Martin M; Pesaresi, Paolo

2015-11-01

In recent years, peptide aptamers have emerged as novel molecular tools that have attracted the attention of researchers in various fields of basic and applied science, ranging from medicine to analytical chemistry. These artificial short peptides are able to specifically bind, track, and inhibit a given target molecule with high affinity, even molecules with poor immunogenicity or high toxicity, and represent a remarkable alternative to antibodies in many different applications. Their use is on the rise, driven mainly by the medical and pharmaceutical sector. Here we discuss the enormous potential of peptide aptamers in both basic and applied aspects of plant biotechnology and food safety. The different peptide aptamer selection methods available both in vivo and in vitro are introduced, and the most important possible applications in plant biotechnology are illustrated. In particular, we discuss the generation of broad-based virus resistance in crops, "reverse genetics" and aptasensors in bioassays for detecting contaminations in food and feed. Furthermore, we suggest an alternative to the transfer of peptide aptamers into plant cells via genetic transformation, based on the use of cell-penetrating peptides that overcome the limits imposed by both crop transformation and Genetically Modified Organism commercialization. © 2015 Institute of Botany, Chinese Academy of Sciences.

Minimalistic peptide supramolecular co-assembly: expanding the conformational space for nanotechnology.

Science.gov (United States)

Makam, Pandeeswar; Gazit, Ehud

2018-05-21

Molecular self-assembly is a ubiquitous process in nature and central to bottom-up nanotechnology. In particular, the organization of peptide building blocks into ordered supramolecular structures has gained much interest due to the unique properties of the products, including biocompatibility, chemical and structural diversity, robustness and ease of large-scale synthesis. In addition, peptides, as short as dipeptides, contain all the molecular information needed to spontaneously form well-ordered structures at both the nano- and the micro-scale. Therefore, peptide supramolecular assembly has been effectively utilized to produce novel materials with tailored properties for various applications in the fields of material science, engineering, medicine, and biology. To further expand the conformational space of peptide assemblies in terms of structural and functional complexity, multicomponent (two or more) peptide supramolecular co-assembly has recently evolved as a promising extended approach, similar to the structural diversity of natural sequence-defined biopolymers (proteins) as well as of synthetic covalent co-polymers. The use of this methodology was recently demonstrated in various applications, such as nanostructure physical dimension control, the creation of non-canonical complex topologies, mechanical strength modulation, the design of light harvesting soft materials, fabrication of electrically conducting devices, induced fluorescence, enzymatic catalysis and tissue engineering. In light of these significant advancements in the field of peptide supramolecular co-assembly in the last few years, in this tutorial review, we provide an updated overview and future prospects of this emerging subject.

Next-generation ELISA diagnostic assay for Chagas Disease based on the combination of short peptidic epitopes

DEFF Research Database (Denmark)

Mucci, Juan; Carmona, Santiago J.; Volcovich, Romina

2017-01-01

Chagas Disease, caused by the protozoan Trypanosoma cruzi, is a major health and economic problem in Latin America for which no vaccine or appropriate drugs for large-scale public health interventions are yet available. Accurate diagnosis is essential for the early identification and follow up....... cruzi linear B-cell epitopes using high-density peptide chips, leading to the identification of several hundred novel sequence signatures associated to chronic Chagas Disease. Here, we performed a serological assessment of 27 selected epitopes and of their use in a novel multipeptide-based diagnostic...... method. A combination of 7 of these peptides were finally evaluated in ELISA format against a panel of 199 sera samples (Chagas-positive and negative, including sera from Leishmaniasis-positive subjects). The multipeptide formulation displayed a high diagnostic performance, with a sensitivity of 96...

Aromatic hydrocarbon concentrations in sediments of Placentia Bay, Newfoundland

International Nuclear Information System (INIS)

Kiceniuk, J.W.

1992-01-01

A study was conducted to examine the potential for contamination of recent sediments with polycyclic aromatic hydrocarbons due to tanker and refinery activity in Placentia Bay, Newfoundland, an area without large local anthropogenic sources of aromatics. Sediment samples were taken from the vicinity of the Come By Chance refinery, Woody Island, Wild Cove, and Port Royal Arm, all in the north end of the bay. The samples were extracted by two methods, dichloromethane extraction of dried sediment for determination of total aromatic hydrocarbon content and hexane extraction of wet sediment for estimation of the bioavailability of hydrocarbons and determination of more volatile compounds. Class analysis of aromatic hydrocarbons was conducted on a NH 2 column with detection at 255 nm. Total concentrations of di-tricyclic aromatics were highest at the Woody Island site (0.6 μg/g). The sediments from the Come By Chance site, Wild Cove, and Port Royal Arm sediments contained 0.3, 0.1, and 0.2 μg/g respectively. The hexane extracts from Come By Chance were lowest in di-tricyclic aromatics (0.007 μg/g), with the other sites being equal in concentration (0.01 μg/g). It is evident from the study that aromatic hydrocarbon concentrations in Placentia Bay are elevated in some parts of the bay in the absence of local combustion sources, and that the most likely source is petroleum. 12 refs., 5 figs., 2 tabs

Fused aromatic thienopyrazines: structure, properties and function

KAUST Repository

Mondal, Rajib

2010-01-01

Recent development of a fused aromatic thieno[3.4-b]pyrazine system and their application in optoelectronic devices are reviewed. Introduction of a fused aromatic unit followed by side chain engineering, dramatically enhanced the charge carrier mobility in thin film transistor devices and mobilities up to 0.2 cm2/Vs were achieved. The optoelectronic properties of these fused aromatic thienopyrazine polymers (Eg = 1.3 to 1.6 eV, HOMO = -4.9 to -5.2 V) were tuned by introduction of various fused aromatic rings within thienopyrazine. By balancing the fundamental properties of these polymers, both high charge carrier mobilities and moderate PCEs in solar cells were achieved. Further, effects of copolymerizing units are discussed. Low band gap semiconducting polymer (Eg ∼ 1 eV) with high field effect mobility (0.044 cm2/Vs) was obtained using cyclopentadithiophene as copolymerizing unit. Finally, a molecular design approach to enhance the absorption coefficients is discussed, which resulted in improved power conversion efficiency in bulk heterojunction solar cells. © 2010 The Royal Society of Chemistry.

An ethnopharmacological study of aromatic Uyghur medicinal plants in Xinjiang, China.

Science.gov (United States)

Zhao, Lu; Tian, Shuge; Wen, E; Upur, Halmuart

2017-12-01

An ethnobotanical survey was completed in a remote village and surrounding country of Xinjiang, where most Uyghur medicinal plants could be collected. This work clarifies and increases ethnobotanical data. We surveyed and organized aromatic medicinal plants that are commonly used in clinical settings to provide a significant reference for studying new medical activities. In the survey, informants who have traditional knowledge on aromatic Uyghur medicinal plants were interviewed between March 2014 and September 2014. Aromatic medicinal plant species and pertinent information were collected. Some therapeutic methods and modes of preparation of traditional aromatic medicinal plants were found. A total of 86 aromatic medicinal plant species belonging to 36 families were included in our study. We identified 34 plant species introduced from different regions such as Europe, India and Mediterranean areas. Fruits and whole plants were the most commonly used parts of plant, and most aromatic medicinal plants could be applied as medicine and food. We assigned the medicinal plants a use value (UV). Knowing the UV of species is useful in determining the use reliability and pharmacological features of related plants. Xinjiang is an area in which indigenous aromatic medicinal plants are diversely used and has therefore established a sound dimensional medical healthcare treatment system. Some aromatic Uyghur medicinal plants are on the verge of extinction. Hence, further strategies for the conservation of these aromatic medicinal plants should be prioritized.

Spectrofluorimetric study of the aromatic carbohydrates of Noriisk petroleum

Energy Technology Data Exchange (ETDEWEB)

Alekseeva, T.A.; Lekveishvili, E.G.; Melikadze, L.D.; Teplitskaia, T.A.; Tevdorashvili, M.N.

1979-01-01

Investigation was made of the specimens of aromatic hydrocarbons which were produced by photochemical decomposition of the products of photocondensation with maleicanhydride of narrow aromatic fractions separated by a system of methods from a high temperature part of Noriisk petroleum. Use was made of a standard spectrofluorimeter of low resolution. A series of aromatic hydrocarbons, naphthalene, benzofluorene, phenantrene, chrizene, pyrene, tetraphene, and 3,4-benzophenantrene were installed in the machine.

Amide I SFG Spectral Line Width Probes the Lipid-Peptide and Peptide-Peptide Interactions at Cell Membrane In Situ and in Real Time.

Science.gov (United States)

Zhang, Baixiong; Tan, Junjun; Li, Chuanzhao; Zhang, Jiahui; Ye, Shuji

2018-06-13

The balance of lipid-peptide and peptide-peptide interactions at cell membrane is essential to a large variety of cellular processes. In this study, we have experimentally demonstrated for the first time that sum frequency generation vibrational spectroscopy can be used to probe the peptide-peptide and lipid-peptide interactions in cell membrane in situ and in real time by determination of the line width of amide I band of protein backbone. Using a "benchmark" model of α-helical WALP23, it is found that the dominated lipid-peptide interaction causes a narrow line width of the amide I band, whereas the peptide-peptide interaction can markedly broaden the line width. When WALP23 molecules insert into the lipid bilayer, a quite narrow line width of the amide I band is observed because of the lipid-peptide interaction. In contrast, when the peptide lies down on the bilayer surface, the line width of amide I band becomes very broad owing to the peptide-peptide interaction. In terms of the real-time change in the line width, the transition from peptide-peptide interaction to lipid-peptide interaction is monitored during the insertion of WALP23 into 1,2-dipalmitoyl- sn-glycero-3-phospho-(1'- rac-glycerol) (DPPG) lipid bilayer. The dephasing time of a pure α-helical WALP23 in 1-palmitoyl-2-oleoyl- sn-glycero-3-phospho-(1'- rac-glycerol) and DPPG bilayer is determined to be 2.2 and 0.64 ps, respectively. The peptide-peptide interaction can largely accelerate the dephasing time.

An alternative bactericidal mechanism of action for lantibiotic peptides that target lipid II

NARCIS (Netherlands)

Hasper, Hester E.; Kramer, Naomi E.; Smith, James L.; Hillman, J. D.; Zachariah, Cherian; Kuipers, Oscar P.; de Kruijff, Ben; Breukink, Eefjan

2006-01-01

Lantibiotics are polycyclic peptides containing unusual amino acids, which have binding specificity for bacterial cells, targeting the bacterial cell wall component lipid II to form pores and thereby lyse the cells. Yet several members of these lipid II - targeted lantibiotics are too short to be

Taylor Dispersion Analysis as a promising tool for assessment of peptide-peptide interactions.

Science.gov (United States)

Høgstedt, Ulrich B; Schwach, Grégoire; van de Weert, Marco; Østergaard, Jesper

2016-10-10

Protein-protein and peptide-peptide (self-)interactions are of key importance in understanding the physiochemical behavior of proteins and peptides in solution. However, due to the small size of peptide molecules, characterization of these interactions is more challenging than for proteins. In this work, we show that protein-protein and peptide-peptide interactions can advantageously be investigated by measurement of the diffusion coefficient using Taylor Dispersion Analysis. Through comparison to Dynamic Light Scattering it was shown that Taylor Dispersion Analysis is well suited for the characterization of protein-protein interactions of solutions of α-lactalbumin and human serum albumin. The peptide-peptide interactions of three selected peptides were then investigated in a concentration range spanning from 0.5mg/ml up to 80mg/ml using Taylor Dispersion Analysis. The peptide-peptide interactions determination indicated that multibody interactions significantly affect the PPIs at concentration levels above 25mg/ml for the two charged peptides. Relative viscosity measurements, performed using the capillary based setup applied for Taylor Dispersion Analysis, showed that the viscosity of the peptide solutions increased with concentration. Our results indicate that a viscosity difference between run buffer and sample in Taylor Dispersion Analysis may result in overestimation of the measured diffusion coefficient. Thus, Taylor Dispersion Analysis provides a practical, but as yet primarily qualitative, approach to assessment of the colloidal stability of both peptide and protein formulations. Copyright © 2016 Elsevier B.V. All rights reserved.

Extraction of aromatics from naphtha with ionic liquids

NARCIS (Netherlands)

Meindersma, G.W.

2005-01-01

The objective of this study was the development of a separation technology for the selective recovery and purification of aromatic compounds benzene, toluene, ethylbenzene and xylenes (BTEX) from liquid ethylene cracker feeds. Most ethylene cracker feeds contain 10 ¿ 25% of aromatic components,

Peptide-mediated lipofection is governed by lipoplex physical properties and the density of surface-displayed amines.

Science.gov (United States)

Rea, Jennifer C; Barron, Annelise E; Shea, Lonnie D

2008-11-01

Peptides can potentiate lipid-mediated gene delivery by modifying lipoplex physiochemical properties to overcome rate-limiting steps to gene transfer. The objectives of this study were to determine the regimes over which cationic peptides enhance lipofection and to investigate the mechanism of action, such as increased cellular association resulting from changes in lipoplex physical properties. Short, cationic peptides were incorporated into lipoplexes by mixing peptide, lipid and DNA. Lipoplexes were characterized using gel retardation, dynamic light scattering, and fluorescent microscopy, and the amount of surface-displayed amines was quantified by fluorescamine. Size, zeta potential, and surface amines for lipoplexes were dependent on peptide/DNA ratio. Inclusion of peptides in lipoplexes resulted in up to a 13-fold increase in percentage of cells transfected, and up to a 76-fold increase in protein expression. This transfection enhancement corresponded to a small particle diameter and positive zeta potential of lipoplexes, as well as increased amount of surface-displayed amines. Relative to lipid alone, these properties of the peptide-modified lipoplexes enhanced cellular association, which has been reported as a rate-limiting step for transfection with lipoplexes. The addition of peptides is a simple method of lipofection enhancement, as direct chemical modification of lipids is not necessary for increased transfection.

Self-assembled electrical materials from contorted aromatics

Science.gov (United States)

Xiao, Shengxiong

This thesis describes the design, synthesis, self-assembly and electrical properties of new types of contorted polycyclic aromatic hydrocarbons. These topologically interesting contorted aromatics show promising transistor characteristics as new building blocks for organic field-effect transistors (OFETs) at different length scales. In chapter 2, a class of pentacenes that are substituted along their long edges with aromatic rings were synthesized. Their solid-state assemblies were studied by X-ray crystallography. Their performance as thin film transistors (TFTs) and single crystal field effect transistors (SCFETs) were systematically evaluated. A structure-property relationship between these highly phenylated pentacenes was found. Chapter 3 explores the new concept of whether a non-planar aromatic core could yield efficacious electronic materials, as the ultimate success in the organic electronics will require a holistic approach to creating new building blocks. Synthesis, functionalization and assembly of a new type of contorted hexabenzocoronene (HBC) whose aromatic core is heavily distorted away from planarity due to the steric congestion around its proximal carbons were discussed. Structural studies by X-ray crystallography showed that these HBC molecules stack into columnar structures in the solid state, which are ideal for conduction. Chapter 4 describes that microscale liquid crystalline thin film OFETs of tetradodecyloxy HBC showed the best transistor properties of all discotic columnar materials. Chapter 5 details the fabrication and characterization of nanoscale single crystalline fiber OFETs of octadodecyloxyl HBC. In Chapter 6 we show that a molecular scale monolayer of HBC acid chlorides could be self-assembled on SiO2 insulating layer and could be organized laterally between the ends of 2 nm carbon nanotube gaps to form high quality FETs that act as environmental and chemical sensors. Chapter 7 details the enforced one-dimensional photoconductivity

Expression of multiple transgenes from a single construct using viral 2A peptides in Drosophila.

Directory of Open Access Journals (Sweden)

Richard W Daniels

Full Text Available Expression of multiple reporter or effector transgenes in the same cell from a single construct is increasingly necessary in various experimental paradigms. The discovery of short, virus-derived peptide sequences that mediate a ribosome-skipping event enables generation of multiple separate peptide products from one mRNA. Here we describe methods and vectors to facilitate easy production of polycistronic-like sequences utilizing these 2A peptides tailored for expression in Drosophila both in vitro and in vivo. We tested the separation efficiency of different viral 2A peptides in cultured Drosophila cells and in vivo and found that the 2A peptides from porcine teschovirus-1 (P2A and Thosea asigna virus (T2A worked best. To demonstrate the utility of this approach, we used the P2A peptide to co-express the red fluorescent protein tdTomato and the genetically-encoded calcium indicator GCaMP5G in larval motorneurons. This technique enabled ratiometric calcium imaging with motion correction allowing us to record synaptic activity at the neuromuscular junction in an intact larval preparation through the cuticle. The tools presented here should greatly facilitate the generation of 2A peptide-mediated expression of multiple transgenes in Drosophila.

In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands.

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Anna Russo

Full Text Available Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.

Antimicrobial Peptides in 2014

Directory of Open Access Journals (Sweden)

Guangshun Wang

2015-03-01

Full Text Available This article highlights new members, novel mechanisms of action, new functions, and interesting applications of antimicrobial peptides reported in 2014. As of December 2014, over 100 new peptides were registered into the Antimicrobial Peptide Database, increasing the total number of entries to 2493. Unique antimicrobial peptides have been identified from marine bacteria, fungi, and plants. Environmental conditions clearly influence peptide activity or function. Human α-defensin HD-6 is only antimicrobial under reduced conditions. The pH-dependent oligomerization of human cathelicidin LL-37 is linked to double-stranded RNA delivery to endosomes, where the acidic pH triggers the dissociation of the peptide aggregate to release its cargo. Proline-rich peptides, previously known to bind to heat shock proteins, are shown to inhibit protein synthesis. A model antimicrobial peptide is demonstrated to have multiple hits on bacteria, including surface protein delocalization. While cell surface modification to decrease cationic peptide binding is a recognized resistance mechanism for pathogenic bacteria, it is also used as a survival strategy for commensal bacteria. The year 2014 also witnessed continued efforts in exploiting potential applications of antimicrobial peptides. We highlight 3D structure-based design of peptide antimicrobials and vaccines, surface coating, delivery systems, and microbial detection devices involving antimicrobial peptides. The 2014 results also support that combination therapy is preferred over monotherapy in treating biofilms.

Antimicrobial Activity and Stability of Short and Long Based Arachnid Synthetic Peptides in the Presence of Commercial Antibiotics.

Science.gov (United States)

Arenas, Ivan; Villegas, Elba; Walls, Oliver; Barrios, Humberto; Rodríguez, Ramon; Corzo, Gerardo

2016-02-17

Four antimicrobial peptides (AMPs) named Pin2[G], Pin2[14], P18K and FA1 were chemically synthesized and purified. The four peptides were evaluated in the presence of eight commercial antibiotics against four microorganisms of medical importance: Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae. The commercial antibiotics used were amoxicillin, azithromycin, ceftriaxone, gentamicin, levofloxacin, sulfamethoxazole, trimethoprim and vancomycin. The best AMP against P. aeruginosa was the peptide FA1, and the best AMP against S. aureus was Pin2[G]. Both FA1 and Pin2[G] were efficient against E. coli, but they were not effective against K. pneumoniae. As K. pneumoniae was resistant to most of the commercial antibiotics, combinations of the AMPs FA1 and Pin2[G] were prepared with these antibiotics. According to the fractional inhibitory concentration (FIC) index, the best antimicrobial combinations were obtained with concomitant applications of mixtures of FA1 with levofloxacin and sulfamethoxazole. However, combinations of FA1 or Pin2[G] with other antibiotics showed that total inhibitory effect of the combinations were greater than the sum of the individual effects of either the antimicrobial peptide or the antibiotic. We also evaluated the stability of the AMPs. The AMP Pin2[G] manifested the best performance in saline buffer, in supernatants of bacterial growth and in human blood plasma. Nevertheless, all AMPs were cleaved using endoproteolytic enzymes. These data show advantages and disadvantages of AMPs for potential clinical treatments of bacterial infections, using them in conjunction with commercial antibiotics.

