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Sample records for lysine residue present

  1. The structural feature surrounding glycated lysine residues in human hemoglobin.

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    Ito, Shigenori; Nakahari, Takashi; Yamamoto, Daisuke

    2011-06-01

    Complications derived from diabetes mellitus are caused by nonenzymatic protein glycation at the specific sites. LC/MS/MS was performed for the identification of the tryptic peptides of glycated hemoglobins using glyceraldehyde. After the identification of the glycation or non-glycation site, computer analysis of the structure surrounding the sites was carried out using PDB data (1BZ0). Five glycated lysine residues (Lys-16(α), -56(α), -8(β), -82(β), and -144(β)) and four non-glycated lysine residues (Lys-7(α), -40(α), -99(α), and -132(β)) were identified. The non-glycated lysine residues, Lys-7(α), -40(α), and -132(β), are most likely to form electrostatic interactions with the β carboxyl group of Asp-74(α), C-terminal His-146(β), and Glu-7(β) by virtue of their proximity, which is 2.67-2.91 Å (N-O). Additionally, there are histidine residues within 4.55-7.38 Å (N-N) around eight sites except for Lys-7(α). We conclude that the following factors seem to be necessary for glycation of lysine residues: (i) the apparent absence of aspartate or glutamate residues to inhibit the glycation reaction by forming an electrostatic interaction, (ii) the presence of histidine residues for acid-base catalysis of the Amadori rearrangement, and (iii) the presence of an amino acid residue capable of stabilizing a phosphate during proton transfer.

  2. Lysine fortification: past, present, and future.

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    Pellett, Peter L; Ghosh, Shibani

    2004-06-01

    Fortification with lysine to improve the protein value of human diets that are heavily based on cereals has received support from the results of these recent studies [1,2]. Support also comes from examination of average food and nutrient availability data derived from food balance sheets. Whereas nutritional status is influenced by the nutrient content of foods consumed in relation to need, the requirements for protein and amino acids are influenced by many additional factors [10, 12, 14, 28, 29]. These include age, sex, body size, physical activity, growth, pregnancy and lactation, infection, and the efficiency of nutrient utilization. Even if the immune response was influenced by the added lysine, adequate water and basic sanitation would remain essential. Acute and chronic undernutrition and most micronutrient deficiencies primarily affect poor and deprived people who do not have access to food of adequate nutritional value, live in unsanitary environments without access to clean water and basic services, and lack access to appropriate education and information [30]. A further variable is the possible interaction between protein and food energy availability [31]. This could affect the protein value of diets when food energy is limiting to a significant degree. Thus, the additional effects of food energy deficiency on protein utilization could well be superimposed on the very poorest. The improvement of dietary diversity must be the long-term aim, with dietary fortification considered only a short-term solution. The former should take place as wealth improves and the gaps between rich and poor diminish. Although such changes are taking place, they are highly uneven. Over the last several decades, increases have occurred in the availability of food energy, total protein, and animal protein for both developed and developing countries. However, for the very poorest developing countries over the same period, changes have been almost nonexistent, and the values for

  3. Role of lysine and acidic amino acid residues on the insecticidal activity of Jackbean urease.

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    Real-Guerra, Rafael; Carlini, Célia Regina; Stanisçuaski, Fernanda

    2013-09-01

    Canavalia ensiformis has three isoforms of urease: Jackbean urease (JBU), Jackbean urease II and canatoxin. These isoforms present several biological activities, independent from the enzymatic property, such as entomotoxicity and antifungal properties. The entomotoxic activity is a property of the whole protein, as well as of a 10 kDa peptide released by insect digestive enzymes. Here we have used chemical modification to observe the influence of lysines and acidic residues on JBU enzymatic and insecticidal activities. Chemical modification of lysine residues was performed with dimethylamine-borane complex and formaldehyde, and acidic residues were modified by 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and ethylenediamine. Derivatized ureases, called JBU-Lys (lysine-modified) and JBU-Ac (acidic residues-modified), were assayed for their biochemical and insecticidal properties. Neither modification altered significantly the kinetic parameters analyzed, indicating that no residue critical for the enzyme activity was affected and that the modifications did not incur in any significant structural alteration. On the other hand, both modifications reduced the toxic activity of the native protein fed to Dysdercus peruvianus. The changes observed in the entomotoxic property of the derivatized proteins reflect alterations in different steps of JBU's toxicity towards insects. JBU-Ac is not susceptible to hydrolysis by insect digestive enzymes, hence impairing the release of toxic peptide(s), while JBU-Lys is processed as the native protein. On the other hand, the antidiuretic effect of JBU on Rhodnius prolixus is altered in JBU-Lys, but not in JBU-Ac. Altogether, these data emphasize the role of lysine and acidic residues on the insecticidal properties of ureases.

  4. Structure-function relationships in scorpion neurotoxins. Identification of the supperreactive lysine residue in toxin I of Androctonus australis Hector.

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    Sampieri, F; Habersetzer-Rochat, C

    1978-07-21

    In a previous article (Habersetzer-Rochat, C. and Sampieri, R. (1976) Biochemistry 15, 2254--2261) it was demonstrated that the toxin I of the North African Scorpion Androctonus australis Hector was inactivated after reaction with iodoacetate; the toxicity loss in mice was correlated with the carboxymethylation of one superreactive residue. In the present work, alkylation of toxin I was performed with iodo[14C]-acetate. Hence, it was possible, after reduction, S-methylation and chymotryptic hydrolysis of this toxin, to isolate the peptide containing the labelled lysine residue. By automatic Edman degradation, this residue was identified as being the penultimate lysine at position 56 in the primary sequence. Comparison of three primary structures of scorpion neurotoxins and comparison in different kinds of activity seem to indicate that this lysine residue is mainly important for toxicity in mice.

  5. Lysine residue 185 of Rad1 is a topological but not a functional counterpart of lysine residue 164 of PCNA.

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    Niek Wit

    Full Text Available Monoubiquitylation of the homotrimeric DNA sliding clamp PCNA at lysine residue 164 (PCNA(K164 is a highly conserved, DNA damage-inducible process that is mediated by the E2/E3 complex Rad6/Rad18. This ubiquitylation event recruits translesion synthesis (TLS polymerases capable of replicating across damaged DNA templates. Besides PCNA, the Rad6/Rad18 complex was recently shown in yeast to ubiquitylate also 9-1-1, a heterotrimeric DNA sliding clamp composed of Rad9, Rad1, and Hus1 in a DNA damage-inducible manner. Based on the highly similar crystal structures of PCNA and 9-1-1, K185 of Rad1 (Rad1(K185 was identified as the only topological equivalent of PCNA(K164. To investigate a potential role of posttranslational modifications of Rad1(K185 in DNA damage management, we here generated a mouse model with a conditional deletable Rad1(K185R allele. The Rad1(K185 residue was found to be dispensable for Chk1 activation, DNA damage survival, and class switch recombination of immunoglobulin genes as well as recruitment of TLS polymerases during somatic hypermutation of immunoglobulin genes. Our data indicate that Rad1(K185 is not a functional counterpart of PCNA(K164.

  6. Studies on the biotin-binding site of avidin. Lysine residues involved in the active site.

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    Gitlin, G; Bayer, E A; Wilchek, M

    1987-01-01

    Egg-white avidin was treated with 1-fluoro-2,4-dinitrobenzene. Modification of an average of one lysine residue per avidin subunit caused the complete loss of biotin binding. Tryptic peptides obtained from the 2,4-dinitrophenylated avidin were fractionated by reversed-phase h.p.l.c. Three peptides contained the 2,4-dinitrophenyl group. Amino acid analysis revealed that lysine residues 45, 94 and 111 are modified and probably comprise part of the biotin-binding site. PMID:3109401

  7. Studies on the biotin-binding site of avidin. Lysine residues involved in the active site.

    OpenAIRE

    Gitlin, G; Bayer, E A; Wilchek, M

    1987-01-01

    Egg-white avidin was treated with 1-fluoro-2,4-dinitrobenzene. Modification of an average of one lysine residue per avidin subunit caused the complete loss of biotin binding. Tryptic peptides obtained from the 2,4-dinitrophenylated avidin were fractionated by reversed-phase h.p.l.c. Three peptides contained the 2,4-dinitrophenyl group. Amino acid analysis revealed that lysine residues 45, 94 and 111 are modified and probably comprise part of the biotin-binding site.

  8. Role of lysine binding residues in the global folding of the lysC riboswitch.

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    Smith-Peter, Erich; Lamontagne, Anne-Marie; Lafontaine, Daniel A

    2015-01-01

    Riboswitches regulate gene expression by rearranging their structure upon metabolite binding. The lysine-sensing lysC riboswitch is a rare example of an RNA aptamer organized around a 5-way helical junction in which ligand binding is performed exclusively through nucleotides located at the junction core. We have probed whether the nucleotides involved in ligand binding play any role in the global folding of the riboswitch. As predicted, our findings indicate that ligand-binding residues are critical for the lysine-dependent gene regulation mechanism. We also find that these residues are not important for the establishment of key magnesium-dependent tertiary interactions, suggesting that folding and ligand recognition are uncoupled in this riboswitch for the formation of specific interactions. However, FRET assays show that lysine binding results in an additional conformational change, indicating that lysine binding may also participate in a specific folding transition. Thus, in contrast to helical junctions being primary determinants in ribozymes and rRNA folding, we speculate that the helical junction of the lysine-sensing lysC riboswitch is not employed as structural a scaffold to direct global folding, but rather has a different role in establishing RNA-ligand interactions required for riboswitch regulation. Our work suggests that helical junctions may adopt different functions such as the coordination of global architecture or the formation of specific ligand binding site.

  9. Regulation of translesion DNA synthesis: Posttranslational modification of lysine residues in key proteins.

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    McIntyre, Justyna; Woodgate, Roger

    2015-05-01

    Posttranslational modification of proteins often controls various aspects of their cellular function. Indeed, over the past decade or so, it has been discovered that posttranslational modification of lysine residues plays a major role in regulating translesion DNA synthesis (TLS) and perhaps the most appreciated lysine modification is that of ubiquitination. Much of the recent interest in ubiquitination stems from the fact that proliferating cell nuclear antigen (PCNA) was previously shown to be specifically ubiquitinated at K164 and that such ubiquitination plays a key role in regulating TLS. In addition, TLS polymerases themselves are now known to be ubiquitinated. In the case of human polymerase η, ubiquitination at four lysine residues in its C-terminus appears to regulate its ability to interact with PCNA and modulate TLS. Within the past few years, advances in global proteomic research have revealed that many proteins involved in TLS are, in fact, subject to a previously underappreciated number of lysine modifications. In this review, we will summarize the known lysine modifications of several key proteins involved in TLS; PCNA and Y-family polymerases η, ι, κ and Rev1 and we will discuss the potential regulatory effects of such modification in controlling TLS in vivo.

  10. Critical lysine residues of Klf4 required for protein stabilization and degradation

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Key-Hwan; Kim, So-Ra; Ramakrishna, Suresh; Baek, Kwang-Hyun, E-mail: baek@cha.ac.kr

    2014-01-24

    Highlights: • Klf4 undergoes the 26S proteasomal degradation by ubiquitination on its multiple lysine residues. • Essential Klf4 ubiquitination sites are accumulated between 190–263 amino acids. • A mutation of lysine at 232 on Klf4 elongates protein turnover. • Klf4 mutants dramatically suppress p53 expression both under normal and UV irradiated conditions. - Abstract: The transcription factor, Krüppel-like factor 4 (Klf4) plays a crucial role in generating induced pluripotent stem cells (iPSCs). As the ubiquitination and degradation of the Klf4 protein have been suggested to play an important role in its function, the identification of specific lysine sites that are responsible for protein degradation is of prime interest to improve protein stability and function. However, the molecular mechanism regulating proteasomal degradation of the Klf4 is poorly understood. In this study, both the analysis of Klf4 ubiquitination sites using several Klf4 deletion fragments and bioinformatics predictions showed that the lysine sites which are signaling for Klf4 protein degradation lie in its N-terminal domain (aa 1–296). The results also showed that Lys32, 52, 232, and 252 of Klf4 are responsible for the proteolysis of the Klf4 protein. These results suggest that Klf4 undergoes proteasomal degradation and that these lysine residues are critical for Klf4 ubiquitination.

  11. SucStruct: Prediction of succinylated lysine residues by using structural properties of amino acids.

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    López, Yosvany; Dehzangi, Abdollah; Lal, Sunil Pranit; Taherzadeh, Ghazaleh; Michaelson, Jacob; Sattar, Abdul; Tsunoda, Tatsuhiko; Sharma, Alok

    2017-03-28

    Post-Translational Modification (PTM) is a biological reaction which contributes to diversify the proteome. Despite many modifications with important roles in the cellular activity, lysine succinylation has recently emerged as an important PTM mark. It alters the chemical structure of lysines, leading to remarkable changes in the structure and function of proteins. Given the huge amount of proteins being sequenced in the post-genome era, the experimental detection of succinylated residues remains expensive, inefficient and time-consuming. Therefore, the development of computational tools for accurately predicting succinylated lysines is an urgent necessity. To date, several approaches have been proposed but their sensitivity has been reportedly poor. In this paper, we propose an approach that utilizes structural features of amino acids to improve lysine succinylation prediction. Succinylated and non-succinylated lysines were first retrieved from 670 proteins and characteristics such as accessible surface area, backbone torsion angles, and local structure conformations were incorporated. We used the k-nearest neighbors cleaning for dealing with class imbalance and designed a pruned decision tree for classification. Our predictor, referred as SucStruct (Succinylation using Structural features), proved to significantly improve performance when compared to previous predictors, with sensitivity, accuracy and Mathew's correlation coefficient equal to 0.7334-0.7946, 0.7444-0.7608 and 0.4884-0.5240, respectively.

  12. Bioconjugation of Oligodeoxynucleotides Carrying 1,4-Dicarbonyl Groups via Reductive Amination with Lysine Residues.

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    Yang, Bo; Jinnouchi, Akiko; Usui, Kazuteru; Katayama, Tsutomu; Fujii, Masayuki; Suemune, Hiroshi; Aso, Mariko

    2015-08-19

    We evaluated the efficacy of bioconjugation of oligodeoxynucleotides (ODNs) containing 1,4-dicarbonyl groups, a C4'-oxidized abasic site (OAS), and a newly designed 2'-methoxy analogue, via reductive amination with lysine residues. Dicarbonyls, aldehyde and ketone at C1- and C4-positions of deoxyribose in the ring-opened form of OAS allowed efficient reaction with amines. Kinetic studies indicated that reductive amination of OAS-containing ODNs with a proximal amine on the complementary strand proceeded 10 times faster than the corresponding reaction of an ODN containing an abasic site with C1-aldehyde. Efficient reductive amination between the DNA-binding domain of Escherichia coli DnaA protein and ODNs carrying OAS in the DnaA-binding sequence proceeded at the lysine residue in proximity to the phosphate group at the 5'-position of the OAS, in contrast to unsuccessful conjugation with abasic site ODNs, even though they have similar aldehydes. Theoretical calculation indicated that the C1-aldehyde of OAS was more accessible to the target lysine than that of the abasic site. These results demonstrate the potential utility of cross-linking strategies that use dicarbonyl-containing ODNs for the study of protein-nucleic acid interactions. Conjugation with a lysine-containing peptide that lacked specific affinity for ODN was also successful, further highlighting the advantages of 1,4-dicarbonyls.

  13. Computational prediction of methylation types of covalently modified lysine and arginine residues in proteins.

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    Deng, Wankun; Wang, Yongbo; Ma, Lili; Zhang, Ying; Ullah, Shahid; Xue, Yu

    2016-05-30

    Protein methylation is an essential posttranslational modification (PTM) mostly occurs at lysine and arginine residues, and regulates a variety of cellular processes. Owing to the rapid progresses in the large-scale identification of methylation sites, the available data set was dramatically expanded, and more attention has been paid on the identification of specific methylation types of modification residues. Here, we briefly summarized the current progresses in computational prediction of methylation sites, which provided an accurate, rapid and efficient approach in contrast with labor-intensive experiments. We collected 5421 methyllysines and methylarginines in 2592 proteins from the literature, and classified most of the sites into different types. Data analyses demonstrated that different types of methylated proteins were preferentially involved in different biological processes and pathways, whereas a unique sequence preference was observed for each type of methylation sites. Thus, we developed a predictor of GPS-MSP, which can predict mono-, di- and tri-methylation types for specific lysines, and mono-, symmetric di- and asymmetrical di-methylation types for specific arginines. We critically evaluated the performance of GPS-MSP, and compared it with other existing tools. The satisfying results exhibited that the classification of methylation sites into different types for training can considerably improve the prediction accuracy. Taken together, we anticipate that our study provides a new lead for future computational analysis of protein methylation, and the prediction of methylation types of covalently modified lysine and arginine residues can generate more useful information for further experimental manipulation.

  14. Effects of lysine residues on structural characteristics and stability of tau proteins

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    Lee, Myeongsang; Baek, Inchul; Choi, Hyunsung; Kim, Jae In; Na, Sungsoo, E-mail: nass@korea.ac.kr

    2015-10-23

    Pathological amyloid proteins have been implicated in neuro-degenerative diseases, specifically Alzheimer's, Parkinson's, Lewy-body diseases and prion related diseases. In prion related diseases, functional tau proteins can be transformed into pathological agents by environmental factors, including oxidative stress, inflammation, Aβ-mediated toxicity and covalent modification. These pathological agents are stable under physiological conditions and are not easily degraded. This un-degradable characteristic of tau proteins enables their utilization as functional materials to capturing the carbon dioxides. For the proper utilization of amyloid proteins as functional materials efficiently, a basic study regarding their structural characteristic is necessary. Here, we investigated the basic tau protein structure of wild-type (WT) and tau proteins with lysine residues mutation at glutamic residue (Q2K) on tau protein at atomistic scale. We also reported the size effect of both the WT and Q2K structures, which allowed us to identify the stability of those amyloid structures. - Highlights: • Lysine mutation effect alters the structure conformation and characteristic of tau. • Over the 15 layers both WT and Q2K models, both tau proteins undergo fractions. • Lysine mutation causes the increment of non-bonded energy and solvent accessible surface area. • Structural instability of Q2K model was proved by the number of hydrogen bonds analysis.

  15. Functional importance of motif I of pseudouridine synthases: mutagenesis of aligned lysine and proline residues.

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    Spedaliere, C J; Hamilton, C S; Mueller, E G

    2000-08-01

    On the basis of sequence alignments, the pseudouridine synthases were grouped into four families that share no statistically significant global sequence similarity, though some common sequence motifs were discovered [Koonin, E. V. (1996) Nucleic Acids. Res. 24, 2411-2415; Gustafsson, C., Reid, R., Greene, P. J., and Santi, D. V. (1996) Nucleic Acids Res. 24, 3756-3762]. We have investigated the functional significance of these alignments by substituting the nearly invariant lysine and proline residues in Motif I of RluA and TruB, pseudouridine synthases belonging to different families. Contrary to our expectations, the altered enzymes display only very mild kinetic impairment. Substitution of the aligned lysine and proline residues does, however, reduce structural stability, consistent with a temperature sensitive phenotype that results from substitution of the cognate proline residue in Cbf5p, a yeast homologue of TruB [Zerbarjadian, Y., King, T., Fournier, M. J., Clarke, L., and Carbon, J. (1999) Mol. Cell. Biol. 19, 7461-7472]. Together, our data support a functional role for Motif I, as predicted by sequence alignments, though the effect of substituting the highly conserved residues was milder than we anticipated. By extrapolation, our findings also support the assignment of pseudouridine synthase function to certain physiologically important eukaryotic proteins that contain Motif I, including the human protein dyskerin, alteration of which leads to the disease dyskeratosis congenita.

  16. Superoxide reduction by a superoxide reductase lacking the highly conserved lysine residue.

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    Pinto, Ana F; Romão, Célia V; Pinto, Liliana C; Huber, Harald; Saraiva, Lígia M; Todorovic, Smilja; Cabelli, Diane; Teixeira, Miguel

    2015-01-01

    Superoxide reductases (SORs) are the most recently identified superoxide detoxification systems, being found in microorganisms from the three domains of life. These enzymes are characterized by a catalytic mononuclear iron site, with one cysteine and four histidine ligands of the ferrous active form. A lysine residue in the -EKHVP- motif, located close to the active site, has been considered to be essential for the enzyme function, by contributing to the positive surface patch that attracts the superoxide anion and by controlling the chemistry of the catalytic mechanism through a hydrogen bond network. However, we show here that this residue is substituted by non-equivalent amino acids in several putative SORs from Archaea and unicellular Eukarya. In this work, we focus on mechanistic and spectroscopic studies of one of these less common enzymes, the SOR from the hyperthermophilic Crenarchaeon Ignicoccus hospitalis. We employ pulse radiolysis fast kinetics and spectroscopic approaches to study the wild-type enzyme (-E23T24HVP-), and two mutants, T24K and E23A, the later mimicking enzymes lacking both the lysine and glutamate (a ferric ion ligand) of the motif. The efficiency of the wild-type protein and mutants in reducing superoxide is comparable to other SORs, revealing the robustness of these enzymes to single mutations.

  17. Lysine Deacetylase Inhibitors in Parasites: Past, Present, and Future Perspectives.

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    Hailu, Gebremedhin S; Robaa, Dina; Forgione, Mariantonietta; Sippl, Wolfgang; Rotili, Dante; Mai, Antonello

    2017-06-22

    Current therapies for human parasite infections rely on a few drugs, most of which have severe side effects, and their helpfulness is being seriously compromised by the drug resistance problem. Globally, this is pushing discovery research of antiparasitic drugs toward new agents endowed with new mechanisms of action. By using a "drug repurposing" strategy, histone deacetylase inhibitors (HDACi), which are presently clinically approved for cancer use, are now under investigation for various parasite infections. Because parasitic Zn(2+)- and NAD(+)-dependent HDACs play crucial roles in the modulation of parasite gene expression and many of them are pro-survival for several parasites under various conditions, they are now emerging as novel potential antiparasitic targets. This Perspective summarizes the state of knowledge of HDACi (both class I/II HDACi and sirtuin inhibitors) targeted to the main human parasitic diseases (schistosomiasis, malaria, trypanosomiasis, leishmaniasis, and toxoplasmosis) and provides visions into the main issues that challenge their development as antiparasitic agents.

  18. The conserved Lysine69 residue plays a catalytic role in Mycobacterium tuberculosis shikimate dehydrogenase

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    Rodrigues Valnês

    2009-01-01

    Full Text Available Abstract Background The shikimate pathway is an attractive target for the development of antitubercular agents because it is essential in Mycobacterium tuberculosis, the causative agent of tuberculosis, but absent in humans. M. tuberculosis aroE-encoded shikimate dehydrogenase catalyzes the forth reaction in the shikimate pathway. Structural and functional studies indicate that Lysine69 may be involved in catalysis and/or substrate binding in M. tuberculosis shikimate dehydrogenase. Investigation of the kinetic properties of mutant enzymes can bring important insights about the role of amino acid residues for M. tuberculosis shikimate dehydrogenase. Findings We have performed site-directed mutagenesis, steady-state kinetics, equilibrium binding measurements and molecular modeling for both the wild-type M. tuberculosis shikimate dehydrogenase and the K69A mutant enzymes. The apparent steady-state kinetic parameters for the M. tuberculosis shikimate dehydrogenase were determined; the catalytic constant value for the wild-type enzyme (50 s-1 is 68-fold larger than that for the mutant K69A (0.73 s-1. There was a modest increase in the Michaelis-Menten constant for DHS (K69A = 76 μM; wild-type = 29 μM and NADPH (K69A = 30 μM; wild-type = 11 μM. The equilibrium dissociation constants for wild-type and K69A mutant enzymes are 32 (± 4 μM and 134 (± 21, respectively. Conclusion Our results show that the residue Lysine69 plays a catalytic role and is not involved in substrate binding for the M. tuberculosis shikimate dehydrogenase. These efforts on M. tuberculosis shikimate dehydrogenase catalytic mechanism determination should help the rational design of specific inhibitors, aiming at the development of antitubercular drugs.

  19. Differential Contributions of Ubiquitin-Modified APOBEC3G Lysine Residues to HIV-1 Vif-Induced Degradation.

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    Turner, Tiffany; Shao, Qiujia; Wang, Weiran; Wang, Yudi; Wang, Chenliang; Kinlock, Ballington; Liu, Bindong

    2016-08-28

    Apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G (A3G) is a host restriction factor that impedes HIV-1 replication. Viral integrity is salvaged by HIV-1 virion infectivity factor (Vif), which mediates A3G polyubiquitination and subsequent cellular depletion. Previous studies have implied that A3G polyubiquitination is essential for Vif-induced degradation. However, the contribution of polyubiquitination to the rate of A3G degradation remains unclear. Here, we show that A3G polyubiquitination is essential for degradation. Inhibition of ubiquitin-activating enzyme E1 by PYR-41 or blocking the formation of ubiquitin chains by over-expressing the lysine to arginine mutation of ubiquitin K48 (K48R) inhibited A3G degradation. Our A3G mutagenesis study showed that lysine residues 297, 301, 303, and 334 were not sufficient to render lysine-free A3G sensitive to Vif-mediated degradation. Our data also confirm that Vif could induce ubiquitin chain formation on lysine residues interspersed throughout A3G. Notably, A3G degradation relied on the lysine residues involved in polyubiquitination. Although A3G and the A3G C-terminal mutant interacted with Vif and were modified by ubiquitin chains, the latter remained more resistant to Vif-induced degradation. Furthermore, the A3G C-terminal mutant, but not the N-terminal mutant, maintained potent antiviral activity in the presence of Vif. Taken together, our results suggest that the location of A3G ubiquitin modification is a determinant for Vif-mediated degradation, implying that in addition to polyubiquitination, other factors may play a key role in the rate of A3G degradation.

  20. Lysine residues at the first and second KTKEGV repeats mediate α-Synuclein binding to membrane phospholipids.

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    Zarbiv, Yonaton; Simhi-Haham, Dganit; Israeli, Eitan; Elhadi, Suaad Abed; Grigoletto, Jessica; Sharon, Ronit

    2014-10-01

    While α-Synuclein (α-Syn) is mainly detected as a cytosolic protein, a portion of it is recovered bound to membranes. It is suggested that binding to membrane phospholipids controls α-Syn structure, physiology and pathogenesis. We aimed at investigating the role, of the positive charged lysine residues at the KTKEGV repeat motif, in mediating α-Syn associations with membrane phospholipids and in α-Syn oligomerization and aggregation. Specifically, two positive lysine (K) residues were replaced with two negative glutamic acid (E) residues at either the first or second KTKEGV repeat motifs. The effect of these mutations on membrane binding was determined by a quantitative phospholipid ELISA assay and compared to wild-type α-Syn and to the Parkinson's disease-causing mutations, A30P, E46K and A53T. We found that the K to E substitutions affected α-Syn binding to phospholipids. In addition, K to E substitutions resulted in a dramatically lower level of soluble α-Syn oligomers and larger intracellular inclusions. Together, our results suggest a critical role for lysine residues at the N-terminal repeat domain in the pathophysiology of α-Syn.