Antimicrobial Activity and Stability of Short and Long Based Arachnid Synthetic Peptides in the Presence of Commercial Antibiotics

Directory of Open Access Journals (Sweden)

Ivan Arenas

2016-02-01

Full Text Available Four antimicrobial peptides (AMPs named Pin2[G], Pin2[14], P18K and FA1 were chemically synthesized and purified. The four peptides were evaluated in the presence of eight commercial antibiotics against four microorganisms of medical importance: Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae. The commercial antibiotics used were amoxicillin, azithromycin, ceftriaxone, gentamicin, levofloxacin, sulfamethoxazole, trimethoprim and vancomycin. The best AMP against P. aeruginosa was the peptide FA1, and the best AMP against S. aureus was Pin2[G]. Both FA1 and Pin2[G] were efficient against E. coli, but they were not effective against K. pneumoniae. As K. pneumoniae was resistant to most of the commercial antibiotics, combinations of the AMPs FA1 and Pin2[G] were prepared with these antibiotics. According to the fractional inhibitory concentration (FIC index, the best antimicrobial combinations were obtained with concomitant applications of mixtures of FA1 with levofloxacin and sulfamethoxazole. However, combinations of FA1 or Pin2[G] with other antibiotics showed that total inhibitory effect of the combinations were greater than the sum of the individual effects of either the antimicrobial peptide or the antibiotic. We also evaluated the stability of the AMPs. The AMP Pin2[G] manifested the best performance in saline buffer, in supernatants of bacterial growth and in human blood plasma. Nevertheless, all AMPs were cleaved using endoproteolytic enzymes. These data show advantages and disadvantages of AMPs for potential clinical treatments of bacterial infections, using them in conjunction with commercial antibiotics.

Anaerobic catabolism of aromatic compounds: a genetic and genomic view.

Science.gov (United States)

Carmona, Manuel; Zamarro, María Teresa; Blázquez, Blas; Durante-Rodríguez, Gonzalo; Juárez, Javier F; Valderrama, J Andrés; Barragán, María J L; García, José Luis; Díaz, Eduardo

2009-03-01

Aromatic compounds belong to one of the most widely distributed classes of organic compounds in nature, and a significant number of xenobiotics belong to this family of compounds. Since many habitats containing large amounts of aromatic compounds are often anoxic, the anaerobic catabolism of aromatic compounds by microorganisms becomes crucial in biogeochemical cycles and in the sustainable development of the biosphere. The mineralization of aromatic compounds by facultative or obligate anaerobic bacteria can be coupled to anaerobic respiration with a variety of electron acceptors as well as to fermentation and anoxygenic photosynthesis. Since the redox potential of the electron-accepting system dictates the degradative strategy, there is wide biochemical diversity among anaerobic aromatic degraders. However, the genetic determinants of all these processes and the mechanisms involved in their regulation are much less studied. This review focuses on the recent findings that standard molecular biology approaches together with new high-throughput technologies (e.g., genome sequencing, transcriptomics, proteomics, and metagenomics) have provided regarding the genetics, regulation, ecophysiology, and evolution of anaerobic aromatic degradation pathways. These studies revealed that the anaerobic catabolism of aromatic compounds is more diverse and widespread than previously thought, and the complex metabolic and stress programs associated with the use of aromatic compounds under anaerobic conditions are starting to be unraveled. Anaerobic biotransformation processes based on unprecedented enzymes and pathways with novel metabolic capabilities, as well as the design of novel regulatory circuits and catabolic networks of great biotechnological potential in synthetic biology, are now feasible to approach.

A Tetrameric Peptide Derived from Bovine Lactoferricin Exhibits Specific Cytotoxic Effects against Oral Squamous-Cell Carcinoma Cell Lines

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Víctor A. Solarte

2015-01-01

Full Text Available Several short linear peptides derived from cyclic bovine lactoferricin were synthesized and tested for their cytotoxic effect against the oral cavity squamous-cell carcinoma (OSCC cell lines CAL27 and SCC15. As a control, an immortalized and nontumorigenic cell line, Het-1A, was used. Linear peptides based on the RRWQWR core sequence showed a moderate cytotoxic effect and specificity towards tumorigenic cells. A tetrameric peptide, LfcinB(20–254, containing the RRWQWR motif, exhibited greater cytotoxic activity (>90% in both OSCC cell lines compared to the linear lactoferricin peptide or the lactoferrin protein. Additionally, this tetrameric peptide showed the highest specificity towards tumorigenic cells among the tested peptides. Interestingly, this effect was very fast, with cell shrinkage, severe damage to cell membrane permeability, and lysis within one hour of treatment. Our results are consistent with a necrotic effect rather than an apoptotic one and suggest that this tetrameric peptide could be considered as a new candidate for the therapeutic treatment of OSCC.

Glucagon-like peptide-2 induces rapid digestive adaptation following intestinal resection in preterm neonates

Science.gov (United States)

Short bowel syndrome (SBS) is a frequent complication after intestinal resection in infants suffering from intestinal disease. We tested whether treatment with the intestinotrophic hormone glucagon-like peptide-2 (GLP-2) increases intestinal volume and function in the period immediately following in...

Geochemical interpretation of distribution of aromatic hydrocarbons in components of geologic environment of Pechora, Barents and Kara seas.

Science.gov (United States)

Kursheva, Anna; Petrova, Vera; Litvinenko, Ivan; Morgunova, Inna

2017-04-01

aromatization and new formation of number of compounds, for example perylene (λmax 405,435 nm). The presence in sediments of highly transformed (post-diagenetic) organic material forms special (for naphthides) type of spectrum (λmax 370-380 nm), which interface is fundamentally different from recent marine sediments. Similar type of spectrum in combination with anomalously high content of aromatic hydrocarbons (ca. 349.1 μg/g) is typical, in particular, for shelf of Spitsbergen archipelago, whose erosion and redeposition of carboniferous rocks play important role in deposits formation. Similar content of aromatic hydrocarbons was noted in sediments of shelf of the Island Kolguev, where exogenous anomaly is caused mainly by anthropogenic factors. This assumption correlates with the results of aromatic hydrocarbons examination where pyrogenic components dominate. The influence of endogenous processes (seepage of hydrocarbons) also may lead to substantial deformation of background spectrum due to formation of intensive peak in short-wave region (λmax max 240-260 nm). Credibility of collected results is proven by significant correlation of quantitative estimation of aromatic hydrocarbons contents conducted using both dispersed organic matter extraction and fractionation and spectrofluorimetry methods. Results, received during GC-MS analysis also prove spectrofluorometric information.

Separation of aromatics by vapor permeation through solvent swollen membrane

Energy Technology Data Exchange (ETDEWEB)

Ito, A.; Adachi, K.; Feng, Y. [Niigata University, Niigata (Japan)

1995-12-20

A vapor permeation process for aromatics separation from a hydrocarbon mixture was studied by means of the simultaneous permeation of dimethylsulfoxide vapor as an agent for membrane swelling and preferential permeation of aromatics. The separation performance of the process was demonstrated by a polyvinylalcohol membrane for mixed vapors of benzene/cyclohexane, xylene/octane and a model gasoline. The aromatic vapors preferentially permeated from these mixed vapor feeds. The separation factor was over 10. The separation mechanism of the process mainly depends on the relative salability of the vapors between aromatics and other hydrocarbons in dimethylsulfoxide. 14 refs., 9 figs., 1 tab.

Does the concept of Clar's aromatic sextet work for dicationic forms of polycyclic aromatic hydrocarbons?--testing the model against charged systems in singlet and triplet states.

Science.gov (United States)

Dominikowska, Justyna; Palusiak, Marcin

2011-07-07

The concept of Clar's π-electron aromatic sextet was tested against a set of polycyclic aromatic hydrocarbons in neutral and doubly charged forms. Systems containing different types of rings (in the context of Clar's concept) were chosen, including benzene, naphthalene, anthracene, phenanthrene and triphenylene. In the case of dicationic structures both singlet and triplet states were considered. It was found that for singlet state dicationic structures the concept of aromatic sextet could be applied and the local aromaticity could be discussed in the context of that model, whereas in the case of triplet state dicationic structures Clar's model rather failed. Different aromaticity indices based on various properties of molecular systems were applied for the purpose of the studies. The discussion about the interdependence between the values of different aromaticity indices applied to neutral and charged systems in singlet and triplet states is also included. This journal is © the Owner Societies 2011

Solvent polarity controls the helical conformation of short peptides rich in Calpha-tetrasubstituted amino acids.

Science.gov (United States)

Bellanda, Massimo; Mammi, Stefano; Geremia, Silvano; Demitri, Nicola; Randaccio, Lucio; Broxterman, Quirinus B; Kaptein, Bernard; Pengo, Paolo; Pasquato, Lucia; Scrimin, Paolo

2007-01-01

The two peptides, rich in C(alpha)-tetrasubstituted amino acids, Ac-[Aib-L-(alphaMe)Val-Aib](2)-L-His-NH(2) (1) and Ac-[Aib-L-(alphaMe)Val-Aib](2)-O-tBu (2 a) are prevalently helical. They present the unique property of changing their conformation from the alpha- to the 3(10)-helix as a function of the polarity of the solvent: alpha in more polar solvents, 3(10) in less polar ones. Conclusive evidence of this reversible change of conformation is reported on the basis of the circular dichroism (CD) spectra and a detailed two-dimensional NMR analysis in two solvents (trifluoroethanol and methanol) refined with molecular dynamics calculations. The X-ray diffractometric analysis of the crystals of both peptides reveals that they assume a prevalent 3(10)-helix conformation in the solid state. This conformation is practically superimposable on that obtained from the NMR analysis of 1 in methanol. The NMR results further validate the reported CD signature of the 3(10)-helix and the use of the CD technique for its assessment.

Deuteration of benzen derivatives and condensed aromatics

International Nuclear Information System (INIS)

Ichikawa, Masaru.

1970-01-01

A process for the deuteration of aromatic compounds (benzene derivatives having one or more cyano, halogeno, nitro or other electron attractive groups, and condensed ring aromatics) is provided. The process comprises reducing said aromatic compound with an alkali metal (preferably K, Rb or Cs) in a solvent (dimethoxyethane, tetrahydrofuran, etc.) to provide an electron-acceptor-donor complex, which is followed by introducing gaseous deuterium into the solution. The deuteration takes place selectively at the position of highest electron density in accordance with nature of the substituent, regardless of steric hindrance. The process is applicable to a wide variety of aromatics to give deuterated compounds in high yields. In one example, 5x10 -3 mole of anthracene (An) was reacted with 2g of metallic potassium in 80cc of dimethoxyethane in a N 2 atmosphere. Into the resulting solution of An=2K + was introduced D 2 gas (30 cmHg) at 25 0 C. After decomposition with air and washing with alcohol, the precipitate was recrystallized from benzene. Yield of recovered AN: more than 90%. Yield of deuteration: 100%. Position of deuteration: 9 and 10 (revealed by NMR and mass spectroscopy). (Kaichi, S.)

Synthesis and bioelectrochemical behavior of aromatic amines.

Science.gov (United States)

Shabbir, Muhammad; Akhter, Zareen; Ahmad, Iqbal; Ahmed, Safeer; Bolte, Michael; McKee, Vickie

2017-12-01

Four aromatic amines 1-amino-4-phenoxybenzene (A 1 ), 4-(4-aminophenyloxy) biphenyl (A 2 ), 1-(4-aminophenoxy) naphthalene (A 3 ) and 2-(4-aminophenoxy) naphthalene (A 4 ) were synthesized and characterized by elemental, spectroscopic (FTIR, NMR), mass spectrometric and single crystal X-ray diffraction methods. The compounds crystallized in monoclinic crystal system with space group P2 1 . Intermolecular hydrogen bonds were observed between the amine group and amine/ether acceptors of neighboring molecules. Electrochemical investigations were done using cyclic voltammetry (CV), square wave voltammetry (SWV) and differential pulse voltammetry (DPV). CV studies showed that oxidation of aromatic amines takes place at about 0.9 V (vs. Ag/AgCl) and the electron transfer (ET) process has irreversible nature. After first scan reactive intermediate were generated electrochemically and some other cathodic and anodic peaks also appeared in the succeeding scans. DPV study revealed that ET process is accompanied by one electron. DNA binding study of aromatic amines was performed by CV and UV-visible spectroscopy. These investigations revealed groove binding mode of interaction of aromatic amines with DNA. Copyright © 2017 Elsevier Inc. All rights reserved.

Oxidative decomposition of aromatic hydrocarbons by electron beam irradiation

Science.gov (United States)

Han, Do-Hung; Stuchinskaya, Tatiana; Won, Yang-Soo; Park, Wan-Sik; Lim, Jae-Kyong

2003-05-01

Decomposition of aromatic volatile organic compounds (VOCs) under electron beam irradiation was studied in order to examine the kinetics of the process, to characterize the reaction product distribution and to develop a process of waste gas control technology. Toluene, ethylbenzene, o-, m-, p-xylenes and chlorobenzene were used as target materials. The experiments were carried out at doses ranging from 0.5 to 10 kGy, using a flow reactor utilized under electron beam irradiation. Maximum degrees of decomposition carried out at 10 kGy in air environment were 55-65% for “non-chlorinated” aromatic VOC and 85% for chlorobenzene. It was found that a combination of aromatic pollutants with chlorobenzene would considerably increase the degradation value up to nearly 50% compared to the same compounds in the absence of chlorine groups. Based on our experimental observation, the degradation mechanism of the aromatic compounds combined with chloro-compound suggests that a chlorine radical, formed from EB irradiation, induces a chain reaction, resulting in an accelerating oxidative destruction of aromatic VOCs.

Comparison of trapping profiles between d-peptides and glutathione in the identification of reactive metabolites

Directory of Open Access Journals (Sweden)

Jaana E. Laine

2015-01-01

Full Text Available Qualitative trapping profile of reactive metabolites arising from six structurally different compounds was tested with three different d-peptide isomers (Peptide 1, gly–tyr–pro–cys–pro–his-pro; Peptide 2, gly–tyr–pro–ala–pro–his–pro; Peptide 3, gly–tyr–arg–pro–cys–pro–his–lys–pro and glutathione (GSH using mouse and human liver microsomes as the biocatalyst. The test compounds were classified either as clinically “safe” (amlodipine, caffeine, ibuprofen, or clinically as “risky” (clozapine, nimesulide, ticlopidine; i.e., associated with severe clinical toxicity outcomes. Our working hypothesis was as follows: could the use of short different amino acid sequence containing d-peptides in adduct detection confer any add-on value to that obtained with GSH? All “risky” agents’ resulted in the formation of several GSH adducts in the incubation mixture and with at least one peptide adduct with both microsomal preparations. Amlodipine did not form any adducts with any of the trapping agents. No GSH and peptide 2 and 3 adducts were found with caffeine, but with peptide 1 one adduct with human liver microsomes was detected. Ibuprofen produced one Peptide 1-adduct with human and mouse liver microsomes but not with GSH. In conclusion, GSH still remains the gold trapping standard for reactive metabolites. However, targeted d-peptides could provide additional information about protein binding potential of electrophilic agents, but their clinical significance needs to be clarified using a wider spectrum of chemicals together with other safety estimates.

Connecting peptide (c-peptide) and the duration of diabetes mellitus ...

African Journals Online (AJOL)

Objective: C-peptide is derived from proinsulin and it is secreted in equimolar concentration with insulin. Plasma C-peptide is more stable than insulin and it provides an indirect measure of insulin secretory reserve and beta cell function. To determine relationship between C-peptide and duration of diabetes mellitus, age, ...

Ampulexins: A New Family of Peptides in Venom of the Emerald Jewel Wasp, Ampulex compressa.

Science.gov (United States)

Moore, Eugene L; Arvidson, Ryan; Banks, Christopher; Urenda, Jean Paul; Duong, Elizabeth; Mohammed, Haroun; Adams, Michael E

2018-03-27

The parasitoid wasp Ampulex compressa injects venom directly into the brain and subesophageal ganglion of the cockroach Periplaneta americana, inducing a 7 to 10 day lethargy termed hypokinesia. Hypokinesia presents as a significant reduction in both escape response and spontaneous walking. We examined aminergic and peptidergic components of milked venom with HPLC and MALDI-TOF mass spectrometry. HPLC coupled with electrochemical detection confirmed the presence of dopamine in milked venom, while mass spectrometry revealed that the venom gland and venom sac have distinct peptide profiles, with milked venom predominantly composed of venom sac peptides. We isolated and characterized novel α-helical, amphipathic venom sac peptides that constitute a new family of venom toxins termed ampulexins. Injection of the most abundant venom peptide, ampulexin 1, into the subesophageal ganglion of cockroaches resulted in a short-term increase in escape threshold. Neither milked venom nor venom peptides interfered with growth of Escherichia coli or Bacillus thuringiensis on agar plates, and exposure to ampulexins or milked venom did not induce cell death in Chinese hamster ovary cells (CHO-K1) or Hi5 cells ( Trichoplusia ni).

Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces.

Science.gov (United States)

Dalgicdir, Cahit; Globisch, Christoph; Peter, Christine; Sayar, Mehmet

2015-08-01

Secondary amphiphilicity is inherent to the secondary structural elements of proteins. By forming energetically favorable contacts with each other these amphiphilic building blocks give rise to the formation of a tertiary structure. Small proteins and peptides, on the other hand, are usually too short to form multiple structural elements and cannot stabilize them internally. Therefore, these molecules are often found to be structurally ambiguous up to the point of a large degree of intrinsic disorder in solution. Consequently, their conformational preference is particularly susceptible to environmental conditions such as pH, salts, or presence of interfaces. In this study we use molecular dynamics simulations to analyze the conformational behavior of two synthetic peptides, LKKLLKLLKKLLKL (LK) and EAALAEALAEALAE (EALA), with built-in secondary amphiphilicity upon forming an alpha-helix. We use these model peptides to systematically study their aggregation and the influence of macroscopic and molecular interfaces on their conformational preferences. We show that the peptides are neither random coils in bulk water nor fully formed alpha helices, but adopt multiple conformations and secondary structure elements with short lifetimes. These provide a basis for conformation-selection and population-shift upon environmental changes. Differences in these peptides' response to macroscopic and molecular interfaces (presented by an aggregation partner) can be linked to their inherent alpha-helical tendencies in bulk water. We find that the peptides' aggregation behavior is also strongly affected by presence or absence of an interface, and rather subtly depends on their surface charge and hydrophobicity.

Microbial degradation of aliphatic and aliphatic-aromatic co-polyesters.

Science.gov (United States)

Shah, Aamer Ali; Kato, Satoshi; Shintani, Noboru; Kamini, Numbi Ramudu; Nakajima-Kambe, Toshiaki

2014-04-01

Biodegradable plastics (BPs) have attracted much attention since more than a decade because they can easily be degraded by microorganisms in the environment. The development of aliphatic-aromatic co-polyesters has combined excellent mechanical properties with biodegradability and an ideal replacement for the conventional nondegradable thermoplastics. The microorganisms degrading these polyesters are widely distributed in various environments. Although various aliphatic, aromatic, and aliphatic-aromatic co-polyester-degrading microorganisms and their enzymes have been studied and characterized, there are still many groups of microorganisms and enzymes with varying properties awaiting various applications. In this review, we have reported some new microorganisms and their enzymes which could degrade various aliphatic, aromatic, as well as aliphatic-aromatic co-polyesters like poly(butylene succinate) (PBS), poly(butylene succinate)-co-(butylene adipate) (PBSA), poly(ε-caprolactone) (PCL), poly(ethylene succinate) (PES), poly(L-lactic acid) (PLA), poly(3-hydroxybutyrate) and poly(3-hydoxybutyrate-co-3-hydroxyvalterate) (PHB/PHBV), poly(ethylene terephthalate) (PET), poly(butylene terephthalate) (PBT), poly(butylene adipate-co-terephthalate (PBAT), poly(butylene succinate-co-terephthalate) (PBST), and poly(butylene succinate/terephthalate/isophthalate)-co-(lactate) (PBSTIL). The mechanism of degradation of aliphatic as well as aliphatic-aromatic co-polyesters has also been discussed. The degradation ability of microorganisms against various polyesters might be useful for the treatment and recycling of biodegradable wastes or bioremediation of the polyester-contaminated environments.

Peptide-Carrier Conjugation

DEFF Research Database (Denmark)

Hansen, Paul Robert

2015-01-01

To produce antibodies against synthetic peptides it is necessary to couple them to a protein carrier. This chapter provides a nonspecialist overview of peptide-carrier conjugation. Furthermore, a protocol for coupling cysteine-containing peptides to bovine serum albumin is outlined....

A microbially derived tyrosine-sulfated peptide mimics a plant peptide hormone.

Science.gov (United States)

Pruitt, Rory N; Joe, Anna; Zhang, Weiguo; Feng, Wei; Stewart, Valley; Schwessinger, Benjamin; Dinneny, José R; Ronald, Pamela C

2017-07-01

The biotrophic pathogen Xanthomonas oryzae pv. oryzae (Xoo) produces a sulfated peptide named RaxX, which shares similarity to peptides in the PSY (plant peptide containing sulfated tyrosine) family. We hypothesize that RaxX mimics the growth-stimulating activity of PSY peptides. Root length was measured in Arabidopsis and rice treated with synthetic RaxX peptides. We also used comparative genomic analyses and reactive oxygen species burst assays to evaluate the activity of RaxX and PSY peptides. Here we found that a synthetic sulfated RaxX derivative comprising 13 residues (RaxX13-sY), highly conserved between RaxX and PSY, induces root growth in Arabidopsis and rice in a manner similar to that triggered by PSY. We identified residues that are required for activation of immunity mediated by the rice XA21 receptor but that are not essential for root growth induced by PSY. Finally, we showed that a Xanthomonas strain lacking raxX is impaired in virulence. These findings suggest that RaxX serves as a molecular mimic of PSY peptides to facilitate Xoo infection and that XA21 has evolved the ability to recognize and respond specifically to the microbial form of the peptide. © 2017 UT-Battelle LLC. New Phytologist © 2017 New Phytologist Trust.

Distributions of Polycyclic Aromatic Hydrocarbons, Aromatic Ketones, Carboxylic Acids, and Trace Metals in Arctic Aerosols: Long-Range Atmospheric Transport, Photochemical Degradation/Production at Polar Sunrise.

Science.gov (United States)

Singh, Dharmendra Kumar; Kawamura, Kimitaka; Yanase, Ayako; Barrie, Leonard A

2017-08-15

The distributions, correlations, and source apportionment of aromatic acids, aromatic ketones, polycyclic aromatic hydrocarbons (PAHs), and trace metals were studied in Canadian high Arctic aerosols. Nineteen PAHs including minor sulfur-containing heterocyclic PAH (dibenzothiophene) and major 6 carcinogenic PAHs were detected with a high proportion of fluoranthene followed by benzo[k]fluoranthene, pyrene, and chrysene. However, in the sunlit period of spring, their concentrations significantly declined likely due to photochemical decomposition. During the polar sunrise from mid-March to mid-April, benzo[a]pyrene to benzo[e]pyrene ratios significantly dropped, and the ratios diminished further from late April to May onward. These results suggest that PAHs transported over the Arctic are subjected to strong photochemical degradation at polar sunrise. Although aromatic ketones decreased in spring, concentrations of some aromatic acids such as benzoic and phthalic acids increased during the course of polar sunrise, suggesting that aromatic hydrocarbons are oxidized to result in aromatic acids. However, PAHs do not act as the major source for low molecular weight (LMW) diacids such as oxalic acid that are largely formed at polar sunrise in the arctic atmosphere because PAHs are 1 to 2 orders of magnitude less abundant than LMW diacids. Correlations of trace metals with organics, their sources, and the possible role of trace transition metals are explained.

Tumor penetrating peptides

Directory of Open Access Journals (Sweden)

Tambet eTeesalu

2013-08-01

Full Text Available Tumor-homing peptides can be used to deliver drugs into tumors. Phage library screening in live mice has recently identified homing peptides that specifically recognize the endothelium of tumor vessels, extravasate, and penetrate deep into the extravascular tumor tissue. The prototypic peptide of this class, iRGD (CRGDKGPDC, contains the integrin-binding RGD motif. RGD mediates tumor homing through binding to αv integrins, which are selectively expressed on various cells in tumors, including tumor endothelial cells. The tumor-penetrating properties of iRGD are mediated by a second sequence motif, R/KXXR/K. This C-end Rule (or CendR motif is active only when the second basic residue is exposed at the C-terminus of the peptide. Proteolytic processing of iRGD in tumors activates the cryptic CendR motif, which then binds to neuropilin-1 activating an endocytic bulk transport pathway through tumor tissue. Phage screening has also yielded tumor-penetrating peptides that function like iRGD in activating the CendR pathway, but bind to a different primary receptor. Moreover, novel tumor-homing peptides can be constructed from tumor-homing motifs, CendR elements and protease cleavage sites. Pathologies other than tumors can be targeted with tissue-penetrating peptides, and the primary receptor can also be a vascular zip code of a normal tissue. The CendR technology provides a solution to a major problem in tumor therapy, poor penetration of drugs into tumors. The tumor-penetrating peptides are capable of taking a payload deep into tumor tissue in mice, and they also penetrate into human tumors ex vivo. Targeting with these peptides specifically increases the accumulation in tumors of a variety of drugs and contrast agents, such as doxorubicin, antibodies and nanoparticle-based compounds. Remarkably the drug to be targeted does not have to be coupled to the peptide; the bulk transport system activated by the peptide sweeps along any compound that is

Identification and characterization of Cd-induced peptides in Egeria densa (water weed): Putative role in Cd detoxification

International Nuclear Information System (INIS)

Malec, Przemyslaw; Maleva, Maria G.; Prasad, M.N.V.; Strzalka, Kazimierz

2009-01-01

Egeria densa has ability to grow in heavy metal contaminated and polluted bodies of water. Shoots exposed to Cd at concentrations up to 300 μM for 7 days showed a pronounced decrease in chlorophyll a and in total protein concentration. Thiol-containing compounds and low-molecular-weight polypeptides were detected in Cd-treated plant extracts by gel filtration chromatography. Two Cd-binding fractions, a thiol-enriched fraction and a non-thiol fraction with a lower molecular weight were identified in extracts by gel filtration. The main fraction of thiol-containing polypeptide, purified by gel filtration and anion-exchange chromatography had a molecular weight of ∼10 kDa. This peptide was characterized by a broad absorption band specific to mercaptide bonds and Cd-sensitive fluorescence emission of aromatic amino acid residues. Our results indicate that cadmium exposure of plants resulted in both a formation of thiol-enriched cadmium complexing peptides and a synthesis of low-molecular-weight metal chelators. The putative role of these compounds in Cd detoxification is discussed.

Diversity, evolution and medical applications of insect antimicrobial peptides

OpenAIRE

Mylonakis, Eleftherios; Podsiadlowski, Lars; Muhammed, Maged; Vilcinskas, Andreas

2016-01-01

Antimicrobial peptides (AMPs) are short proteins with antimicrobial activity. A large portion of known AMPs originate from insects, and the number and diversity of these molecules in different species varies considerably. Insect AMPs represent a potential source of alternative antibiotics to address the limitation of current antibiotics, which has been caused by the emergence and spread of multidrug-resistant pathogens. To get more insight into AMPs, we investigated the diversity and evolutio...

Aromatic graphene

Energy Technology Data Exchange (ETDEWEB)

Das, D. K., E-mail: gour.netai@gmail.com [Department of Metallurgical and Material Science Engineering, National Institute of Technology Durgapur-713209, West Bengal (India); Sahoo, S., E-mail: sukadevsahoo@yahoo.com [Department of Physics, National Institute of Technology Durgapur-713209, West Bengal (India)

2016-04-13

In recent years graphene attracts the scientific and engineering communities due to its outstanding electronic, thermal, mechanical and optical properties and many potential applications. Recently, Popov et al. [1] have studied the properties of graphene and proved that it is aromatic but without fragrance. In this paper, we present a theory to prepare graphene with fragrance. This can be used as scented pencils, perfumes, room and car fresheners, cosmetics and many other useful household substances.

Aromatic graphene

International Nuclear Information System (INIS)

Das, D. K.; Sahoo, S.

2016-01-01

In recent years graphene attracts the scientific and engineering communities due to its outstanding electronic, thermal, mechanical and optical properties and many potential applications. Recently, Popov et al. [1] have studied the properties of graphene and proved that it is aromatic but without fragrance. In this paper, we present a theory to prepare graphene with fragrance. This can be used as scented pencils, perfumes, room and car fresheners, cosmetics and many other useful household substances.

Effects of treatment with glucagon-like peptide-2 on bone resorption in colectomized patients with distal ileostomy or jejunostomy and short-bowel syndrome

DEFF Research Database (Denmark)

Gottschalck, Ida B; Jeppesen, Palle B; Hartmann, Bolette

2008-01-01

OBJECTIVE: The gut hormone GLP-2 (glucagon-like peptide-2) seems to be involved in the circadian pattern of bone resorption, whereas parathyroid hormone (PTH) is an established key hormone in bone turnover. Endogenous GLP-2 secretion is lacking in colectomized patients with short-bowel syndrome...... (SBS) and they have reduced bone mineral density (BMD). The aim of the study was to investigate the anti-resorptive effect (assessed by s-CTX) of 14 days of GLP-2 treatment in these patients and to determine whether 56 days of treatment would improve BMD. PTH secretion in response to GLP-2 was also...... in the SBS patients, and after 56 days of GLP-2 treatment there was no improvement in BMD. A significant reduction in PTH secretion in response to GLP-2 was observed only in patients with ileostomy. CONCLUSIONS: The decreased bone resorption in response to GLP-2 injections cannot be elicited in SBS patients...

ArrayPitope: Automated Analysis of Amino Acid Substitutions for Peptide Microarray-Based Antibody Epitope Mapping

DEFF Research Database (Denmark)

Hansen, Christian Skjødt; Østerbye, Thomas; Marcatili, Paolo

2017-01-01

-reactivity. B cell epitopes are typically classified as either linear epitopes, i.e. short consecutive segments from the protein sequence or conformational epitopes adapted through native protein folding. Recent advances in high-density peptide microarrays enable high-throughput, high-resolution identification...

Peptide Nucleic Acids

DEFF Research Database (Denmark)

2003-01-01

A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

Peptide Nucleic Acids

DEFF Research Database (Denmark)

1998-01-01

A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

PeptideAtlas

Data.gov (United States)

U.S. Department of Health & Human Services — PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass...

Synthetic peptide vaccines: palmitoylation of peptide antigens by a thioester bond increases immunogenicity

DEFF Research Database (Denmark)

Beekman, N.J.C.M.; Schaaper, W.M.M.; Tesser, G.I.

1997-01-01

Synthetic peptides have frequently been used to immunize animals. However, peptides less than about 20 to 30 amino acids long are poor immunogens. In general, to increase its immunogenicity, the presentation of the peptide should be improved, and molecular weight needs to be increased. Many...... or an amide bond. It was found that these S-palmitoylated peptides were much more immunogenic than N-palmitoylated peptides and at least similar to KLH-conjugated peptides with respect to appearance and magnitude of induced antibodies (canine parvovirus) or immunocastration effect (gonadotropin...

Global simulation of aromatic volatile organic compounds in the atmosphere

Science.gov (United States)

Cabrera Perez, David; Taraborrelli, Domenico; Pozzer, Andrea

2015-04-01

Among the large number of chemical compounds in the atmosphere, the organic group plays a key role in the tropospheric chemistry. Specifically the subgroup called aromatics is of great interest. Aromatics are the predominant trace gases in urban areas due to high emissions, primarily by vehicle exhausts and fuel evaporation. They are also present in areas where biofuel is used (i.e residential wood burning). Emissions of aromatic compounds are a substantial fraction of the total emissions of the volatile organic compounds (VOC). Impact of aromatics on human health is very important, as they do not only contribute to the ozone formation in the urban environment, but they are also highly toxic themselves, especially in the case of benzene which is able to trigger a range of illness under long exposure, and of nitro-phenols which cause detrimental for humans and vegetation even at very low concentrations. The aim of this work is to assess the atmospheric impacts of aromatic compounds on the global scale. The main goals are: lifetime and budget estimation, mixing ratios distribution, net effect on ozone production and OH loss for the most emitted aromatic compounds (benzene, toluene, xylenes, ethylbenzene, styrene and trimethylbenzenes). For this purpose, we use the numerical chemistry and climate simulation ECHAM/MESSy Atmospheric Chemistry (EMAC) model to build the global atmospheric budget for the most emitted and predominant aromatic compounds in the atmosphere. A set of emissions was prepared in order to include biomass burning, vegetation and anthropogenic sources of aromatics into the model. A chemical mechanism based on the Master Chemical Mechanism (MCM) was developed to describe the chemical oxidation in the gas phase of these aromatic compounds. MCM have been reduced in terms of number of chemical equation and species in order to make it affordable in a 3D model. Additionally other features have been added, for instance the production of HONO via ortho

Comparison Review of Short-Acting and Long-Acting Glucagon-like Peptide-1 Receptor Agonists

OpenAIRE

Uccellatore, Annachiara; Genovese, Stefano; Dicembrini, Ilaria; Mannucci, Edoardo; Ceriello, Antonio

2015-01-01

Glucagon-like peptide-1 (GLP-1) receptor agonists (GLP-1 RAs) are useful tools for treating type 2 diabetes mellitus. In their recent position statement, the American Diabetes Association and European Association for the Study of Diabetes recommend GLP1-RAs as add-on to metformin when therapeutic goals are not achieved with monotherapy, particularly for patients who wish to avoid weight gain or hypoglycemia. GLP1-RAs differ substantially in their duration of action, frequency of administratio...

Global aromatics supply. Today and tomorrow

Energy Technology Data Exchange (ETDEWEB)

Bender, M. [BASF SE, Ludwigshafen (Germany)

2013-11-01

Aromatics are the essential building blocks for some of the largest petrochemical products in today's use. To the vast majority they are consumed to produce intermediates for polymer products and, hence, contribute to our modern lifestyle. Their growth rates are expected to be in line with GDP growth in future. This contrasts the significantly lower growth rates of the primary sources for aromatics - fuel processing and steam cracking of naphtha fractions. A supply gap can be expected to open up in future for which creative solutions will be required. (orig.)

Silicone elastomers with aromatic voltage stabilizers

DEFF Research Database (Denmark)

A Razak, Aliff Hisyam; Skov, Anne Ladegaard

of electron-trapping by aromatic compounds grafted to silicone backbones in a crosslinked PDMS is illustrated in Fig. 1. The electrical breakdown strength, the storage modulus and the loss modulus of the elastomer were investigated, as well as the excitation energy from the collision between electron carriers...... and benzene rings in PDMS-PPMS copolymer was measured by UV-vis spectroscopy. The developed elastomers were inherently soft with enhanced electrical breakdown strength due to delocalized pi-electrons of aromatic rings attached to the silicone backbone. The dielectric relative permittivity of PDMS...

Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins II reactions at side-chain loci in model systems

International Nuclear Information System (INIS)

Garrison, W.M.

1983-11-01

The major emphasis in radiation biology at the molecular level has been on the nucleic acid component of the nucleic acid-protein complex because of its primary genetic importance. But there is increasing evidence that radiation damage to the protein component also has important biological implications. Damage to capsid protein now appears to be a major factor in the radiation inactivation of phage and other viruses. And, there is increasing evidence that radiation-chemical change in the protein component of chromation leads to changes in the stability of the repressor-operator complexes involved in gene expression. Knowledge of the radiation chemistry of protein is also of importance in other fields such as the application of radiation sterilization to foods and drugs. Recent findings that a class of compounds, the α,α'-diaminodicarboxylic acids, not normally present in food proteins, are formed in protein radiolysis is of particular significance since certain of their peptide derivatives have been showing to exhibit immunological activity. The purpose of this review is to bring together and to correlate our present knowledge of products and mechanisms in the radiolysis of peptides, polypeptides and proteins both aqueous and solid-state. In part 1 we presented a discussion of the radiation-induced reactions of the peptide main-chain in model peptide and polypeptide systems. Here in part 2 the emphasis is on the competing radiation chemistry at side-chain loci of peptide derivatives of aliphatic, aromatic-unsaturated and sulfur-containing amino acids in similar systems. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis, and ESR spectroscopy are included

How proteases from Enterococcus faecalis contribute to its resistance to short alpha-helical antimicrobial peptides

Czech Academy of Sciences Publication Activity Database

Nešuta, Ondřej; Buděšínský, Miloš; Hadravová, Romana; Monincová, Lenka; Humpolíčková, Jana; Čeřovský, Václav

2017-01-01

Roč. 75, č. 7 (2017), č. článku ftx091. ISSN 2049-632X R&D Projects: GA TA ČR(CZ) TA04010638; GA MZd(CZ) NV16-27726A Institutional support: RVO:61388963 Keywords : antimicrobial peptides * biofilm * C-terminal deamidation * gelatinase * protease Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 2.335, year: 2016

[New strategy for RNA vectorization in mammalian cells. Use of a peptide vector].