  1. A noncanonical function of sortase enables site-specific conjugation of small molecules to lysine residues in proteins.

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    Bellucci, Joseph J; Bhattacharyya, Jayanta; Chilkoti, Ashutosh

    2015-01-07

    We provide the first demonstration that isopeptide ligation, a noncanonical activity of the enzyme sortase A, can be used to modify recombinant proteins. This reaction was used in vitro to conjugate small molecules to a peptide, an engineered targeting protein, and a full-length monoclonal antibody with an exquisite level of control over the site of conjugation. Attachment to the protein substrate occurred exclusively through isopeptide bonds at a lysine ε-amino group within a specific amino acid sequence. This reaction allows more than one molecule to be site-specifically conjugated to a protein at internal sites, thereby overcoming significant limitations of the canonical native peptide ligation reaction catalyzed by sortase A. Our method provides a unique chemical ligation procedure that is orthogonal to existing methods, supplying a new method to site-specifically modify lysine residues that will be a valuable addition to the protein conjugation toolbox.

  2. Elicitin-Induced Distal Systemic Resistance in Plants is Mediated Through the Protein-Protein Interactions Influenced by Selected Lysine Residues.

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    Uhlíková, Hana; Obořil, Michal; Klempová, Jitka; Šedo, Ondrej; Zdráhal, Zbyněk; Kašparovský, Tomáš; Skládal, Petr; Lochman, Jan

    2016-01-01

    Elicitins are a family of small proteins with sterol-binding activity that are secreted by Phytophthora and Pythium sp. classified as oomycete PAMPs. Although α- and β-elicitins bind with the same affinity to one high affinity binding site on the plasma membrane, β-elicitins (possessing 6-7 lysine residues) are generally 50- to 100-fold more active at inducing distal HR and systemic resistance than the α-isoforms (with only 1-3 lysine residues). To examine the role of lysine residues in elicitin biological activity, we employed site-directed mutagenesis to prepare a series of β-elicitin cryptogein variants with mutations on specific lysine residues. In contrast to direct infiltration of protein into leaves, application to the stem revealed a rough correlation between protein's charge and biological activity, resulting in protection against Phytophthora parasitica. A detailed analysis of proteins' movement in plants showed no substantial differences in distribution through phloem indicating differences in consequent apoplastic or symplastic transport. In this process, an important role of homodimer formation together with the ability to form a heterodimer with potential partner represented by endogenous plants LTPs is suggested. Our work demonstrates a key role of selected lysine residues in these interactions and stresses the importance of processes preceding elicitin recognition responsible for induction of distal systemic resistance.

  3. Elicitin-induced distal systemic resistance in plants is mediated through the protein-protein interactions influenced by selected lysine residues

    Directory of Open Access Journals (Sweden)

    Hana eUhlíková

    2016-02-01

    Full Text Available Elicitins are a family of small proteins with sterol-binding activity that are secreted by Phytophthora and Pythium spp. classified as oomycete PAMPs. Although alfa- and beta-elicitins bind with the same affinity to one high affinity binding site on the plasma membrane, beta-elicitins (possessing 6-7 lysine residues are generally 50- to 100-fold more active at inducing distal HR and systemic resistance than the alfa-isoforms (with only 1-3 lysine residues.To examine the role of lysine residues in elicitin biological activity, we employed site-directed mutagenesis to prepare a series of beta-elicitin cryptogein variants with mutations on specific lysine residues. In contrast to direct infiltration of protein into leaves, application to the stem revealed a rough correlation between protein’s charge and biological activity, resulting in protection against Phytophthora parasitica. A detailed analysis of proteins’ movement in plants showed no substantial differences in distribution through phloem indicating differences in consequent apoplastic or symplastic transport. In this process, an important role of homodimer formation together with the ability to form a heterodimer with potential partner represented by endogenous plants LTPs is suggested. Our work demonstrates a key role of selected lysine residues in these interactions and stresses the importance of processes preceding elicitin recognition responsible for induction of distal systemic resistance.

  4. Oxidative deamination of benzylamine and lysine residue in bovine serum albumin by green tea, black tea, and coffee.

    Science.gov (United States)

    Akagawa, Mitsugu; Shigemitsu, Tomoko; Suyama, Kyozo

    2005-10-01

    Oxidative deamination by various polyphenolic compounds is presumed to be due to the oxidative conversion of polyphenols to the corresponding quinones through autoxidation. Here we examined the oxidative deamination by the polyphenol-rich beverages green tea, black tea, and coffee at a physiological pH and temperature. Green tea, black tea, and coffee extracts oxidatively deaminated benzylamine and the lysine residues of bovine serum albumin to benzaldehyde and alpha-aminoadipic delta-semialdehyde residues, respectively, in sodium phosphate buffer (pH 7.4) at 37 degrees C in both the presence and absence of Cu2+, indicating the occurrence of an amine (lysyl) oxidase-like reaction. We also examined the effects of pH and metal ions on the reaction. The possible biological effects of drinking polyphenol-rich beverages on human are also discussed.

  5. Substitution of glutamate residue by lysine in the dimerization domain affects DNA binding ability of HapR by inducing structural deformity in the DNA binding domain.

    Directory of Open Access Journals (Sweden)

    Richa Singh

    Full Text Available HapR has been given the status of a high cell density master regulatory protein in Vibrio cholerae. Though many facts are known regarding its structural and functional aspects, much still can be learnt from natural variants of the wild type protein. This work aims at investigating the nature of functional inertness of a HapR natural variant harboring a substitution of a conserved glutamate residue at position 117 which participates in forming a salt bridge by lysine (HapRV2G-E(117K. Experimental evidence presented here reveals the inability of this variant to interact with various cognate promoters by in vitro gel shift assay. Furthermore, the elution profiles of HapRV2G-E(117K protein along with the wild type functional HapRV2G in size-exclusion chromatography as well as circular dichroism spectra did not reflect any significant differences in its structure, thereby indicating the intactness of dimer in the variant protein. To gain further insight into the global shape of the proteins, small angle X-ray scattering analysis (SAXS was performed. Intriguingly, increased radius of gyration of HapRV2G-E(117K of 27.5 Å in comparison to the wild type protein from SAXS data analyses implied a significant alteration in the global shape of the dimeric HapRV2G-E(117K protein. Structure reconstruction brought forth that the DNA binding domains were substantially "parted away" in this variant. Taken together, our data illustrates that substitution of the conserved glutamate residue by lysine in the dimerization domain induces separation of the two DNA binding domains from their native-like positioning without altering the dimeric status of HapR variant.

  6. Substitution of glutamate residue by lysine in the dimerization domain affects DNA binding ability of HapR by inducing structural deformity in the DNA binding domain.

    Science.gov (United States)

    Singh, Richa; Rathore, Yogendra Singh; Singh, Naorem Santa; Peddada, Nagesh; Ashish; Raychaudhuri, Saumya

    2013-01-01

    HapR has been given the status of a high cell density master regulatory protein in Vibrio cholerae. Though many facts are known regarding its structural and functional aspects, much still can be learnt from natural variants of the wild type protein. This work aims at investigating the nature of functional inertness of a HapR natural variant harboring a substitution of a conserved glutamate residue at position 117 which participates in forming a salt bridge by lysine (HapRV2G-E(117)K). Experimental evidence presented here reveals the inability of this variant to interact with various cognate promoters by in vitro gel shift assay. Furthermore, the elution profiles of HapRV2G-E(117)K protein along with the wild type functional HapRV2G in size-exclusion chromatography as well as circular dichroism spectra did not reflect any significant differences in its structure, thereby indicating the intactness of dimer in the variant protein. To gain further insight into the global shape of the proteins, small angle X-ray scattering analysis (SAXS) was performed. Intriguingly, increased radius of gyration of HapRV2G-E(117)K of 27.5 Å in comparison to the wild type protein from SAXS data analyses implied a significant alteration in the global shape of the dimeric HapRV2G-E(117)K protein. Structure reconstruction brought forth that the DNA binding domains were substantially "parted away" in this variant. Taken together, our data illustrates that substitution of the conserved glutamate residue by lysine in the dimerization domain induces separation of the two DNA binding domains from their native-like positioning without altering the dimeric status of HapR variant.

  7. SITE-SPECIFIC LABELING OF A PROTEIN LYSINE RESIDUE BY NOVEL KINETIC LABELING COMBINATORIAL LIBRARIES

    Directory of Open Access Journals (Sweden)

    Allen Krantz

    2014-03-01

    Full Text Available The first example of a kinetic labeling library designed to enable the discovery of affinity labels is presented. Each library component (1 consists of a variable peptidyl component linked to a biotinyl moiety by a 4-mercaptobenzoyl linker in thioester format. We demonstrate that an affinity label can be uncovered by measuring reaction rates between library pools and the protein target, human serum albumin (HSA and identifying significant outliers. By choosing peptide functionality compatible with a potentially reactive thioester labeling entity, libraries can be screened in pools. It is noteworthy that a limited subset of amino acids (R, S, E, F, Y, l, M, W, and Q that compose the affinity moiety is sufficient to produce rate variances that guide the discovery process. After two rounds of deconvolution, J-FLYEE-NH2 (7-E emerges as a bona fide affinity label of HSA. Unlike known affinity labels, the affinity moiety is not retained in the protein product, but is extruded upon acylation of the protein. This feature affords a method of introducing various payloads, without extraneous elements, onto protein frameworks.

  8. Inhibition of Alkaline Phosphatase from Pearl Oyster Pinctada fucata by o-Phthalaldehyde: Involvement of Lysine and Histidine Residues at the Active Site

    Institute of Scientific and Technical Information of China (English)

    CHEN Hongtao; XIE Liping; YU Zhenyan; ZHANG Rongqing

    2005-01-01

    Alkaline phosphatase from Pinctada fucata was inactivated by o-phthalaldehyde (OPA). The inactivation followed pseudo first-order kinetics with a second rate constant of 0.167 (mmol/L)-1·min-1 at pH 7.5 and 25°C. A Tsou's plot analysis showed that inactivation occurred upon formation of one isoindole group. The OPA-modified enzyme lost the ability to bind with the specific affinity column and the presence of substrates or competitive inhibitors protected the enzyme from inactivation. The results revealed that the OPA-reaction site was at the enzyme substrate binding site. Prior modification of the enzyme by lysine or histidine specific reagent abolished formation of the isoindole derivatives, suggesting that lysine and histidine residues were involved in the OPA-induced inactivation. Taken together, OPA inactivated the alkaline phosphatase from Pinctada fucata by cross-linking lysine and histidine residues at the active site and formed an isoindole group at the substrate binding site of the enzyme.

  9. Piscidin-1-analogs with double L- and D-lysine residues exhibited different conformations in lipopolysaccharide but comparable anti-endotoxin activities

    Science.gov (United States)

    Kumar, Amit; Mahajan, Mukesh; Awasthi, Bhanupriya; Tandon, Anshika; Harioudh, Munesh Kumar; Shree, Sonal; Singh, Pratiksha; Shukla, Praveen Kumar; Ramachandran, Ravishankar; Mitra, Kalyan; Bhattacharjya, Surajit; Ghosh, Jimut Kanti

    2017-01-01

    To become clinically effective, antimicrobial peptides (AMPs) should be non-cytotoxic to host cells. Piscidins are a group of fish-derived AMPs with potent antimicrobial and antiendotoxin activities but limited by extreme cytotoxicity. We conjectured that introduction of cationic residue(s) at the interface of polar and non-polar faces of piscidins may control their insertion into hydrophobic mammalian cell membrane and thereby reducing cytotoxicity. We have designed several novel analogs of piscidin-1 by substituting threonine residue(s) with L and D-lysine residue(s). L/D-lysine-substituted analogs showed significantly reduced cytotoxicity but exhibited either higher or comparable antibacterial activity akin to piscidin-1. Piscidin-1-analogs demonstrated higher efficacy than piscidin-1 in inhibiting lipopolysaccharide (LPS)-induced pro-inflammatory responses in THP-1 cells. T15,21K-piscidin-1 (0.5 mg/Kg) and T15,21dK-piscidin-1 (1.0 mg/Kg) demonstrated 100% survival of LPS (12.0 mg/Kg)-administered mice. High resolution NMR studies revealed that both piscidin-1 and T15,21K-piscidin-1 adopted helical structures, with latter showing a shorter helix, higher amphipathicity and cationic residues placed at optimal distances to form ionic/hydrogen bond with lipid A of LPS. Remarkably, T15,21dK-piscidin-1 showed a helix-loop-helix structure in LPS and its interactions with LPS could be sustained by the distance of separation of side chains of R7 and D-Lys-15 which is close to the inter-phosphate distance of lipid A. PMID:28051162

  10. The roles of selected arginine and lysine residues of TAFI (Pro-CPU) in its activation to TAFIa by the thrombin-thrombomodulin complex.

    Science.gov (United States)

    Wu, Chengliang; Kim, Paul Y; Manuel, Reg; Seto, Marian; Whitlow, Marc; Nagashima, Mariko; Morser, John; Gils, Ann; Declerck, Paul; Nesheim, Michael E

    2009-03-13

    Thrombomodulin (TM) increases the catalytic efficiency of thrombin (IIa)-mediated activation of thrombin-activable fibrinolysis inhibitor (TAFI) 1250-fold. Negatively charged residues of the C-loop of TM-EGF-like domain 3 are required for TAFI activation. Molecular models suggested several positively charged residues of TAFI with which the C-loop residues could interact. Seven TAFI mutants were constructed to determine if these residues are required for efficient TAFI activation. TAFI wild-type or mutants were activated in the presence or absence of TM and the kinetic parameters of TAFI activation were determined. When the three consecutive lysine residues in the activation peptide of TAFI were substituted with alanine (K42/43/44A), the catalytic efficiencies for TAFI activation with TM decreased 8-fold. When other positively charged surface residues of TAFI (Lys-133, Lys-211, Lys-212, Arg-220, Lys-240, or Arg-275) were mutated to alanine, the catalytic efficiencies for TAFI activation with TM decreased by 1.7-2.7-fold. All decreases were highly statistically significant. In the absence of TM, catalytic efficiencies ranged from 2.8-fold lower to 1.24-fold higher than wild-type. None of these, except the 2.8-fold lower value, was statistically significant. The average half-life of the TAFIa mutants was 8.1+/-0.6 min, and that of wild type was 8.4+/-0.3 min at 37 degrees C. Our data show that these residues are important in the activation of TAFI by IIa, especially in the presence of TM. Whether the mutated residues promote a TAFI-TM or TAFI-IIa interaction remains to be determined. In addition, these residues do not influence spontaneous inactivation of TAFIa.

  11. Expansion of the Lysine Acylation Landscape

    DEFF Research Database (Denmark)

    Olsen, Christian A.

    2012-01-01

    Leaving marks: The number of known posttranslational modifications for lysine has been expanded considerably. In addition to acetylation of side-chain amino functionalities of lysine residues in proteins, crotonylation, succinylation, and malonylation have now been identified as posttranslational...

  12. Contribution of a lysine residue in the first transmembrane segment to the selectivity filter region in the CFTR chloride channel.

    Science.gov (United States)

    Negoda, Alexander; El Hiani, Yassine; Cowley, Elizabeth A; Linsdell, Paul

    2017-02-21

    The anion selectivity and conductance of the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel are determined predominantly by interactions between permeant anions and the narrow region of the channel pore. This narrow region has therefore been described as functioning as the "selectivity filter" of the channel. Multiple pore-lining transmembrane segments (TMs) have previously been shown to contribute to the selectivity filter region. However, little is known about the three-dimensional organization of this region, or how multiple TMs combine to determine its functional properties. In the present study we have used patch clamp recording to identify changes in channel function associated with the formation of disulfide cross-links between cysteine residues introduced into different TMs within the selectivity filter. Cysteine introduced at position L102 in TM1 was able to form disulfide bonds with F337C and T338C in TM6, two positions that are known to play key roles in determining anion permeation properties. Consistent with this proximal arrangement of L102, F337 and T338, different mutations at L102 altered anion selectivity and conductance properties in a way that suggests that this residue plays an important role in determining selectivity filter function, albeit a much lesser role than that of F337. These results suggest an asymmetric three-dimensional arrangement of the key selectivity filter region of the pore, as well as having important implications regarding the molecular mechanism of anion permeation.

  13. Present-day dynamic and residual topography in Central Anatolia

    Science.gov (United States)

    Şengül Uluocak, Ebru; Pysklywec, Russell; Göǧüş, Oǧuz H.

    2016-09-01

    The Central Anatolian orogenic plateau is represented by young volcanism, rapid plateau uplift and distinctive (past and active) tectonic deformation. In this study, we consider observational data in terms of regional present-day geodynamics in the region. The residual topography of Central Anatolia was derived to define the regional isostatic conditions according to Airy isostasy and infer the potential role of `dynamic topography'. 2-D thermomechanical forward models for coupled mantle-lithosphere flow/deformation were conducted along an N-S directional profile through the region (e.g. northern/Pontides, interior and southern/Taurides). These models were based on seismic tomography data that provide estimates about the present-day mantle thermal structure beneath the Anatolian plate. We compare the modelling results with calculated residual topography and independent data sets of geological deformation, gravity and high surface heat flow/widespread geothermal activity. Model results suggest that there is ˜1 km of mantle flow induced dynamic topography associated with the sublithospheric flow driven by the seismically inferred mantle structure. The uprising mantle may have also driven the asthenospheric source of volcanism in the north (e.g. Galatia volcanic province) and the Cappadocia volcanic province in the south while elevating the surface in the last 10 Myr. Our dynamic topography calculations emphasize the role of vertical forcing under other orogenic plateaux underlain by relatively thin crust and low-density asthenospheric mantle.

  14. Present-day dynamic and residual topography in Central Anatolia

    Science.gov (United States)

    Şengül Uluocak, Ebru; Pysklywec, Russell; Göǧüş, Oǧuz H.

    2016-09-01

    The Central Anatolian orogenic plateau is represented by young volcanism, rapid plateau uplift and distinctive (past and active) tectonic deformation. In this study, we consider observational data in terms of regional present-day geodynamics in the region. The residual topography of Central Anatolia was derived to define the regional isostatic conditions according to Airy isostasy and infer the potential role of `dynamic topography'. 2-D thermomechanical forward models for coupled mantle-lithosphere flow/deformation were conducted along an N-S directional profile through the region (e.g. northern/Pontides, interior and southern/Taurides). These models were based on seismic tomography data that provide estimates about the present-day mantle thermal structure beneath the Anatolian plate. We compare the modelling results with calculated residual topography and independent data sets of geological deformation, gravity and high surface heat flow/widespread geothermal activity. Model results suggest that there is ˜1 km of mantle flow induced dynamic topography associated with the sublithospheric flow driven by the seismically inferred mantle structure. The uprising mantle may have also driven the asthenospheric source of volcanism in the north (e.g. Galatia volcanic province) and the Cappadocia volcanic province in the south while elevating the surface in the last 10 Myr. Our dynamic topography calculations emphasize the role of vertical forcing under other orogenic plateaux underlain by relatively thin crust and low-density asthenospheric mantle.

  15. Lysine221 is the general base residue of the isochorismate synthase from Pseudomonas aeruginosa (PchA) in a reaction that is diffusion limited.

    Science.gov (United States)

    Meneely, Kathleen M; Luo, Qianyi; Dhar, Prajnaparamita; Lamb, Audrey L

    2013-10-01

    The isochorismate synthase from Pseudomonas aeruginosa (PchA) catalyzes the conversion of chorismate to isochorismate, which is subsequently converted by a second enzyme (PchB) to salicylate for incorporation into the salicylate-capped siderophore pyochelin. PchA is a member of the MST family of enzymes, which includes the structurally homologous isochorismate synthases from Escherichia coli (EntC and MenF) and salicylate synthases from Yersinia enterocolitica (Irp9) and Mycobacterium tuberculosis (MbtI). The latter enzymes generate isochorismate as an intermediate before generating salicylate and pyruvate. General acid-general base catalysis has been proposed for isochorismate synthesis in all five enzymes, but the residues required for the isomerization are a matter of debate, with both lysine221 and glutamate313 proposed as the general base (PchA numbering). This work includes a classical characterization of PchA with steady state kinetic analysis, solvent kinetic isotope effect analysis and by measuring the effect of viscosogens on catalysis. The results suggest that isochorismate production from chorismate by the MST enzymes is the result of general acid-general base catalysis with a lysine as the base and a glutamic acid as the acid, in reverse protonation states. Chemistry is determined to not be rate limiting, favoring the hypothesis of a conformational or binding step as the slow step.

  16. Lysine residues in N-terminal and C-terminal regions of human histone H2A are targets for biotinylation by biotinidase.

    Science.gov (United States)

    Chew, Yap Ching; Camporeale, Gabriela; Kothapalli, Nagarama; Sarath, Gautam; Zempleni, Janos

    2006-04-01

    In eukaryotic cell nuclei, DNA associates with the core histones H2A, H2B, H3 and H4 to form nucleosomal core particles. DNA binding to histones is regulated by posttranslational modifications of N-terminal tails (e.g., acetylation and methylation of histones). These modifications play important roles in the epigenetic control of chromatin structure. Recently, evidence that biotinidase and holocarboxylase synthetase (HCS) catalyze the covalent binding of biotin to histones has been provided. The primary aim of this study was to identify biotinylation sites in histone H2A and its variant H2AX. Secondary aims were to determine whether acetylation and methylation of histone H2A affect subsequent biotinylation and whether biotinidase and HCS localize to the nucleus in human cells. Biotinylation sites were identified using synthetic peptides as substrates for biotinidase. These studies provided evidence that K9 and K13 in the N-terminus of human histones H2A and H2AX are targets for biotinylation and that K125, K127 and K129 in the C-terminus of histone H2A are targets for biotinylation. Biotinylation of lysine residues was decreased by acetylation of adjacent lysines but was increased by dimethylation of adjacent arginines. The existence of biotinylated histone H2A in vivo was confirmed by using modification-specific antibodies. Antibodies to biotinidase and HCS localized primarily to the nuclear compartment, consistent with a role for these enzymes in regulating chromatin structure. Collectively, these studies have identified five novel biotinylation sites in human histones; histone H2A is unique among histones in that its biotinylation sites include amino acid residues from the C-terminus.

  17. Acetylation and glycation of fibrinogen in vitro occur at specific lysine residues in a concentration dependent manner: A mass spectrometric and isotope labeling study

    Energy Technology Data Exchange (ETDEWEB)

    Svensson, Jan, E-mail: jan.svensson@ki.se [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden); Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden); Bergman, Ann-Charlotte [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden); Adamson, Ulf [Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden); Blombaeck, Margareta [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden); Wallen, Hakan; Joerneskog, Gun [Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden)

    2012-05-04

    Highlights: Black-Right-Pointing-Pointer Fibrinogen was incubated in vitro with glucose or aspirin. Black-Right-Pointing-Pointer Acetylations and glycations were found at twelve lysine sites by mass spectrometry. Black-Right-Pointing-Pointer The labeling by aspirin and glucose occurred dose-dependently. Black-Right-Pointing-Pointer No competition between glucose and aspirin for binding to fibrinogen was found. -- Abstract: Aspirin may exert part of its antithrombotic effects through platelet-independent mechanisms. Diabetes is a condition in which the beneficial effects of aspirin are less prominent or absent - a phenomenon called 'aspirin resistance'. We investigated whether acetylation and glycation occur at specific sites in fibrinogen and if competition between glucose and aspirin in binding to fibrinogen occurs. Our hypothesis was that such competition might be one explanation to 'aspirin resistance' in diabetes. After incubation of fibrinogen in vitro with aspirin (0.8 mM, 24 h) or glucose (100 mM, 5-10 days), we found 12 modified sites with mass spectrometric techniques. Acetylations in the {alpha}-chain: {alpha}K191, {alpha}K208, {alpha}K224, {alpha}K429, {alpha}K457, {alpha}K539, {alpha}K562, in the {beta}-chain: {beta}K233, and in the {gamma}-chain: {gamma}K170 and {gamma}K273. Glycations were found at {beta}K133 and {gamma}K75, alternatively {gamma}K85. Notably, the lysine 539 is a site involved in FXIII-mediated cross-linking of fibrin. With isotope labeling in vitro, using [{sup 14}C-acetyl]salicylic acid and [{sup 14}C]glucose, a labeling of 0.013-0.084 and 0.12-0.5 mol of acetylated and glycated adduct/mol fibrinogen, respectively, was found for clinically (12.9-100 {mu}M aspirin) and physiologically (2-8 mM glucose) relevant plasma concentrations. No competition between acetylation and glycation could be demonstrated. Thus, fibrinogen is acetylated at several lysine residues, some of which are involved in the cross-linking of

  18. Significant residual fluorinated alcohols present in various fluorinated materials.

    Science.gov (United States)

    Dinglasan-Panlilio, Mary Joyce A; Mabury, Scott A

    2006-03-01

    Polyfluorinated telomer alcohols and sulfonamides are classes of compounds recently identified as precursor molecules to the perfluorinated acids detected in the environment. Despite the detection and quantification of these volatile compounds in the atmosphere, their sources remain unknown. Both classes of compounds are used in the synthesis of various fluorosurfactants and incorporated in polymeric materials used extensively in the carpet, textile, and paper industries. This study has identified the presence of residual unbound fluoro telomer alcohols (FTOHs) in varying chain lengths (C6-C14) in several commercially available and industrially applied polymeric and surfactant materials. NMeFOSE, a perfluoroalkyl sulfonamido alcohol, was also detected in a commercially available carpet protector product. A method was developed to remove these residual compounds from polymeric and surfactant materials by dispersion in water and stripping of the volatiles using a constant flow of air and trapping on XAD resin. Using gas chromatography mass spectrometry analysis, it was determined that the fluorinated materials examined consist of 0.04-3.8% residual alcohols on a fluoro alcohol to dry mass basis. These values indicate that residual alcohols, left unreacted and unbound from the manufacturing process of fluorinated polymers and surfactants, could be a significant source of the polyfluorinated telomer alcohols and sulfonamides released into the environment. This study suggests that elimination or reduction of these residual alcohols from all marketed fluorinated polymers and fluorosurfactants is key in reducing the prevalence of perfluorinated acids formed in the environment.