Science.gov (United States)

Vidal, P; Morris, M C; Chaloin, L; Heitz, F; Divita, G

1997-04-01

A major barrier for gene delivery is the low permeability of nucleic acids to cellular membranes. The development of antisenses and gene therapy has focused mainly on improving methods of oligonucleotide or gene delivery to the cell. In this report we described a new strategy for RNA cell delivery, based on a short single peptide. This peptide vector is derived from both the fusion domain of the gp41 protein of HIV and the nuclear localization sequence of the SV40 large T antigen. This peptide vector localizes rapidly to the cytoplasm then to the nucleus of human fibroblasts (HS-68) within a few minutes and exhibits a high affinity for a single-stranded mRNA encoding the p66 subunit of the HIV-1 reverse transcriptase (in a 100 nM range). The peptide/RNA complex formation involves mainly electrostatic interactions between the basic residues of the peptide and the charges on the phosphate group of the RNA. In the presence of the peptide-vector fluorescently-labelled mRNA is delivered into the cytoplasm of mammalian cells (HS68 human fibroblasts) in less than 1 h with a relatively high efficiency (80%). This new concept based on a peptide-derived vector offers several advantages compared to other compounds commonly used in gene delivery. This vector is highly soluble and exhibits no cytotoxicity at the concentrations used for optimal gene delivery. This result clearly supports the fact that this peptide vector is a powerful tool and that it can be used widely, as much for laboratory research as for new applications and development in gene and/or antisense therapy.

Polycyclic Aromatic Hydrocarbons

Science.gov (United States)

Salama, Farid

2010-01-01

Carbonaceous materials play an important role in space. Polycyclic Aromatic Hydrocarbons (PAHs) are a ubiquitous component of the carbonaceous materials. PAHs are the best-known candidates to account for the IR emission bands. They are also thought to be among the carriers of the diffuse interstellar absorption bands (DIBs). PAH ionization states reflect the ionization balance of the medium while PAH size, composition, and structure reflect the energetic and chemical history of the medium. A major challenge is to reproduce in the laboratory the physical conditions that exist in the emission and absorption interstellar zones. The harsh physical conditions of the ISM -low temperature, collisionless, strong UV radiation fields- are simulated in the laboratory by associating a molecular beam with an ionizing discharge to generate a cold plasma expansion. PAH ions and radicals are formed from the neutral precursors in an isolated environment at low temperature and probed with high-sensitivity cavity ringdown spectroscopy in the NUV-NIR range. Carbon nanoparticles are also formed during the short residence time of the precursors in the plasma and are characterized with time-offlight mass spectrometry. These experiments provide unique information on the spectra of large carbonaceous molecules and ions in the gas phase that can now be directly compared to interstellar and circumstellar observations (IR emission bands, DIBs, extinction curve). These findings also hold great potential for understanding the formation process of interstellar carbonaceous grains. We will review recent progress in the experimental and theoretical studies of PAHs, compare the laboratory data with astronomical observations and discuss the global implications.

Equilibrium studies of the adsorption of aromatic disulfonates by Mg-Al oxide

Science.gov (United States)

Kameda, Tomohito; Umetsu, Mami; Kumagai, Shogo; Yoshioka, Toshiaki

2018-03-01

The removal of m-benzenedisulfonate (BDS2-) and 2,6-naphthalenedisulfonate (NDS2-) anions by Mg-Al oxide was investigated. Langmuir model best describes the adsorption of both aromatic disulfonate anions, with the maximum amount of uptake higher for BDS2-. Mg-Al oxide reacts easier with the aromatic disulfonate anion with higher charge density, a trend that is the opposite of that observed in aromatic sulfonate anions. After increasing the charge from -1 to -2, the removal of aromatic disulfonates by Mg-Al oxide is controlled by electrostatic interactions, instead of hydrophobic interactions that are dominant for aromatic sulfonate anions.

Diversity-oriented peptide stapling

DEFF Research Database (Denmark)

Tran, Thu Phuong; Larsen, Christian Ørnbøl; Røndbjerg, Tobias

2017-01-01

as a powerful method for peptide stapling. However, to date CuAAC stapling has not provided a simple method for obtaining peptides that are easily diversified further. In the present study, we report a new diversity-oriented peptide stapling (DOPS) methodology based on CuAAC chemistry. Stapling of peptides...

Alzheimer's disease against peptides products of enzymatic cleavage APP protein: Biological, pathobiological and physico-chemical properties of fibrillating peptides.

Science.gov (United States)

Marszałek, Małgorzata

2017-05-17

Various peptides products of enzymatic cleavage of key for Alzheimer's disease Amyloid Precursor Protein (APP) are well known, but still are matter of scientific debate. The Aβ type products are especially challenging for experimental and medical research. This paper outlines several, still poorly known, biological and medical processes such as peptides biology, i.e., formation, biodistribution, translocation, transport and finally removal from brain compartments and body fluids like Intracellular Fluid (ICF), Cerebrospinal Fluid (CSF), Interstitial Fluid (ISF), blood serum or urine. In addition, the following studies concerning AD patients might prove challenging and simultaneously promising: peptides translocation through Blood-Brain - Barrier (BBB) and Blood-Cerebrospinal Fluid Barrier (BCSFB) and their removal from the brain according to a new concept of glymphatic system; - diagnostic difficulties that stem from physico-chemical properties and the nature of proteins or fibrillating peptides itself like low concentration, short half-live and from experimental-technical problems as well like high adsorption or low solubility of Aβ, tau or amylin. The study of diagnostic parameters is very important, as it may better reflect early changes before the disease develops; one such parameter is the Aβ42/Aβ40 ratio, or the ratio with the total tau concentration combination and other new biomarkers like Aβ1-38; other factors include oxidative stress and inflammation process proteins, complement factor H, alpha-2-macroglobulin, or clusterin. The study of various forms of pathological amyloid deposits that emerge in different but specific brain regions AD patients seems to be crucial as well. The composition of the first initial pathological, pre-fibrillating monomers of fibrillating peptides and their role in AD development and disease progression have been described as well. They are even more challenging for science and simultaneously might be more promising in

B-type natriuretic peptides. A diagnostic breakthrough in heart failure.

Science.gov (United States)

McCullough, P A

2003-04-01

B-type natriuretic peptide (BNP) is a neurohormone synthesized in the cardiac ventricles, which is released as N-terminal pro-brain natriuretic peptide (NT-proBNP) and then enzymatically cleaved in to the NT fragment and the immunoreactive BNP. Both tests have been used to identify patients with congestive heart failure (CHF). Important considerations for these tests include their half-lives in plasma, dependence on renal function for clearance, and the interpretation of their units of measure. In general, a BNP level below 100 pg/mL has strong negative predictive value in the assessment of patients with dyspnea caused by a disorder other than CHF. In addition, BNP levels can be used to gauge the effect of short-term treatment of acutely decompensated heart failure, and the peptide has been shown to be a reliable independent predictor of sudden cardiac death. In the absence of renal dysfunction NT-proBNP has also been shown to be an independent predictor of sudden death in CHF patients. Because both a large area of myonecrosis or concomitant left ventricular failure are related to prognosis in acute coronary syndromes, B-type natriuretic peptides have also been linked to outcomes in this condition. This article describes the physiology and timing of release of B-type natriuretic peptides and the rationale for their use in the following settings: 1) evaluation of decompensated CHF, 2) screening for chronic CHF, 3) prognosis of CHF and sudden death, and 4) prognosis in acute coronary syndromes with inferred left ventricular dysfunction.

Effect of a Fusion Peptide by Covalent Conjugation of a Mitochondrial Cell-Penetrating Peptide and a Glutathione Analog Peptide

Directory of Open Access Journals (Sweden)

Carmine Pasquale Cerrato

2017-06-01

Full Text Available Previously, we designed and synthesized a library of mitochondrial antioxidative cell-penetrating peptides (mtCPPs superior to the parent peptide, SS31, to protect mitochondria from oxidative damage. A library of antioxidative glutathione analogs called glutathione peptides (UPFs, exceptional in hydroxyl radical elimination compared with glutathione, were also designed and synthesized. Here, a follow-up study is described, investigating the effects of the most promising members from both libraries on reactive oxidative species scavenging ability. None of the peptides influenced cell viability at the concentrations used. Fluorescence microscopy studies showed that the fluorescein-mtCPP1-UPF25 (mtgCPP internalized into cells, and spectrofluorometric analysis determined the presence and extent of peptide into different cell compartments. mtgCPP has superior antioxidative activity compared with mtCPP1 and UPF25 against H2O2 insult, preventing ROS formation by 2- and 3-fold, respectively. Moreover, we neither observed effects on mitochondrial membrane potential nor production of ATP. These data indicate that mtgCPP is targeting mitochondria, protecting them from oxidative damage, while also being present in the cytosol. Our hypothesis is based on a synergistic effect resulting from the fused peptide. The mitochondrial peptide segment is targeting mitochondria, whereas the glutathione analog peptide segment is active in the cytosol, resulting in increased scavenging ability.

Peptide-membrane interactions of arginine-tryptophan peptides probed using quartz crystal microbalance with dissipation monitoring.

KAUST Repository

Rydberg, Hanna A

2014-04-18

Membrane-active peptides include peptides that can cross cellular membranes and deliver macromolecular cargo as well as peptides that inhibit bacterial growth. Some of these peptides can act as both transporters and antibacterial agents. It is desirable to combine the knowledge from these two different fields of membrane-active peptides into design of new peptides with tailored actions, as transporters of cargo or as antibacterial substances, targeting specific membranes. We have previously shown that the position of the amino acid tryptophan in the peptide sequence of three arginine-tryptophan peptides affects their uptake and intracellular localization in live mammalian cells, as well as their ability to inhibit bacterial growth. Here, we use quartz crystal microbalance with dissipation monitoring to assess the induced changes caused by binding of the three peptides to supported model membranes composed of POPC, POPC/POPG, POPC/POPG/cholesterol or POPC/lactosyl PE. Our results indicate that the tryptophan position in the peptide sequence affects the way these peptides interact with the different model membranes and that the presence of cholesterol in particular seems to affect the membrane interaction of the peptide with an even distribution of tryptophans in the peptide sequence. These results give mechanistic insight into the function of these peptides and may aid in the design of membrane-active peptides with specified cellular targets and actions.

Peptide-membrane interactions of arginine-tryptophan peptides probed using quartz crystal microbalance with dissipation monitoring.

KAUST Repository

Rydberg, Hanna A; Kunze, Angelika; Carlsson, Nils; Altgä rde, Noomi; Svedhem, Sofia; Nordé n, Bengt

2014-01-01

Membrane-active peptides include peptides that can cross cellular membranes and deliver macromolecular cargo as well as peptides that inhibit bacterial growth. Some of these peptides can act as both transporters and antibacterial agents. It is desirable to combine the knowledge from these two different fields of membrane-active peptides into design of new peptides with tailored actions, as transporters of cargo or as antibacterial substances, targeting specific membranes. We have previously shown that the position of the amino acid tryptophan in the peptide sequence of three arginine-tryptophan peptides affects their uptake and intracellular localization in live mammalian cells, as well as their ability to inhibit bacterial growth. Here, we use quartz crystal microbalance with dissipation monitoring to assess the induced changes caused by binding of the three peptides to supported model membranes composed of POPC, POPC/POPG, POPC/POPG/cholesterol or POPC/lactosyl PE. Our results indicate that the tryptophan position in the peptide sequence affects the way these peptides interact with the different model membranes and that the presence of cholesterol in particular seems to affect the membrane interaction of the peptide with an even distribution of tryptophans in the peptide sequence. These results give mechanistic insight into the function of these peptides and may aid in the design of membrane-active peptides with specified cellular targets and actions.

Automated solid-phase peptide synthesis to obtain therapeutic peptides

Directory of Open Access Journals (Sweden)

Veronika Mäde

2014-05-01

Full Text Available The great versatility and the inherent high affinities of peptides for their respective targets have led to tremendous progress for therapeutic applications in the last years. In order to increase the drugability of these frequently unstable and rapidly cleared molecules, chemical modifications are of great interest. Automated solid-phase peptide synthesis (SPPS offers a suitable technology to produce chemically engineered peptides. This review concentrates on the application of SPPS by Fmoc/t-Bu protecting-group strategy, which is most commonly used. Critical issues and suggestions for the synthesis are covered. The development of automated methods from conventional to essentially improved microwave-assisted instruments is discussed. In order to improve pharmacokinetic properties of peptides, lipidation and PEGylation are described as covalent conjugation methods, which can be applied by a combination of automated and manual synthesis approaches. The synthesis and application of SPPS is described for neuropeptide Y receptor analogs as an example for bioactive hormones. The applied strategies represent innovative and potent methods for the development of novel peptide drug candidates that can be manufactured with optimized automated synthesis technologies.

Ion beam irradiation effects on aromatic polymers

International Nuclear Information System (INIS)

Shukushima, Satoshi; Ueno, Keiji

1995-01-01

We studied the optical and thermal properties of aromatic polymer films which had been irradiated with 1 MeV H + , H 2 + and He + ions. The examined aromatic polymers were polyetherether ketone(PEEK), polyetherimide(PEI), polyether sulfon(PES), polysulfon(PSF), and polyphenylene sulfide(PPS). The optical densities at 300nm of PES and PSF greatly increased after the irradiation. The optical densities at 400nm of all the examined polymer lineally increased with the irradiation dose. The PEEK film which had been irradiated with 1 MeV H + was not deformed above melting point. This demonstrates that cross-linking occurs in PEEK films by ion beam irradiation. As for the effects, depending on the mass of the irradiated ions, it was found that the ions with a high mass induced larger effects on the aromatic polymers for the same absorption energy. (author)

Determination of aromatic and PAH (polycyclic aromatic hydrocarbons) content of oily wastewaters

Energy Technology Data Exchange (ETDEWEB)

Lysyj, I.; Russell, E.C.

1978-08-01

An analytical scheme was developed for determining the total organic content and hydrocarbon concentration from a one-liter portion of a wastewater sample, and determining the volatile, suspended, and water-soluble fractions from a second, two-liter portion. Analyses of untreated and treated bilge wastewater from the U.S. Army Fort Eustis, Va., facility showed 10-300 ppm suspended organics and 10-300 ppm dissolved organics in the untreated bilge, and no suspended matter, but 700-2000 ppm dissolved organics, in the treated bilge wastewaters. Of the dissolved organics in untreated and treated wastewater, 70 and 10%, respectively, were extracted with chloroform; the organics in the treated water were probably biologically derived from petroleum degradation. Gas chromatographic/mass spectroscopic and high-pressure liquid chromatographic analyses of the chloroform extracts showed about equal parts of phenolic compounds and aromatic hydrocarbons, small amounts of heterocyclics, and traces of polycyclic aromatics in the untreated wastewater, and mainly phenolics in the treated water.

The effect of a beta-lactamase inhibitor peptide on bacterial membrane structure and integrity: a comparative study.

Science.gov (United States)

Alaybeyoglu, Begum; Uluocak, Bilge Gedik; Akbulut, Berna Sariyar; Ozkirimli, Elif

2017-05-01

Co-administration of beta-lactam antibiotics and beta-lactamase inhibitors has been a favored treatment strategy against beta-lactamase-mediated bacterial antibiotic resistance, but the emergence of beta-lactamases resistant to current inhibitors necessitates the discovery of novel non-beta-lactam inhibitors. Peptides derived from the Ala46-Tyr51 region of the beta-lactamase inhibitor protein are considered as potent inhibitors of beta-lactamase; unfortunately, peptide delivery into the cell limits their potential. The properties of cell-penetrating peptides could guide the design of beta-lactamase inhibitory peptides. Here, our goal is to modify the peptide with the sequence RRGHYY that possesses beta-lactamase inhibitory activity under in vitro conditions. Inspired by the work on the cell-penetrating peptide pVEC, our approach involved the addition of the N-terminal hydrophobic residues, LLIIL, from pVEC to the inhibitor peptide to build a chimera. These residues have been reported to be critical in the uptake of pVEC. We tested the potential of RRGHYY and its chimeric derivative as a beta-lactamase inhibitory peptide on Escherichia coli cells and compared the results with the action of the antimicrobial peptide melittin, the beta-lactam antibiotic ampicillin, and the beta-lactamase inhibitor potassium clavulanate to get mechanistic details on their action. Our results show that the addition of LLIIL to the N-terminus of the beta-lactamase inhibitory peptide RRGHYY increases its membrane permeabilizing potential. Interestingly, the addition of this short stretch of hydrophobic residues also modified the inhibitory peptide such that it acquired antimicrobial property. We propose that addition of the hydrophobic LLIIL residues to the peptide N-terminus offers a promising strategy to design novel antimicrobial peptides in the battle against antibiotic resistance. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2017 European

Production of peptide antisera specific for mouse and rat proinsulin C-peptide 2

DEFF Research Database (Denmark)

Blume, N; Madsen, O D; Kofod, Hans

1990-01-01

for antibody binding to the immunizing antigen. Antisera to C-peptide 2, stained islet beta-cells on mouse and rat, but not monkey pancreas sections in immunocytochemical analysis. Preabsorption to the synthetic C-peptide 2, but not the synthetic mouse and rat C-peptide 1 abolished staining. In conclusion we......Mice and rats have two functional non-allelic insulin genes. By using a synthetic peptide representing a common sequence in mouse and rat C-peptide 2 as antigen, we have produced rabbit antisera specific for an epitope which is not present in mouse or rat C-peptide 1. Long-term immunization did...... not seem to increase the end point titre as tested in direct ELISA. The specificity of the antiserum was determined by competitive ELISA and histochemistry on pancreas sections. Only the synthetic C-peptide 2, but not the homologous synthetic C-peptide 1 from mouse and rat competed efficiently in ELISA...

Therapeutic peptides for cancer therapy. Part I - peptide inhibitors of signal transduction cascades.

Science.gov (United States)

Bidwell, Gene L; Raucher, Drazen

2009-10-01

Therapeutic peptides have great potential as anticancer agents owing to their ease of rational design and target specificity. However, their utility in vivo is limited by low stability and poor tumor penetration. The authors review the development of peptide inhibitors with potential for cancer therapy. Peptides that inhibit signal transduction cascades are discussed. The authors searched Medline for articles concerning the development of therapeutic peptides and their delivery. Given our current knowledge of protein sequences, structures and interaction interfaces, therapeutic peptides that inhibit interactions of interest are easily designed. These peptides are advantageous because they are highly specific for the interaction of interest, and they are much more easily developed than small molecule inhibitors of the same interactions. The main hurdle to application of peptides for cancer therapy is their poor pharmacokinetic and biodistribution parameters. Therefore, successful development of peptide delivery vectors could potentially make possible the use of this new and very promising class of anticancer agents.

Identification of Four-Jointed Box 1 (FJX1-Specific Peptides for Immunotherapy of Nasopharyngeal Carcinoma.

Directory of Open Access Journals (Sweden)

San Jiun Chai

Full Text Available Nasopharyngeal carcinoma (NPC is highly prevalent in South East Asia and China. The poor outcome is due to late presentation, recurrence, distant metastasis and limited therapeutic options. For improved treatment outcome, immunotherapeutic approaches focusing on dendritic and autologous cytotoxic T-cell based therapies have been developed, but cost and infrastructure remain barriers for implementing these in low-resource settings. As our prior observations had found that four-jointed box 1 (FJX1, a tumor antigen, is overexpressed in NPCs, we investigated if short 9-20 amino acid sequence specific peptides matching to FJX1 requiring only intramuscular immunization to train host immune systems would be a better treatment option for this disease. Thus, we designed 8 FJX1-specific peptides and implemented an assay system to first, assess the binding of these peptides to HLA-A2 molecules on T2 cells. After, ELISPOT assays were used to determine the peptides immunogenicity and ability to induce potential cytotoxicity activity towards cancer cells. Also, T-cell proliferation assay was used to evaluate the potential of MHC class II peptides to stimulate the expansion of isolated T-cells. Our results demonstrate that these peptides are immunogenic and peptide stimulated T-cells were able to induce peptide-specific cytolytic activity specifically against FJX1-expressing cancer cells. In addition, we demonstrated that the MHC class II peptides were capable of inducing T-cell proliferation. Our results suggest that these peptides are capable of inducing specific cytotoxic cytokines secretion against FJX1-expressing cancer cells and serve as a potential vaccine-based therapy for NPC patients.