  19. Site-specific methylation and acetylation of lysine residues in the C-terminal domain (CTD) of RNA polymerase II

    Science.gov (United States)

    Voss, Kirsten; Forné, Ignasi; Descostes, Nicolas; Hintermair, Corinna; Schüller, Roland; Maqbool, Muhammad Ahmad; Heidemann, Martin; Flatley, Andrew; Imhof, Axel; Gut, Marta; Gut, Ivo; Kremmer, Elisabeth; Andrau, Jean-Christophe; Eick, Dirk

    2015-01-01

    Dynamic modification of heptad-repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 of RNA polymerase II (RNAPII) C-terminal domain (CTD) regulates transcription-coupled processes. Mass spectrometry analysis revealed that K7-residues in non-consensus repeats of human RNAPII are modified by acetylation, or mono-, di-, and tri-methylation. K7ac, K7me2, and K7me3 were found exclusively associated with phosphorylated CTD peptides, while K7me1 occurred also in non-phosphorylated CTD. The monoclonal antibody 1F5 recognizes K7me1/2 residues in CTD and reacts with RNAPIIA. Treatment of cellular extracts with phosphatase or of cells with the kinase inhibitor flavopiridol unmasked the K7me1/2 epitope in RNAPII0, consistent with the association of K7me1/2 marks with phosphorylated CTD peptides. Genome-wide profiling revealed high levels of K7me1/2 marks at the transcriptional start site of genes for sense and antisense transcribing RNAPII. The new K7 modifications further expand the mammalian CTD code to allow regulation of differential gene expression. PMID:26566685

  20. Site-specific methylation and acetylation of lysine residues in the C-terminal domain (CTD) of RNA polymerase II.

    Science.gov (United States)

    Voss, Kirsten; Forné, Ignasi; Descostes, Nicolas; Hintermair, Corinna; Schüller, Roland; Maqbool, Muhammad Ahmad; Heidemann, Martin; Flatley, Andrew; Imhof, Axel; Gut, Marta; Gut, Ivo; Kremmer, Elisabeth; Andrau, Jean-Christophe; Eick, Dirk

    2015-01-01

    Dynamic modification of heptad-repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 of RNA polymerase II (RNAPII) C-terminal domain (CTD) regulates transcription-coupled processes. Mass spectrometry analysis revealed that K7-residues in non-consensus repeats of human RNAPII are modified by acetylation, or mono-, di-, and tri-methylation. K7ac, K7me2, and K7me3 were found exclusively associated with phosphorylated CTD peptides, while K7me1 occurred also in non-phosphorylated CTD. The monoclonal antibody 1F5 recognizes K7me1/2 residues in CTD and reacts with RNAPIIA. Treatment of cellular extracts with phosphatase or of cells with the kinase inhibitor flavopiridol unmasked the K7me1/2 epitope in RNAPII0, consistent with the association of K7me1/2 marks with phosphorylated CTD peptides. Genome-wide profiling revealed high levels of K7me1/2 marks at the transcriptional start site of genes for sense and antisense transcribing RNAPII. The new K7 modifications further expand the mammalian CTD code to allow regulation of differential gene expression.

  1. Role of lysine and tryptophan residues in the biological activity of toxin VII (Ts gamma) from the scorpion Tityus serrulatus.

    Science.gov (United States)

    Hassani, O; Mansuelle, P; Cestèle, S; Bourdeaux, M; Rochat, H; Sampieri, F

    1999-02-01

    Toxin VII (TsVII), also known as Ts gamma, is the most potent neurotoxin in the venom of the Brazilian scorpion Tityus serrulatus. It has been purified to homogeneity using a new fast and efficient method. Chemical modification of TsVII with the tryptophan-specific reagent o-nitrophenylsulfenyl chloride yielded three modified derivatives (residues Trp39, Trp50 and Trp54). Acetylation of TsVII mostly generated the monoacetylated Lys12 derivative. No side reactions were detected, as indicated by endoproteinase Lys-C peptide mapping, Edman degradation and electrospray mass spectrometry. Circular dichroism and fluorimetric measurements showed that none of the chemical modifications altered the overall structure of the derivatives. The acetylation of Lys12 or the sulfenylation of Trp39 or Trp54 led to a loss of both toxicity in mice and apparent binding affinity for rat brain and cockroach synaptosomal preparations. Sulfenylation of Trp50, however, moderately affected the toxicity of TsVII in mice and had almost no effect on its binding properties. A 3-dimensional model of TsVII was constructed by homology modeling. It suggests that the most reactive residues (Lys12 and Trp39 and Trp54) are all important in the functional disruption of neuronal sodium channels by TsVII, and are close to each other in the hydrophobic conserved region.

  2. SIRT1 Regulates Thyroid-Stimulating Hormone Release by Enhancing PIP5Kgamma Activity through Deacetylation of Specific Lysine Residues in Mammals.

    Directory of Open Access Journals (Sweden)

    Sayaka Akieda-Asai

    Full Text Available BACKGROUND: SIRT1, a NAD-dependent deacetylase, has diverse roles in a variety of organs such as regulation of endocrine function and metabolism. However, it remains to be addressed how it regulates hormone release there. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report that SIRT1 is abundantly expressed in pituitary thyrotropes and regulates thyroid hormone secretion. Manipulation of SIRT1 level revealed that SIRT1 positively regulated the exocytosis of TSH-containing granules. Using LC/MS-based interactomics, phosphatidylinositol-4-phosphate 5-kinase (PIP5Kgamma was identified as a SIRT1 binding partner and deacetylation substrate. SIRT1 deacetylated two specific lysine residues (K265/K268 in PIP5Kgamma and enhanced PIP5Kgamma enzyme activity. SIRT1-mediated TSH secretion was abolished by PIP5Kgamma knockdown. SIRT1 knockdown decreased the levels of deacetylated PIP5Kgamma, PI(4,5P(2, and reduced the secretion of TSH from pituitary cells. These results were also observed in SIRT1-knockout mice. CONCLUSIONS/SIGNIFICANCE: Our findings indicated that the control of TSH release by the SIRT1-PIP5Kgamma pathway is important for regulating the metabolism of the whole body.

  3. Conserved aspartate and lysine residues of RcsB are required for amylovoran biosynthesis, virulence, and DNA binding in Erwinia amylovora.

    Science.gov (United States)

    Ancona, Veronica; Chatnaparat, Tiyakhon; Zhao, Youfu

    2015-08-01

    In Erwinia amylovora, the Rcs phosphorelay system is essential for amylovoran production and virulence. To further understand the role of conserved aspartate residue (D56) in the phosphor receiver (PR) domain and lysine (K180) residue in the function domain of RcsB, amino acid substitutions of RcsB mutant alleles were generated by site-directed mutagenesis and complementation of various rcs mutants were performed. A D56E substitution of RcsB, which mimics the phosphorylation state of RcsB, complemented the rcsB mutant, resulting in increased amylovoran production and gene expression, reduced swarming motility, and restored pathogenicity. In contrast, D56N and K180A or K180Q substitutions of RcsB did not complement the rcsB mutant. Electrophoresis mobility shift assays showed that D56E, but not D56N, K180Q and K180A substitutions of RcsB bound to promoters of amsG and flhD, indicating that both D56 and K180 are required for DNA binding. Interestingly, the RcsBD56E allele could also complement rcsAB, rcsBC and rcsABCD mutants with restored virulence and increased amylovoran production, indicating that RcsB phosphorylation is essential for virulence of E. amylovora. In addition, mutations of T904 and A905, but not phosphorylation mimic mutation of D876 in the PR domain of RcsC, constitutively activate the Rcs system, suggesting that phosphor transfer is required for activating the Rcs system and indicating both A905 and T904 are required for the phosphatase activity of RcsC. Our results demonstrated that RcsB phosphorylation and dephosphorylation, phosphor transfer from RcsC are essential for the function of the Rcs system, and also suggested that constitutive activation of the Rcs system could reduce the fitness of E. amylovora.

  4. Residue control in the European Union, the present and future challenges. Experiences from the Netherlands

    NARCIS (Netherlands)

    Sterk, S.S.

    2015-01-01

    Residue control in the European Union has the primary goal to protect consumers from intolerable health hazards which may be associated with residues of veterinary drugs or non-licensed or forbidden substances in animal products. The present situation regarding residue control in the EU is discussed

  5. The valine and lysine residues in the conserved FxVTxK motif are important for the function of phylogenetically distant plant cellulose synthases.

    Science.gov (United States)

    Slabaugh, Erin; Scavuzzo-Duggan, Tess; Chaves, Arielle; Wilson, Liza; Wilson, Carmen; Davis, Jonathan K; Cosgrove, Daniel J; Anderson, Charles T; Roberts, Alison W; Haigler, Candace H

    2016-05-01

    Cellulose synthases (CESAs) synthesize the β-1,4-glucan chains that coalesce to form cellulose microfibrils in plant cell walls. In addition to a large cytosolic (catalytic) domain, CESAs have eight predicted transmembrane helices (TMHs). However, analogous to the structure of BcsA, a bacterial CESA, predicted TMH5 in CESA may instead be an interfacial helix. This would place the conserved FxVTxK motif in the plant cell cytosol where it could function as a substrate-gating loop as occurs in BcsA. To define the functional importance of the CESA region containing FxVTxK, we tested five parallel mutations in Arabidopsis thaliana CESA1 and Physcomitrella patens CESA5 in complementation assays of the relevant cesa mutants. In both organisms, the substitution of the valine or lysine residues in FxVTxK severely affected CESA function. In Arabidopsis roots, both changes were correlated with lower cellulose anisotropy, as revealed by Pontamine Fast Scarlet. Analysis of hypocotyl inner cell wall layers by atomic force microscopy showed that two altered versions of Atcesa1 could rescue cell wall phenotypes observed in the mutant background line. Overall, the data show that the FxVTxK motif is functionally important in two phylogenetically distant plant CESAs. The results show that Physcomitrella provides an efficient model for assessing the effects of engineered CESA mutations affecting primary cell wall synthesis and that diverse testing systems can lead to nuanced insights into CESA structure-function relationships. Although CESA membrane topology needs to be experimentally determined, the results support the possibility that the FxVTxK region functions similarly in CESA and BcsA.

  6. Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit.

    Directory of Open Access Journals (Sweden)

    Franck Tarendeau

    Full Text Available Understanding how avian influenza viruses adapt to human hosts is critical for the monitoring and prevention of future pandemics. Host specificity is determined by multiple sites in different viral proteins, and mutation of only a limited number of these sites can lead to inter-species transmission. Several of these sites have been identified in the viral polymerase, the best characterised being position 627 in the PB2 subunit. Efficient viral replication at the relatively low temperature of the human respiratory tract requires lysine 627 rather than the glutamic acid variant found systematically in avian viruses. However, the molecular mechanism by which any of these host specific sites determine host range are unknown, although adaptation to host factors is frequently evoked. We used ESPRIT, a library screening method, to identify a new PB2 domain that contains a high density of putative host specific sites, including residue 627. The X-ray structure of this domain (denoted the 627-domain exhibits a novel fold with the side-chain of Lys627 solvent exposed. The structure of the K627E mutated domain shows no structural differences but the charge reversal disrupts a striking basic patch on the domain surface. Five other recently proposed host determining sites of PB2 are also located on the 627-domain surface. The structure of the complete C-terminal region of PB2 comprising the 627-domain and the previously identified NLS-domain, which binds the host nuclear import factor importin alpha, was also determined. The two domains are found to pack together with a largely hydrophilic interface. These data enable a three-dimensional mapping of approximately half of PB2 sites implicated in cross-species transfer onto a single structural unit. Their surface location is consistent with roles in interactions with other viral proteins or host factors. The identification and structural characterization of these well-defined PB2 domains will help design

  7. Molecular and structural insight into lysine selection on substrate and ubiquitin lysine 48 by the ubiquitin-conjugating enzyme Cdc34

    DEFF Research Database (Denmark)

    Suryadinata, Randy; Holien, Jessica K; Yang, George

    2013-01-01

    The attachment of ubiquitin (Ub) to lysines on substrates or itself by ubiquitin-conjugating (E2) and ubiquitin ligase (E3) enzymes results in protein ubiquitination. Lysine selection is important for generating diverse substrate-Ub structures and targeting proteins to different fates; however......, the mechanisms of lysine selection are not clearly understood. The positioning of lysine(s) toward the E2/E3 active site and residues proximal to lysines are critical in their selection. We investigated determinants of lysine specificity of the ubiquitin-conjugating enzyme Cdc34, toward substrate and Ub lysines....... Evaluation of the relative importance of different residues positioned -2, -1, +1 and +2 toward ubiquitination of its substrate, Sic1, on lysine 50 showed that charged residues in the -1 and -2 positions negatively impact on ubiquitination. Modeling suggests that charged residues at these positions alter...

  8. Reactive lysine content in commercially available pet foods

    NARCIS (Netherlands)

    Rooijen, van C.; Bosch, G.; Poel, van der A.F.B.; Wierenga, P.A.; Alexander, L.; Hendriks, W.H.

    2014-01-01

    The Maillard reaction can occur during processing of pet foods. During this reaction, the e-amino group of lysine reacts with reducing sugars to become unavailable for metabolism. The aim of the present study was to determine the reactive lysine (RL; the remaining available lysine) to total lysine (

  9. Analysis of the components of residual deformity in clubfeet presenting for reoperation.

    Science.gov (United States)

    Tarraf, Y N; Carroll, N C

    1992-01-01

    We reviewed the records and radiographs of 125 children with 159 clubfeet reoperated for residual deformity after operative repair (210 reoperations). We concluded that residual forefoot adduction and supination were the most common persistent deformities (present in 95% of the feet) and that these deformities resulted from undercorrection at the time of primary operation. Although not then apparent, the persistent deformities became more evident with growth, and additional treatment became necessary. Undercorrection resulted from not releasing the calcaneocuboid joint and plantar fascia and failure to recognize residual forefoot adduction on the interoperative radiographs at primary operation.

  10. Oligo-lysine Induced Formation of Silica Particles in Neutral Silicate Solution

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Oligo-(lysine)n (n = 1-4) containing different numbers of lysine residues was used to induce the condensation of silicic acid to form silica particles in neutral silicate solution. It was found that the condensation rate and the formation of silica particles are dependent on the number of lysine residues in an oligo-lysine. Oligo-lysine with more lysine residues can link more silicic acid together to form a matrix that promotes the effective aggregation of the condensed silica pieces to form large silica particles.

  11. Hypochlorite-induced damage to proteins: formation of nitrogen-centred radicals from lysine residues and their role in protein fragmentation.

    Science.gov (United States)

    Hawkins, C L; Davies, M J

    1998-01-01

    Stimulated monocytes and neutrophils generate hypochlorite (HOCl) via the release of the enzyme myeloperoxidase and hydrogen peroxide. HOCl damages proteins by reaction with amino acid side-chains or backbone cleavage. Little information is available about the mechanisms and intermediates involved in these reactions. EPR spin trapping has been employed to identify radicals on proteins, peptides and amino acids after treatment with HOCl. Reaction with HOCl gives both high- and low-molecular-mass nitrogen-centred, protein-derived radicals; the yield of the latter increases with both higher HOCl:protein ratios and enzymic digestion. These radicals, which arise from lysine side-chain amino groups, react with ascorbate, glutathione and Trolox. Reaction of HOCl-treated proteins with excess methionine eliminates radical formation, which is consistent with lysine-derived chloramines (via homolysis of N-Cl bonds) being the radical source. Incubation of HOCl-treated proteins, after removal of excess oxidant, gives rise to both nitrogen-centred radicals, over a period of hours, and time-dependent fragmentation of the protein. Treatment with excess methionine or antioxidants (Trolox, ascorbate, glutathione) protects against fragmentation; urate and bilirubin do not. Chloramine formation and nitrogen-centred radicals are therefore key species in HOCl-induced protein fragmentation. PMID:9620862

  12. Bioavailability of free lysine and protein-bound lysine from casein and fishmeal in juvenile turbot (Psetta maxima).

    Science.gov (United States)

    Kroeckel, Saskia; Dietz, Carsten; Schulz, Carsten; Susenbeth, Andreas

    2015-03-14

    In the present study, a linear regression analysis between lysine intake and lysine retention was conducted to investigate the efficiency of lysine utilisation (k(Lys)) at marginal lysine intake of either protein-bound or free lysine sources in juvenile turbot (Psetta maxima). For this purpose, nine isonitrogenous and isoenergetic diets were formulated to contain 2·25-4·12 g lysine/100 g crude protein (CP) to ensure that lysine was the first-limiting amino acid in all diets. The basal diet contained 2·25 g lysine/100 g CP. Graded levels of casein (Cas), fishmeal (FM) and L-lysine HCl (Lys) were added to the experimental diets to achieve stepwise lysine increments. A total of 240 fish (initial weight 50·1 g) were hand-fed all the experimental diets once daily until apparent satiation over a period of 56 d. Feed intake was significantly affected by dietary lysine concentration rather than by dietary lysine source. Specific growth rate increased significantly at higher lysine concentrations (PCas, Lys or FM were 0·833, 0·857 and 0·684, respectively. The bioavailability of lysine from the respective lysine sources was determined by a slope-ratio approach. The bioavailability of lysine (relative to the reference lysine source Cas) from FM and Lys was 82·1 and 103 %, respectively. Nutrient requirement for maintenance was in the range of 16·7-23·4 mg/kg(0·8) per d, and did not differ between the treatments. There were no significant differences in lysine utilisation efficiency or bioavailability of protein-bound or crystalline lysine from the respective sources observed when lysine was confirmed to be the first-limiting nutrient.

  13. Tetranectin-binding site on plasminogen kringle 4 involves the lysine-binding pocket and at least one additional amino acid residue

    DEFF Research Database (Denmark)

    Graversen, Jonas Heilskov; Sigurskjold, B W; Thøgersen, H C

    2000-01-01

    that all amino acid residues of plasminogen kringle 4 found to be involved in t-AMCHA binding are also involved in binding tetranectin. Notably, one amino acid residue of plasminogen kringle 4, Arg 32, not involved in binding t-AMCHA, is critical for binding tetranectin. We also find that Asp 57 and Asp 55......, we analyze the interaction of wild-type and six single-residue mutants of recombinant plasminogen kringle 4 expressed in Escherichia coli with the recombinant C-type lectin domain of tetranectin and trans-aminomethyl-cyclohexanoic acid (t-AMCHA) using isothermal titration calorimetry. We find...

  14. Probing China's Lysine Market

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ The lysine sector in China developed further in 2006. Both the capacity and the output hit new highs and China had a major impact on the global lysine market. The import amount of lysine satisfied only a very small portion of the domestic market's demand.

  15. 4'-CyanoPLP presents better prospect for the experimental detection of elusive cyclic intermediate radical in the reaction of lysine 5,6-aminomutase.

    Science.gov (United States)

    Maity, Amarendra Nath; Ke, Shyue-Chu

    2015-02-01

    The results of our calculations suggest that the reaction of 4'-cyanoPLP with lysine 5,6-aminomutase offers better prospect for the experimental detection of elusive cyclic azacyclopropylcarbinyl radical (I), which is proposed to be a key intermediate in the reaction of pyridoxal-5'-phosphate dependent radical aminomutases. We have calculated the corresponding hyperfine coupling constants (HFCCs) for (14)N and (13)C of cyano group using several basis sets to help the characterization of 4'-cyanoI.

  16. A group-specific inhibitor of lysosomal cysteine proteinases selectively inhibits both proteolytic degradation and presentation of the antigen dinitrophenyl-poly-L-lysine by guinea pig accessory cells to T cells

    DEFF Research Database (Denmark)

    Buus, S; Werdelin, O

    1986-01-01

    of antigens by guinea pig accessory cells. The proteinase inhibitor benzyloxycarbonyl-phenylalanylalanine-diazomethyl-ketone, which selectively inhibits cysteine proteinases, was used to block this set of enzymes in cultured cells. We demonstrate that the selective inhibition of the cysteine proteinases...... inhibitor. Another inhibitor, pepstatin A, which selectively blocks aspartic proteinases, did not block the presentation of dinitrophenyl-poly-L-lysine. The results identify cysteine proteinases, probably lysosomal, as one of the groups of enzymes involved in antigen processing....

  17. An update on histone lysine methylation in plants

    Institute of Scientific and Technical Information of China (English)

    Yu Yu; Zhongyuan Bu; Wen-Hui Shen; Aiwu Dong

    2009-01-01

    Histone methylation plays crucial roles in epigenetic regulation.The SET domain proteins are now recognized as generally having methyltransferase activity targeted to specific lysine residues of histones.The enzymes and their specific histone lysine methylation have enormous impacts on the regulation of chromatin structure and function.In this review,we discuss recent advances made on histone lysine methylations and their diverse functions in plant growth and development.

  18. Installation of site-specific methylation into histones using methyl lysine analogs.

    Science.gov (United States)

    Simon, Matthew D

    2010-04-01

    Chromatin structure is influenced by post-translational modifications on histones, the principal basic protein component of chromatin. In order to study one of these modifications, lysine methylation, in the context of reconstituted chromatin, this unit describes the installation of analogs of methyl lysine residues into recombinant histones. The modification site is specified by mutating the lysine of interest to cysteine. The mutant histones are expressed and purified, and the cysteine residue alkylated to produce N-methyl aminoethylcysteine, an isosteric analog of methyl lysine. Using different alkylating reagents, it is possible to install analogs of mono-, di-, or trimethyl lysine. While these analogs are not identical to methyl lysine residues, they show similar biochemical properties to their natural counterparts. The ease of synthesis of methyl lysine analog (MLA) histones, especially on a large scale, makes them particularly useful reagents for studying the effects of histone lysine methylation on chromatin structure, biophysics and biochemistry. (c) 2010 by John Wiley & Sons, Inc.

  19. 4′-CyanoPLP presents better prospect for the experimental detection of elusive cyclic intermediate radical in the reaction of lysine 5,6-aminomutase

    Energy Technology Data Exchange (ETDEWEB)

    Maity, Amarendra Nath; Ke, Shyue-Chu, E-mail: ke@mail.ndhu.edu.tw

    2015-02-06

    Graphical abstract: The results of our calculations suggest that the reaction of 4′-cyanoPLP with lysine 5,6-aminomutase offers better prospect for the experimental detection of elusive cyclic azacyclopropylcarbinyl radical, which is proposed to be a key intermediate in the reaction of pyridoxal-5′-phosphate dependent radical aminomutases. - Highlights: • 4′-CyanoI{sup ·} is the lowest energy radical intermediate in the reaction of 5,6-LAM. • 4′-CyanoPLP offers good prospect for the experimental observation of elusive I{sup ·}. • The calculated HFCCs would help to characterize 4′-cyanoI{sup ·} by EPR. - Abstract: The results of our calculations suggest that the reaction of 4′-cyanoPLP with lysine 5,6-aminomutase offers better prospect for the experimental detection of elusive cyclic azacyclopropylcarbinyl radical (I{sup ·}), which is proposed to be a key intermediate in the reaction of pyridoxal-5′-phosphate dependent radical aminomutases. We have calculated the corresponding hyperfine coupling constants (HFCCs) for {sup 14}N and {sup 13}C of cyano group using several basis sets to help the characterization of 4′-cyanoI{sup ·}.

  20. PLMD: An updated data resource of protein lysine modifications.

    Science.gov (United States)

    Xu, Haodong; Zhou, Jiaqi; Lin, Shaofeng; Deng, Wankun; Zhang, Ying; Xue, Yu

    2017-05-20

    Post-translational modifications (PTMs) occurring at protein lysine residues, or protein lysine modifications (PLMs), play critical roles in regulating biological processes. Due to the explosive expansion of the amount of PLM substrates and the discovery of novel PLM types, here we greatly updated our previous studies, and presented a much more integrative resource of protein lysine modification database (PLMD). In PLMD, we totally collected and integrated 284,780 modification events in 53,501 proteins across 176 eukaryotes and prokaryotes for up to 20 types of PLMs, including ubiquitination, acetylation, sumoylation, methylation, succinylation, malonylation, glutarylation, glycation, formylation, hydroxylation, butyrylation, propionylation, crotonylation, pupylation, neddylation, 2-hydroxyisobutyrylation, phosphoglycerylation, carboxylation, lipoylation and biotinylation. Using the data set, a motif-based analysis was performed for each PLM type, and the results demonstrated that different PLM types preferentially recognize distinct sequence motifs for the modifications. Moreover, various PLMs synergistically orchestrate specific cellular biological processes by mutual crosstalks with each other, and we totally found 65,297 PLM events involved in 90 types of PLM co-occurrences on the same lysine residues. Finally, various options were provided for accessing the data, while original references and other annotations were also present for each PLM substrate. Taken together, we anticipated the PLMD database can serve as a useful resource for further researches of PLMs. PLMD 3.0 was implemented in PHP + MySQL and freely available at http://plmd.biocuckoo.org. Copyright © 2017 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

  1. Characterizing T Cells in SCID Patients Presenting with Reactive or Residual T Lymphocytes

    Directory of Open Access Journals (Sweden)

    Atar Lev

    2012-01-01

    Full Text Available Introduction. Patients with severe combined immunodeficiency (SCID may present with residual circulating T cells. While all cells are functionally deficient, resulting in high susceptibility to infections, only some of these cells are causing autoimmune symptoms. Methods. Here we compared T-cell functions including the number of circulating CD3+ T cells, in vitro responses to mitogens, T-cell receptor (TCR repertoire, TCR excision circles (TREC levels, and regulatory T cells (Tregs enumeration in several immunodeficinecy subtypes, clinically presenting with nonreactive residual cells (MHC-II deficiency or reactive cells. The latter includes patients with autoreactive clonal expanded T cell and patients with alloreactive transplacentally maternal T cells. Results. MHC-II deficient patients had slightly reduced T-cell function, normal TRECs, TCR repertoires, and normal Tregs enumeration. In contrast, patients with reactive T cells exhibited poor T-cell differentiation and activity. While the autoreactive cells displayed significantly reduced Tregs numbers, the alloreactive transplacentally acquired maternal lymphocytes had high functional Tregs. Conclusion. SCID patients presenting with circulating T cells show different patterns of T-cell activity and regulatory T cells enumeration that dictates the immunodeficient and autoimmune manifestations. We suggest that a high-tolerance capacity of the alloreactive transplacentally acquired maternal lymphocytes represents a toleration advantage, yet still associated with severe immunodeficiency.

  2. Characterizing T cells in SCID patients presenting with reactive or residual T lymphocytes.

    Science.gov (United States)

    Lev, Atar; Simon, Amos J; Trakhtenbrot, Luba; Goldstein, Itamar; Nagar, Meital; Stepensky, Polina; Rechavi, Gideon; Amariglio, Ninette; Somech, Raz

    2012-01-01

    Patients with severe combined immunodeficiency (SCID) may present with residual circulating T cells. While all cells are functionally deficient, resulting in high susceptibility to infections, only some of these cells are causing autoimmune symptoms. Here we compared T-cell functions including the number of circulating CD3(+) T cells, in vitro responses to mitogens, T-cell receptor (TCR) repertoire, TCR excision circles (TREC) levels, and regulatory T cells (Tregs) enumeration in several immunodeficinecy subtypes, clinically presenting with nonreactive residual cells (MHC-II deficiency) or reactive cells. The latter includes patients with autoreactive clonal expanded T cell and patients with alloreactive transplacentally maternal T cells. MHC-II deficient patients had slightly reduced T-cell function, normal TRECs, TCR repertoires, and normal Tregs enumeration. In contrast, patients with reactive T cells exhibited poor T-cell differentiation and activity. While the autoreactive cells displayed significantly reduced Tregs numbers, the alloreactive transplacentally acquired maternal lymphocytes had high functional Tregs. SCID patients presenting with circulating T cells show different patterns of T-cell activity and regulatory T cells enumeration that dictates the immunodeficient and autoimmune manifestations. We suggest that a high-tolerance capacity of the alloreactive transplacentally acquired maternal lymphocytes represents a toleration advantage, yet still associated with severe immunodeficiency.

  3. Mutational, kinetic, and NMR studies of the roles of conserved glutamate residues and of lysine-39 in the mechanism of the MutT pyrophosphohydrolase.

    Science.gov (United States)

    Harris, T K; Wu, G; Massiah, M A; Mildvan, A S

    2000-02-22

    The MutT enzyme catalyzes the hydrolysis of nucleoside triphosphates (NTP) to NMP and PP(i) by nucleophilic substitution at the rarely attacked beta-phosphorus. The solution structure of the quaternary E-M(2+)-AMPCPP-M(2+) complex indicated that conserved residues Glu-53, -56, -57, and -98 are at the active site near the bound divalent cation possibly serving as metal ligands, Lys-39 is positioned to promote departure of the NMP leaving group, and Glu-44 precedes helix I (residues 47-59) possibly stabilizing this helix which contributes four catalytic residues to the active site [Lin, J. , Abeygunawardana, C., Frick, D. N., Bessman, M. J., and Mildvan, A. S. (1997) Biochemistry 36, 1199-1211]. To test these proposed roles, the effects of mutations of each of these residues on the kinetic parameters and on the Mn(2+), Mg(2+), and substrate binding properties were examined. The largest decreases in k(cat) for the Mg(2+)-activated enzyme of 10(4.7)- and 10(2.6)-fold were observed for the E53Q and E53D mutants, respectively, while 97-, 48-, 25-, and 14-fold decreases were observed for the E44D, E56D, E56Q, and E44Q mutations, respectively. Smaller effects on k(cat) were observed for mutations of Glu-98 and Lys-39. For wild type MutT and its E53D and E44D mutants, plots of log(k(cat)) versus pH exhibited a limiting slope of 1 on the ascending limb and then a hump, i.e., a sharply defined maximum near pH 8 followed by a plateau, yielding apparent pK(a) values of 7.6 +/- 0.3 and 8.4 +/- 0.4 for an essential base and a nonessential acid catalyst, respectively, in the active quaternary MutT-Mg(2+)-dGTP-Mg(2+) complex. The pK(a) of 7.6 is assigned to Glu-53, functioning as a base catalyst in the active quaternary complex, on the basis of the disappearance of the ascending limb of the pH-rate profile of the E53Q mutant, and its restoration in the E53D mutant with a 10(1.9)-fold increase in (k(cat))(max). The pK(a) of 8.4 is assigned to Lys-39 on the basis of the disappearance

  4. Exploiting Oceanic Residual Depth to Quantify Present-day Dynamic Topography at the Earth's Surface

    Science.gov (United States)

    Hoggard, Mark; White, Nicky

    2014-05-01

    Convective circulation within the mantle causes vertical motions at the Earth's surface. This dynamic topography is time dependent and occurs on wavelengths of 1000s km with maximum amplitudes of ±2 km. Convective simulation models have been used extensively to make predictions of dynamic topography and have thus far out-paced observational constraints. Here, the well-established relationship between seafloor subsidence and age is used to produce a global map of residual depth anomalies in the oceanic realm. Care is taken to remove other causes of topography, including an isostatic correction for sedimentary loading that takes compaction into account, a correction for variable oceanic crustal thickness, and lithospheric thickening with age away from mid-ocean ridge spreading centres. A dataset including over 1000 seismic reflection profiles and 300 modern wide-angle refraction experiments has been amassed, primarily on old ocean floor adjacent to the continents. Calculation of residual depth yields a map of present-day dynamic topography with amplitudes significantly larger than the errors associated with the corrections. One of the most interesting results occurs along the west coast of Africa, where two full 2000 km wavelengths of dynamic topography have been captured with amplitudes ±1 km that correlate well with the long-wavelength free air gravity anomaly. Comparison with predictive models reveal poor to moderate correlations. This is a direct result of the limited resolution of the mantle tomography models used to set-up convection simulations and also the currently poor understanding of viscosity structure within the Earth. It is hoped that this residual depth dataset should provide an excellent surface boundary constraint for future convective simulation.

  5. Elucidating the effects of arginine and lysine on a monoclonal antibody C-terminal lysine variation in CHO cell cultures.

    Science.gov (United States)

    Zhang, Xintao; Tang, Hongping; Sun, Ya-Ting; Liu, Xuping; Tan, Wen-Song; Fan, Li

    2015-08-01

    C-terminal lysine variants are commonly observed in monoclonal antibodies (mAbs) and found sensitive to process conditions, especially specific components in culture medium. The potential roles of media arginine (Arg) and lysine (Lys) in mAb heavy chain C-terminal lysine processing were investigated by monitoring the lysine variant levels under various Arg and Lys concentrations. Both Arg and Lys were found to significantly affect lysine variant level. Specifically, lysine variant level increased from 18.7 to 31.8 % when Arg and Lys concentrations were increased from 2 to 10 mM. Since heterogeneity of C-terminal lysine residues is due to the varying degree of proteolysis by basic carboxypeptidases (Cps), enzyme (basic Cps) level, pH conditions, and product (Arg and Lys) inhibition, which potentially affect the enzymatic reaction, were investigated under various Arg and Lys conditions. Enzyme level and pH conditions were found not to account for the different lysine variant levels, which was evident from the minimal variation in transcription level and intracellular pH. On the other hand, product inhibition effect of Arg and Lys on basic Cps was evident from the notable intracellular and extracellular Arg and Lys concentrations comparable with Ki values (inhibition constant) of basic Cps and further confirmed by cell-free assays. Additionally, a kinetic study of lysine variant level during the cell culture process enabled further characterization of the C-terminal lysine processing.

  6. Effect of dietary lysine on hepatic lysine catabolism in broilers

    Science.gov (United States)

    Lysine is frequently a first- or second-limiting amino acid in poultry diets. Improving the efficiency of lysine use for protein synthesis would effectively lower the lysine requirement and decrease feed costs. Understanding how lysine is degraded and how the degradation is regulated would identif...

  7. Structure of lysine adducts with 16 alpha-hydroxyestrone and cortisol.

    Science.gov (United States)

    Bucala, R; Ulrich, P C; Chait, B T; Bencsath, F A; Cerami, A

    1986-07-01

    Recent studies indicate that steroids containing a vicinal hydroxyketone moiety can react with proteins both in vitro and in vivo to form covalent addition products. This reaction is non-enzymatic and occurs via the Heyns rearrangement of an initial Schiff base adduct between the steroid carbonyl and the epsilon-amino group of lysine residues. The present study describes the synthesis, isolation, and structural analysis of model adducts prepared by the incubation of 16 alpha-hydroxyesterone or cortisol with NaCNBH3 and lysine derivatives blocked in the N alpha-position. The product formed from the reaction of 16 alpha-hydroxyesterone and lysine was found to have the structure predicted for a reduced Schiff base between these molecules. A stable, cortisol-lysine adduct was similarly synthesized and isolated. This conjugate was found not to be the expected reduced Schiff base but rather a C-20 cyano amine. This compound most likely was formed by the nucleophilic addition of cyanide during the course of the incubation. The observation that the cortisol-lysine Schiff base is not reducible with NaCNBH3 accounts for the observation that the incorporation rate of glucocorticoids into proteins is not increased by the presence of NaCNBH3.

  8. Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants.

    Directory of Open Access Journals (Sweden)

    Hsin-Mao Wu

    Full Text Available Lysine racemase, a pyridoxal 5'-phosphate (PLP-dependent amino acid racemase that catalyzes the interconversion of lysine enantiomers, is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants. Here, we have determined the first crystal structure of a lysine racemase (Lyr from Proteus mirabilis BCRC10725, which shows the highest activity toward lysine and weaker activity towards arginine. In addition, we establish the first broad-specificity amino acid racemase (Bar structure from Pseudomonas putida DSM84, which presents not only the highest activity toward lysine but also remarkably broad substrate specificity. A complex structure of Bar-lysine is also established here. These structures demonstrate the similar fold of alanine racemase, which is a head-to-tail homodimer with each protomer containing an N-terminal (α/β(8 barrel and a C-terminal β-stranded domain. The active-site residues are located at the protomer interface that is a funnel-like cavity with two catalytic bases, one from each protomer, and the PLP binding site is at the bottom of this cavity. Structural comparisons, site-directed mutagenesis, kinetic, and modeling studies identify a conserved arginine and an adjacent conserved asparagine that fix the orientation of the PLP O3 atom in both structures and assist in the enzyme activity. Furthermore, side chains of two residues in α-helix 10 have been discovered to point toward the cavity and define the substrate specificity. Our results provide a structural foundation for the design of racemases with pre-determined substrate specificity and for the development of the non-antibiotic selection system in transgenic plants.

  9. A Novel Staphylococcus Podophage Encodes a Unique Lysin with Unusual Modular Design

    Science.gov (United States)

    Cater, Katie; Dandu, Vidya Sree; Bari, S. M. Nayeemul; Lackey, Kim; Everett, Gabriel F. K.

    2017-01-01

    ABSTRACT Drug-resistant staphylococci, particularly Staphylococcus aureus and Staphylococcus epidermidis, are leading causes of hospital-acquired infections. Bacteriophages and their peptidoglycan hydrolytic enzymes (lysins) are currently being explored as alternatives to conventional antibiotics; however, only a limited diversity of staphylococcal phages and their lysins has yet been characterized. Here, we describe a novel staphylococcal phage and its lysins. Bacteriophage Andhra is the first reported S. epidermidis phage belonging to the family Podoviridae. Andhra possesses an 18,546-nucleotide genome with 20 open reading frames. BLASTp searches revealed that gene product 10 (gp10) and gp14 harbor putative catalytic domains with predicted peptidase and amidase activities, characteristic functions of phage lysins. We purified these proteins and show that both Andhra_gp10 and Andhra_gp14 inhibit growth and degrade cell walls of diverse staphylococci, with Andhra_gp10 exhibiting more robust activity against the panel of cell wall substrates tested. Site-directed mutagenesis of its predicted catalytic residues abrogated the activity of Andhra_gp10, consistent with the presence of a catalytic CHAP domain on its C terminus. The active site location combined with the absence of an SH3b cell wall binding domain distinguishes Andhra_gp10 from the majority of staphylococcal lysins characterized to date. Importantly, close homologs of Andhra_gp10 are present in related staphylococcal podophages, and we propose that these constitute a new class of phage-encoded lysins. Altogether, our results reveal insights into the biology of a rare family of staphylococcal phages while adding to the arsenal of antimicrobials with potential for therapeutic use. IMPORTANCE The spread of antibiotic resistance among bacterial pathogens is inciting a global public health crisis. Drug-resistant Staphylococcus species, especially S. aureus and S. epidermidis, have emerged in both hospital

  10. [The effect of the raw protein supply on the lysine requirements of young pigs of 12-40 kg. 1. Report. Feeding studies with wheat-peanut extraction residue rations].

    Science.gov (United States)

    Schüler, D; Bodenstein, K H; Hennig, A

    1976-09-01

    10 feedings trials were carried out with a total of more than 500 pigs weighing 12 to 40 kgs. To investigate the lysine needs of growing pigs, the animals were fed rations of wheat + extracted ground nut meal. Different food mixtures were tested containing 5 levels of crude protein (19%, 17%, 15%, 13% and 11% of the dry feed. Within each crude protein level 6 graded lysine supplements were added to the ration. The trial showed that the lysine requirements of the weaned pigs were in a decisive measure determined by the percentage proportion of crude protein contained in the ration. The crude protein portion may be calculated (for the liveweight range tested) by using the following regression equation: y=0.28+0.075x (y=lysine requirements expressed as % of the air-dried ration; x=percentage proportion of crude protein in the ration). Rations containing only protein sources of vegetable origin, with a minimum protein content of 15%, produced the same daily weight gains (520 g) as a standard diet, if the lysine demands were met through the supplementation of synthetic lysine.

  11. Interaction of L-lysine and soluble elastin with the semicarbazide-sensitive amine oxidase in the context of its vascular-adhesion and tissue maturation functions.

    LENUS (Irish Health Repository)

    Olivieri, Aldo

    2010-04-01

    The copper-containing quinoenzyme semicarbazide-sensitive amine oxidase (EC 1.4.3.21; SSAO) is a multifunctional protein. In some tissues, such as the endothelium, it also acts as vascular-adhesion protein 1 (VAP-1), which is involved in inflammatory responses and in the chemotaxis of leukocytes. Earlier work had suggested that lysine might function as a recognition molecule for SSAO\\/VAP-1. The present work reports the kinetics of the interaction of L-lysine and some of its derivatives with SSAO. Binding was shown to be saturable, time-dependent but reversible and to cause uncompetitive inhibition with respect to the amine substrate. It was also specific, since D-lysine, L-lysine ethyl ester and epsilon-acetyl-L-lysine, for example, did not bind to the enzyme. The lysine-rich protein soluble elastin bound to the enzyme relatively tightly, which may have relevance to the reported roles of SSAO in maintaining the extracellular matrix (ECM) and in the maturation of elastin. Our data show that lysyl residues are not oxidized by SSAO, but they bind tightly to the enzyme in the presence of hydrogen peroxide. This suggests that binding in vivo of SSAO to lysyl residues in physiological targets might be regulated in the presence of H(2)O(2), formed during the oxidation of a physiological SSAO substrate, yet to be identified.

  12. Residual polar motion caused by coseismic and interseismic deformations from 1900 to present

    Science.gov (United States)

    Cambiotti, G.; Wang, X.; Sabadini, R.; Yuen, D. A.

    2016-05-01

    We challenge the perspective that seismicity could contribute to polar motion by arguing quantitatively that, in first approximation and on the average, interseismic deformations can compensate for it. This point is important because what we must simulate and observe in Earth Orientation Parameter time-series over intermediate timescales of decades or centuries is the residual polar motion resulting from the two opposing processes of coseismic and interseismic deformations. In this framework, we first simulate the polar motion caused by only coseismic deformations during the longest period available of instrumental seismicity, from 1900 to present, using both the CMT and ISC-GEM catalogues. The instrumental seismicity covering a little longer than one century does not represent yet the average seismicity that we should expect on the long term. Indeed, although the simulation shows a tendency to move the Earth rotation pole towards 133°E at the average rate of 16.5 mm yr-1, this trend is still sensitive to individual megathrust earthquakes, particularly to the 1960 Chile and 1964 Alaska earthquakes. In order to further investigate this issue, we develop a global seismicity model (GSM) that is independent from any earthquake catalogue and that describes the average seismicity along plate boundaries on the long term by combining information about present-day plate kinematics with the Anderson theory of faulting, the seismic moment conservation principle and a few other assumptions. Within this framework, we obtain a secular polar motion of 8 mm yr-1 towards 112.5°E that is comparable with that estimated from 1900 to present using the earthquake catalogues, although smaller by a factor of 2 in amplitude and different by 20° in direction. Afterwards, in order to reconcile the idea of a secular polar motion caused by earthquakes with our simplest understanding of the seismic cycle, we adapt the GSM in order to account for interseismic deformations and we use it to

  13. Lysine methylation: beyond histones

    Institute of Scientific and Technical Information of China (English)

    Xi Zhang; Hong Wen; Xiaobing Shi

    2012-01-01

    Posttranslational modifications (PTMs) of histone proteins,such as acetylation,methylation,phosphorylation,and ubiquitylation,play essential roles in regulating chromatin dynamics.Combinations of different modifications on the histone proteins,termed 'histone code' in many cases,extend the information potential of the genetic code by regulating DNA at the epigenetic level.Many PTMs occur on non-histone proteins as well as histones,regulating protein-protein interactions,stability,localization,and/or enzymatic activities of proteins involved in diverse cellular processes.Although protein phosphorylation,ubiquitylation,and acetylation have been extensively studied,only a few proteins other than histones have been reported that can be modified by lysine methylation.This review summarizes the current progress on lysine methylation of nonhistone proteins,and we propose that lysine methylation,like phosphorylation and acetylation,is a common PTM that regulates proteins in diverse cellular processes.

  14. ß-Lysine discrimination by lysyl-tRNA synthetase

    DEFF Research Database (Denmark)

    Gilreath, Marla S; Roy, Hervé; Bullwinkle, Tammy J

    2011-01-01

    guided by the PoxA structure. A233S LysRS behaved as wild type with a-lysine, while the G469A and A233S/G469A variants decreased stable a-lysyl-adenylate formation. A233S LysRS recognized ß-lysine better than wildtype, suggesting a role for this residue in discriminating a- and ß-amino acids. Both...

  15. NMR determination of lysine pKa values in the Pol lambda lyase domain: mechanistic implications.

    Science.gov (United States)

    Gao, Guanghua; DeRose, Eugene F; Kirby, Thomas W; London, Robert E

    2006-02-14

    increase in the Hill coefficients observed in the complex is consistent with the screening of the interacting lysine residues by the DNA. The pKa of K312 residue increased to 10.58 in the complex, probably due to salt bridge formation with the 5'-phosphate group of the DNA. The pKa values obtained for the lyase domain of Pol lambda in the present study are consistent with recent crystallographic studies of Pol beta complexed with 5-phosphorylated abasic sugar analogues in nicked DNA which reveal an open site with no obvious interactions that would significantly depress the pK value for the active site lysine residue. It is suggested that due to the heterogeneity of the damaged DNA substrates with which Pol lambda as well as other related polymerases may be required to bind, the unexpectedly poor optimization of the lyase catalytic site may reflect a compromise of flexibility with catalytic efficiency.

  16. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level

    DEFF Research Database (Denmark)

    Danielsen, Jannie M R; Sylvestersen, Kathrine B; Bekker-Jensen, Simon;

    2011-01-01

    The covalent attachment of ubiquitin to proteins regulates numerous processes in eukaryotic cells. Here we report the identification of 753 unique lysine ubiquitylation sites on 471 proteins using higher-energy collisional dissociation on the LTQ Orbitrap Velos. In total 5756 putative ubiquitin...... substrates were identified. Lysine residues targeted by the ubiquitin-ligase system show no unique sequence feature. Surface accessible lysine residues located in ordered secondary regions, surrounded by smaller and positively charged amino acids are preferred sites of ubiquitylation. Lysine ubiquitylation...

  17. Deregulation of histone lysine methyltransferases contributes to oncogenic transformation of human bronchoepithelial cells

    Directory of Open Access Journals (Sweden)

    Yoda Satoshi

    2008-11-01

    Full Text Available Abstract Background Alterations in the processing of the genetic information in carcinogenesis result from stable genetic mutations or epigenetic modifications. It is becoming clear that nucleosomal histones are central to proper gene expression and that aberrant DNA methylation of genes and histone methylation plays important roles in tumor progression. To date, several histone lysine methyltransferases (HKMTs have been identified and histone lysine methylation is now considered to be a critical regulator of transcription. However, still relatively little is known about the role of HKMTs in tumorigenesis. Results We observed differential HKMT expression in a lung cancer model in which normal human bronchial epithelial (NHBE cells expressing telomerase, SV40 large T antigen, and Ras were immortal, formed colonies in soft agar, and expressed specific HKMTs for H3 lysine 9 and 27 residues but not for H3 lysine 4 residue. Modifications in the H3 tails affect the binding of proteins to the histone tails and regulate protein function and the position of lysine methylation marks a gene to be either activated or repressed. In the present study, suppression by siRNA of HKMTs (EZH2, G9A, SETDB1 and SUV39H1 that are over-expressed in immortalized and transformed cells lead to reduced cell proliferation and much less anchorage-independent colony growth. We also found that the suppression of H3-K9, G9A and SUV39H1 induced apoptosis and the suppression of H3-K27, EZH2 caused G1 arrest. Conclusion Our results indicate the potential of these HKMTs in addition to the other targets for epigenetics such as DNMTs and HDACs to be interesting therapeutic targets.

  18. Bioavailability of lysine in heat-treated foods and feedstuffs

    NARCIS (Netherlands)

    McArtney Rutherfurd, S.

    2010-01-01

    During the processing of foodstuffs, lysine can react with other compounds present to form nutritionally unavailable derivatives, the most common example of which are Maillard products. Maillard products can cause serious problems when determining the available lysine content of processed foods or f

  19. Bioavailability of lysine in heat-treated foods and feedstuffs

    NARCIS (Netherlands)

    McArtney Rutherfurd, S.

    2010-01-01

    During the processing of foodstuffs, lysine can react with other compounds present to form nutritionally unavailable derivatives, the most common example of which are Maillard products. Maillard products can cause serious problems when determining the available lysine content of processed foods or

  20. Chemical tools for unraveling the substrate specificity of the lysine deacylase enzymes

    DEFF Research Database (Denmark)

    Madsen, Andreas Stahl; Olsen, Christian Adam

    The lysine deacylase (KDAC) enzymes catalyze hydrolytic removal of acyl functionalities from theε-amino group of lysine residues ina variety of proteins including histones, and KDAC-mediated deacetylation of proteins has been established as a key epigeneticandmetabolic regulator. Recent studies h......-dependent HDACs 1–11 as well as NAD + -dependent sirtuins (SIRT1–7) will be discussed....

  1. Creative lysins: Listeria and the engineering of antimicrobial enzymes.

    Science.gov (United States)

    Van Tassell, Maxwell L; Angela Daum, M; Kim, Jun-Seob; Miller, Michael J

    2016-02-01

    Cell wall lytic enzymes have been of increasing interest as antimicrobials for targeting Gram-positive spoilage and pathogenic bacteria, largely due to the development of strains resistant to antibiotics and bacteriophage therapy. Such lysins show considerable promise against Listeria monocytogenes, a primary concern in food-processing environments, but there is room for improvement via protein engineering. Advances in antilisterial applications could benefit from recent developments in lysin biotechnology that have largely targeted other organisms. Herein we present various considerations for the future development of lysins, including environmental factors, cell physiology concerns, and dynamics of protein architecture. Our goal is to review key developments in lysin biotechnology to provide a contextual framework for the current models of lysin-cell interactions and highlight key considerations for the characterization and design of novel lytic enzymes.

  2. Structural basis for the site-specific incorporation of lysine derivatives into proteins.

    Directory of Open Access Journals (Sweden)

    Veronika Flügel

    Full Text Available Posttranslational modifications (PTMs of proteins determine their structure-function relationships, interaction partners, as well as their fate in the cell and are crucial for many cellular key processes. For instance chromatin structure and hence gene expression is epigenetically regulated by acetylation or methylation of lysine residues in histones, a phenomenon known as the 'histone code'. Recently it was shown that these lysine residues can furthermore be malonylated, succinylated, butyrylated, propionylated and crotonylated, resulting in significant alteration of gene expression patterns. However the functional implications of these PTMs, which only differ marginally in their chemical structure, is not yet understood. Therefore generation of proteins containing these modified amino acids site specifically is an important tool. In the last decade methods for the translational incorporation of non-natural amino acids using orthogonal aminoacyl-tRNA synthetase (aaRS:tRNAaaCUA pairs were developed. A number of studies show that aaRS can be evolved to use non-natural amino acids and expand the genetic code. Nevertheless the wild type pyrrolysyl-tRNA synthetase (PylRS from Methanosarcina mazei readily accepts a number of lysine derivatives as substrates. This enzyme can further be engineered by mutagenesis to utilize a range of non-natural amino acids. Here we present structural data on the wild type enzyme in complex with adenylated ε-N-alkynyl-, ε-N-butyryl-, ε-N-crotonyl- and ε-N-propionyl-lysine providing insights into the plasticity of the PylRS active site. This shows that given certain key features in the non-natural amino acid to be incorporated, directed evolution of this enzyme is not necessary for substrate tolerance.

  3. Characterization and crystal structure of lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase (cDHDPS) protein.

    Science.gov (United States)

    Rice, Elena A; Bannon, Gary A; Glenn, Kevin C; Jeong, Soon Seog; Sturman, Eric J; Rydel, Timothy J

    2008-12-15

    The lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase enzyme (cDHDPS) was recently successfully introduced into maize plants to enhance the level of lysine in the grain. To better understand lysine insensitivity of the cDHDPS, we expressed, purified, kinetically characterized the protein, and solved its X-ray crystal structure. The cDHDPS enzyme has a fold and overall structure that is highly similar to other DHDPS proteins. A noteworthy feature of the active site is the evidence that the catalytic lysine residue forms a Schiff base adduct with pyruvate. Analyses of the cDHDPS structure in the vicinity of the putative binding site for S-lysine revealed that the allosteric binding site in the Escherichia coli DHDPS protein does not exist in cDHDPS due to three non-conservative amino acids substitutions, and this is likely why cDHDPS is not feedback inhibited by lysine.

  4. (R)-β-lysine-modified elongation factor P functions in translation elongation

    DEFF Research Database (Denmark)

    Bullwinkle, Tammy J; Zou, S Betty; Rajkovic, Andrei

    2013-01-01

    Post-translational modification of bacterial elongation factor P (EF-P) with (R)-β-lysine at a conserved lysine residue activates the protein in vivo and increases puromycin reactivity of the ribosome in vitro. The additional hydroxylation of EF-P at the same lysine residue by the YfcM protein has......-(β)-lysyl-EF-P showed 30% increased puromycin reactivity but no differences in dipeptide synthesis rates when compared with the β-lysylated form. Unlike disruption of the other genes required for EF-P modification, deletion of yfcM had no phenotypic consequences in Salmonella. Taken together, our findings indicate...

  5. Polar Volatiles on Mars--Theory versus Observation: Excess solid carbon dioxide is probably present in the north residual cap.