Identification of Four-Jointed Box 1 (FJX1)-Specific Peptides for Immunotherapy of Nasopharyngeal Carcinoma

Science.gov (United States)

Chai, San Jiun; Yap, Yoke Yeow; Foo, Yoke Ching; Yap, Lee Fah; Ponniah, Sathibalan; Teo, Soo Hwang; Cheong, Sok Ching; Patel, Vyomesh; Lim, Kue Peng

2015-01-01

Nasopharyngeal carcinoma (NPC) is highly prevalent in South East Asia and China. The poor outcome is due to late presentation, recurrence, distant metastasis and limited therapeutic options. For improved treatment outcome, immunotherapeutic approaches focusing on dendritic and autologous cytotoxic T-cell based therapies have been developed, but cost and infrastructure remain barriers for implementing these in low-resource settings. As our prior observations had found that four-jointed box 1 (FJX1), a tumor antigen, is overexpressed in NPCs, we investigated if short 9–20 amino acid sequence specific peptides matching to FJX1 requiring only intramuscular immunization to train host immune systems would be a better treatment option for this disease. Thus, we designed 8 FJX1-specific peptides and implemented an assay system to first, assess the binding of these peptides to HLA-A2 molecules on T2 cells. After, ELISPOT assays were used to determine the peptides immunogenicity and ability to induce potential cytotoxicity activity towards cancer cells. Also, T-cell proliferation assay was used to evaluate the potential of MHC class II peptides to stimulate the expansion of isolated T-cells. Our results demonstrate that these peptides are immunogenic and peptide stimulated T-cells were able to induce peptide-specific cytolytic activity specifically against FJX1-expressing cancer cells. In addition, we demonstrated that the MHC class II peptides were capable of inducing T-cell proliferation. Our results suggest that these peptides are capable of inducing specific cytotoxic cytokines secretion against FJX1-expressing cancer cells and serve as a potential vaccine-based therapy for NPC patients. PMID:26536470

Infrared Spectroscopy of Matrix-Isolated Polycyclic Aromatic Nitrogen Heterocycles (PANHs)

Science.gov (United States)

Mattioda, A. L.; Hudgins, D. M.; Bauschlicher, C. W.; Allamandola, L. J.; Biemesderfer, C. D.; Rosi, M.

2002-01-01

The mid-infrared spectra of the nitrogen-containing heterocyclic polycyclic aromatic compounds 1-azabenz[a]-anthracene; 2-azabenz[a]anthracene; 1-azachrysene; 2-azachrysene; 4-azachrysene; 2-azapyrene, and 7,8 benzoquinoline in their neutral and cation forms were investigated. The spectra of these species isolated in an argon matrix have been measured. Band frequencies and intensities were tabulated and these data compared with spectra computed using density functional theory at the B3LYP level. The overall agreement between experiment and theory is quite good, in keeping with earlier results on homonuclear polycyclic aromatic hydrocarbons. The differences between the spectral properties of nitrogen bearing aromatics and non-substituted, neutral polycyclic aromatic hydrocarbons will be discussed.

SEDIMENT-ASSOCIATED REACTIONS OF AROMATIC AMINES. 2. QSAR DEVELOPMENT

Science.gov (United States)

The fate of aromatic amines in soils and sediments is dominated by irreversible binding through nucleophilic addition and oxidative radical coupling. Despite the common occurrence of the aromatic amine functional group in organic chemicals, the molecular properties useful for pr...

Purification and use of E. coli peptide deformylase for peptide deprotection in chemoenzymatic peptide synthesis

NARCIS (Netherlands)

Di Toma, Claudia; Sonke, Theo; Quaedflieg, Peter J.; Janssen, Dick B.

Peptide deformylases (PDFs) catalyze the removal of the formyl group from the N-terminal methionine residue in nascent polypeptide chains in prokaryotes. Its deformylation activity makes PDF an attractive candidate for the biocatalytic deprotection of formylated peptides that are used in

Antioxidant activity of yoghurt peptides: Part 2 – Characterisationof peptide fractions

DEFF Research Database (Denmark)

Farvin, Sabeena; Baron, Caroline; Nielsen, Nina Skall

2010-01-01

the peptides identified contained at least one proline residue. Some of the identified peptides included the hydrophobic amino acid residues Val or Leu at the N-terminus and Pro, His or Tyr in the amino acid sequence, which is characteristic of antioxidant peptides. In addition, the yoghurt contained...

Ligand-regulated peptide aptamers.

Science.gov (United States)

Miller, Russell A

2009-01-01

The peptide aptamer approach employs high-throughput selection to identify members of a randomized peptide library displayed from a scaffold protein by virtue of their interaction with a target molecule. Extending this approach, we have developed a peptide aptamer scaffold protein that can impart small-molecule control over the aptamer-target interaction. This ligand-regulated peptide (LiRP) scaffold, consisting of the protein domains FKBP12, FRB, and GST, binds to the cell-permeable small-molecule rapamycin and the binding of this molecule can prevent the interaction of the randomizable linker region connecting FKBP12 with FRB. Here we present a detailed protocol for the creation of a peptide aptamer plasmid library, selection of peptide aptamers using the LiRP scaffold in a yeast two-hybrid system, and the screening of those peptide aptamers for a ligand-regulated interaction.

A novel aromatic alcohol dehydrogenase in higher plants: molecular cloning and expression.

Science.gov (United States)

Goffner, D; Van Doorsselaere, J; Yahiaoui, N; Samaj, J; Grima-Pettenati, J; Boudet, A M

1998-03-01

Cinnamyl alcohol dehydrogenase (CAD; EC 1.1.195) catalyses the conversion of p-hydroxy-cinnamaldehydes to the corresponding alcohols and is considered a key enzyme in lignin biosynthesis. In a previous study, an atypical form of CAD (CAD 1) was identified in Eucalyptus gunnii [12]. We report here the molecular cloning and characterization of the corresponding cDNA, CAD 1-5, which encodes this novel aromatic alcohol dehydrogenase. The identity of CAD 1-5 was unambiguously confirmed by sequence comparison of the cDNA with peptide sequences derived from purified CAD 1 protein and by functional expression of CAD 1 recombinant protein in Escherichia coli. Both native and recombinant CAD 1 exhibit high affinity towards lignin precursors including 4-coumaraldehyde and coniferaldehyde, but they do not accept sinapaldehyde. Moreover, recombinant CAD 1 can also utilize a wide range of aromatic substrates including unsubstituted and substituted benzaldehydes. The open reading frame of CAD 1-5 encodes a protein with a calculated molecular mass of 35,790 Da and an isoelectric point of 8.1. Although sequence comparisons with proteins in databases revealed significant similarities with dihydroflavonol-4-reductases (DFR; EC 1.1.1.219) from a wide range of plant species, the most striking similarity was found with cinnamoyl-CoA reductase (CCR; EC 1.2.1.44), the enzyme which directly precedes CAD in the lignin biosynthetic pathway. RNA blot analysis and immunolocalization experiments indicated that CAD 1 is expressed in both lignified and unlignified tissues/cells. Based on the catalytic activity of CAD 1 in vitro and its localization in planta, CAD 1 may function as an 'alternative' enzyme in the lignin biosynthetic pathway. However, additional roles in phenolic metabolism are not excluded.

Aromatic products from reaction of lignin model compounds with UV-alkaline peroxide

International Nuclear Information System (INIS)

Sun, Y.P.; Wallis, A.F.A.; Nguyen, K.L.

1997-01-01

A series of guaiacyl and syringyl lignin model compounds and their methylated analogues were reacted with alkaline hydrogen peroxide while irradiating with UV light at 254 nm. The aromatic products obtained were investigated by gas chromatography-mass spectrometry (GC-MS). Guaiacol, syringol and veratrol gave no detectable aromatic products. However, syringol methyl ether gave small amounts of aromatic products, resulting from ring substitution and methoxyl displacement by hydroxyl radicals. Reaction of vanillin and syringaldehyde gave the Dakin reaction products, methoxy-1,4-hydroquinones, while reaction of their methyl ethers yielded benzoic acids. Acetoguaiacone, acetosyringone and their methyl ethers afforded several hydroxylated aromatic products, but no aromatic products were identified in the reaction mixtures from guaiacylpropane and syringylpropane. In contrast, veratrylpropane gave a mixture from which 17 aromatic hydroxylated compounds were identified. It is concluded that for phenolic lignin model compounds, particularly those possessing electrondonating aromatic ring substituents, ring-cleavage reactions involving superoxide radical anions are dominant, whereas for non-phenolic lignin models, hydroxylation reactions through attack of hydroxyl radicals prevail

A distributive peptide cyclase processes multiple microviridin core peptides within a single polypeptide substrate.

Science.gov (United States)

Zhang, Yi; Li, Kunhua; Yang, Guang; McBride, Joshua L; Bruner, Steven D; Ding, Yousong

2018-05-03

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important family of natural products. Their biosynthesis follows a common scheme in which the leader peptide of a precursor peptide guides the modifications of a single core peptide. Here we describe biochemical studies of the processing of multiple core peptides within a precursor peptide, rare in RiPP biosynthesis. In a cyanobacterial microviridin pathway, an ATP-grasp ligase, AMdnC, installs up to two macrolactones on each of the three core peptides within AMdnA. The enzyme catalysis occurs in a distributive fashion and follows an unstrict N-to-C overall directionality, but a strict order in macrolactonizing each core peptide. Furthermore, AMdnC is catalytically versatile to process unnatural substrates carrying one to four core peptides, and kinetic studies provide insights into its catalytic properties. Collectively, our results reveal a distinct biosynthetic logic of RiPPs, opening up the possibility of modular production via synthetic biology approaches.

Superior Antifouling Performance of a Zwitterionic Peptide Compared to an Amphiphilic, Non-Ionic Peptide.

Science.gov (United States)

Ye, Huijun; Wang, Libing; Huang, Renliang; Su, Rongxin; Liu, Boshi; Qi, Wei; He, Zhimin

2015-10-14

The aim of this study was to explore the influence of amphiphilic and zwitterionic structures on the resistance of protein adsorption to peptide self-assembled monolayers (SAMs) and gain insight into the associated antifouling mechanism. Two kinds of cysteine-terminated heptapeptides were studied. One peptide had alternating hydrophobic and hydrophilic residues with an amphiphilic sequence of CYSYSYS. The other peptide (CRERERE) was zwitterionic. Both peptides were covalently attached onto gold substrates via gold-thiol bond formation. Surface plasmon resonance analysis results showed that both peptide SAMs had ultralow or low protein adsorption amounts of 1.97-11.78 ng/cm2 in the presence of single proteins. The zwitterionic peptide showed relatively higher antifouling ability with single proteins and natural complex protein media. We performed molecular dynamics simulations to understand their respective antifouling behaviors. The results indicated that strong surface hydration of peptide SAMs contributes to fouling resistance by impeding interactions with proteins. Compared to the CYSYSYS peptide, more water molecules were predicted to form hydrogen-bonding interactions with the zwitterionic CRERERE peptide, which is in agreement with the antifouling test results. These findings reveal a clear relation between peptide structures and resistance to protein adsorption, facilitating the development of novel peptide-containing antifouling materials.

A Review of Polycyclic Aromatic Hydrocarbons and Heavy Metal ...

African Journals Online (AJOL)

A Review of Polycyclic Aromatic Hydrocarbons and Heavy Metal Contamination of Fish from Fish Farms. ... Journal of Applied Sciences and Environmental Management ... Polycyclic aromatic hydrocarbons (PAHs) and heavy metals contribute to pollutants in aquaculture facilities and thus need to be further investigated.

Metal Triflates for the Production of Aromatics from Lignin

NARCIS (Netherlands)

Deuss, Peter J.; Lahive, Ciaran W.; Lancefield, Christopher S.; Westwood, Nicholas J.; Kamer, Paul C. J.; Barta, Katalin; de Vries, Johannes G.

2016-01-01

The depolymerization of lignin into valuable aromatic chemicals is one of the key goals towards establishing economically viable biorefineries. In this contribution we present a simple approach for converting lignin to aromatic monomers in high yields under mild reaction conditions. The methodology

Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces.

Directory of Open Access Journals (Sweden)

Cahit Dalgicdir

2015-08-01

Full Text Available Secondary amphiphilicity is inherent to the secondary structural elements of proteins. By forming energetically favorable contacts with each other these amphiphilic building blocks give rise to the formation of a tertiary structure. Small proteins and peptides, on the other hand, are usually too short to form multiple structural elements and cannot stabilize them internally. Therefore, these molecules are often found to be structurally ambiguous up to the point of a large degree of intrinsic disorder in solution. Consequently, their conformational preference is particularly susceptible to environmental conditions such as pH, salts, or presence of interfaces. In this study we use molecular dynamics simulations to analyze the conformational behavior of two synthetic peptides, LKKLLKLLKKLLKL (LK and EAALAEALAEALAE (EALA, with built-in secondary amphiphilicity upon forming an alpha-helix. We use these model peptides to systematically study their aggregation and the influence of macroscopic and molecular interfaces on their conformational preferences. We show that the peptides are neither random coils in bulk water nor fully formed alpha helices, but adopt multiple conformations and secondary structure elements with short lifetimes. These provide a basis for conformation-selection and population-shift upon environmental changes. Differences in these peptides' response to macroscopic and molecular interfaces (presented by an aggregation partner can be linked to their inherent alpha-helical tendencies in bulk water. We find that the peptides' aggregation behavior is also strongly affected by presence or absence of an interface, and rather subtly depends on their surface charge and hydrophobicity.

Reduction of Aromatic and Heterocyclic Aromatic N-Hydroxylamines by Human Cytochrome P450 2S1

Science.gov (United States)

Wang, Kai; Guengerich, F. Peter

2013-01-01

Many aromatic amines and heterocyclic aromatic amines (HAAs) are known carcinogens for animals and there is also strong evidence for some in human cancer. The activation of these compounds, including some arylamine drugs, involves N-hydroxylation, usually by cytochrome P450 enzymes (P450) in Family 1 (1A2, 1A1, and 1B1). We previously demonstrated that the bioactivation product of the anti-cancer agent 2-(4-amino-3-methylphenyl)-5-fluorobenzothiazole (5F 203), an N-hydroxylamine, can be reduced by P450 2S1 to its amine precursor under anaerobic conditions and, to a lesser extent, under aerobic conditions (Wang, K., and Guengerich, F. P. (2012) Chem. Res. Toxicol. 25, 1740–1751). In the present study, we tested the hypothesis that P450 2S1 is involved in the reductive biotransformation of known carcinogenic aromatic amines and HAAs. The N-hydroxylamines of 4-aminobiphenyl (4-ABP), 2-naphthylamine (2-NA), and 2-aminofluorene (2-AF) were synthesized and found to be reduced by P450 2S1 under both anaerobic and aerobic conditions. The formation of amines due to P450 2S1 reduction also occurred under aerobic conditions but was less apparent because the competitive disproportionation reactions (of the N-hydroxylamines) also yielded amines. Further, some nitroso and nitro derivatives of the arylamines could also be reduced by P450 2S1. None of the amines tested were oxidized by P450 2S1. These results suggest that P450 2S1 may be involved in the reductive detoxication of several of the activated products of carcinogenic aromatic amines and HAAs. PMID:23682735

Global atmospheric budget of simple monocyclic aromatic compounds

Directory of Open Access Journals (Sweden)

D. Cabrera-Perez

2016-06-01

Full Text Available The global atmospheric budget and distribution of monocyclic aromatic compounds is estimated, using an atmospheric chemistry general circulation model. Simulation results are evaluated with an ensemble of surface and aircraft observations with the goal of understanding emission, production and removal of these compounds.Anthropogenic emissions provided by the RCP database represent the largest source of aromatics in the model (≃ 23 TgC year−1 and biomass burning from the GFAS inventory the second largest (≃ 5 TgC year−1. The simulated chemical production of aromatics accounts for  ≃ 5 TgC year−1. The atmospheric burden of aromatics sums up to 0.3 TgC. The main removal process of aromatics is photochemical decomposition (≃ 27 TgC  year−1, while wet and dry deposition are responsible for a removal of  ≃ 4 TgC year−1.Simulated mixing ratios at the surface and elsewhere in the troposphere show good spatial and temporal agreement with the observations for benzene, although the model generally underestimates mixing ratios. Toluene is generally well reproduced by the model at the surface, but mixing ratios in the free troposphere are underestimated. Finally, larger discrepancies are found for xylenes: surface mixing ratios are not only overestimated but also a low temporal correlation is found with respect to in situ observations.

Antimicrobial Peptides in Reptiles

Science.gov (United States)

van Hoek, Monique L.

2014-01-01

Reptiles are among the oldest known amniotes and are highly diverse in their morphology and ecological niches. These animals have an evolutionarily ancient innate-immune system that is of great interest to scientists trying to identify new and useful antimicrobial peptides. Significant work in the last decade in the fields of biochemistry, proteomics and genomics has begun to reveal the complexity of reptilian antimicrobial peptides. Here, the current knowledge about antimicrobial peptides in reptiles is reviewed, with specific examples in each of the four orders: Testudines (turtles and tortosises), Sphenodontia (tuataras), Squamata (snakes and lizards), and Crocodilia (crocodilans). Examples are presented of the major classes of antimicrobial peptides expressed by reptiles including defensins, cathelicidins, liver-expressed peptides (hepcidin and LEAP-2), lysozyme, crotamine, and others. Some of these peptides have been identified and tested for their antibacterial or antiviral activity; others are only predicted as possible genes from genomic sequencing. Bioinformatic analysis of the reptile genomes is presented, revealing many predicted candidate antimicrobial peptides genes across this diverse class. The study of how these ancient creatures use antimicrobial peptides within their innate immune systems may reveal new understandings of our mammalian innate immune system and may also provide new and powerful antimicrobial peptides as scaffolds for potential therapeutic development. PMID:24918867

Biodegradation of Various Aromatic Compounds by Enriched Bacterial Cultures: Part A-Monocyclic and Polycyclic Aromatic Hydrocarbons.