    Science.gov (United States)

    Murray, B C; Malin, M C

    1973-11-02

    The residual frost caps of Mars are probably water-ice. They may be the source of the water vapor associated with seasonal polar hoods. A permanent reservoir of solid CO(2) is also probably present within the north residual cap and may comprise a mass of CO(2) some two to five times that of the present atmosphere of Mars. The martian atmospheric pressure is probably regulated by the temperature of the reservoir and not by the annual heat balance of exposed solid CO(2) (37). The present reservoir temperature presumably reflects a long-term average of the polar heat balance. The question of a large permanent north polar cap is reexamined in light of the Mariner 9 data. The lower general elevation of the north polar region compared to the south and the resulting occurrence in the north of a permanent CO(2) deposit are probably responsible for the differences in size and shape of the two residual caps. The details of the processes involved are less apparent, however. It might be argued that the stability of water-ice deposits depends on both insolation and altitude. The present north and south residual caps should be symmetrically located with respect to such a hypothetical stability field. However, the offset of the south cap from the geometrical pole, the non-symmetrical outline of the north cap, and the apparently uniform thickness of the thin, widespread water-ice all argue against control by simple solid-vapor equilibrium of water under present environmental conditions. We think that the present location of the water-ice may reflect, in part, the past location of the permanent CO(2) reservoir. The extreme stability of polar water-ice deposits increases the likelihood that past environmental conditions may be recorded there. Detailed information on elevations in the vicinity of the residual caps is needed before we can further elucidate the nature and history of the residual caps. This, along with measurements of polar infrared emission, should be given high

  6. Induction by fructose force-feeding of histone H3 and H4 acetylation at their lysine residues around the Slc2a5 gene and its expression in mice.

    Science.gov (United States)

    Honma, Kazue; Mochizuki, Kazuki; Goda, Toshinao

    2013-01-01

    It has been reported that fructose force-feeding rapidly induced jejunal Slc2a5 gene expression in rodents. We demonstrate in this study that acetylation at lysine (K) 9 of histone H3 and acetylation at K5 and K16 of histone H4 were more enhanced in the promoter/enhancer to transcribed regions of the Slc2a5 gene in fructose force-fed mice than in glucose force-fed mice. However, fructose force-feeding did not induce acetylation at K14 of histone H3, or at K8 and K12 of histone H4 around the Slc2a5 gene. These results suggest that fructose force-feeding induced selective histone acetylation, particularly of H3 and H4, around the jejunal Slc2a5 gene in mice.

  7. New lysine-acetylated proteins screened by immunoaffinity and liquid chromatography-mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The lack of selective extraction specific for lysine-acetylated proteins has been a major problem in the field of acetylation biology,though acetylation plays a key role in many biological processes.In this paper,we report for the first time the proteomic screening of lysine-acetylated proteins from a mouse liver tissue,by a new approach of immunoaffinity purification of lysine-acetylated peptides combined with nano-HPLC/MS/MS analysis.We have found 20 lysine-acetylated proteins with 21 lysine-acetylated sites,among which 12 lysine-acetylated proteins and 16 lysine-acetylated sites have never been reported before.Notably,three acetyltransferases harboring in mitochondrion are newly discovered acetyltransferases responsible for the acetylation of nonhistone proteins.We have explored the significant patterns of residue preference by the hierarchical clustering analysis of amino acid residues surrounding acetylation sites,which could be helpful to the prediction of new sites of lysine acetylation.Our findings provide more candidates for studying the important roles played by acetylation in diverse cellular pathways and related human diseases.

  8. Effects of fortified lysine on the amino acid profile and sensory qualities of deep-fried and dried noodles.

    Science.gov (United States)

    Polpuech, C; Chavasit, V; Srichakwal, P; Paniangvait, P

    2011-08-01

    Lysine fortification of wheat flour has been used toward reducing protein energy malnutrition in developing countries. The feasibility of fortifying instant noodles with lysine was evaluated based on sensory qualities and the residual lysine content. Fifty grams of deep-fried and dried instant noodles were fortified with 0.23 and 0.21 g lysine, respectively. The production temperatures used for deep-frying were 165-175 degrees C and for drying, 80-105 degrees C; these are the temperatures used in the industrial production of both kinds of noodles. Lysine fortification was then performed at the local factories using the commercial production lines and packaging for both types of instant noodles. Both fortified and unfortified deep-fried and dried instant noodles were stored at 50 degrees C under fluorescent light for 2 and 4 months, respectively. The fortified products were tested for residual lysine content and sensory qualities as compared with unfortified noodles. The results show fortified products from the tested processing temperatures were all accepted. After storage, significant losses of lysine were not found in both types of noodles analysed. The lysine-fortified noodles had amino acid scores of 102% and 122%, respectively. After 2 months, the sensory quality of fortified deep-fried noodles was still acceptable; however, the dried noodles turned to an unacceptable dark colour. This study shows that it is feasible to fortify deep-fried instant noodles with lysine, though lysine fortification exhibited an undesirable colour in the dried instant noodles after storage.

  9. Effect of heat damage in an autoclave on the reactive lysine contents of soy products and corn distillers dried grains with solubles. Use of the results to check on lysine damage in common qualities of these ingredients.

    Science.gov (United States)

    Fontaine, Johannes; Zimmer, Ulrike; Moughan, Paul J; Rutherfurd, Shane M

    2007-12-26

    The suitability of the homoarginine reaction for determining the reactive lysine in soy products and corn distillers dried grain with solubles (DDGS) was tested. For this purpose, some batches were subjected to deliberate heat damage for up to 30 min in an autoclave with 135 degrees C hot steam, and the samples were analyzed for total lysine and reactive lysine. In addition, 84 samples of common soy and 80 samples of corn DDGS were tested for their content of total and reactive lysine, and the contents were compared with those of the autoclave tests. For soy products conclusive results were obtained. In the case of heat treatment, both total lysine and reactive lysine decrease, but the latter is clearly a more sensitive indicator of lysine damage. Most normal products are quite similar, with toasting-induced damage to reactive lysine of ca. 15% compared to untoasted beans. The cause of the constantly occurring residual lysine after guanidination and the poorer reaction balance in the case of damage were explained. For common DDGS samples, however, less favorable results were obtained. Reactive and total lysine decreased almost in parallel due to heat damage, showing a great gap between them. Results showed indeed that variation of total and reactive lysine in DDGS is high, proving that its production conditions are not yet optimal for a feed ingredient.

  10. Carbonaceous material production from vegetable residue and their use in the removal of textile dyes present in wastewater

    Science.gov (United States)

    Peláez-Cid, A. A.; Tlalpa-Galán, M. A.; Herrera-González, A. M.

    2013-06-01

    This paper presents the adsorption results of acid, basic, direct, vat, and reactive-type dyes on carbonaceous adsorbent materials prepared starting off vegetable residue such as Opuntia ficus indica and Casimiroa edulis fruit wastes. The adsorbents prepared from Opuntia ficus indica waste were designated: TunaAsh, CarTunaT, and CarTunaQ. The materials obtained from Casimiroa edulis waste were named: CenZAP, CarZAPT, and CarZAPQ. TunaAsh and CenZAP consist of ashes obtained at 550 °C CarTunaT and CarZAPT consist of the materials carbonized at 400 °C lastly, CarTunaQ and CarZAPQ consist of chemically activated carbons using H3PO4 at 400 °C. Only the chemically activated materials were washed with distilled water until a neutral pH was obtained after their carbonization. All materials were ground and sieved to obtain a particle size ranging from 0.25 to 0.84 mm. The static adsorption results showed that both ashes and chemically activated carbon are more efficient at dye removal for both vegetable residues. For TunaAsh and CarTunaQ, removal rates of up to 100% in the cases of basic, acid, and direct dyes were achieved. Regarding wastewater containing reactive dyes, the efficiency ranged from 60 to 100%. For vat effluents, it ranged from 42 to 52%. In the case of CenZAP and CarZAPQ, it was possible to treat reactive effluents with rates ranging between 63 and 91%. Regarding vat effluents, it ranged from 57 to 68%. The process of characterization for all materials was done using scanning electron microscopy and infrared spectroscopy.

  11. Systemic lupus erythematosus patients contain significantly less igm against mono-methylated lysine than healthy subjects.

    Directory of Open Access Journals (Sweden)

    Sha Guo

    Full Text Available Post-translational modifications on proteins are important in biological processes but may create neo-epitopes that induce autoimmune responses. In this study, we measured the serum IgG and IgM response to a set of non-modified or acetyl- and methyl-modified peptides corresponding to residues 1-19 of the histone 3 N-terminal tail in systemic lupus erythematosus (SLE patients and healthy subjects. Our results indicated that the SLE patients and healthy subjects produced antibodies (Abs to the peptides, but the two groups had different Ab isotype and epitope preferences. Abs to the non-modified form, H31-19, were of the IgG isotype and produced by SLE patients. They could not recognize the scrambled H31-19, which contained the same amino acid composition but a different sequence as H31-19. In comparison, healthy subjects in general did not produce IgG against H31-19. However, about 70% of the healthy subjects produced IgM Abs against mono-methylated K9 of H31-19 (H31-19K9me. Our further studies revealed that ε-amine mono-methylated lysine could completely inhibit the IgM binding to H31-19K9me, but lysine had no inhibitory effect. In addition, the IgM Abs could bind peptides containing a mono-methylated lysine residue but with totally different sequences. Thus, mono-methylated lysine was the sole epitope for the IgM. Interestingly, SLE patients had much lower levels of this type of IgM. There was no obvious correlation between the IgM levels and disease activity and the decreased IgM was unlikely caused by medical treatments.We also found that the IgM Abs were not polyreactive to dsDNA, ssDNA, lipopolysaccharide (LPS or insulin and they did not exist in umbilical cord serum, implying that they were not natural Abs. The IgM Abs against mono-methylated lysine are present in healthy subjects but are significantly lower in SLE patients, suggesting a distinct origin of production and special physiological functions.

  12. Coarse-grained simulations of hemolytic peptide δ-lysin interacting with a POPC bilayer.

    Science.gov (United States)

    King, Mariah J; Bennett, Ashley L; Almeida, Paulo F; Lee, Hee-Seung

    2016-12-01

    δ-lysin, secreted by a Gram-positive bacterium Staphylococcus aureus, is a 26-residue membrane active peptide that shares many common features with antimicrobial peptides (AMPs). However, it possesses a few unique features that differentiate itself from typical AMPs. In particular, δ-lysin has zero net charge, even though it has many charged residues, and it preferentially lyses eukaryotic cells over bacterial cells. Here, we present the results of coarse-grained molecular dynamics simulations of δ-lysin interacting with a zwitterionic membrane over a wide range of peptide concentrations. When the peptides concentration is low, spontaneous dimerization of peptides is observed on the membrane surface, but deep insertion of peptides or pore formation was not observed. However, the calculated free energy of peptide insertion suggests that a small fraction of peptides is likely to be present inside the membrane at the peptide concentrations typically seen in dye efflux experiments. When the simulations with multiple peptides are carried out with a single pre-inserted transmembrane peptide, spontaneous pore formation occurs with a peptide-to-lipid ratio (P/L) as low as P/L=1:42. Inter-peptide salt bridges among the transmembrane peptides seem to play a role in creating compact pores with very low level of hydration. More importantly, the transmembrane peptides making up the pore are constantly pushed to the opposite side of the membrane when the mass imbalance between the two sides of membrane is significant. Thus, the pore is very dynamic, allowing multiple peptides to translocate across the membrane simultaneously.

  13. Present Situation and Control Countermeasures of Pesticide Residue on Crops in Yinzhou District of Ningbo City, China

    Directory of Open Access Journals (Sweden)

    XU Pei-juan

    2014-02-01

    Full Text Available Tatal of 411 batches of rice, leaf vegetables, fruits, beans, solanums and tubers were sampled monthly, in accordance with related national regulations on 22 detected pesticides in the Yinzhou District, Ningbo City. The results showed that the pesticide detection rate was0.3%, the qualified rate of pesticide residues in agricultural products was 97.82%. Pesticide residues detection accounted for 88.89%. The samples beyond the pesticide residue standard were mainly vegetables from May to October. Leaf vegetables exceeding the standard sample rate reached 3.72%. Pesticide residue samples exceeding the standard were found in retail in plain and coastal areas, but were found in all scale farming in mountainous areas. The rate of exceeding the pesticide residues standard of farmers with primary school education level was4.50%, which was 6.16 times higher than that farmers with university education. In order to reduce the pesticide residual in Yinzhou District,we put forward control countermeasures in 5 aspects.

  14. Digestible Lysine on Live Performance of Chicken Type Naked Neck During the Starter Phase

    Directory of Open Access Journals (Sweden)

    RG de Oliveira

    2015-12-01

    Full Text Available ABSTRACT The poultry market has changed due to a higher consumer interest on products with differentiated organoleptic characteristics, making of free-range broiler production a promising activity. This experiment was conducted to determine the digestible lysine requirements of Redbro Cou Nu male and female chickens during the starter phase (one to 21 days of age. Six hundred and thirty Redbro Cou Nu broilers were distributed into 30 pens (21 chickens/pen according to a randomized complete design in a 5 x 2 factorial arrangement, consisting of five levels of digestible lysine and two sexes, with three replicates (pens per treatments. Diets with increasing digestible lysine levels (8.1, 9.5, 10.9, 12.3 and 13.7 g of digestible lysine per kg of diet were offered ad libitum. The following performance traits were evaluated at the end of the experiment (d 21: feed intake, lysine intake, body weight gain, and feed conversion ratio. No interaction between dietary lysine level and sex was observed for the evaluated traits. The effect of sex was only detected on body weight gain, while effects of dietary lysine level were only detected on the feed intake. Males presented higher body weight gain than females. Lysine intake and body weight gain increased, and feed conversion ratio decreased as the level of dietary lysine increased. The best feed conversion ratio was obtained when birds were fed 12.95 g of digestible lysine per kg of diet.

  15. l-lysine production by Bacillus methanolicus: Genome-based mutational analysis and l-lysine secretion engineering.

    Science.gov (United States)

    Nærdal, Ingemar; Netzer, Roman; Irla, Marta; Krog, Anne; Heggeset, Tonje Marita Bjerkan; Wendisch, Volker F; Brautaset, Trygve

    2017-02-20

    Bacillus methanolicus is a methylotrophic bacterium with an increasing interest in academic research and for biotechnological applications. This bacterium was previously applied for methanol-based production of l-glutamate, l-lysine and the five-carbon diamine cadaverine by wild type, classical mutant and recombinant strains. The genomes of two different l-lysine secreting B. methanolicus classical mutant strains, NOA2#13A52-8A66 and M168-20, were sequenced. We focused on mutational mapping in genes present in l-lysine and other relevant amino acid biosynthetic pathways, as well as in the primary cell metabolism important for precursor supply. In addition to mutations in the aspartate pathway genes dapG, lysA and hom-1, new mutational target genes like alr, proA, proB1, leuC, odhA and pdhD were identified. Surprisingly, no mutations were found in the putative l-lysine transporter gene lysE(MGA3). Inspection of the wild type B. methanolicus strain PB1 genome sequence identified two homologous putative l-lysine transporter genes, lysE(PB1) and lysE2(PB1). The biological role of these putative l-lysine transporter genes, together with the heterologous l-lysine exporter gene lysE(Cg) from Corynebacterium glutamicum, were therefore investigated. Our results demonstrated that the titer of secreted l-lysine in B. methanolicus was significantly increased by overexpression of lysE(Cg) while overexpression of lysE(MGA3), lysE(PB1) and lysE2(PB1) had no measurable effect.

  16. Digestible lysine requirements of broilers

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    LEP Bernal

    2014-03-01

    Full Text Available Modern broilers have been submitted to continuous genetic improvement, and therefore, their nutritional requirements must be constantly updated to ensure their performance. Two experiments were carried out to evaluate different digestible lysine levels for starter (1021 days and grower (22-35 days phases. The experiments were carried out with male and female Cobb 500 broilers, distributed according to a randomized block experimental design in a 5x2 factorial arrangement (5 increasing digestible lysine levels x 2 sexes, totaling 10 treatments, with 8 replicates of 22 and 20 birds during the starter and grower phase, respectively. Digestible lysine levels of 1.06, 1.12, 1.18, 1.24, and 1.30 were used in the starter diets (10-21 days and 0.9, 0.98, 1.04, 1.10, and 1.16% in the grower diets (22-35 days. Based on the statistical analyses of the evaluated performance parameters, digestible lysine requirements for maximum performance were determined as 1.22% for males and 1.24% for females in the starter phase, and 1.16% for both sexes in the grower phase. Carcass and performance results indicate that digestible lysine requirements vary with sex and evaluated production parameter. Considering the most relevant broiler production parameters, in 22- to 35-d-old males, digestible lysine requirement for breast meat yield (1.16% was higher than those for feed conversion ratio (1.07% and weight gain (1.05%.

  17. DNA Damage-Induced Acetylation of Lysine 3016 of ATM Activates ATM Kinase Activity▿ †

    OpenAIRE

    Sun, Yingli; Xu, Ye; Roy, Kanaklata; Price, Brendan D.

    2007-01-01

    The ATM protein kinase is essential for cells to repair and survive genotoxic events. The activation of ATM's kinase activity involves acetylation of ATM by the Tip60 histone acetyltransferase. In this study, systematic mutagenesis of lysine residues was used to identify regulatory ATM acetylation sites. The results identify a single acetylation site at lysine 3016, which is located in the highly conserved C-terminal FATC domain adjacent to the kinase domain. Antibodies specific for acetyl-ly...

  18. Systematic Analysis of the Functions of Lysine Acetylation in the Regulation of Tat Activity.

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    Minghao He

    Full Text Available The Tat protein of HIV-1 has several well-known properties, such as nucleocytoplasmic trafficking, transactivation of transcription, interaction with tubulin, regulation of mitotic progression, and induction of apoptosis. Previous studies have identified a couple of lysine residues in Tat that are essential for its functions. In order to analyze the functions of all the lysine residues in Tat, we mutated them individually to alanine, glutamine, and arginine. Through systematic analysis of the lysine mutants, we discovered several previously unidentified characteristics of Tat. We found that lysine acetylation could modulate the subcellular localization of Tat, in addition to the regulation of its transactivation activity. Our data also revealed that lysine mutations had distinct effects on microtubule assembly and Tat binding to bromodomain proteins. By correlation analysis, we further found that the effects of Tat on apoptosis and mitotic progression were not entirely attributed to its effect on microtubule assembly. Our findings suggest that Tat may regulate diverse cellular activities through binding to different proteins and that the acetylation of distinct lysine residues in Tat may modulate its interaction with various partners.

  19. Apolipoprotein A-I lysine modification: effects on helical content, lipid binding and cholesterol acceptor activity.

    Science.gov (United States)

    Brubaker, Gregory; Peng, Dao-Quan; Somerlot, Benjamin; Abdollahian, Davood J; Smith, Jonathan D

    2006-01-01

    We examined the role of the positively charged lysine residues in apoAI by chemical modification. Lysine modification by reductive methylation did not alter apoAI's net charge, secondary or tertiary structure as observed by circular dichroism and trytophan fluorescence, respectively, or have much impact on lipid binding or ABCA1-dependent cholesterol acceptor activity. Acetylation of lysine residues lowered the isoelectric point of apoAI, altered its secondary and tertiary structure, and led to a 40% decrease in cholesterol acceptor activity, while maintaining 93% of its lipid binding activity. Exhaustive lysine acetoacetylation lowered apoAI's isoelectric point, profoundly disrupted its secondary and tertiary structure, and led to 90% and 82% reductions in cholesterol acceptor and lipid binding activities, respectively. The dose-dependent acetoacetylation of an increasing proportion of apoAI lysine residues demonstrated that cholesterol acceptor activity was more sensitive to this modification than lipid binding activity, suggesting that apoAI lysine positive charges play an important role in ABCA1 mediated lipid efflux beyond the role needed to maintain alpha-helical content and lipid binding activity.

  20. Using a bacteriocin structure to engineer a phage lysin that targets Yersinia pestis.

    Science.gov (United States)

    Lukacik, Petra; Barnard, Travis J; Buchanan, Susan K

    2012-12-01

    Purified phage lysins present an alternative to traditional antibiotics and work by hydrolysing peptidoglycan. Phage lysins have been developed against Gram-positive pathogens such as Bacillus anthracis and Streptococcus pneumoniae, where the peptidoglycan layer is exposed on the cell surface. Addition of the lysin to a bacterial culture results in rapid death of the organism. Gram-negative bacteria are resistant to phage lysins because they contain an outer membrane that protects the peptidoglycan from degradation. We solved crystal structures of a Yersinia pestis outer-membrane protein and the bacteriocin that targets it, which informed engineering of a bacterial-phage hybrid lysin that can be transported across the outer membrane to kill specific Gram-negative bacteria. This work provides a template for engineering phage lysins against a wide variety of bacterial pathogens.

  1. Presentation

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    Paulo Henrique Freire Vieira

    2013-12-01

    Full Text Available This dossier focuses on one of the essential debate topics today about the territorial dimension of the new development strategies concerned with the worsening of the global socioecological crisis, that is: the challenges related to the activation and integration in networks of localized agri-food systems. For its composition, some contributions presented and debated during the VI International Conference on Localized Agri-food System - The LAFS facing the opportunities and challenges of the new global context have been gathered. The event took place in the city of Florianópolis, from May 21th to 25th of 2013. The event was promoted by the Federal University of Santa Catarina (UFSC and by the Center for the International Cooperation on Agricultural Research for Development (CIRAD. Besides UFSC and CIRAD, EPAGRI, State University of Santa Catarina (UDESC, as well as research institutes and universities from other states (UFMG, IEA/SP, UFS, UFRGS and Mexican and Argentinian partners from the RED SIAL Latino Americana also participated in the organization of lectures, discussion tables and workshops.

  2. Presentation

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    Eduardo Vicente

    2013-06-01

    Full Text Available In the present edition of Significação – Scientific Journal for Audiovisual Culture and in the others to follow something new is brought: the presence of thematic dossiers which are to be organized by invited scholars. The appointed subject for the very first one of them was Radio and the invited scholar, Eduardo Vicente, professor at the Graduate Course in Audiovisual and at the Postgraduate Program in Audiovisual Media and Processes of the School of Communication and Arts of the University of São Paulo (ECA-USP. Entitled Radio Beyond Borders the dossier gathers six articles and the intention of reuniting works on the perspectives of usage of such media as much as on the new possibilities of aesthetical experimenting being build up for it, especially considering the new digital technologies and technological convergences. It also intends to present works with original theoretical approach and original reflections able to reset the way we look at what is today already a centennial media. Having broadened the meaning of “beyond borders”, four foreign authors were invited to join the dossier. This is the first time they are being published in this country and so, in all cases, the articles where either written or translated into Portuguese.The dossier begins with “Radio is dead…Long live to the sound”, which is the transcription of a thought provoking lecture given by Armand Balsebre (Autonomous University of Barcelona – one of the most influential authors in the world on the Radio study field. It addresses the challenges such media is to face so that it can become “a new sound media, in the context of a new soundscape or sound-sphere, for the new listeners”. Andrew Dubber (Birmingham City University regarding the challenges posed by a Digital Era argues for a theoretical approach in radio studies which can consider a Media Ecology. The author understands the form and discourse of radio as a negotiation of affordances and

  3. Presentation

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    Helmut Renders

    2008-10-01

    Full Text Available We present to our esteemed readers the second edition of our journal for 2008. We have chosen the theme “The life and work of Prof. Dr. Jürgen Moltmann” as its special emphasis. It is our way to pay homage to J. Moltmann in the year the Universidade Metodista de São Paulo awards him an honorary Doctor Honoris Causa degree. Sincethe seventies, Moltmann and Latin America have been in dialog. In his emblematic work “A Theology of Liberation”, Gustavo Gutiérrez, the Catholic, discussed with Moltmann, the Reformed, the relationship between eschatology and history (GUTIÉRREZ, Gustavo.Teologia da Libertação. 5ª edição. Petrópolis, RJ: Vozes, 1985, p. 27, 137-139. A dialog held in the premises of IMS, which nowadays is called UMESP, has produced the little book “Passion for life” (MOLTMANN, Jürgen. Paixão pela vida. São Paulo, SP: ASTE - Associaçãode Seminários Teológicos Evangélicos, 1978.In the following years, the wide theological work of J. Moltmann went all the way from debates to congresses and has conquered the classrooms. Most probably, J. Moltmann is nowadays the most widely read European author in Brazilian theological seminaries. Thisrecognition can only be held in unison and the wide response to our request for articles confirms the huge repercussion that Moltmann’s work has been having up to today in Brazil. The ecumenical theologian J. Moltmann is ecumenically read. We believe that thisway we may be better equipped to answer to anyone who asks us for the reason there is hope in us. We have organized the articles on J. Moltmann’s theology according to the original publication date of the books dealt with in each essay. We also communicate that some articles which were originally requested for this edition of the journal will be published in the journal Estudos de Regilião in May 2009.As it is usual with the journal Caminhando, we have, besides this thematic emphasis, yet other contributions in the areas of

  4. Presentation

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    Nicanor Lopes

    2010-11-01

    Full Text Available The Journal Caminhando debuts with a new editorial format: eachmagazine will have a Dossier.In 2010 Christianity celebrated the centenary of Edinburgh. TheWorld Missionary Conference in Edinburgh in 1910 is regarded by manyas missiological watershed in the missionary and ecumenical movement.So the Faculty of Theology of the Methodist Church (FATEO decidedto organize a Wesleyan Week discussing the issue of mission. For anevent of this magnitude FATEO invited the Rev. Dr. Wesley Ariarajah,Methodist pastor and teacher of Sri Lanka with extensive experience inpastoral ministry in local churches and professor of History of Religionsand the New Testament at the Theological College of Lanka, maintainedby the Protestant Churches in Sri Lanka. In 1981 he was invited to jointhe World Council of Churches, where he presided for over ten years theCouncil of Interreligious Dialogue. From 1992 he served as Deputy GeneralSecretary of the WCC.The following texts are not the speeches of the Rev. Dr. WesleyAriarajah, for they will be published separately. Nevertheless, the journaldialogs with the celebrations of the centenary of Edinburgh, parting formthe intriguing theme: "Mission in the 21st century in Brazil". After all, howis it that mission takes place among us in personal, church, and communityactivities?Within the Dossier, as common to the journal, the textos are organizedas follows: Bible, Theology / History and Pastoral Care. Other items thatdo not fit within the Dossier, but, do articulate mission, can be found inthe section Declarations and Documents and Book Reviews.The authors of the Dossier have important considerations in buildinga contemporary missiological concept considering Brazilian reality.Anderson de Oliveira, in the Bible-Section, presents a significantexegeses of Matthew 26.6-13. What does it mean when Jesus is quotedwith the words: "For the poor always ye have with you, but me ye havenot always." Is this declaration challenging the gospels

  5. A de novo NADPH generation pathway for improving lysine production of Corynebacterium glutamicum by rational design of the coenzyme specificity of glyceraldehyde 3-phosphate dehydrogenase.

    Science.gov (United States)

    Bommareddy, Rajesh Reddy; Chen, Zhen; Rappert, Sugima; Zeng, An-Ping

    2014-09-01

    Engineering the cofactor availability is a common strategy of metabolic engineering to improve the production of many industrially important compounds. In this work, a de novo NADPH generation pathway is proposed by altering the coenzyme specificity of a native NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (GAPDH) to NADP, which consequently has the potential to produce additional NADPH in the glycolytic pathway. Specifically, the coenzyme specificity of GAPDH of Corynebacterium glutamicum is systematically manipulated by rational protein design and the effect of the manipulation for cellular metabolism and lysine production is evaluated. By a combinatorial modification of four key residues within the coenzyme binding sites, different GAPDH mutants with varied coenzyme specificity were constructed. While increasing the catalytic efficiency of GAPDH towards NADP enhanced lysine production in all of the tested mutants, the most significant improvement of lysine production (~60%) was achieved with the mutant showing similar preference towards both NAD and NADP. Metabolic flux analysis with (13)C isotope studies confirmed that there was no significant change of flux towards the pentose phosphate pathway and the increased lysine yield was mainly attributed to the NADPH generated by the mutated GAPDH. The present study highlights the importance of protein engineering as a key strategy in de novo pathway design and overproduction of desired products.

  6. Lysine Ubiquitination and Acetylation of Human Cardiac 20S Proteasomes

    Science.gov (United States)

    Lau, Edward; Choi, Howard JH; Ng, Dominic CM; Meyer, David; Fang, Caiyun; Li, Haomin; Wang, Ding; Zelaya, Ivette M; Yates, John R; Lam, Maggie PY

    2016-01-01

    Purpose Altered proteasome functions are associated with multiple cardiomyopathies. While the proteasome targets poly-ubiquitinated proteins for destruction, it itself is modifiable by ubiquitination. We aim to identify the exact ubiquitination sites on cardiac proteasomes and examine whether they are also subject to acetylations. Experimental design Assembled cardiac 20S proteasome complexes were purified from five human hearts with ischemic cardiomyopathy, then analyzed by high-resolution MS to identify ubiquitination and acetylation sites. We developed a library search strategy that may be used to complement database search in identifying PTM in different samples. Results We identified 63 ubiquitinated lysines from intact human cardiac 20S proteasomes. In parallel, 65 acetylated residues were also discovered, 39 of which shared with ubiquitination sites. Conclusion and clinical relevance This is the most comprehensive characterization of cardiac proteasome ubiquitination to-date. There are significant overlaps between the discovered ubiquitination and acetylation sites, permitting potential crosstalk in regulating proteasome functions. The information presented here will aid future therapeutic strategies aimed at regulating the functions of cardiac proteasomes. PMID:24957502

  7. Available lysine in canned fish

    OpenAIRE

    Rao, D. Ramananda; Gadre, Ujjwala V.

    1984-01-01

    Otolithus argenteus was canned in brine by heat processing at two different steam pressures either at 0.70 kg/cm super(2) or 1.05 kg/cm super(2) for 25 minutes. The nutritive value of canned fish as evaluated by the total nitrogen and available lysine did not alter much either during heat processing or during storage over a period of nine months at 28 degree plus or minus 5 degree C.

  8. BIOLOGICAL ADHESIVES. Adaptive synergy between catechol and lysine promotes wet adhesion by surface salt displacement.

    Science.gov (United States)

    Maier, Greg P; Rapp, Michael V; Waite, J Herbert; Israelachvili, Jacob N; Butler, Alison

    2015-08-01

    In physiological fluids and seawater, adhesion of synthetic polymers to solid surfaces is severely limited by high salt, pH, and hydration, yet these conditions have not deterred the evolution of effective adhesion by mussels. Mussel foot proteins provide insights about adhesive adaptations: Notably, the abundance and proximity of catecholic Dopa (3,4-dihydroxyphenylalanine) and lysine residues hint at a synergistic interplay in adhesion. Certain siderophores—bacterial iron chelators—consist of paired catechol and lysine functionalities, thereby providing a convenient experimental platform to explore molecular synergies in bioadhesion. These siderophores and synthetic analogs exhibit robust adhesion energies (E(ad) ≥-15 millijoules per square meter) to mica in saline pH 3.5 to 7.5 and resist oxidation. The adjacent catechol-lysine placement provides a "one-two punch," whereby lysine evicts hydrated cations from the mineral surface, allowing catechol binding to underlying oxides.

  9. Identification and characterization of lysine-methylated sites on histones and non-histone proteins.

    Science.gov (United States)

    Lee, Tzong-Yi; Chang, Cheng-Wei; Lu, Cheng-Tzung; Cheng, Tzu-Hsiu; Chang, Tzu-Hao

    2014-06-01

    Protein methylation is a kind of post-translational modification (PTM), and typically takes place on lysine and arginine amino acid residues. Protein methylation is involved in many important biological processes, and most recent studies focused on lysine methylation of histones due to its critical roles in regulating transcriptional repression and activation. Histones possess highly conserved sequences and are homologous in most species. However, there is much less sequence conservation among non-histone proteins. Therefore, mechanisms for identifying lysine-methylated sites may greatly differ between histones and non-histone proteins. Nevertheless, this point of view was not considered in previous studies. Here we constructed two support vector machine (SVM) models by using lysine-methylated data from histones and non-histone proteins for predictions of lysine-methylated sites. Numerous features, such as the amino acid composition (AAC) and accessible surface area (ASA), were used in the SVM models, and the predictive performance was evaluated using five-fold cross-validations. For histones, the predictive sensitivity was 85.62% and specificity was 80.32%. For non-histone proteins, the predictive sensitivity was 69.1% and specificity was 88.72%. Results showed that our model significantly improved the predictive accuracy of histones compared to previous approaches. In addition, features of the flanking region of lysine-methylated sites on histones and non-histone proteins were also characterized and are discussed. A gene ontology functional analysis of lysine-methylated proteins and correlations of lysine-methylated sites with other PTMs in histones were also analyzed in detail. Finally, a web server, MethyK, was constructed to identify lysine-methylated sites. MethK now is available at http://csb.cse.yzu.edu.tw/MethK/.

  10. Analysis of the organic matter which are present in solid organic wastes from urban areas; Analise da materia organica presente em residues organicos solidos de origem urbana

    Energy Technology Data Exchange (ETDEWEB)

    Canellas, Luciano Pasqualoto; Santos, Gabriel de Araujo; Amarai Sobrinho, Nelson Moura Brasil do; Mazur, Nelson [Universidade Federal Rural do Rio de Janeiro, RJ (Brazil). Dept. de Solos. E-mail: canellas@ufrrj.br; Moraes, Anselmo Alpande [Universidade Federal Rural do Rio de Janeiro, RJ (Brazil). Dept. de Quimica

    1997-07-01

    This study analyses the organic matter which are present in the solid wastes from the Rio de Janeiro city - Brazil. The humic acids were extracted and purified. After the purification, the humic acids were dried by lyophilization. Visible UV, infrared and NMR spectra were obtained for the humic acids extracted.

  11. Effect of bacteriophage lysin on lysogens

    Institute of Scientific and Technical Information of China (English)

    Balaji Subramanyam; Vanaja Kumar

    2011-01-01

    Objective: To study the effect of phage lysin on the growth of lysogens. Methods: Sputum specimens processed by modified Petroff's method were respectively treated with phagebiotics in combination with lysin and lysin alone. The specimens were incubated at 37℃ for 4 days. At the end of day 1, 2, 3 and day 4, the specimens were streaked on blood agar plates and incubated at 37℃ for 18-24 hours. The growth of normal flora observed after day 1 was considered as lysogens.Results:When specimens treated with lysin alone, lysogen formation was avoided and normal flora was controlled. Conclusions: Lysin may have no effect on the growth of lysogens. Sputum specimens treated with phagebiotics-lysin showed the growth of lysogens.

  12. Recognition and Survey the Productive Residues of the Curing Centers and Presenting the Management Methods. (The case study: the 7th zone of Karaj municipality

    Directory of Open Access Journals (Sweden)

    P. Gohari Mokammel

    2016-06-01

    Full Text Available The high risk of residues of curing centre and extensive use of them endangered all over the world. According to the reports of the world health organization (WHO 75-90% of productive residue of curing centre is usual kind and is out of danger and management of them is like the urban waste material. On the basis of this reports 10 to 25% (percent of the mentioned residues are placed in the group of dangerous residues, and it needs a precise and wise management program. The aim of this research in the first step is to recognize and survey the sources of productive hospital residues and in the next step physical analysis of them. Finally, by considering the taken results, the suitable management methods for the zone would be presentable. On the basis of the available statistics, the seventh zone of Karaj municipality has 174280 per population (89059 per men and 85221 per women.In this zone totally one hospital with 316 beds Approval and 278 beds are used, 14 clinic 35 Medical recognition laboratory 69 Drugstore and there are nine rehabilitate centre, the way of study is descriptive interruptive. In this research recognition of productive source of hospital residue taken and process, sampling, analyzing of the data and presenting appropriate management methods suitable with the zone. At last after the taken data analysis, the results are described as follows: The average of infectious and disinfections residue of Alborz hospital, clinics and medical recognition laboratory by order 55, 45 and 23 , 77 and 15.7, 84.3 percent are obtained. The average of plastic and paper in productive residues of Alborz hospital, drugstores and rehabilitate centre by order 43.8, 8.4 and17.2, 67.6 and 0.2, 20.3 percent are calculated. Daily economical benefit in the case of performing the recovery plan for the Alborz hospital, 69 drugstores and 9 health centre totally 1369355 Rials calculated, and of this rate plastic with 923211 Rials is placed on the first grade. The

  13. Hemoglobin Labeled by Radioactive Lysine

    Science.gov (United States)

    Bale, W. F.; Yuile, C. L.; DeLaVergne, L.; Miller, L. L.; Whipple, G. H.

    1949-12-08

    This paper reports on the utilization of tagged epsilon carbon of DL-lysine by a dog both anemic and hypoproteinemic due to repeated bleeding plus a diet low in protein. The experiment extended over period of 234 days, a time sufficient to indicate an erythrocyte life span of at least 115 days based upon the rate of replacement of labeled red cell proteins. The proteins of broken down red cells seem not to be used with any great preference for the synthesis of new hemoglobin.

  14. Autoacetylation of the MYST lysine acetyltransferase MOF protein.

    Science.gov (United States)

    Yang, Chao; Wu, Jiang; Sinha, Sarmistha H; Neveu, John M; Zheng, Yujun George

    2012-10-12

    The MYST family of histone acetyltransferases (HATs) plays critical roles in diverse cellular processes, such as the epigenetic regulation of gene expression. Lysine autoacetylation of the MYST HATs has recently received considerable attention. Nonetheless, the mechanism and function of the autoacetylation process are not well defined. To better understand the biochemical mechanism of MYST autoacetylation and the impact of autoacetylation on the cognate histone acetylation, we carried out detailed analyses of males-absent-on-the-first (MOF), a key member of the MYST family. A number of mutant MOF proteins were produced with point mutations at several key residues near the active site of the enzyme. Autoradiography and immunoblotting data showed that mutation of these residues affects the autoacetylation activity and HAT activity of MOF by various degrees demonstrating that MOF activity is highly sensitive to the chemical changes in those residues. We produced MOF protein in the deacetylated form by using a nonspecific lysine deacetylase. Interestingly, both the autoacetylation activity and the histone acetylation activity of the deacetylated MOF were found to be very close to that of wild-type MOF, suggesting that autoacetylation of MOF only marginally modulates the enzymatic activity. Also, we found that the autoacetylation rates of MOF and deacetylated MOF were much slower than the cognate substrate acetylation. Thus, autoacetylation does not seem to contribute to the intrinsic enzymatic activity in a significant manner. These data provide new insights into the mechanism and function of MYST HAT autoacetylation.

  15. Autoacetylation of the MYST Lysine Acetyltransferase MOF Protein*

    Science.gov (United States)

    Yang, Chao; Wu, Jiang; Sinha, Sarmistha H.; Neveu, John M.; Zheng, Yujun George

    2012-01-01

    The MYST family of histone acetyltransferases (HATs) plays critical roles in diverse cellular processes, such as the epigenetic regulation of gene expression. Lysine autoacetylation of the MYST HATs has recently received considerable attention. Nonetheless, the mechanism and function of the autoacetylation process are not well defined. To better understand the biochemical mechanism of MYST autoacetylation and the impact of autoacetylation on the cognate histone acetylation, we carried out detailed analyses of males-absent-on-the-first (MOF), a key member of the MYST family. A number of mutant MOF proteins were produced with point mutations at several key residues near the active site of the enzyme. Autoradiography and immunoblotting data showed that mutation of these residues affects the autoacetylation activity and HAT activity of MOF by various degrees demonstrating that MOF activity is highly sensitive to the chemical changes in those residues. We produced MOF protein in the deacetylated form by using a nonspecific lysine deacetylase. Interestingly, both the autoacetylation activity and the histone acetylation activity of the deacetylated MOF were found to be very close to that of wild-type MOF, suggesting that autoacetylation of MOF only marginally modulates the enzymatic activity. Also, we found that the autoacetylation rates of MOF and deacetylated MOF were much slower than the cognate substrate acetylation. Thus, autoacetylation does not seem to contribute to the intrinsic enzymatic activity in a significant manner. These data provide new insights into the mechanism and function of MYST HAT autoacetylation. PMID:22918831

  16. PENILAIAN PENGARUH PENAMBAHAN LYSINE PADA NASI

    Directory of Open Access Journals (Sweden)

    Ignatius Tarwotjo

    2012-11-01

    Full Text Available Pengaruh penambahan lysine pada mutu protein nasi dilakukan pada tikus putih dengan mengukur Protein Efficiency Ratio. Nasi dan Nasi dengan sayur beserta laukpauk, seperti dikonsumsi oleh kebanyakan keluarga di Indonesia, yang berasnya lebih dulu ditambahi butiran premix berisi lysine, thiamine dan riboflavin ternaya menghasilkan Protein Efficiency Ratio lebih tinggi dari pada yang tidak ditambahi.

  17. Structural Insights Into Amino Acid Binding and Gene Control by a Lysine Riboswitch

    Energy Technology Data Exchange (ETDEWEB)

    Serganov, A.; Huang, L; Patel, D

    2008-01-01

    In bacteria, the intracellular concentration of several amino acids is controlled by riboswitches1, 2, 3, 4. One of the important regulatory circuits involves lysine-specific riboswitches, which direct the biosynthesis and transport of lysine and precursors common for lysine and other amino acids. To understand the molecular basis of amino acid recognition by riboswitches, here we present the crystal structure of the 174-nucleotide sensing domain of the Thermotoga maritima lysine riboswitch in the lysine-bound (1.9 A) and free (3.1 A) states. The riboswitch features an unusual and intricate architecture, involving three-helical and two-helical bundles connected by a compact five-helical junction and stabilized by various long-range tertiary interactions. Lysine interacts with the junctional core of the riboswitch and is specifically recognized through shape-complementarity within the elongated binding pocket and through several direct and K+-mediated hydrogen bonds to its charged ends. Our structural and biochemical studies indicate preformation of the riboswitch scaffold and identify conformational changes associated with the formation of a stable lysine-bound state, which prevents alternative folding of the riboswitch and facilitates formation of downstream regulatory elements. We have also determined several structures of the riboswitch bound to different lysine analogues5, including antibiotics, in an effort to understand the ligand-binding capabilities of the lysine riboswitch and understand the nature of antibiotic resistance. Our results provide insights into a mechanism of lysine-riboswitch-dependent gene control at the molecular level, thereby contributing to continuing efforts at exploration of the pharmaceutical and biotechnological potential of riboswitches.

  18. 含砷废渣处理现状及对策%THE PRESENT SITUATION AND THE COUNTERMEASURE OF THE PROCESSING OF ARSENIC RESIDUES

    Institute of Scientific and Technical Information of China (English)

    徐建兵; 沈强华; 陈雯; 曹忠华

    2017-01-01

    伴随着优质矿逐渐被消耗,复杂含砷矿逐渐被开采出来,含砷废渣的产量不断增加,而砷及含砷化合物毒性很大,因此如何有效的处理含砷废渣使其无害化变得非常迫切.介绍了砷的危害,含砷废渣的来源,综述了含砷废渣处理方法的现状及存在的问题.目前,处理含砷废渣的方法主要有硫酸铜置换法、硫酸铁法和碱浸法等资源化处理,以及水泥固化、钙盐稳定化等固化稳定化处理.但这些方法都存在相应的不足,为了能有效地解决含砷废渣的问题,提出了合成臭葱石固化砷是处理含砷废渣的对策.%With the gradual depletion of high quality ore,comnplicated ore containing arsenic was gradually being mined,and the production of arsenic residues increased continuously.As the toxicity of arsenic and arsenic compounds are quite strong,so how to effectively deal with arsenic residues to make it harmless become very urgent.The detriment of arsenic and the origin of arsenic-containing wastes are introduced,the present situation and existing problems of the processing is reviewed.Currently,major treatment methods for the resource utilization of arsenic residues include copper sulfate cementation process,ferric sulfate leaching process,alkali leaching process etc.and the solidification-stabilization of arsenic residues include cement solidification process,calcium salt stabilization process etc.But all these methods have their respective shortcomings.In order to effectively solve the problem of arsenic residues,a process of stabilizing arsenic by synthesizing scorodite is proposed as the countermeasure for treatment of arsenic residues.

  19. Engineering a Lysine-ON Riboswitch for Metabolic Control of Lysine Production in Corynebacterium glutamicum.

    Science.gov (United States)

    Zhou, Li-Bang; Zeng, An-Ping

    2015-12-18

    Riboswitches are natural RNA elements that regulate gene expression by binding a ligand. Here, we demonstrate the possibility of altering a natural lysine-OFF riboswitch from Eschericia coli (ECRS) to a synthetic lysine-ON riboswitch and using it for metabolic control. To this end, a lysine-ON riboswitch library was constructed using tetA-based dual genetic selection. After screening the library, the functionality of the selected lysine-ON riboswitches was examined using a report gene, lacZ. Selected lysine-ON riboswitches were introduced into the lysE gene (encoding a lysine transport protein) of Corynebacterium glutamicum and used to achieve dynamic control of lysine transport in a recombinant lysine-producing strain, C. glutamicum LPECRS, which bears a deregulated aspartokinase and a lysine-OFF riboswitch for dynamic control of the enzyme citrate synthase. Batch fermentation results of the strains showed that the C. glutamicum LPECRS strain with an additional lysine-ON riboswitch for the control of lysE achieved a 21% increase in the yield of lysine compared to that of the C. glutamicum LPECRS strain and even a 89% increase in yield compared to that of the strain with deregulated aspartokinase. This work provides a useful approach to generate lysine-ON riboswitches for C. glutamicum metabolic engineering and demonstrates for the first time a synergetic effect of lysine-ON and -OFF riboswitches for improving lysine production in this industrially important microorganism. The approach can be used to dynamically control other genes and can be applied to other microorganisms.

  20. The biology of lysine acetylation integrates transcriptional programming and metabolism

    Directory of Open Access Journals (Sweden)

    Mujtaba Shiraz

    2011-03-01

    Full Text Available Abstract The biochemical landscape of lysine acetylation has expanded from a small number of proteins in the nucleus to a multitude of proteins in the cytoplasm. Since the first report confirming acetylation of the tumor suppressor protein p53 by a lysine acetyltransferase (KAT, there has been a surge in the identification of new, non-histone targets of KATs. Added to the known substrates of KATs are metabolic enzymes, cytoskeletal proteins, molecular chaperones, ribosomal proteins and nuclear import factors. Emerging studies demonstrate that no fewer than 2000 proteins in any particular cell type may undergo lysine acetylation. As described in this review, our analyses of cellular acetylated proteins using DAVID 6.7 bioinformatics resources have facilitated organization of acetylated proteins into functional clusters integral to cell signaling, the stress response, proteolysis, apoptosis, metabolism, and neuronal development. In addition, these clusters also depict association of acetylated proteins with human diseases. These findings not only support lysine acetylation as a widespread cellular phenomenon, but also impel questions to clarify the underlying molecular and cellular mechanisms governing target selectivity by KATs. Present challenges are to understand the molecular basis for the overlapping roles of KAT-containing co-activators, to differentiate between global versus dynamic acetylation marks, and to elucidate the physiological roles of acetylated proteins in biochemical pathways. In addition to discussing the cellular 'acetylome', a focus of this work is to present the widespread and dynamic nature of lysine acetylation and highlight the nexus that exists between epigenetic-directed transcriptional regulation and metabolism.

  1. IDENTIFICATION OF ACTIVE SITE RESIDUES IN DEXTRANSUCRASE FROM Weissella cibaria JAG8

    Directory of Open Access Journals (Sweden)

    Tingirikari Jagan Mohan Rao

    2013-12-01

    Full Text Available Dextransucrase isolated from Weissella cibaria JAG8 was subjected to chemical modification by bifunctional inhibitor o-phthalaldehyde to know the involvement of lysine and cysteine residues in its activity. The enzyme lost 97% of its activity in presence of 10 mM o-phthalaldehyde. The enzyme inhibitor complex gave absorbance maxima at 334 nm and fluorescence emission maxima at 418 nm, which confirmed the isoindole derivative formation. Sucrose protected the enzyme against o-phthalaldehyde inactivation. Denaturation with urea decreased the fluorescence emission showing that the native form of enzyme is essential for isoindole formation. Dextransucrase pre-treated with pyridoxal-5’-phosphate followed by o-phthalaldehyde treatment showed an increase in fluorescence intensity at 418 nm after dialysis, when compared with fluorescence intensity before dialysis, indicated that both the inhibitors bind to same lysine residues present at (or near the active site of enzyme. The results showed that both lysine and cysteine are the key amino acid residues which are present at the active site and are essential for dextransucrase activity.

  2. Site-Specific Conjugation to Native and Engineered Lysines in Human Immunoglobulins by Microbial Transglutaminase.

    Science.gov (United States)

    Spidel, Jared L; Vaessen, Benjamin; Albone, Earl F; Cheng, Xin; Verdi, Arielle; Kline, J Bradford

    2017-09-20

    The use of microbial transglutaminase (MTG) to produce site-specific antibody-drug conjugates (ADCs) has thus far focused on the transamidation of engineered acyl donor glutamine residues in an antibody based on the hypothesis that the lower specificity of MTG for acyl acceptor lysines may result in the transamidation of multiple native lysine residues, thereby yielding heterogeneous products. We investigated the utilization of native IgG lysines as acyl acceptor sites for glutamine-based acyl donor substrates. Of the approximately 80 lysines in multiple recombinant IgG monoclonal antibodies (mAbs), none were transamidated. Because recombinant mAbs lack the C-terminal Lys447 due to cleavage by carboxypeptidase B in the production cell host, we explored whether blocking the cleavage of Lys447 by the addition of a C-terminal amino acid could result in transamidation of Lys447 by a variety of acyl donor substrates. MTG efficiently transamidated Lys447 in the presence of any nonacidic, nonproline amino acid residue at position 448. Lysine scanning mutagenesis throughout the antibody further revealed several transamidation sites in both the heavy- and light-chain constant regions. Additionally, scanning mutagenesis of the hinge region in a Fab' fragment revealed sites of transamidation that were not reactive in the context of the full-length mAb. Here, we demonstrate the utility of single lysine substitutions and the C-terminal Lys447 for engineering efficient acyl acceptor sites suitable for site-specific conjugation to a range of glutamine-based acyl donor substrates.

  3. Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli

    DEFF Research Database (Denmark)

    Weinert, Brian T; Iesmantavicius, Vytautas; Wagner, Sebastian A

    2013-01-01

    Lysine acetylation is a frequently occurring posttranslational modification in bacteria; however, little is known about its origin and regulation. Using the model bacterium Escherichia coli (E. coli), we found that most acetylation occurred at a low level and accumulated in growth-arrested cells...... acetylate lysine residues in vitro and that AcP levels are correlated with acetylation levels in vivo, suggesting that AcP may acetylate proteins nonenzymatically in cells. These results uncover a critical role for AcP in bacterial acetylation and indicate that most acetylation in E. coli occurs at a low...

  4. Enhanced Amelioration of High-Fat Diet-Induced Fatty Liver by Docosahexaenoic Acid and Lysine Supplementations

    Directory of Open Access Journals (Sweden)

    Hsin-Yu Lin

    2014-01-01

    Full Text Available Fatty liver disease is the most common pathological condition in the liver. Here, we generated high-fat diet-(HFD- induced nonalcoholic fatty liver disease (NAFLD in mice and tested the effects of docosahexaenoic acid (DHA and lysine during a four-week regular chow (RCfeeding. Our results showed that 1% lysine and the combination of 1% lysine + 1% DHA reduced body weight. Moreover, serum triglyceride levels were reduced by 1% DHA and 1% lysine, whereas serum alanine transaminase activity was reduced by 1% DHA and 1% DHA + 0.5% lysine. Switching to RC reduced hepatic lipid droplet accumulation, which was further reduced by the addition of DHA or lysine. Furthermore, the mRNA expressions of hepatic proinflammatory cytokines were suppressed by DHA and combinations of DHA + lysine, whereas the mRNA for the lipogenic gene, acetyl-CoA carboxylase 1 (ACC1, was suppressed by DHA. In the gonadal adipose tissues, combinations of DHA and lysine inhibited mRNA expression of lipid metabolism-associated genes, including ACC1, fatty acid synthase, lipoprotein lipase, and perilipin. In conclusion, the present study demonstrated that, in conjunction with RC-induced benefits, supplementation with DHA or lysine further ameliorated the high-fat diet-induced NAFLD and provided an alternative strategy to treat, and potentially prevent, NAFLD.

  5. A novel amperometric biosensor based on a co-crosslinked L-lysine-α-oxidase/overoxidized polypyrrole bilayer for the highly selective determination of L-lysine.

    Science.gov (United States)

    Guerrieri, Antonio; Ciriello, Rosanna; Cataldi, Tommaso R I

    2013-09-17

    An amperometric biosensor for the determination of L-lysine based on L-lysine-α-oxidase immobilized by co-crosslinking on a platinum electrode previously modified by an overoxidized polypyrrole film is described. The optimization of experimental parameters, such as pH and flow rate, permitted to minimize significantly substrate interferences even using a low specific, commercial enzyme. The relevant biases introduced in the measurement of lysine were just about 1% for L-arginine, L-histidine and L-ornithine, roughly 4% for L-phenylalanine and L-tyrosine. The developed approach allowed linear lysine responses from 0.02 mM up to 2 mM with a sensitivity of 41 nA/(mM × mm(2)) and a detection limit of 4 μM (S/N=3). No appreciable loss in lysine sensitivity was observed up to about 40 days. Allowing polypyrrole layer to remove interference from electroactive compounds, the present method revealed suitable to detect L-lysine in a pharmaceutical and cheese sample, showing a good agreement with the expected values. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Residual thymic tissue and lymph node involvement by acute myeloid leukaemia presenting as mediastinal, strongly (18) FDG-PET-positive masses.