Science.gov (United States)

Oberoi, Akashdeep Singh; Philip, Ligy; Bhallamudi, S Murty

2015-08-01

Present study focused on the screening of bacterial consortium for biodegradation of monocyclic aromatic hydrocarbon (MAH) and polycyclic aromatic hydrocarbons (PAHs). Target compounds in the present study were naphthalene, acenaphthene, phenanthrene (PAHs), and benzene (MAH). Microbial consortia enriched with the above target compounds were used in screening experiments. Naphthalene-enriched consortium was found to be the most efficient consortium, based on its substrate degradation rate and its ability to degrade other aromatic pollutants with significantly high efficiency. Substrate degradation rate with naphthalene-enriched culture followed the order benzene > naphthalene > acenaphthene > phenanthrene. Chryseobacterium and Rhodobacter were discerned as the predominant species in naphthalene-enriched culture. They are closely associated to the type strain Chryseobacterium arthrosphaerae and Rhodobacter maris, respectively. Single substrate biodegradation studies with naphthalene (PAH) and benzene (MAH) were carried out using naphthalene-enriched microbial consortium (NAPH). Phenol and 2-hydroxybenzaldehyde were identified as the predominant intermediates during benzene and naphthalene degradation, respectively. Biodegradation of toluene, ethyl benzene, xylene, phenol, and indole by NAPH was also investigated. Monod inhibition model was able to simulate biodegradation kinetics for benzene, whereas multiple substrate biodegradation model was able to simulate biodegradation kinetics for naphthalene.

Designer lipid-like peptides: a class of detergents for studying functional olfactory receptors using commercial cell-free systems.

Science.gov (United States)

Corin, Karolina; Baaske, Philipp; Ravel, Deepali B; Song, Junyao; Brown, Emily; Wang, Xiaoqiang; Wienken, Christoph J; Jerabek-Willemsen, Moran; Duhr, Stefan; Luo, Yuan; Braun, Dieter; Zhang, Shuguang

2011-01-01

A crucial bottleneck in membrane protein studies, particularly G-protein coupled receptors, is the notorious difficulty of finding an optimal detergent that can solubilize them and maintain their stability and function. Here we report rapid production of 12 unique mammalian olfactory receptors using short designer lipid-like peptides as detergents. The peptides were able to solubilize and stabilize each receptor. Circular dichroism showed that the purified olfactory receptors had alpha-helical secondary structures. Microscale thermophoresis suggested that the receptors were functional and bound their odorants. Blot intensity measurements indicated that milligram quantities of each olfactory receptor could be produced with at least one peptide detergent. The peptide detergents' capability was comparable to that of the detergent Brij-35. The ability of 10 peptide detergents to functionally solubilize 12 olfactory receptors demonstrates their usefulness as a new class of detergents for olfactory receptors, and possibly other G-protein coupled receptors and membrane proteins.

Designer lipid-like peptides: a class of detergents for studying functional olfactory receptors using commercial cell-free systems.

Directory of Open Access Journals (Sweden)

Karolina Corin

Full Text Available A crucial bottleneck in membrane protein studies, particularly G-protein coupled receptors, is the notorious difficulty of finding an optimal detergent that can solubilize them and maintain their stability and function. Here we report rapid production of 12 unique mammalian olfactory receptors using short designer lipid-like peptides as detergents. The peptides were able to solubilize and stabilize each receptor. Circular dichroism showed that the purified olfactory receptors had alpha-helical secondary structures. Microscale thermophoresis suggested that the receptors were functional and bound their odorants. Blot intensity measurements indicated that milligram quantities of each olfactory receptor could be produced with at least one peptide detergent. The peptide detergents' capability was comparable to that of the detergent Brij-35. The ability of 10 peptide detergents to functionally solubilize 12 olfactory receptors demonstrates their usefulness as a new class of detergents for olfactory receptors, and possibly other G-protein coupled receptors and membrane proteins.

Signal-BNF: A Bayesian Network Fusing Approach to Predict Signal Peptides

Directory of Open Access Journals (Sweden)

Zhi Zheng

2012-01-01

Full Text Available A signal peptide is a short peptide chain that directs the transport of a protein and has become the crucial vehicle in finding new drugs or reprogramming cells for gene therapy. As the avalanche of new protein sequences generated in the postgenomic era, the challenge of identifying new signal sequences has become even more urgent and critical in biomedical engineering. In this paper, we propose a novel predictor called Signal-BNF to predict the N-terminal signal peptide as well as its cleavage site based on Bayesian reasoning network. Signal-BNF is formed by fusing the results of different Bayesian classifiers which used different feature datasets as its input through weighted voting system. Experiment results show that Signal-BNF is superior to the popular online predictors such as Signal-3L and PrediSi. Signal-BNF is featured by high prediction accuracy that may serve as a useful tool for further investigating many unclear details regarding the molecular mechanism of the zip code protein-sorting system in cells.

Structure of genes for dermaseptins B, antimicrobial peptides from frog skin. Exon 1-encoded prepropeptide is conserved in genes for peptides of highly different structures and activities.

Science.gov (United States)

Vouille, V; Amiche, M; Nicolas, P

1997-09-01

We cloned the genes of two members of the dermaseptin family, broad-spectrum antimicrobial peptides isolated from the skin of the arboreal frog Phyllomedusa bicolor. The dermaseptin gene Drg2 has a 2-exon coding structure interrupted by a small 137-bp intron, wherein exon 1 encoded a 22-residue hydrophobic signal peptide and the first three amino acids of the acidic propiece; exon 2 contained the 18 additional acidic residues of the propiece plus a typical prohormone processing signal Lys-Arg and a 32-residue dermaseptin progenitor sequence. The dermaseptin genes Drg2 and Drg1g2 have conserved sequences at both untranslated ends and in the first and second coding exons. In contrast, Drg1g2 comprises a third coding exon for a short version of the acidic propiece and a second dermaseptin progenitor sequence. Structural conservation between the two genes suggests that Drg1g2 arose recently from an ancestral Drg2-like gene through amplification of part of the second coding exon and 3'-untranslated region. Analysis of the cDNAs coding precursors for several frog skin peptides of highly different structures and activities demonstrates that the signal peptides and part of the acidic propieces are encoded by conserved nucleotides encompassed by the first coding exon of the dermaseptin genes. The organization of the genes that belong to this family, with the signal peptide and the progenitor sequence on separate exons, permits strikingly different peptides to be directed into the secretory pathway. The recruitment of such a homologous 'secretory' exon by otherwise non-homologous genes may have been an early event in the evolution of amphibian.

Aromatics saturation, opening and cleavage technology for middle distillates

Energy Technology Data Exchange (ETDEWEB)

Oballa, M.C.; Simanzhenkov, V.; Kim, G. [NOVA Chemicals Corp., Calgary, AB (Canada)

2009-07-01

In order to address environmental concerns, there is a need to develop technologies to reformulate or adjust the quality of transportation fuels. The purpose is to reduce the concentration of the compounds which negatively affect the air that people breathe. One of those targeted is the aromatics content of diesel, because high aromatics content results in low cetane number of diesel, as well as higher emission of particulate matter. Less conventional sources of hydrocarbon feedstock such as oil from oil sands and/or shale oil are being exploited in Alberta. These feeds contain multiple fused aromatic ring compounds. NOVA Chemicals would like to use these potentially abundant liquids as feed, but they must first be transformed into a more user friendly state. This paper discussed the development of a process technology that could saturate the aromatic rings, open up the saturated rings and cleave them to get smaller paraffinic molecules. The products then comprised of lower paraffins are suitable as feed to steam crackers for the production of ethylene and propylene, higher paraffins suitable for blending into gasoline and mono aromatic ring compounds which may be further treated through alkylation of benzene to ethylbenzene and dealkylation to styrene. The paper discussed the process steps and highlighted the catalysts. Research results were also shown. It was concluded that the critical technology gaps, as well as solutions, which would enable overcoming the challenges related to handling of aromatic bitumen feedstock, entail the development of two different catalysts, which are on two different technology platforms. 7 refs., 3 tabs., 5 figs.

Carbohydrate protease conjugates: Stabilized proteases for peptide synthesis

Energy Technology Data Exchange (ETDEWEB)

Wartchow, C.A.; Wang, Peng; Bednarski, M.D.; Callstrom, M.R. [Ohio State Univ., Columbus, OH (United States)]|[Lawrence Berkeley Lab., CA (United States)

1995-12-31

The synthesis of oligopeptides using stable carbohydrate protease conjugates (CPCs) was examined in acetonitrile solvent systems. CPC[{alpha}-chymotrypsin] was used for the preparation of peptides containing histidine, phenylalanine, tryptophan in the P{sub 1} position in 60-93% yield. The CPC[{alpha}-chymotrypsin]-catalyzed synthesis of octamer Z-Gly-Gly-Phe-Gly-Gly-Phe-Gly-Gly-OEt from Z-Gly-Gly-Phe-Gly-Gly-Phe-OMe was achieved in 71% yield demonstrating that synthesis peptides containing both hydrophylic and hydrophobic amino acids. The P{sub 2} specificity of papain for aromatic residues was utilized for the 2 + 3 coupling of Z-Tyr-Gly-OMe to H{sub 2}N-Gly-Phe-Leu-OH to generate the leucine enkephalin derivative in 79% yield. Although papain is nonspecific for the hydrolysis of N-benzyloxycarbonyl amino acid methyl esters in aqueous solution, the rates of synthesis for these derivitives with nucleophile leucine tert-butyl ester differed by nearly 2 orders of magnitude. CPC[thermolysin] was used to prepare the aspartame precursor Z-Asp-Phe-OMe in 90% yield. The increased stability of CPCs prepared from periodate-modified poly(2-methacryl- amido-2-deoxy-D-glucose), poly(2-methacrylamido-2-deoxy-D-galactose), and poly(5-methacryl-amido-5-deoxy-D-ribose), carbohydrate materials designed to increase the aldehyde concentration in aqueous solution, suggests that the stability of CPCs is directly related to the aldehyde concentration of the carbohydrate material. Periodate oxidation of poly(2-methacrylamido-2-deoxy-D-glucose) followed by covalent attachment to {alpha}-chymotrypsin gave a CPC with catalytic activity in potassium phosphate buffer at 90{degrees}C for 2 h. 1 fig., 1 tab., 40 refs.

Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions

DEFF Research Database (Denmark)

Khandelia, Himanshu; Langham, Allison A; Kaznessis, Yiannis N

2006-01-01

Simulations of antimicrobial peptides in membrane mimics can provide the high resolution, atomistic picture that is necessary to decipher which sequence and structure components are responsible for activity and toxicity. With such detailed insight, engineering new sequences that are active but non...... peptides and their interaction with membrane mimics. In this article, we discuss the promise and the challenges of widely used models and detail our recent work on peptide-micelle simulations as an attractive alternative to peptide-bilayer simulations. We detail our results with two large structural...... classes of peptides, helical and beta-sheet and demonstrate how simulations can assist in engineering of novel antimicrobials with therapeutic potential....

Application of aromatization catalyst in synthesis of carbon nanotubes

Indian Academy of Sciences (India)

In a typical chemical vapour deposition (CVD) process for synthesizing carbon nanotubes (CNTs), it was found that the aromatization catalysts could promote effectively the formation of CNT. The essence of this phenomenon was attributed to the fact that the aromatization catalyst can accelerate the ...

Alkylation of organic aromatic compounds

Science.gov (United States)

Smith, Jr., Lawrence A.

1989-01-01

Aromatic compounds are alkylated in a catalytic distillation, wherein the catalyst structure also serves as a distillation component by contacting the aromatic compound with a C.sub.2 to C.sub.10 olefin in the catalyst bed under 0.25 to 50 atmospheres of pressure and at temperatures in the range of 80.degree. C. to 500.degree. C., using as the catalyst a mole sieve characterized as acidic or an acidic cation exchange resin. For example, ethyl benzene is produced by feeding ethylene below the catalyst bed while benzene is conveniently added through the reflux in molar excess to that required to react with ethylene, thereby reacting substantially all of the ethylene and recovering benzene as the principal overhead and ethyl benzene in the bottoms.

Alkylation of organic aromatic compounds

Science.gov (United States)

Smith, L.A. Jr.

1989-07-18

Aromatic compounds are alkylated in a catalytic distillation, wherein the catalyst structure also serves as a distillation component by contacting the aromatic compound with a C[sub 2] to C[sub 10] olefin in the catalyst bed under 0.25 to 50 atmospheres of pressure and at temperatures in the range of 80 C to 500 C, using as the catalyst a mole sieve characterized as acidic or an acidic cation exchange resin. For example, ethyl benzene is produced by feeding ethylene below the catalyst bed while benzene is conveniently added through the reflux in molar excess to that required to react with ethylene, thereby reacting substantially all of the ethylene and recovering benzene as the principal overhead and ethyl benzene in the bottoms. 1 fig.

Substituted Phthalic Anhydrides from Biobased Furanics : A New Approach to Renewable Aromatics

NARCIS (Netherlands)

Thiyagarajan, Shanmugam; Genuino, Homer C.|info:eu-repo/dai/nl/371571685; Sliwa, Michal; van der Waal, Jan C.; de Jong, Ed; van Haveren, Jacco; Weckhuysen, Bert M.|info:eu-repo/dai/nl/285484397; Bruijnincx, Pieter C. A.|info:eu-repo/dai/nl/33799529X; van Es, Daan S.

2015-01-01

A novel route for the production of renewable aromatic chemicals, particularly substituted phthalic acid anhydrides, is presented. The classical two-step approach to furanics-derived aromatics via Diels-Alder (DA) aromatization has been modified into a three-step procedure to address the general

Cation Radical Accelerated Nucleophilic Aromatic Substitution via Organic Photoredox Catalysis.

Science.gov (United States)

Tay, Nicholas E S; Nicewicz, David A

2017-11-15

Nucleophilic aromatic substitution (S N Ar) is a direct method for arene functionalization; however, it can be hampered by low reactivity of arene substrates and their availability. Herein we describe a cation radical-accelerated nucleophilic aromatic substitution using methoxy- and benzyloxy-groups as nucleofuges. In particular, lignin-derived aromatics containing guaiacol and veratrole motifs were competent substrates for functionalization. We also demonstrate an example of site-selective substitutive oxygenation with trifluoroethanol to afford the desired trifluoromethylaryl ether.

Catalytic oxidation of o-aminophenols and aromatic amines by mushroom tyrosinase.

Science.gov (United States)

Muñoz-Muñoz, Jose Luis; Garcia-Molina, Francisco; Garcia-Ruiz, Pedro Antonio; Varon, Ramon; Tudela, Jose; Rodriguez-Lopez, Jose N; Garcia-Canovas, Francisco

2011-12-01

The kinetics of tyrosinase acting on o-aminophenols and aromatic amines as substrates was studied. The catalytic constants of aromatic monoamines and o-diamines were both low, these results are consistent with our previous mechanism in which the slow step is the transfer of a proton by a hydroxyl to the peroxide in oxy-tyrosinase (Fenoll et al., Biochem. J. 380 (2004) 643-650). In the case of o-aminophenols, the hydroxyl group indirectly cooperates in the transfer of the proton and consequently the catalytic constants in the action of tyrosinase on these compounds are higher. In the case of aromatic monoamines, the Michaelis constants are of the same order of magnitude than for monophenols, which suggests that the monophenols bind better (higher binding constant) to the enzyme to facilitate the π-π interactions between the aromatic ring and a possible histidine of the active site. In the case of aromatic o-diamines, both the catalytic and Michaelis constants are low, the values of the catalytic constants being lower than those of the corresponding o-diphenols. The values of the Michaelis constants of the aromatic o-diamines are slightly lower than those of their corresponding o-diphenols, confirming that the aromatic o-diamines bind less well (lower binding constant) to the enzyme. Copyright © 2011 Elsevier B.V. All rights reserved.

Palladium-catalysed electrophilic aromatic C-H fluorination

Science.gov (United States)

Yamamoto, Kumiko; Li, Jiakun; Garber, Jeffrey A. O.; Rolfes, Julian D.; Boursalian, Gregory B.; Borghs, Jannik C.; Genicot, Christophe; Jacq, Jérôme; van Gastel, Maurice; Neese, Frank; Ritter, Tobias

2018-02-01

Aryl fluorides are widely used in the pharmaceutical and agrochemical industries, and recent advances have enabled their synthesis through the conversion of various functional groups. However, there is a lack of general methods for direct aromatic carbon-hydrogen (C-H) fluorination. Conventional methods require the use of either strong fluorinating reagents, which are often unselective and difficult to handle, such as elemental fluorine, or less reactive reagents that attack only the most activated arenes, which reduces the substrate scope. A method for the direct fluorination of aromatic C-H bonds could facilitate access to fluorinated derivatives of functional molecules that would otherwise be difficult to produce. For example, drug candidates with improved properties, such as increased metabolic stability or better blood-brain-barrier penetration, may become available. Here we describe an approach to catalysis and the resulting development of an undirected, palladium-catalysed method for aromatic C-H fluorination using mild electrophilic fluorinating reagents. The reaction involves a mode of catalysis that is unusual in aromatic C-H functionalization because no organometallic intermediate is formed; instead, a reactive transition-metal-fluoride electrophile is generated catalytically for the fluorination of arenes that do not otherwise react with mild fluorinating reagents. The scope and functional-group tolerance of this reaction could provide access to functional fluorinated molecules in pharmaceutical and agrochemical development that would otherwise not be readily accessible.

Temperature-dependent loop formation kinetics in flexible peptides studied by time-resolved fluorescence spectroscopy

Directory of Open Access Journals (Sweden)

Harekrushna Sahoo

2006-01-01

Full Text Available Looping rates in short polypeptides can be determined by intramolecular fluorescence quenching of a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo by tryptophan. By this methodology, the looping rates in glycine-serine peptides with the structure Trp-(Gly-Sern-Dbo-NH2 of different lengths (n = 0–10 were determined in dependence on temperature in D2O and the activation parameters were derived. In general, the looping rate increases with decreasing peptide length, but the shortest peptide (n=0 shows exceptional behavior because its looping rate is slower than that for the next longer ones (n=1,2. The activation energies increase from 17.5 kJ mol−1 for the longest peptide (n=10 to 20.5 kJ mol−1 for the shortest one (n=0, while the pre-exponential factors (log⁡(A/s−1 range from 10.20 to 11.38. The data are interpreted in terms of an interplay between internal friction (stiffness of the biopolymer backbone and steric hindrance effects and solvent friction (viscosity-limited diffusion. For the longest peptides, the activation energies resemble more and more the value expected for solvent viscous flow. Internal friction is most important for the shortest peptides, causing a negative curvature and a smaller than ideal slope (ca. –1.1 of the double-logarithmic plots of the looping rates versus the number of peptide chain segments (N. Interestingly, the corresponding plot for the pre-exponential factors (logA versus logN shows the ideal slope (–1.5. While the looping rates can be used to assess the flexibility of peptides in a global way, it is suggested that the activation energies provide a measure of the “thermodynamic” flexibility of a peptide, while the pre-exponential factors reflect the “dynamic” flexibility.

Flanking signal and mature peptide residues influence signal peptide cleavage

Directory of Open Access Journals (Sweden)

Ranganathan Shoba

2008-12-01

Full Text Available Abstract Background Signal peptides (SPs mediate the targeting of secretory precursor proteins to the correct subcellular compartments in prokaryotes and eukaryotes. Identifying these transient peptides is crucial to the medical, food and beverage and biotechnology industries yet our understanding of these peptides remains limited. This paper examines the most common type of signal peptides cleavable by the endoprotease signal peptidase I (SPase I, and the residues flanking the cleavage sites of three groups of signal peptide sequences, namely (i eukaryotes (Euk (ii Gram-positive (Gram+ bacteria, and (iii Gram-negative (Gram- bacteria. Results In this study, 2352 secretory peptide sequences from a variety of organisms with amino-terminal SPs are extracted from the manually curated SPdb database for analysis based on physicochemical properties such as pI, aliphatic index, GRAVY score, hydrophobicity, net charge and position-specific residue preferences. Our findings show that the three groups share several similarities in general, but they display distinctive features upon examination in terms of their amino acid compositions and frequencies, and various physico-chemical properties. Thus, analysis or prediction of their sequences should be separated and treated as distinct groups. Conclusion We conclude that the peptide segment recognized by SPase I extends to the start of the mature protein to a limited extent, upon our survey of the amino acid residues surrounding the cleavage processing site. These flanking residues possibly influence the cleavage processing and contribute to non-canonical cleavage sites. Our findings are applicable in defining more accurate prediction tools for recognition and identification of cleavage site of SPs.

Analysis of peptide uptake and location of root hair-promoting peptide accumulation in plant roots.

Science.gov (United States)

Matsumiya, Yoshiki; Taniguchi, Rikiya; Kubo, Motoki

2012-03-01

Peptide uptake by plant roots from degraded soybean-meal products was analyzed in Brassica rapa and Solanum lycopersicum. B. rapa absorbed about 40% of the initial water volume, whereas peptide concentration was decreased by 75% after 24 h. Analysis by reversed-phase HPLC showed that number of peptides was absorbed by the roots during soaking in degraded soybean-meal products for 24 h. Carboxyfluorescein-labeled root hair-promoting peptide was synthesized, and its localization, movement, and accumulation in roots were investigated. The peptide appeared to be absorbed by root hairs and then moved to trichoblasts. Furthermore, the peptide was moved from trichoblasts to atrichoblasts after 24 h. The peptide was accumulated in epidermal cells, suggesting that the peptide may have a function in both trichoblasts and atrichoblasts. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.

Oxidation of protein tyrosine or methionine residues: From the amino acid to the peptide

Energy Technology Data Exchange (ETDEWEB)

Berges, J [Universite Pierre et Marie Curie, UMR 7616, Laboratoire de Chimie Theorique, 75005 Paris (France); Trouillas, P [EA 4021 Faculte de Pharmacie, 2 Rue du Dr. Marcland, 87025 Limoges Cedex (France); Houee-Levin, C, E-mail: jb@lct.jussieu.fr, E-mail: patrick.trouillas@unilim.fr, E-mail: chantal.houee@u-psud.fr [Universite Paris Sud, UMR 8000, Laboratoire de Chimie Physique, 91405 Orsay (France) (France)

2011-01-01

Methionine and tyrosine are competing targets of oxidizing free radicals in peptides or proteins. The first step is the addition of OH radicals either on the sulphur atom of methionine, followed by OH{sup -} elimination, or on the aromatic cycle of tyrosine. The next step can be stabilization of methionine radical cation by a two centre-three electron bond, or intramolecular electron transfer from tyrosine to the methionine radical cation. In this latter case a tyrosine radical is formed, which appears deprotonated. In a first step we have compared the stability of the OH radical adducts on Methionine or on Tyrosine. In agreement with experimental results, the thermodynamical data indicate that the OH adduct on Tyrosine and the radical cation are more stable than those on methionine. In a second step we have investigated the stabilization of the radical cations of Methionine by formation of intramolecular S:X two-center three-electron bond (X=S, N, O). Finally we have compared the spin densities on separated amino acids to that in a radical pentapeptide, methionine enkephalin. One observes a delocalisation of the orbital of the odd electron on the sulfur atom of Met and on the cycle of Tyr. The peptidic chain is also concerned.

Oxidation of protein tyrosine or methionine residues: From the amino acid to the peptide

International Nuclear Information System (INIS)

Berges, J; Trouillas, P; Houee-Levin, C

2011-01-01

Methionine and tyrosine are competing targets of oxidizing free radicals in peptides or proteins. The first step is the addition of OH radicals either on the sulphur atom of methionine, followed by OH - elimination, or on the aromatic cycle of tyrosine. The next step can be stabilization of methionine radical cation by a two centre-three electron bond, or intramolecular electron transfer from tyrosine to the methionine radical cation. In this latter case a tyrosine radical is formed, which appears deprotonated. In a first step we have compared the stability of the OH radical adducts on Methionine or on Tyrosine. In agreement with experimental results, the thermodynamical data indicate that the OH adduct on Tyrosine and the radical cation are more stable than those on methionine. In a second step we have investigated the stabilization of the radical cations of Methionine by formation of intramolecular S:X two-center three-electron bond (X=S, N, O). Finally we have compared the spin densities on separated amino acids to that in a radical pentapeptide, methionine enkephalin. One observes a delocalisation of the orbital of the odd electron on the sulfur atom of Met and on the cycle of Tyr. The peptidic chain is also concerned.

Extraction of Aromatics from Heavy Naphtha Using Different Solvents

International Nuclear Information System (INIS)

EI-Bassuoni, A.A.; Esmael, K.K.

2004-01-01

Aromatic hydrocarbons are very important to the petrochemical industry. Among these are benzene, toluene and xylene (BTX), which are basic raw materials for the production of a number of important petrochemicals. There are many processes used to separate aromatic from non aromatic such as fractionation, azeotropic distillation and liquid I liquid extraction, etc. Liquid - liquid extraction is unique, efficiently used for heat sensitive, close boiling components and for separation of components not possible by other unit operations and it could be done at ambient temperature makes it more energy efficient. The choice of solvent depends on the properties and boiling range of the feedstock. Through the years, a lot of selective solvents has been proposed and selected for the physical separation of aromatics in liquid liquid extraction. Among the selection criteria are the stability,. chemical compatibility, availability, environmental hazards and price of the solvent. But the basic solvent properties that make it efficient are selectivity and capacity

Human Platelet-Rich Plasma- and Extracellular Matrix-Derived Peptides Promote Impaired Cutaneous Wound Healing In Vivo

Science.gov (United States)

Demidova-Rice, Tatiana N.; Wolf, Lindsey; Deckenback, Jeffry; Hamblin, Michael R.; Herman, Ira M.

2012-01-01

Previous work in our laboratory has described several pro-angiogenic short peptides derived from endothelial extracellular matrices degraded by bacterial collagenase. Here we tested whether these peptides could stimulate wound healing in vivo. Our experiments demonstrated that a peptide created as combination of fragments of tenascin X and fibrillin 1 (comb1) applied into cranial dermal wounds created in mice treated with cyclophosphamide to impair wound healing, can improve the rate of wound closure. Furthermore, we identify and characterize a novel peptide (UN3) created and modified from two naturally-occurring peptides, which are present in human platelet-rich plasma. In vitro testing of UN3 demonstrates that it causes a 50% increase in endothelial proliferation, 250% increase in angiogenic response and a tripling of epithelial cell migration in response to injury. Results of in vivo experiments where comb1 and UN3 peptides were added together to cranial wounds in cyclophosphamide-treated mice leads to improvement of wound vascularization as shown by an increase of the number of blood vessels present in the wound beds. Application of the peptides markedly promotes cellular responses to injury and essentially restores wound healing dynamics to those of normal, acute wounds in the absence of cyclophosphamide impairment. Our current work is aimed at understanding the mechanisms underlying the stimulatory effects of these peptides as well as identification of the cellular receptors mediating these effects. PMID:22384158

Formation and fragmentation of radical peptide anions: insights from vacuum ultra violet spectroscopy.

Science.gov (United States)

Brunet, Claire; Antoine, Rodolphe; Dugourd, Philippe; Canon, Francis; Giuliani, Alexandre; Nahon, Laurent

2012-02-01

We have studied the photodissociation of gas-phase deprotonated caerulein anions by vacuum ultraviolet (VUV) photons in the 4.5 to 20 eV range, as provided by the DESIRS beamline at the synchrotron radiation facility SOLEIL (France). Caerulein is a sulphated peptide with three aromatic residues and nine amide bonds. Electron loss is found to be the major relaxation channel at every photon energy. However, an increase in the fragmentation efficiency (neutral losses and peptide backbone cleavages) as a function of the energy is also observed. The oxidized ions, generated by electron photodetachment were further isolated and activated by collision (CID) in a MS(3) scheme. The branching ratios of the different fragments observed by CID as a function of the initial VUV photon energy are found to be independent of the initial photon energy. Thus, there is no memory effect of the initial excitation energy on the fragmentation channels of the oxidized species on the time scale of our tandem MS experiment. We also report photofragment yields as a function of photon energy for doubly deprotonated caerulein ions, for both closed-shell ([M-2H](2-)) non-radical ions and open-shell ([M-3H](2-•)) radical ions. These latter ions are generated by electron photodetachment from [M-3H](3-) precursor ions. The detachment yield increases monotonically with the energy with the appearance of several absorption bands. Spectra for radical and non-radical ions are quite similar in terms of observed bands; however, the VUV fragmentation yield is enhanced by the presence of a radical in caerulein peptides. © American Society for Mass Spectrometry, 2011

Human Milk: Bioactive Proteins/Peptides and Functional Properties.

Science.gov (United States)

Lönnerdal, Bo

2016-06-23

Breastfeeding has been associated with many benefits, both in the short and in the long term. Infants being breastfed generally have less illness and have better cognitive development at 1 year of age than formula-fed infants. Later in life, they have a lower risk of obesity, diabetes and cardiovascular disease. Several components in breast milk may be responsible for these different outcomes, but bioactive proteins/peptides likely play a major role. Some proteins in breast milk are comparatively resistant towards digestion and may therefore exert their functions in the gastrointestinal tract in intact form or as larger fragments. Other milk proteins may be partially digested in the upper small intestine and the resulting peptides may exert functions in the lower small intestine. Lactoferrin, lysozyme and secretory IgA have been found intact in the stool of breastfed infants and are therefore examples of proteins that are resistant against proteolytic degradation in the gut. Together, these proteins serve protective roles against infection and support immune function in the immature infant. α-lactalbumin, β-casein, κ-casein and osteopontin are examples of proteins that are partially digested in the upper small intestine, and the resulting peptides influence functions in the gut. Such functions include stimulation of immune function, mineral and trace element absorption and defense against infection. © 2016 Nestec Ltd., Vevey/S. Karger AG, Basel.

Diversity, evolution and medical applications of insect antimicrobial peptides.

Science.gov (United States)

Mylonakis, Eleftherios; Podsiadlowski, Lars; Muhammed, Maged; Vilcinskas, Andreas

2016-05-26

Antimicrobial peptides (AMPs) are short proteins with antimicrobial activity. A large portion of known AMPs originate from insects, and the number and diversity of these molecules in different species varies considerably. Insect AMPs represent a potential source of alternative antibiotics to address the limitation of current antibiotics, which has been caused by the emergence and spread of multidrug-resistant pathogens. To get more insight into AMPs, we investigated the diversity and evolution of insect AMPs by mapping their phylogenetic distribution, allowing us to predict the evolutionary origins of selected AMP families and to identify evolutionarily conserved and taxon-specific families. Furthermore, we highlight the use of the nematode Caenorhabditis elegans as a whole-animal model in high-throughput screening methods to identify AMPs with efficacy against human pathogens, including Acinetobacter baumanii and methicillin-resistant Staphylococcus aureus We also discuss the potential medical applications of AMPs, including their use as alternatives for conventional antibiotics in ectopic therapies, their combined use with antibiotics to restore the susceptibility of multidrug-resistant pathogens, and their use as templates for the rational design of peptidomimetic drugs that overcome the disadvantages of therapeutic peptides.The article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'. © 2016 The Authors.

Transformations of Aromatic Compounds by Nitrosomonas europaea

OpenAIRE

Keener, William K.; Arp, Daniel J.

1994-01-01

Benzene and a variety of substituted benzenes inhibited ammonia oxidation by intact cells of Nitrosomonas europaea. In most cases, the inhibition was accompanied by transformation of the aromatic compound to a more oxidized product or products. All products detected were aromatic, and substituents were often oxidized but were not separated from the benzene ring. Most transformations were enhanced by (NH4)2SO4 (12.5 mM) and were prevented by C2H2, a mechanism-based inactivator of ammonia monoo...

Far UV irradiation of DNA in the presence of proteins, amino acids or peptides

International Nuclear Information System (INIS)

Larcom, L.L.; Rains, C.A.

1985-01-01

The DNA of bacteriophage SPO2c12 was subjected to 254 nm irradiation in solutions containing lysozyme or histone. The sensitivity of phage DNA to biological inactivation by UV increased as the amount of lysozyme bound per DNA strand increased. Although binding constants could not be measured for the DNA-histone interaction, this protein had a protective effect which was greater under conditions which cause enhanced binding. No crosslinking of either protein could be detected. Irradiation was also performed in the presence of various amino acids and short peptides. These were chosen to include amino acids which: (1) are positively charged, (2) absorb UV of this wavelength or (3) form UV-induced crosslinks to DNA. None of the amino acids tested affected sensitivity of the DNA to biological inactivation. Peptides containing a UV-absorbing amino acid and a positively charged amino acid enhanced sensitivity. For each of these peptides, a mixture of the constituent amino acids had the same effect as the peptide itself. Under the conditions used, no evidence for formation of DNA-amino acid crosslinks was found. The results indicate that proteins and peptides can sensitize DNA to UV inactivation by mechanisms other than covalent crosslink formation. (author)

The direct aromatization of methane

Energy Technology Data Exchange (ETDEWEB)

Marcelin, G.; Oukaci, R.; Migone, R.A.; Kazi, A.M. [Altamira Instruments, Pittsburgh, PA (United States)

1995-12-31

The thermal decomposition of methane shows significant potential as a process for the production of higher unsaturated and aromatic hydrocarbons when the extent of the reaction is limited. Thermodynamic calculations have shown that when the reaction is limited to the formation of C{sub 2} to C{sub 10} products, yields of aromatics can exceed 40% at temperatures of 1200{degrees}C. Preliminary experiments have shown that when the reaction is limited to the formation of C{sub 2} to C{sub 10} products, yields of aromatics can exceed 40% at temperatures of 1200{degrees}C. Preliminary experiments have shown that cooling the product and reacting gases as the reaction proceeds can significantly reduce or eliminate the formation of solid carbon and heavier (C{sub 10+}) materials. Much work remains to be done in optimizing the quenching process and this is one of the goals of this program. Means to lower the temperature of the reaction are being studied as this result in a more feasible commercial process due to savings realized in energy and material of construction costs. The use of free-radical generators and catalysts will be investigated as a means of lowering the reaction temperature thus allowing faster quenching. It is highly likely that such studies will lead to a successful direct methane to higher hydrocarbon process.

Prediction of Scylla olivacea (Crustacea; Brachyura) peptide hormones using publicly accessible transcriptome shotgun assembly (TSA) sequences.

Science.gov (United States)

Christie, Andrew E

2016-05-01

The aquaculture of crabs from the genus Scylla is of increasing economic importance for many Southeast Asian countries. Expansion of Scylla farming has led to increased efforts to understand the physiology and behavior of these crabs, and as such, there are growing molecular resources for them. Here, publicly accessible Scylla olivacea transcriptomic data were mined for putative peptide-encoding transcripts; the proteins deduced from the identified sequences were then used to predict the structures of mature peptide hormones. Forty-nine pre/preprohormone-encoding transcripts were identified, allowing for the prediction of 187 distinct mature peptides. The identified peptides included isoforms of adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin B, allatostatin C, bursicon β, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/molt-inhibiting hormone, diuretic hormone 31, eclosion hormone, FMRFamide-like peptide, HIGSLYRamide, insulin-like peptide, intocin, leucokinin, myosuppressin, neuroparsin, neuropeptide F, orcokinin, pigment dispersing hormone, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, SIFamide and tachykinin-related peptide, all well-known neuropeptide families. Surprisingly, the tissue used to generate the transcriptome mined here is reported to be testis. Whether or not the testis samples had neural contamination is unknown. However, if the peptides are truly produced by this reproductive organ, it could have far reaching consequences for the study of crustacean endocrinology, particularly in the area of reproductive control. Regardless, this peptidome is the largest thus far predicted for any brachyuran (true crab) species, and will serve as a foundation for future studies of peptidergic control in members of the commercially important genus Scylla. Copyright © 2016 Elsevier Inc. All rights reserved.

Alkyne Benzannulation Reactions for the Synthesis of Novel Aromatic Architectures.

Science.gov (United States)

Hein, Samuel J; Lehnherr, Dan; Arslan, Hasan; J Uribe-Romo, Fernando; Dichtel, William R

2017-11-21

Aromatic compounds and polymers are integrated into organic field effect transistors, light-emitting diodes, photovoltaic devices, and redox-flow batteries. These compounds and materials feature increasingly complex designs, and substituents influence energy levels, bandgaps, solution conformation, and crystal packing, all of which impact performance. However, many polycyclic aromatic hydrocarbons of interest are difficult to prepare because their substitution patterns lie outside the scope of current synthetic methods, as strategies for functionalizing benzene are often unselective when applied to naphthalene or larger systems. For example, cross-coupling and nucleophilic aromatic substitution reactions rely on prefunctionalized arenes, and even directed metalation methods most often modify positions near Lewis basic sites. Similarly, electrophilic aromatic substitutions access single regioisomers under substrate control. Cycloadditions provide a convergent route to densely functionalized aromatic compounds that compliment the above methods. After surveying cycloaddition reactions that might be used to modify the conjugated backbone of poly(phenylene ethynylene)s, we discovered that the Asao-Yamamoto benzannulation reaction is notably efficient. Although this reaction had been reported a decade earlier, its scope and usefulness for synthesizing complex aromatic systems had been under-recognized. This benzannulation reaction combines substituted 2-(phenylethynyl)benzaldehydes and substituted alkynes to form 2,3-substituted naphthalenes. The reaction tolerates a variety of sterically congested alkynes, making it well-suited for accessing poly- and oligo(ortho-arylene)s and contorted hexabenzocoronenes. In many cases in which asymmetric benzaldehyde and alkyne cycloaddition partners are used, the reaction is regiospecific based on the electronic character of the alkyne substrate. Recognizing these desirable features, we broadened the substrate scope to include silyl

A non-covalent peptide-based carrier for in vivo delivery of DNA mimics.

Science.gov (United States)

Morris, May C; Gros, Edwige; Aldrian-Herrada, Gudrun; Choob, Michael; Archdeacon, John; Heitz, Frederic; Divita, Gilles

2007-01-01

The dramatic acceleration in identification of new nucleic-acid-based therapeutic molecules has provided new perspectives in pharmaceutical research. However, their development is limited by their poor cellular uptake and inefficient trafficking. Here we describe a short amphipathic peptide, Pep-3, that combines a tryptophan/phenylalanine domain with a lysine/arginine-rich hydrophilic motif. Pep-3 forms stable nano-size complexes with peptide-nucleic acid analogues and promotes their efficient delivery into a wide variety of cell lines, including primary and suspension lines, without any associated cytotoxicity. We demonstrate that Pep-3-mediated delivery of antisense-cyclin B1-charged-PNA blocks tumour growth in vivo upon intratumoral and intravenous injection. Moreover, we show that PEGylation of Pep-3 significantly improves complex stability in vivo and consequently the efficiency of antisense cyclin B1 administered intravenously. Given the biological characteristics of these vectors, we believe that peptide-based delivery technologies hold a true promise for therapeutic applications of DNA mimics.