    Science.gov (United States)

    Maschmeyer, Georg; Brink, Ingo; Jähne, Doris; Arnold, Renate; Schega, Olaf

    2017-09-01

    We report on a multidisciplinary management of a 68-year-old AML patient presenting with a PET-positive mediastinal tumour typical for lymph node metastasis. It was removed via minimally invasive thoracoscopic intervention and was identified as a thymus residual infiltrated by AML. Follow-up PET-CT scan after resection and remission induction chemotherapy was completely normal. To our knowledge, this is the first documented case report of AML presenting with PET-positive infiltrates of thymic and lymph node tissue along the aortic bow mimicking a second intrathoracic malignancy. Our observation indicates the usefulness of this imaging technique and supports clarification of these unusual findings in AML patients, in case of need also by invasive diagnostic procedures, to enable an adequate therapeutic decision. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  7. SPOTing Acetyl-Lysine Dependent Interactions

    Directory of Open Access Journals (Sweden)

    Sarah Picaud

    2015-08-01

    Full Text Available Post translational modifications have been recognized as chemical signals that create docking sites for evolutionary conserved effector modules, allowing for signal integration within large networks of interactions. Lysine acetylation in particular has attracted attention as a regulatory modification, affecting chromatin structure and linking to transcriptional activation. Advances in peptide array technologies have facilitated the study of acetyl-lysine-containing linear motifs interacting with the evolutionary conserved bromodomain module, which specifically recognizes and binds to acetylated sequences in histones and other proteins. Here we summarize recent work employing SPOT peptide technology to identify acetyl-lysine dependent interactions and document the protocols adapted in our lab, as well as our efforts to characterize such bromodomain-histone interactions. Our results highlight the versatility of SPOT methods and establish an affordable tool for rapid access to potential protein/modified-peptide interactions involving lysine acetylation.

  8. Oligo(L-lysine)-induced titanium dioxide: Effects of consecutive lysine on precipitation

    Science.gov (United States)

    Ahn, Sungjun; Park, Sangwoo; Lee, Sang-Yup

    2011-11-01

    Biomineralization of metal oxide utilizes biomolecular substances, such as peptides and proteins, to induce mineralization of metal precursors in a mild aqueous solution. In this study, we investigated biomineralization of an abiological substance, titanium dioxide (TiO 2), by oligo(L-lysine). Specifically, we systemically studied the influence of the number of consecutive lysine on TiO 2 precipitation. Oligo(L-lysine) was chosen as a homopeptide lysine source whose lysine quantity was adjusted. When oligo(L-lysine) contains more than three consecutive lysine, it induces notably fast precipitation, while single and dilysine do not readily form TiO 2 precipitates. Precipitation of TiO 2 was promoted with the length of oligo(L-lysine). The oligo(L-lysine) was associated with TiO 2 precipitate, which was confirmed by spectroscopic and thermogravitational analyses. The outcomes of this research provide a plausible rationale for explaining precipitation of the Ti precursor that is highly dependent on peptide sequences.

  9. Lysine requirement of growing male Pekin ducks.

    Science.gov (United States)

    Bons, A; Timmler, R; Jeroch, H

    2002-12-01

    1. One growth experiment and one balance test were conducted to study the response to increasing levels of dietary lysine supplementation in male Pekin ducks with special reference to the growth periods from 1 to 3 weeks and 4 to 7 weeks of age. 2. Two different low-lysine diets were used as basal diets in both periods. The basal lysine levels were 7.6 g/kg (d 1 to 21) and 6.2 g/kg (d 22 to 49) and the ranges in lysine concentration were 7.6 to 12.6 g/kg (d 1 to 21) and 6.2 to 11.2 g/kg (d 22 to 49). 3. Growth performance, feed conversion efficiency and meat yield increased (P < 0.05) with increasing lysine concentration (requirement defined as 95% of the asymptote). 4. It is concluded that the dietary lysine concentration should be 0.93 g/MJ nitrogen corrected apparent metabolisable energy (AMEN) (11.7 g/kg) for the starter period (until d 21) and 0.75 g/MJ AMEN (10.0 g/kg) for the grower period (from d 22 onwards).

  10. Antibacterial activity of a newly developed peptide-modified lysin against Acinetobacter baumannii and Pseudomonas aeruginosa

    Directory of Open Access Journals (Sweden)

    Hang eYang

    2015-12-01

    Full Text Available The global emergence of multidrug-resistant (MDR bacteria is a growing threat to public health worldwide. Natural bacteriophage lysins are promising alternatives in the treatment of infections caused by Gram-positive pathogens, but not Gram-negative ones, like Acinetobacter baumannii and Pseudomonas aeruginosa, due to the barriers posed by their outer membranes. Recently, modifying a natural lysin with an antimicrobial peptide was found able to break the barriers, and to kill Gram-negative pathogens. Herein, a new peptide-modified lysin (PlyA was constructed by fusing the cecropin A peptide residues 1–8 (KWKLFKKI with the OBPgp279 lysin and its antibacterial activity was studied. PlyA showed good and broad antibacterial activities against logarithmic phase A. baumannii and P. aeruginosa, but much reduced activities against the cells in stationary phase. Addition of outer membrane permeabilizers (EDTA and citric acid could enhance the antibacterial activity of PlyA against stationary phase cells. Finally, no antibacterial activity of PlyA could be observed in some bio-matrices, such as culture media, milk, and sera. In conclusion, we reported here a novel peptide-modified lysin with significant antibacterial activity against both logarithmic (without OMPs and stationary phase (with OMPs A. baumannii and P. aeruginosa cells in buffer, but further optimization is needed to achieve broad activity in diverse bio-matrices.

  11. Determination of activity by gamma spectrometry of radionuclides present in drums of residues generated in nuclear centrals; Determinacion de actividad por espectrometria gamma de radionucleidos presentes en tambores de residuos generados en centrales nucleares

    Energy Technology Data Exchange (ETDEWEB)

    Aguiar, J.C.; Fernandez, J. [Autoridad Regulatoria Nuclear, Av. Del Libertador 8250, Ciudad Autonoma de Buenos Aires (Argentina)]. e-mail: jaguiar@cae.arn.gov.ar

    2006-07-01

    The generation of radioactive residuals in nuclear centrals as CNA I (Atucha I Nuclear Central) and CNE (Embalse Nuclear Central) makes that the measurement of those radionuclides has been a previous stage to the waste management. A method used in those nuclear centrals it is the gamma spectrometry with HPGe detectors, previous to the immobilization of the residual in a cemented matrix, with this the contact with the external agents and its possible dispersion to the atmosphere in the short term is avoided. The ARN (Nuclear Regulatory Authority) of Argentina it carries out periodically intercomparisons and evaluations of the measurement and procedures systems used in the nuclear power stations for the correct measurement and determination of activity of radioactive residuals by gamma spectrometry. In this work an independent method of measurement is exposed to the nuclear power stations. To determine the activity of the residuals by gamma spectrometry deposited in drums, it is required of the precise knowledge of the efficiency curve for such geometry and matrix. Due to the RNA doesn't have a pattern of these characteristics, a mathematical model has been used to obtain this efficiency curve. For it, it is necessary to determine previously: 1) the geometric efficiency or solid angle sustained by the source-detector system (drum-detector) applying a mathematical model described in this work. 2) To estimate the auto-attenuation factor that present the photons in the cemented matrix, these calculations are carried out with a simple equation and its are verified with the Micro Shield 6.10 program. The container commonly used by these nuclear power stations its are drums for 220 liters constructed with SAE 1010 steel and with a thickness of 0.127 cm, with an approximate weight 7.73 Kg., internal diameter of 57.1 cm, and height: 87 cm. The results obtained until the moment register a discrepancy from 5 to 10% with relationship to the measurements carried out by the

  12. Differences in lysine pKa values may be used to improve NMR signal dispersion in reductively methylated proteins

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, Sherwin J. [University of Illinois at Chicago, Department of Biochemistry and Molecular Genetics (United States); Kobayashi, Tomoyoshi; John Solaro, R. [University of Illinois at Chicago, Department of Physiology and Biophysics, Center for Cardiovascular Research (United States); Gaponenko, Vadim [University of Illinois at Chicago, Department of Biochemistry and Molecular Genetics (United States)], E-mail: vadimg@uic.edu

    2009-04-15

    Reductive methylation of lysine residues in proteins offers a way to introduce {sup 13}C methyl groups into otherwise unlabeled molecules. The {sup 13}C methyl groups on lysines possess favorable relaxation properties that allow highly sensitive NMR signal detection. One of the major limitations in the use of reductive methylation in NMR is the signal overlap of {sup 13}C methyl groups in NMR spectra. Here we show that the uniform influence of the solvent on chemical shifts of exposed lysine methyl groups could be overcome by adjusting the pH of the buffering solution closer to the pKa of lysine side chains. Under these conditions, due to variable pKa values of individual lysine side chains in the protein of interest different levels of lysine protonation are observed. These differences are reflected in the chemical shift differences of methyl groups in reductively methylated lysines. We show that this approach is successful in four different proteins including Ca{sup 2+}-bound Calmodulin, Lysozyme, Ca{sup 2+}-bound Troponin C, and Glutathione S-Transferase. In all cases significant improvement in NMR spectral resolution of methyl signals in reductively methylated proteins was obtained. The increased spectral resolution helps with more precise characterization of protein structural rearrangements caused by ligand binding as shown by studying binding of Calmodulin antagonist trifluoperazine to Calmodulin. Thus, this approach may be used to increase resolution in NMR spectra of {sup 13}C methyl groups on lysine residues in reductively methylated proteins that enhances the accuracy of protein structural assessment.

  13. Structure and Histone Binding Properties of the Vps75-Rtt109 Chaperone-Lysine Acetyltransferase Complex

    Energy Technology Data Exchange (ETDEWEB)

    Su, Dan; Hu, Qi; Zhou, Hui; Thompson, James R.; Xu, Rui-Ming; Zhang, Zhiguo; Mer, Georges (Mayo); (Chinese Aca. Sci.)

    2011-11-02

    The histone chaperone Vps75 presents the remarkable property of stimulating the Rtt109-dependent acetylation of several histone H3 lysine residues within (H3-H4){sub 2} tetramers. To investigate this activation mechanism, we determined x-ray structures of full-length Vps75 in complex with full-length Rtt109 in two crystal forms. Both structures show similar asymmetric assemblies of a Vps75 dimer bound to an Rtt109 monomer. In the Vps75-Rtt109 complexes, the catalytic site of Rtt109 is confined to an enclosed space that can accommodate the N-terminal tail of histone H3 in (H3-H4){sub 2}. Investigation of Vps75-Rtt109-(H3-H4)2 and Vps75-(H3-H4)2 complexes by NMR spectroscopy-probed hydrogen/deuterium exchange suggests that Vps75 guides histone H3 in the catalytic enclosure. These findings clarify the basis for the enhanced acetylation of histone H3 tail residues by Vps75-Rtt109.

  14. Lysine-Rich Proteins in High-Lysine Hordeum Vulgare Grain

    DEFF Research Database (Denmark)

    Ingversen, J.; Køie, B.

    1973-01-01

    The salt-soluble proteins in barley grain selected for high-lysine content (Hiproly, CI 7115 and the mutants 29 and 86) and of a control (Carlsberg II) with normal lysine content, contain identical major proteins as determined by MW and electrophoretic mobility. The concentration of a protein group...

  15. Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs.

    Science.gov (United States)

    Fischle, Wolfgang; Franz, Henriette; Jacobs, Steven A; Allis, C David; Khorasanizadeh, Sepideh

    2008-07-11

    Previous studies have shown two homologous chromodomain modules in the HP1 and Polycomb proteins exhibit discriminatory binding to related methyllysine residues (embedded in ARKS motifs) of the histone H3 tail. Methylated ARK(S/T) motifs have recently been identified in other chromatin factors (e.g. linker histone H1.4 and lysine methyltransferase G9a). These are thought to function as peripheral docking sites for the HP1 chromodomain. In vertebrates, HP1-like chromodomains are also present in the chromodomain Y chromosome (CDY) family of proteins adjacent to a putative catalytic motif. The human genome encodes three CDY family proteins, CDY, CDYL, and CDYL2. These have putative functions ranging from establishment of histone H4 acetylation during spermiogenesis to regulation of transcription co-repressor complexes. To delineate the biochemical functions of the CDY family chromodomains, we analyzed their specificity of methyllysine recognition. We detected substantial differences among these factors. The CDY chromodomain exhibits discriminatory binding to lysine-methylated ARK(S/T) motifs, whereas the CDYL2 chromodomain binds with comparable strength to multiple ARK(S/T) motifs. Interestingly, subtle amino acid changes in the CDYL chromodomain prohibit such binding interactions in vitro and in vivo. However, point mutations can rescue binding. In support of the in vitro binding properties of the chromodomains, the full-length CDY family proteins exhibit substantial variability in chromatin localization. Our studies underscore the significance of subtle sequence differences in a conserved signaling module for diverse epigenetic regulatory pathways.

  16. Present Study and Prospect of Friction Stir Welding Residual Stress%搅拌摩擦焊残余应力研究现状及展望

    Institute of Scientific and Technical Information of China (English)

    牛鹏亮; 李文亚

    2015-01-01

    搅拌摩擦焊是一种新型的固相焊接技术,目前国内外的研究主要集中在工艺、组织、力学性能等方面,而有关搅拌摩擦焊缝内部残余应力的研究相对较少。由于检测设备的限制,国内主要采用有损检测方法,无损检测方法却很少。详细综述了国内有关搅拌摩擦焊件内部残余应力测试的钻孔法、云纹干涉法,以及国内外无损检测方法中的X射线衍射法、中子衍射法和高能同步辐射法的研究概况,讨论了各种检测方法的优缺点,对未来搅拌摩擦焊残余应力的研究作了展望。%Friction stir welding is a new solid-state welding technology. At present, studies of domestic and overseas focus on processes, microstructure and mechanical properties. Studies on the initial residual stress of friction stir welding are relative fewer. Because of the limited testing equipment, the destructive tests are usually adopted by domestic research-ers, but the non-destructive tests are so fewer. The destructive, such as hole-drilling and moire interferometry, and non-destructive tests, such as X-ray diffraction, neutron diffraction and synchrotron radiation, are summarized in detail. Mean-while, the advantages and disadvantages of the detection methods are discussed and a prospection for the study of friction stir welding residual stress is made.

  17. Evaluation of dose due to the liberation of the radioactive content present in systems of final disposal of radioactive residues; Evaluacion de la dosis debida a la liberacion del contenido radiactivo presente en sistemas de disposicion final de residuos radiactivos

    Energy Technology Data Exchange (ETDEWEB)

    Amado, V.; Lopez, F. [Autoridad Regulatoria Nuclear, Av. Del Libertador 8250, Ciudad Autonoma de Buenos Aires (C1429BNP) (Argentina)]. e-mail: vamado@cae.arn.gov.ar

    2006-07-01

    The disposal systems of radioactive residuals well-known as repositories near to the surface, are used to dispose residuals that can contain high concentrations of radionuclides of period of short semi disintegration, which they would decay at levels radiologically insignificant in some few decades or in some centuries: and acceptably low concentrations of radionuclides of period of long semi disintegration. The dose that would receive the critic group due to these systems it could be increased by cause of discreet events that affect the foreseen retard time, or by the gradual degradation of the barriers. To this last case it contributes the presence of water, because it implies leaching and dissolution that can give place to radionuclide concentrations in the underground water greater to the prospective ones. The dosimetric evaluation is important because it offers useful objective information to decide if a given repository is adjusted to the purposes of its design and it fulfills the regulatory requirements. In this work a simplified evaluation of the dose that would receive the critic group due to the liberation of contained radionuclides in a hypothetical system of final disposition of radioactive residuals is presented. For it, they are considered representative values of the usually contained activities in this type of systems and they are carried out some approaches of the source term. The study is developed in two stages. In the first one, by means of the Radionuclide pollutant scattering pattern in phreatic aquifers (DRAF) it is considered the scattering of the pollutants in the phreatic aquifer, until the discharge point in the course of the nearest surface water. This model, developed originally in the regulatory branch of the National Commission of Argentine Atomic Energy (CNEA); it solves the transport equation of solutes in porous means in three dimensions, by the finite differences method having in account the soil retention and the radioactive

  18. Snorkeling of lysine side chains in transmembrane helices: how easy can it get?

    Science.gov (United States)

    Strandberg, Erik; Killian, J Antoinette

    2003-06-05

    Transmembrane segments of proteins are often flanked by lysine residues. The side chains of these residues may snorkel, i.e. they may bury themselves with their aliphatic part in the hydrophobic region of the lipid bilayer, while positioning the charged amino group in the more polar interface. Here we estimate the free energy cost of snorkeling from thermodynamical calculations based on studies with synthetic transmembrane peptides [Strandberg et al. (2002) Biochemistry 41, 7190-7198]. The value is estimated to be between 0.07 and 0.7 kcal mol(-1) for a lysine side chain. This very low value indicates that snorkeling may be a common process, which should be taken into consideration both in experimental and in theoretical studies on protein-lipid interactions.

  19. Transporte no solo de solutos presentes na água residuária de café conilon = Soil transportedsolutes found in conilon coffee wastewater

    Directory of Open Access Journals (Sweden)

    Paulo Afonso Ferreira

    2006-01-01

    Full Text Available Neste estudo, determinaramse em colunas de solos os fatores de retardamento, coeficientes dispersivodifusivos e curvas de efluente, assim como a concentração residente dos íons potássio, sódio, cálcio e magnésio presentes na água residuária da lavagem e despolpa de frutos do cafeeiro conilon. Inicialmente, as colunas foram interligadas a frascos de Mariotte contendo água destilada, durante período suficiente para passar dois volumes de poros e, em seguida, a frascos contendo a água residuária. As concentrações relativas das amostras oriundas do efluente, correspondentes aos respectivos volumes de poros, foram utilizadas a fim de obter as curvas experimentais de efluente para sódio, potássio, cálcio e magnésio. Modelos matemáticos para concentração no fluxo foram ajustados aos pontos amostrais das curvas de efluente, permitindo, assim, obter os valores dos fatores de retardamento e coeficientes dispersivodifusivospara os íons. Para o latossolo, os fatores de retardamento foram superiores àqueles encontrados para o aluvial e argissolo. Por outro lado, os coeficientes dispersivodifusivos não apresentaram tendência entre os três solos. As concentrações residentes dos solutos apresentaram a ordem de grandeza: aluvialThis study was carried out to determine the retardation factors, diffusivedispersive coefficients and effluent curves, as well as the resident concentration of potassium, sodium, calcium and magnesium ions found in the wastewater from washing and pulping of the conilon coffee cherries. Initially, the columns were interlinked to Mariotte flasks containing distilled water, over period enough to pass two pore volumes of the soil, and then being linked to flasks containing this wastewater. The relative concentrations of the samples from the effluent, corresponding to the respective pore volumes, were used in order to obtain the experimental effluent curves for sodium, potassium, calcium and magnesium. Mathematical

  20. Lysine methylation regulates the pRb tumour suppressor protein.

    Science.gov (United States)

    Munro, S; Khaire, N; Inche, A; Carr, S; La Thangue, N B

    2010-04-22

    The pRb tumour suppressor protein has a central role in coordinating early cell cycle progression. An important level of control imposed on pRb occurs through post-translational modification, for example, phosphorylation. We describe here a new level of regulation on pRb, mediated through the targeted methylation of lysine residues, by the methyltransferase Set7/9. Set7/9 methylates the C-terminal region of pRb, both in vitro and in cells, and methylated pRb interacts with heterochromatin protein HP1. pRb methylation is required for pRb-dependent cell cycle arrest and transcriptional repression, as well as pRb-dependent differentiation. Our results indicate that methylation can influence the properties of pRb, and raise the interesting possibility that methylation modulates pRb tumour suppressor activity.

  1. A mechanism-based potent sirtuin inhibitor containing Nε-thiocarbamoyl-lysine (TuAcK)

    OpenAIRE

    2011-01-01

    In the current study, we have identified Nε-thiocarbamoyl-lysine (TuAcK) as a general sirtuin inhibitory warhead which was shown to be able to confer potent sirtuin inhibition. This inhibition was also shown to be mechanism-based in that the TuAck residue was able to be processed by a sirtuin enzyme with the formation of a stalled S-alkylamidate intermediate.

  2. SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

    Energy Technology Data Exchange (ETDEWEB)

    Del Rizzo, Paul A.; Couture, Jean-François; Dirk, Lynnette M.A.; Strunk, Bethany S.; Roiko, Marijo S.; Brunzelle, Joseph S.; Houtz, Robert L.; Trievel, Raymond C. (Michigan); (NWU); (Kentucky)

    2010-11-15

    SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine {epsilon}-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine {epsilon}-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated {epsilon}-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes.

  3. A study on the effect of surface lysine to arginine mutagenesis on protein stability and structure using green fluorescent protein.

    Directory of Open Access Journals (Sweden)

    Sriram Sokalingam

    Full Text Available Two positively charged basic amino acids, arginine and lysine, are mostly exposed to protein surface, and play important roles in protein stability by forming electrostatic interactions. In particular, the guanidinium group of arginine allows interactions in three possible directions, which enables arginine to form a larger number of electrostatic interactions compared to lysine. The higher pKa of the basic residue in arginine may also generate more stable ionic interactions than lysine. This paper reports an investigation whether the advantageous properties of arginine over lysine can be utilized to enhance protein stability. A variant of green fluorescent protein (GFP was created by mutating the maximum possible number of lysine residues on the surface to arginines while retaining the activity. When the stability of the variant was examined under a range of denaturing conditions, the variant was relatively more stable compared to control GFP in the presence of chemical denaturants such as urea, alkaline pH and ionic detergents, but the thermal stability of the protein was not changed. The modeled structure of the variant indicated putative new salt bridges and hydrogen bond interactions that help improve the rigidity of the protein against different chemical denaturants. Structural analyses of the electrostatic interactions also confirmed that the geometric properties of the guanidinium group in arginine had such effects. On the other hand, the altered electrostatic interactions induced by the mutagenesis of surface lysines to arginines adversely affected protein folding, which decreased the productivity of the functional form of the variant. These results suggest that the surface lysine mutagenesis to arginines can be considered one of the parameters in protein stability engineering.

  4. Efficient Production of Enantiopure d-Lysine from l-Lysine by a Two-Enzyme Cascade System

    Directory of Open Access Journals (Sweden)

    Xin Wang

    2016-10-01

    Full Text Available The microbial production of d-lysine has been of great interest as a medicinal raw material. Here, a two-step process for d-lysine production from l-lysine by the successive microbial racemization and asymmetric degradation with lysine racemase and decarboxylase was developed. The whole-cell activities of engineered Escherichia coli expressing racemases from the strains Proteus mirabilis (LYR and Lactobacillus paracasei (AAR were first investigated comparatively. When the strain BL21-LYR with higher racemization activity was employed, l-lysine was rapidly racemized to give dl-lysine, and the d-lysine yield was approximately 48% after 0.5 h. Next, l-lysine was selectively catabolized to generate cadaverine by lysine decarboxylase. The comparative analysis of the decarboxylation activities of resting whole cells, permeabilized cells, and crude enzyme revealed that the crude enzyme was the best biocatalyst for enantiopure d-lysine production. The reaction temperature, pH, metal ion additive, and pyridoxal 5′-phosphate content of this two-step production process were subsequently optimized. Under optimal conditions, 750.7 mmol/L d-lysine was finally obtained from 1710 mmol/L l-lysine after 1 h of racemization reaction and 0.5 h of decarboxylation reaction. d-lysine yield could reach 48.8% with enantiomeric excess (ee ≥ 99%.

  5. Radioactive Lysine in Protein Metabolism Studies

    Science.gov (United States)

    Miller, L. L.; Bale, W. F.; Yuile, C. L.; Masters, R. E.; Tishkoff, G. H.; Whipple,, G. H.

    1950-01-09

    Studies of incorporation of DL-lysine in various body proteins of the dog; the time course of labeled blood proteins; and apparent rate of disappearance of labeled plasma proteins for comparison of behavior of the plasma albumin and globulin fractions; shows more rapid turn over of globulin fraction.

  6. Lysine and arginine requirements of Salminus brasiliensis

    Directory of Open Access Journals (Sweden)

    Jony Koji Dairiki

    2013-08-01

    Full Text Available The objective of this work was to determine the dietary lysine (DL and dietary arginine (DA requirements of dourado (Salminus brasiliensis, through dose-response trials using the amino acid profiles of whole carcasses as a reference. Two experiments were carried out in a completely randomized design (n=4. In the first experiment, groups of 12 feed-conditioned dourado juveniles (11.4±0.2 g were stocked in 60 L cages placed in 300 L plastic indoor tanks in a closed circulation system. Fish were fed for 60 days on diets containing 1.0, 1.5, 2.0, 2.5, 3.0, or 3.5 % dietary lysine. In the second experiment, dourado juveniles (27.0±0.8 g were fed for 60 days on semipurified diets containing arginine at 1.0, 1.5, 2.0, 2.5 or 3.0%, in similar conditions to those of the first experiment. Optimal DL requirements, as determined by broken-line analysis method for final weight, weight gain and specific growth rate, were 2.15% DL or 5% lysine in dietary protein, and 1.48% DA or 3.43% arginine in dietary protein. The best feed conversion ratio is attained with 2.5% DL or 5.8% lysine in dietary protein and 1.4% DA or 3.25% arginine in dietary protein.

  7. Lysine kinetics in preterm infants: the importance of enteral feeding

    NARCIS (Netherlands)

    S.R.D. van der Schoor (Sophie); P.J. Reeds; F. Stellaard; J.L.D. Wattimena (Josias); P.J.J. Sauer (Pieter); H.A. Büller (Hans); J.B. van Goudoever (Hans)

    2004-01-01

    textabstractINTRODUCTION: Lysine is the first limiting essential amino acid in the diet of newborns. First pass metabolism by the intestine of dietary lysine has a direct effect on systemic availability. We investigated whether first pass lysine metabolism in the intestine is high

  8. Lysine kinetics in preterm infants : the importance of enteral feeding

    NARCIS (Netherlands)

    van der Schoor, SRD; Reeds, PJ; Stellaard, F; Wattimena, JDL; Sauer, PJJ; Buller, HA; van Goudoever, JB

    2004-01-01

    Introduction: Lysine is the first limiting essential amino acid in the diet of newborns. First pass metabolism by the intestine of dietary lysine has a direct effect on systemic availability. We investigated whether first pass lysine metabolism in the intestine is high in preterm infants, particular

  9. Charged Residues at the First Transmembrane Region Contribute to the Voltage Dependence of the Slow Gate of Connexins.