STUDY OF FACTORS AFFECTING DEVELOPMENT OF FOOD AROMATIZATION

Directory of Open Access Journals (Sweden)

Н.Ye. Dubova

2017-10-01

Full Text Available The specific understanding of food philosophy according to the facts of development of cooking technologies and growth rate of food range is given. As it has been proven by historical stages of production of flavorings, aroma is one of the important organoleptic ingredients for food developers. A review of food production based on development of nanotechnologies, as well as promising and cautioning publications on nanotechnologies in the food sector is presented. On the basis of the literary analysis, the future impact of nanotechnologies on the evolution of the aromatization process of food products is predicted. It has been determined that the peculiarity of the development mentioned above lies in the use of plant enzymes and / or flavor precursors in the nanoscale range. The example of enzymatic breakdown of polyunsaturated fatty acids of plant cell membranes as one of the ways of creating fresh flavor of many fruits, namely C6-C9 aldehydes and alcohols, is considered. It is noted that green fresh aromatic ingredients are needed to improve the organoleptic profile of foods from heat-treated vegetables, melons and gourds. The following factors affecting the development of food aromatization are defined: the decreased differentiation of principles of healthy nutrition and fast food, repetition of natural processes of aroma formation, application of wild green leafy vegetables, and evolution of medical nutrition. The information on food aromatization by packing with autonomous mixing and their approximate assortment is given. The innovations in food aromatization are aimed at quality nutrition, time saving, recreation and entertainment, meeting specific needs (vegetarian dishes, restrictive diets.

Insulin C-peptide test

Science.gov (United States)

C-peptide ... the test depends on the reason for the C-peptide measurement. Ask your health care provider if ... C-peptide is measured to tell the difference between insulin the body produces and insulin someone injects ...

What are the ideal properties for functional food peptides with antihypertensive effect? A computational peptidology approach.

Science.gov (United States)

Zhou, Peng; Yang, Chao; Ren, Yanrong; Wang, Congcong; Tian, Feifei

2013-12-01

Peptides with antihypertensive potency have long been attractive to the medical and food communities. However, serving as food additives, rather than therapeutic agents, peptides should have a good taste. In the present study, we explore the intrinsic relationship between the angiotensin I-converting enzyme (ACE) inhibition and bitterness of short peptides in the framework of computational peptidology, attempting to find out the appropriate properties for functional food peptides with satisfactory bioactivities. As might be expected, quantitative structure-activity relationship modeling reveals a significant positive correlation between the ACE inhibition and bitterness of dipeptides, but this correlation is quite modest for tripeptides and, particularly, tetrapeptides. Moreover, quantum mechanics/molecular mechanics analysis of the structural basis and energetic profile involved in ACE-peptide complexes unravels that peptides of up to 4 amino acids long are sufficient to have efficient binding to ACE, and more additional residues do not bring with substantial enhance in their ACE-binding affinity and, thus, antihypertensive capability. All of above, it is coming together to suggest that the tripeptides and tetrapeptides could be considered as ideal candidates for seeking potential functional food additives with both high antihypertensive activity and low bitterness. Copyright © 2013 Elsevier Ltd. All rights reserved.

Double-Stranded Peptide Nucleic Acids

DEFF Research Database (Denmark)

2001-01-01

A novel class of compounds, known as peptide nucleic acids, form double-stranded structures with one another and with ssDNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker.......A novel class of compounds, known as peptide nucleic acids, form double-stranded structures with one another and with ssDNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

Rational Design of Cyclic Antimicrobial Peptides Based on BPC194 and BPC198

Directory of Open Access Journals (Sweden)

Anna D. Cirac

2017-06-01

Full Text Available A strategy for the design of antimicrobial cyclic peptides derived from the lead compounds c(KKLKKFKKLQ (BPC194 and c(KLKKKFKKLQ (BPC198 is reported. First, the secondary β-structure of BPC194 and BPC198 was analyzed by carrying out molecular dynamics (MD simulations. Then, based on the sequence pattern and the β-structure of BPC194 or BPC198, fifteen analogues were designed and synthesized on solid-phase. The best peptides (BPC490, BPC918, and BPC924 showed minimum inhibitory concentration (MIC values <6.2 μM against Pseudomonas syringae pv. syringae and Xanthomonas axonopodis pv. vesicatoria, and an MIC value of 12.5 to 25 μM against Erwinia amylovora, being as active as BPC194 and BPC198. Interestingly, these three analogues followed the structural pattern defined from the MD simulations of the parent peptides. Thus, BPC490 maintained the parallel alignment of the hydrophilic pairs K1–K8, K2–K7, and K4–K5, whereas BPC918 and BPC924 included the two hydrophilic interactions K3–Q10 and K5–K8. In short, MD simulations have proved to be very useful for ascertaining the structural features of cyclic peptides that are crucial for their biological activity. Such approaches could be further employed for the development of new antibacterial cyclic peptides.

Nanoscale dynamics and aging of fibrous peptide-based gels

Energy Technology Data Exchange (ETDEWEB)

Dudukovic, Nikola A., E-mail: dudukov1@illinois.edu [Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Zukoski, Charles F. [Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, New York 14222 (United States)

2014-10-28

Solutions of the aromatic dipeptide derivative molecule fluorenylmethoxycarbonyl-diphenylalanine (Fmoc-FF) in dimethyl sulfoxide produce fibrous gels when mixed with water. We study the evolution of density fluctuations of this three-component system using X-ray photon correlation spectroscopy (XPCS) and compare these results to the macroscopic rheology of the gels and optical observations of the microstructure evolution. At the investigated scattering angles, the intensity autocorrelation functions do not follow behavior expected for simple diffusion of individual Fmoc-FF molecules localized within cages of nearest neighbors. Instead, the dynamics are associated with density fluctuations on length scales of ∼10–100 nm arising from disaggregation and reformation of fibers, leading to an increasingly uniform network. This process is correlated with the growth of the elastic modulus, which saturates at long times. Autocorrelation functions and relaxation times acquired from XPCS measurements are consistent with relaxation rates of structures at dynamic equilibrium. This study provides further support to the concept of exploring peptide-based gelators as valence-limited patchy particles capable of forming equilibrium gels.

Ambient aromatic hydrocarbon measurements at Welgegund, South Africa

Science.gov (United States)

Jaars, K.; Beukes, J. P.; van Zyl, P. G.; Venter, A. D.; Josipovic, M.; Pienaar, J. J.; Vakkari, V.; Aaltonen, H.; Laakso, H.; Kulmala, M.; Tiitta, P.; Guenther, A.; Hellén, H.; Laakso, L.; Hakola, H.

2014-07-01

Aromatic hydrocarbons are associated with direct adverse human health effects and can have negative impacts on ecosystems due to their toxicity, as well as indirect negative effects through the formation of tropospheric ozone and secondary organic aerosol, which affect human health, crop production and regional climate. Measurements of aromatic hydrocarbons were conducted at the Welgegund measurement station (South Africa), which is considered to be a regionally representative background site. However, the site is occasionally impacted by plumes from major anthropogenic source regions in the interior of South Africa, which include the western Bushveld Igneous Complex (e.g. platinum, base metal and ferrochrome smelters), the eastern Bushveld Igneous Complex (platinum and ferrochrome smelters), the Johannesburg-Pretoria metropolitan conurbation (> 10 million people), the Vaal Triangle (e.g. petrochemical and pyrometallurgical industries), the Mpumalanga Highveld (e.g. coal-fired power plants and petrochemical industry) and also a region of anticyclonic recirculation of air mass over the interior of South Africa. The aromatic hydrocarbon measurements were conducted with an automated sampler on Tenax-TA and Carbopack-B adsorbent tubes with heated inlet for 1 year. Samples were collected twice a week for 2 h during daytime and 2 h during night-time. A thermal desorption unit, connected to a gas chromatograph and a mass selective detector was used for sample preparation and analysis. Results indicated that the monthly median (mean) total aromatic hydrocarbon concentrations ranged between 0.01 (0.011) and 3.1 (3.2) ppb. Benzene levels did not exceed the local air quality standard limit, i.e. annual mean of 1.6 ppb. Toluene was the most abundant compound, with an annual median (mean) concentration of 0.63 (0.89) ppb. No statistically significant differences in the concentrations measured during daytime and night-time were found, and no distinct seasonal patterns were

Applications of electrochemically-modulated liquid chromatography (EMLC): Separations of aromatic amino acids and polycyclic aromatic hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

Deng, Li [Iowa State Univ., Ames, IA (United States)

1998-03-27

The research in this thesis explores the separation capabilities of a new technique termed electrochemically-modulated liquid chromatography (EMLC). The thesis begins with a general introduction section which provides a literature review of this technique as well as a brief background discussion of the two research projects in each of the next two chapters. The two papers which follow investigate the application of EMLC to the separation of a mixture of aromatic amino acids and of a mixture of polycyclic aromatic hydrocarbons (PAHs). The last section presents general conclusions and summarizes the thesis. References are compiled in the reference section of each chapter. The two papers have been removed for separate processing.

Wheat straw lignin degradation induction to aromatics by por Aspergillus spp. and Penicillium chrysogenum

Directory of Open Access Journals (Sweden)

Baltierra-Trejo Eduardo

2016-02-01

Full Text Available Wheat straw is a recalcitrant agricultural waste; incineration of this material represents an important environmental impact. Different reports have been made regarding the use of the structural components of wheat straw, i.e. cellulose, hemicellulose and lignin; however, lignin has been less exploited because it is largely considered the recalcitrant part. Residual wheat straw lignin (REWSLI has a potential biotech-nological value if depolymerization is attained to produce aromatics. Ligninolytic mitosporic fungus represent an alternative where very little research has been done, even though they are capable of depol-ymerize REWSLI in simple nutritional conditions in relatively short periods, when compared to basidio-mycetes. The aim of this research was to study the depolymerization activity of Aspergillus spp and Penicillium spp on semipurified REWSLI as the sole carbon source to produce aromatics. The depoly-merization capacity was determined by the activity of the laccase, lignin peroxidase and manganese peroxidase enzymes. The generated aromatics derived from the REWSLI depolymerization were identi-fied by gas chromatography. Obtained results revealed that Penicillium chrysogenum depolymerized the lignin material by 34.8% during the 28-day experimentation period. Laccase activity showed the largest activity with 111 U L-1 in a seven-day period, this enzyme induction was detected in a smaller period than that required by basidiomycetes to induce it. Moreover, the enzymatic activity was produced with-out the addition of an extra carbon source as metabolic inductor. Aspergillus spp and Penicillium spp generated guaiacol, vanillin, and hydroxybenzoic, vanillinic, syringic and ferulic acid with a maximum weekly production of 3.5, 3.3, 3.2, 3.3, 10.1 and 21.9 mg mL-1, respectively.

Application of synthetic peptides for detection of anti-citrullinated peptide antibodies

DEFF Research Database (Denmark)

Trier, Nicole Hartwig; Holm, Bettina Eide; Slot, Ole

2016-01-01

Anti-citrullinated protein antibodies (ACPAs) are a hallmark of rheumatoid arthritis (RA) and represent an important tool for the serological diagnosis of RA. In this study, we describe ACPA reactivity to overlapping citrullinated Epstein-Barr virus nuclear antigen-1 (EBNA-1)-derived peptides...... (n=40), systemic lupus erythematosus (n=20), Sjögren's syndrome (n=40)) were screened for antibody reactivity. Antibodies to a panel of five citrullinated EBNA-1 peptides were found in 67% of RA sera, exclusively of the IgG isotype, while 53% of the patient sera reacted with a single peptide......, ARGGSRERARGRGRG-Cit-GEKR, accounting for more than half of the ACPA reactivity alone. Moreover, these antibodies were detected in 10% of CCP2-negative RA sera. In addition, 47% of the RA sera reacted with two or three citrullinated EBNA-1 peptides from the selected peptide panel. Furthermore, a negative...

Primary structure and conformational analysis of peptide methionine-tyrosine, a peptide related to neuropeptide Y and peptide YY isolated from lamprey intestine

DEFF Research Database (Denmark)

Conlon, J M; Bjørnholm, B; Jørgensen, Flemming Steen

1991-01-01

A peptide belonging to the pancreatic-polypeptide-fold family of regulatory peptides has been isolated from the intestine of an Agnathan, the sea lamprey (Petromyzon marinus). The primary structure of the peptide (termed peptide methionine-tyrosine) was established as Met-Pro-Pro-Lys-Pro-Asp-Asn-...... in a preferred structure in which the conformation of the beta-turn between the two helical domains (residues 9-14) is appreciably different....

Self-assembly behaviours of peptide-drug conjugates: influence of multiple factors on aggregate morphology and potential self-assembly mechanism

Science.gov (United States)

Fan, Qin; Ji, Yujie; Wang, Jingjing; Wu, Li; Li, Weidong; Chen, Rui; Chen, Zhipeng

2018-04-01

Peptide-drug conjugates (PDCs) as self-assembly prodrugs have the unique and specific features to build one-component nanomedicines. Supramolecular structure based on PDCs could form various morphologies ranging from nanotube, nanofibre, nanobelt to hydrogel. However, the assembly process of PDCs is too complex to predict or control. Herein, we investigated the effects of extrinsic factors on assembly morphology and the possible formation of nanostructures based on PDCs. To this end, we designed a PDC consisting of hydrophobic drug (S)-ketoprofen (Ket) and valine-glutamic acid dimeric repeats peptide (L-VEVE) to study their assembly behaviour. Our results showed that the critical assembly concentration of Ket-L-VEVE was 0.32 mM in water to form various nanostructures which experienced from micelle, nanorod, nanofibre to nanoribbon. The morphology was influenced by multiple factors including molecular design, assembly time, pH and hydrogen bond inhibitor. On the basis of experimental results, we speculated the possible assembly mechanism of Ket-L-VEVE. The π-π stacking interaction between Ket molecules could serve as an anchor, and hydrogen bonded-induced β-sheets and hydrophilic/hydrophobic balance between L-VEVE peptide play structure-directing role in forming filament-like or nanoribbon morphology. This work provides a new sight to rationally design and precisely control the nanostructure of PDCs based on aromatic fragment.

Improving Peptide Applications Using Nanotechnology.

Science.gov (United States)

Narayanaswamy, Radhika; Wang, Tao; Torchilin, Vladimir P

2016-01-01

Peptides are being successfully used in various fields including therapy and drug delivery. With advancement in nanotechnology and targeted delivery carrier systems, suitable modification of peptides has enabled achievement of many desirable goals over-riding some of the major disadvantages associated with the delivery of peptides in vivo. Conjugation or physical encapsulation of peptides to various nanocarriers, such as liposomes, micelles and solid-lipid nanoparticles, has improved their in vivo performance multi-fold. The amenability of peptides to modification in chemistry and functionalization with suitable nanocarriers are very relevant aspects in their use and have led to the use of 'smart' nanoparticles with suitable linker chemistries that favor peptide targeting or release at the desired sites, minimizing off-target effects. This review focuses on how nanotechnology has been used to improve the number of peptide applications. The paper also focuses on the chemistry behind peptide conjugation to nanocarriers, the commonly employed linker chemistries and the several improvements that have already been achieved in the areas of peptide use with the help of nanotechnology.

Peptide and Peptide-Dependent Motions in MHC Proteins: Immunological Implications and Biophysical Underpinnings

Directory of Open Access Journals (Sweden)

Cory M. Ayres

2017-08-01

Full Text Available Structural biology of peptides presented by class I and class II MHC proteins has transformed immunology, impacting our understanding of fundamental immune mechanisms and allowing researchers to rationalize immunogenicity and design novel vaccines. However, proteins are not static structures as often inferred from crystallographic structures. Their components move and breathe individually and collectively over a range of timescales. Peptides bound within MHC peptide-binding grooves are no exception and their motions have been shown to impact recognition by T cell and other receptors in ways that influence function. Furthermore, peptides tune the motions of MHC proteins themselves, which impacts recognition of peptide/MHC complexes by other proteins. Here, we review the motional properties of peptides in MHC binding grooves and discuss how peptide properties can influence MHC motions. We briefly review theoretical concepts about protein motion and highlight key data that illustrate immunological consequences. We focus primarily on class I systems due to greater availability of data, but segue into class II systems as the concepts and consequences overlap. We suggest that characterization of the dynamic “energy landscapes” of peptide/MHC complexes and the resulting functional consequences is one of the next frontiers in structural immunology.

Antibacterial activity of synthetic peptides derived from lactoferricin against Escherichia coli ATCC 25922 and Enterococcus faecalis ATCC 29212.

Science.gov (United States)

León-Calvijo, María A; Leal-Castro, Aura L; Almanzar-Reina, Giovanni A; Rosas-Pérez, Jaiver E; García-Castañeda, Javier E; Rivera-Monroy, Zuly J

2015-01-01

Peptides derived from human and bovine lactoferricin were designed, synthesized, purified, and characterized using RP-HPLC and MALDI-TOF-MS. Specific changes in the sequences were designed as (i) the incorporation of unnatural amino acids in the sequence, the (ii) reduction or (iii) elongation of the peptide chain length, and (iv) synthesis of molecules with different number of branches containing the same sequence. For each peptide, the antibacterial activity against Escherichia coli ATCC 25922 and Enterococcus faecalis ATCC 29212 was evaluated. Our results showed that Peptides I.2 (RWQWRWQWR) and I.4 ((RRWQWR)4K2Ahx2C2) exhibit bigger or similar activity against E. coli (MIC 4-33 μM) and E. faecalis (MIC 10-33 μM) when they were compared with lactoferricin protein (LF) and some of its derivate peptides as II.1 (FKCRRWQWRMKKLGA) and IV.1 (FKCRRWQWRMKKLGAPSITCVRRAE). It should be pointed out that Peptides I.2 and I.4, containing the RWQWR motif, are short and easy to synthesize; our results demonstrate that it is possible to design and obtain synthetic peptides that exhibit enhanced antibacterial activity using a methodology that is fast and low-cost and that allows obtaining products with a high degree of purity and high yield.

Antibacterial Activity of Synthetic Peptides Derived from Lactoferricin against Escherichia coli ATCC 25922 and Enterococcus faecalis ATCC 29212

Directory of Open Access Journals (Sweden)

María A. León-Calvijo

2015-01-01

Full Text Available Peptides derived from human and bovine lactoferricin were designed, synthesized, purified, and characterized using RP-HPLC and MALDI-TOF-MS. Specific changes in the sequences were designed as (i the incorporation of unnatural amino acids in the sequence, the (ii reduction or (iii elongation of the peptide chain length, and (iv synthesis of molecules with different number of branches containing the same sequence. For each peptide, the antibacterial activity against Escherichia coli ATCC 25922 and Enterococcus faecalis ATCC 29212 was evaluated. Our results showed that Peptides I.2 (RWQWRWQWR and I.4 ((RRWQWR4K2Ahx2C2 exhibit bigger or similar activity against E. coli (MIC 4–33 μM and E. faecalis (MIC 10–33 μM when they were compared with lactoferricin protein (LF and some of its derivate peptides as II.1 (FKCRRWQWRMKKLGA and IV.1 (FKCRRWQWRMKKLGAPSITCVRRAE. It should be pointed out that Peptides I.2 and I.4, containing the RWQWR motif, are short and easy to synthesize; our results demonstrate that it is possible to design and obtain synthetic peptides that exhibit enhanced antibacterial activity using a methodology that is fast and low-cost and that allows obtaining products with a high degree of purity and high yield.