    Science.gov (United States)

    Pinto, Bernardo I; García, Isaac E; Pupo, Amaury; Retamal, Mauricio A; Martínez, Agustín D; Latorre, Ramón; González, Carlos

    2016-07-22

    Connexins (Cxs) are a family of membrane-spanning proteins that form gap junction channels and hemichannels. Connexin-based channels exhibit two distinct voltage-dependent gating mechanisms termed slow and fast gating. Residues located at the C terminus of the first transmembrane segment (TM-1) are important structural components of the slow gate. Here, we determined the role of the charged residues at the end of TM-1 in voltage sensing in Cx26, Cx46, and Cx50. Conductance/voltage curves obtained from tail currents together with kinetics analysis reveal that the fast and slow gates of Cx26 involves the movement of two and four charges across the electric field, respectively. Primary sequence alignment of different Cxs shows the presence of well conserved glutamate residues in the C terminus of TM-1; only Cx26 contains a lysine in that position (lysine 41). Neutralization of lysine 41 in Cx26 increases the voltage dependence of the slow gate. Swapping of lysine 41 with glutamate 42 maintains the voltage dependence. In Cx46, neutralization of negative charges or addition of a positive charge in the Cx26 equivalent region reduced the slow gate voltage dependence. In Cx50, the addition of a glutamate in the same region decreased the voltage dependence, and the neutralization of a negative charge increased it. These results indicate that the charges at the end of TM-1 are part of the slow gate voltage sensor in Cxs. The fact that Cx42, which has no charge in this region, still presents voltage-dependent slow gating suggests that charges still unidentified also contribute to the slow gate voltage sensitivity.

  10. The Mycobacterium tuberculosis LipB enzyme functions as a cysteine/lysine dyad acyltransferase.

    Science.gov (United States)

    Ma, Qingjun; Zhao, Xin; Nasser Eddine, Ali; Geerlof, Arie; Li, Xinping; Cronan, John E; Kaufmann, Stefan H E; Wilmanns, Matthias

    2006-06-06

    Lipoic acid is essential for the activation of a number of protein complexes involved in key metabolic processes. Growth of Mycobacterium tuberculosis relies on a pathway in which the lipoate attachment group is synthesized from an endogenously produced octanoic acid moiety. In patients with multiple-drug-resistant M. tuberculosis, expression of one gene from this pathway, lipB, encoding for octanoyl-[acyl carrier protein]-protein acyltransferase is considerably up-regulated, thus making it a potential target in the search for novel antiinfectives against tuberculosis. Here we present the crystal structure of the M. tuberculosis LipB protein at atomic resolution, showing an unexpected thioether-linked active-site complex with decanoic acid. We provide evidence that the transferase functions as a cysteine/lysine dyad acyltransferase, in which two invariant residues (Lys-142 and Cys-176) are likely to function as acid/base catalysts. Analysis by MS reveals that the LipB catalytic reaction proceeds by means of an internal thioesteracyl intermediate. Structural comparison of LipB with lipoate protein ligase A indicates that, despite conserved structural and sequence active-site features in the two enzymes, 4'-phosphopantetheine-bound octanoic acid recognition is a specific property of LipB.

  11. Effects of dietary digestible lysine levels on protein and fat deposition in the carcass of broilers

    Directory of Open Access Journals (Sweden)

    F de C Tavernari

    2009-06-01

    Full Text Available An experiment was carried out to evaluate the effects of different levels of digestible lysine in the diets of male and female broilers on protein and fat deposition. A total of 2160 Avian Farms broilers. A completely randomized experimental design was applied, and treatments consisted of the effects of three digestible lysine levels nested within each sex, with 12 replicates and 30 birds per experimental unit. The adopted digestible lysine levels corresponded to 92.5, 100.0, and 107.5% of the nutritional requirements of phases 1 to 21 days, 22 to 42 days, and 43 to 56 days of age, respectively. In each phase, the experimental diets contained similar calorie and protein levels within each sex. No significant effects of lysine levels were found on dry matter and fat percentages in the carcass of birds during the evaluated periods. Also, there were no significant effects of lysine levels on protein and fat deposition in males or females. However, males presented higher protein deposition and lower fat deposition than females during the total experimental period. Gompertz equations showed that females deposit more fat and less protein than males, and that this affected the fall in the curve of protein deposition, when the curve of fat deposition was still rising. Therefore, it was concluded that the older the broilers at slaughter, the higher their body fat content and the lower their body protein content, particularly in females.

  12. A lysinated thiophene-based semiconductor as a multifunctional neural bioorganic interface.

    Science.gov (United States)

    Bonetti, Simone; Pistone, Assunta; Brucale, Marco; Karges, Saskia; Favaretto, Laura; Zambianchi, Massimo; Posati, Tamara; Sagnella, Anna; Caprini, Marco; Toffanin, Stefano; Zamboni, Roberto; Camaioni, Nadia; Muccini, Michele; Melucci, Manuela; Benfenati, Valentina

    2015-06-03

    Lysinated molecular organic semiconductors are introduced as valuable multifunctional platforms for neural cells growth and interfacing. Cast films of quaterthiophene (T4) semiconductor covalently modified with lysine-end moieties (T4Lys) are fabricated and their stability, morphology, optical/electrical, and biocompatibility properties are characterized. T4Lys films exhibit fluorescence and electronic transport as generally observed for unsubstituted oligothiophenes combined to humidity-activated ionic conduction promoted by the charged lysine-end moieties. The Lys insertion in T4 enables adhesion of primary culture of rat dorsal root ganglion (DRG), which is not achievable by plating cells on T4. Notably, on T4Lys, the number on adhering neurons/area is higher and displays a twofold longer neurite length than neurons plated on glass coated with poly-l-lysine. Finally, by whole-cell patch-clamp, it is shown that the biofunctionality of neurons cultured on T4Lys is preserved. The present study introduces an innovative concept for organic material neural interface that combines optical and iono-electronic functionalities with improved biocompatibility and neuron affinity promoted by Lys linkage and the softness of organic semiconductors. Lysinated organic semiconductors could set the scene for the fabrication of simplified bioorganic devices geometry for cells bidirectional communication or optoelectronic control of neural cells biofunctionality.

  13. Gastroprotective effects of L-lysine salification of ketoprofen in ethanol-injured gastric mucosa.

    Science.gov (United States)

    Cimini, Annamaria; Brandolini, Laura; Gentile, Roberta; Cristiano, Loredana; Menghini, Paola; Fidoamore, Alessia; Antonosante, Andrea; Benedetti, Elisabetta; Giordano, Antonio; Allegretti, Marcello

    2015-04-01

    Ketoprofen L-lysine salt (KLS), a NSAID, is widely used for its analgesic efficacy and tolerability. L-lysine salification was reported to increase the solubility and the gastric absorption and tolerance of ketoprofen. Since the management of NSAIDs gastrotoxicity still represents a major limitation in prolonged therapies, mainly when gastric lesions are present, this study investigated the gastro-protective activity of L-lysine by using a well-established model of gastric mucosa injury, the ethanol-gastric injury model. Several evidences show that the damaging action of ethanol could be attributed to the increase of ROS, which plays a key role in the increase of lipid peroxidation products, including malonyldialdehyde and 4-hydroxy-2-nonenal. With the aim to unravel the mechanism of L-lysine gastroprotection, cellular MDA levels and 4-HNE protein adducts as markers of lipid peroxidation and a panel of key endogenous gastro-protective proteins were assayed. The data obtained indicate a gastroprotective effect of L-lysine on gastric mucosa integrity.

  14. Cyclic lipodepsipeptides produced by Pseudomonas spp. naturally present in raw milk induce inhibitory effects on microbiological inhibitor assays for antibiotic residue screening.

    Directory of Open Access Journals (Sweden)

    Wim Reybroeck

    Full Text Available Two Pseudomonas strains, identified as closely related to Pseudomonas tolaasii, were isolated from milk of a farm with frequent false-positive Delvotest results for screening putative antibiotic residues in raw milk executed as part of the regulatory quality programme. Growth at 5 to 7°C of these isolates in milk resulted in high lipolysis and the production of bacterial inhibitors. The two main bacterial inhibitors have a molecular weight of 1168.7 and 1140.7 Da respectively, are heat-tolerant and inhibit Geobacillus stearothermophilus var. calidolactis, the test strain of most of the commercially available microbiological inhibitor tests for screening of antibiotic residues in milk. Furthermore, these bacterial inhibitors show antimicrobial activity against Staphylococcus aureus, Bacillus cereus and B. subtilis and also interfere negatively with yoghurt production. Following their isolation and purification with RP-HPLC, the inhibitors were identified by NMR analysis as cyclic lipodepsipeptides of the viscosin group. Our findings bring to light a new challenge for quality control in the dairy industry. By prolonging the refrigerated storage of raw milk, the keeping quality of milk is influenced by growth and metabolic activities of psychrotrophic bacteria such as pseudomonads. Besides an increased risk of possible spoilage of long shelf-life milk, the production at low temperature of natural bacterial inhibitors may also result in false-positive results for antibiotic residue screening tests based on microbial inhibitor assays thus leading to undue production loss.

  15. Expression and purification of histone H3 proteins containing multiple sites of lysine acetylation using nonsense suppression.

    Science.gov (United States)

    Young, Isaac A; Mittal, Chitvan; Shogren-Knaak, Michael A

    2016-02-01

    Lysine acetylation is a common post-translational modification, which is especially prevalent in histone proteins in chromatin. A number of strategies exist for generating histone proteins containing lysine acetylation, but an especially attractive approach is to genetically encode acetyl-lysine residues using nonsense suppression. This strategy has been successfully applied to single sites of histone acetylation. However, because histone acetylation can often occur at multiple sites simultaneously, we were interested in determining whether this approach could be extended. Here we show that we can express histone H3 proteins that incorporate up to four sites of lysine acetylation on the histone tail. Because the amount of expressed multi-acetylated histone is reduced relative to the wild type, a purification strategy involving affinity purification and ion exchange chromatography was optimized. This expression and purification strategy ultimately generates H3 histone uniformly acetylated at the desired position at levels and purity sufficient to assemble histone octamers. Histone octamers containing four sites of lysine acetylation were assembled into mononucleosomes and enzymatic assays confirmed that this acetylation largely blocks further acetylation by the yeast SAGA acetyltransferase complex.

  16. Lysine conservation and context in TGFbeta and Wnt signaling suggest new targets and general themes for posttranslational modification.

    Science.gov (United States)

    Konikoff, Charlotte E; Wisotzkey, Robert G; Newfeld, Stuart J

    2008-10-01

    TGFbeta and Wnt pathways play important roles in the development of animals from sponges to humans. In both pathways posttranslational modification as a means of regulating their function, such as lysine modification by ubiquitination and sumoylation, has been observed. However, a gap exists between the immunological observation of posttranslational modification and the identification of the target lysine. To fill this gap, we conducted a phylogenetic analysis of lysine conservation and context in TGFbeta and Wnt pathway receptors and signal transducers and suggest numerous high-probability candidates for posttranslational modification. Further comparison of results from both pathways suggests two general features for biochemical regulation of intercellular signaling: receptors are less frequent targets for modification than signal transduction agonists, and a lysine adjacent to an upstream hydrophobic residue may be a preferred context for modification. Overall the results suggest numerous applications for an evolutionary approach to the biochemical regulation of developmental pathways, including (1) streamlining of the identification of the target lysine, (2) determination of when members of a multigene family acquire distinct activities, (3) application to any conserved protein family, and (4) application to any modification of a specific amino acid.

  17. Antioxidant activity of carbocysteine lysine salt monohydrate.

    Science.gov (United States)

    Pinamonti, S; Venturoli, L; Leis, M; Chicca, M; Barbieri, A; Sostero, S; Ravenna, F; Daffonchio, L; Novellini, R; Ciaccia, A

    2001-09-01

    Reactive oxygen radicals are involved in many respiratory diseases, including chronic obstructive pulmonary disease (COPD). Carbocysteine lysine salt monohydrate (CLS) is a mucoactive drug effective in the treatment of bronchopulmonary diseases characterized by mucus alterations, including COPD. In the present study, the antioxidant activity of CLS was studied in vitro in three different oxygen radical producing systems, i.e. bronchoalveolar lavages (BAL) from patients affected by COPD, ultrasound treated human serum and cultured human lung endothelial cells challenged with elastase. BAL, exposed or not to different concentrations of CLS (1.5-30 mM), was assayed for free radical content by fluorometric analysis of DNA unwinding (FADU) or by cytochrome c reduction kinetics. Human serum was treated with ultrasound in the presence or absence of CLS (1.5, 2.5 mM) or N-acetyl cysteine (NAC; 4, 5 mM) and assayed for free radical content by FADU. Human endothelial cells cultured in vitro from pulmonary artery were incubated with elastase (0.3 IU/mL), in the presence or absence of glutathione (GSH; 0.65 mM) or CLS (0.16 mM). The supernatant was tested for cytochrome c reduction kinetics whereas cell homogenates were assessed for xanthine oxidase (XO) content by SDS-PAGE. Results showed that CLS is more effective as an in vitro scavenger in comparison to GSH and NAC. CLS reduced the damage of DNA from healthy donors exposed to COPD-BAL and was able to quench clastogenic activity induced in human serum by exposure to ultrasound at concentrations as low as 2.5 mM. NAC protect DNA from radical damage, starting from 5 mM. In human lung endothelial cells cultured in presence of elastase, CLS (0.16 mM) decreased xanthine oxidase activity. These results suggest that CLS could act by interfering with the conversion of xanthine dehydrogenase into superoxide-producing xanthine oxidase. The antioxidant activity of CLS could contribute to its therapeutic activity by reducing radical

  18. Differences in lysine adduction by acrolein and methyl vinyl ketone: implications for cytotoxicity in cultured hepatocytes.

    Science.gov (United States)

    Kaminskas, Lisa M; Pyke, Simon M; Burcham, Philip C

    2005-11-01

    Acrolein is a highly toxic environmental pollutant that readily alkylates the epsilon-amino group of lysine residues in proteins. In model systems, such chemistry involves sequential addition of two acrolein molecules to a given nitrogen, forming bis-Michael-adducted species that undergo aldol condensation and dehydration to form Nepsilon-(3-formyl-3,4-dehydropiperidino)lysine. Whether this ability to form cyclic adducts participates in the toxicity of acrolein is unknown. To address this issue, we compared the chemistry of protein adduction by acrolein to that of its close structural analogue methyl vinyl ketone, expecting that the alpha-methyl group would hinder the intramolecular cyclization of any bis-adducted species formed by methyl vinyl ketone. Both acrolein and methyl vinyl ketone displayed comparable protein carbonylating activity during in vitro studies with the model protein bovine serum albumin, confirming the alpha,beta,-unsaturated bond of both compounds is an efficient Michael acceptor for protein nucleophiles. However, differences in adduction chemistry became apparent during the use of electrospray ionization-MS to monitor reaction products in a lysine-containing peptide after modification by each compound. For example, although a Schiff base adduct was detected following reaction of the peptide with acrolein, an analogous species was not formed by methyl vinyl ketone. Furthermore, while ions corresponding to mono- and bis-Michael adducts were detected at the N-terminus and lysine residues following peptide modification by both carbonyls, only acrolein modification generated ions attributable to cyclic adducts. Despite these differences in adduction chemistry, in mouse hepatocytes, the two compounds exhibited very comparable abilities to induce rapid, concentration-dependent cell death as well as protein carbonylation. These findings suggest that the acute toxicity of short-chain alpha,beta-unsaturated carbonyl compounds involves their ability to

  19. Non-Invasive Evaluation of Alginate/Poly-L-lysine/Alginate Microcapsules by Magnetic Resonance Microscopy

    OpenAIRE

    Constantinidis, Ioannis; Grant, Samuel C.; Celper, Susanne; Gauffin-Holmberg, Isabel; Agering, Kristina; Oca-Cossio, Jose A.; Bui, Jonathan D.; Flint, Jeremy; Hamaty, Christine; Simpson, Nicholas E.; Blackband, Stephen J.

    2007-01-01

    In this report, we present data to demonstrate the utility of 1H MR microscopy to noninvasively examine alginate/poly-L-lysine/alginate (APA) microcapsules. Specifically, high-resolution images were used to visualize and quantify the poly-L-lysine (PLL) layer, and monitor temporal changes in the alginate gel microstructure during a month long in vitro culture. The thickness of the alginate/PLL layer was quantified to be 40.6±6.2 μm regardless of the alginate composition used to generate the b...

  20. Catalytic roles of lysines (K9, K27, K31) in the N-terminal domain in human adenylate kinase by random site-directed mutagenesis.

    Science.gov (United States)

    Ayabe, T; Park, S K; Takenaka, H; Sumida, M; Uesugi, S; Takenaka, O; Hamada, M

    1996-11-01

    To elucidate lysine residues in the N-terminal domain of human cytosolic adenylate kinase (hAK1, EC 2.7.4.3), random site-directed mutagenesis of K9, K27, and K31 residues was performed, and six mutants were analyzed by steady-state kinetics. K9 residue may play an important role in catalysis by interacting with AMP2-. K27 and K31 residues appear to play a functional role in catalysis by interacting with MgATP2-. In human AK, the epsilon-amino group in the side chain of these lysine residues would be essential for phosphoryl transfer between MgATP2- and AMP2- during transition state.

  1. Differentiation of compact and extended conformations of di-ubiquitin conjugates with lysine-specific isopeptide linkages by ion mobility-mass spectrometry.

    Science.gov (United States)

    Jung, Ji Eun; Pierson, Nicholas A; Marquardt, Andreas; Scheffner, Martin; Przybylski, Michael; Clemmer, David E

    2011-08-01

    Modification of ubiquitin, a key cellular regulatory polypeptide of 76 amino acids, to polyubiquitin conjugates by lysine-specific isopeptide linkage at one of its seven lysine residues has been recognized as a central pathway determining its biochemical properties and cellular functions. Structural details and differences of distinct lysine-isopeptidyl ubiquitin conjugates that reflect their different functions and reactivities, however, are only partially understood. Ion mobility spectrometry (IMS) combined with mass spectrometry (MS) has recently emerged as a powerful tool for probing conformations and topology involved in protein interactions by an electric field-driven separation of polypeptide ions through a drift gas. Here we report the conformational characterization and differentiation of Lys63- and Lys48-linked ubiquitin conjugates by IMS-MS. Lys63- and Lys48-linked di-ubiquitin conjugates were prepared by recombinant bacterial expression and by chemical synthesis using a specific chemical ligation strategy, and characterized by high-resolution Fourier transform ion cyclotron resonance mass spectrometry, circular dichroism spectroscopy, and molecular modeling. IMS-MS was found to be an effective tool for the identification of structural differences of ubiquitin complexes in the gas phase. The comparison of collision cross-sections of Lys63- and Lys48-linked di-ubiquitin conjugates showed a more elongated conformation of Lys63-linked di-ubiquitin. In contrast, the Lys48-linked di-ubiquitin conjugate showed a more compact conformation. The IMS-MS results are consistent with published structural data and a comparative molecular modeling study of the Lys63- and Lys48-linked conjugates. The results presented here suggest IMS techniques can provide information that complements MS measurements in differentiating higher-order polyubiquitins and other isomeric protein linkages.

  2. Charge neutralization of the central lysine cluster in prion protein (PrP) promotes PrP(Sc)-like folding of recombinant PrP amyloids.

    Science.gov (United States)

    Groveman, Bradley R; Kraus, Allison; Raymond, Lynne D; Dolan, Michael A; Anson, Kelsie J; Dorward, David W; Caughey, Byron

    2015-01-09

    The structure of the infectious form of prion protein, PrP(Sc), remains unclear. Most pure recombinant prion protein (PrP) amyloids generated in vitro are not infectious and lack the extent of the protease-resistant core and solvent exclusion of infectious PrP(Sc), especially within residues ∼90-160. Polyanionic cofactors can enhance infectivity and PrP(Sc)-like characteristics of such fibrils, but the mechanism of this enhancement is unknown. In considering structural models of PrP(Sc) multimers, we identified an obstacle to tight packing that might be overcome with polyanionic cofactors, namely, electrostatic repulsion between four closely spaced cationic lysines within a central lysine cluster of residues 101-110. For example, in our parallel in-register intermolecular β-sheet model of PrP(Sc), not only would these lysines be clustered within the 101-110 region of the primary sequence, but they would have intermolecular spacings of only ∼4.8 Å between stacked β-strands. We have now performed molecular dynamics simulations predicting that neutralization of the charges on these lysine residues would allow more stable parallel in-register packing in this region. We also show empirically that substitution of these clustered lysine residues with alanines or asparagines results in recombinant PrP amyloid fibrils with extended proteinase-K resistant β-sheet cores and infrared spectra that are more reminiscent of bona fide PrP(Sc). These findings indicate that charge neutralization at the central lysine cluster is critical for the folding and tight packing of N-proximal residues within PrP amyloid fibrils. This charge neutralization may be a key aspect of the mechanism by which anionic cofactors promote PrP(Sc) formation.

  3. Annatto seed residue (Bixa orellana L.: nutritional quality

    Directory of Open Access Journals (Sweden)

    Melissa Alessandra Valério

    2015-06-01

    Full Text Available Considering that annatto seeds are rich in protein, the present work aimed to evaluate the biological quality of this nutrient in the meal residue originating from annatto seed processing. We determined the general composition, mineral levels, amino acid composition and chemical scores, antinutritional factors, and protein quality using biological assays. The following values were obtained: 11.50% protein, 6.74% moisture, 5.22% ash, 2.22% lipids, 42.19% total carbohydrates and 28.45% fiber. The residue proved to be a food rich in fiber and also a protein source. Antinutritional factors were not detected. The most abundant amino acids were lysine, phenylalanine + tyrosine, leucine and isoleucine. Valine was the most limiting amino acid (chemical score 0.22. The protein quality of the seed residue and the isolated protein showed no significant differences. The biological value was lower than that of the control protein but higher than that found in other vegetables. Among the biochemical analyses, only creatinine level was decreased in the two test groups compared to the control group. Enzyme tests did not indicate liver toxicity. The results showed favorable aspects for the use of annatto seed residue in the human diet, meriting further research.

  4. Exploring lysine riboswitch for metabolic flux control and improvement of L-lysine synthesis in Corynebacterium glutamicum.

    Science.gov (United States)

    Zhou, Li-Bang; Zeng, An-Ping

    2015-06-19

    Riboswitch, a regulatory part of an mRNA molecule that can specifically bind a metabolite and regulate gene expression, is attractive for engineering biological systems, especially for the control of metabolic fluxes in industrial microorganisms. Here, we demonstrate the use of lysine riboswitch and intracellular l-lysine as a signal to control the competing but essential metabolic by-pathways of lysine biosynthesis. To this end, we first examined the natural lysine riboswitches of Eschericia coli (ECRS) and Bacillus subtilis (BSRS) to control the expression of citrate synthase (gltA) and thus the metabolic flux in the tricarboxylic acid (TCA) cycle in E. coli. ECRS and BSRS were then successfully used to control the gltA gene and TCA cycle activity in a lysine producing strain Corynebacterium glutamicum LP917, respectively. Compared with the strain LP917, the growth of both lysine riboswitch-gltA mutants was slower, suggesting a reduced TCA cycle activity. The lysine production was 63% higher in the mutant ECRS-gltA and 38% higher in the mutant BSRS-gltA, indicating a higher metabolic flux into the lysine synthesis pathway. This is the first report on using an amino acid riboswitch for improvement of lysine biosynthesis. The lysine riboswitches can be easily adapted to dynamically control other essential but competing metabolic pathways or even be engineered as an "on-switch" to enhance the metabolic fluxes of desired metabolic pathways.

  5. Antimicrobial activity of chicken NK-lysin against Eimeria sporozoites.

    Science.gov (United States)

    Hong, Yeong H; Lillehoj, Hyun S; Siragusa, Gregory R; Bannerman, Douglas D; Lillehoj, Erik P

    2008-06-01

    NK-lysin is an antimicrobial and antitumor polypeptide that is considered to play an important role in innate immunity. Chicken NK-lysin is a member of the saposin-like protein family and exhibits potent antitumor cell activity. To evaluate the antimicrobial properties of chicken NK-lysin, we examined its ability to reduce the viability of various bacterial strains and two species of Eimeria parasites. Culture supernatants from COS7 cells transfected with a chicken NK-lysin cDNA and His-tagged purified NK-lysin from the transfected cells both showed high cytotoxic activity against Eimeria acervulina and Eimeria maxima sporozoites. In contrast, no bactericidal activity was observed. Further studies using synthetic peptides derived from NK-lysin may be useful for pharmaceutical and agricultural uses in the food animal industry.

  6. Progress in biogas. Biogas production from agricultural biomass and organic residues. Pt. 1 and 2. Proceedings (oral presentations and poster presentations); Fortschritt beim Biogas. Biogas aus landwirtschaftlicher Biomasse and organischen Reststoffen. T. 1 und 2. Tagungsband. Vortraege and Poster

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2007-07-01

    Within the International Conference ''Progress in Biogas - Biogas production from agricultural biomass and organic residues'' at the University Hohenheim (Stuttgart, Federal Republic of Germany) from 18th to 21st September, 2007, the following lectures were held: (1) Global relevance and potential of bioenergy for regional development; (2) Biogas electricity for France feed-in tariff and some other things to know before entering French market; (3) Policy drivers and future prospects for on-farm anaerobic digestion in Northern Ireland; (4) Biogas in Belgium, a swot analysis; (5) Status and prospects of biogas energy use in Ukraine; (6) Recent developments in Chinese agricultural biogas production; (7) Opportunities for agricultural based biogas systems in the province of Ontario, Canada; (8) Pre-treatment and digestion of separated collected household waste in Sweden; (9) To the problem of monitoring measures and prophylaxis measures with the utilization of organic residual substances in biological gas facilities from hygienic view; (10) Fermenting residues from biological gas facilities - nutrients and pollutants, possibilities of application in the agriculture; (11) Treatment and utilization of fermentation residues; (12) Potential of residual gas of NaWaRo feeded biogas plants in Baden-Wuerttemberg; (13) Operating analytics of biogas plants to improve efficiency and to ensure process stability; (14) The potential of biogas and electric power production from subproducts in the sugar and alcohol industries by the application of anaerobic digestion; (15) Co-digestion plant in dairy cattle farm in Emilia Romagna region (Italy); (16) Facing operational problems in a biodigeser in Yuvientsa - Amazonian Region of Ecuador; (17) Biogas plant instead of milk cow - payment and occupation with the use of grassilage; (18) Biogas in ecologic agriculture - experiences from 3 years of fermentation of grass-clover ley; (19) Combined solar-biogas basis for the

  7. 赖氨酸乙酰化作用:更为广泛的蛋白调控方式%Lysine acetylation, a more prevalent posttranslational regulation of protein function

    Institute of Scientific and Technical Information of China (English)

    黄的; 张华凤

    2012-01-01

    Acetylation of proteins on lysine residues,including non-histones lysine acetylation, is a prevalent and reversible posttranslational modification. Technological limitations in this field have long impeded the progress in analysis of lysine acetylation's cellular roles. In the past several years,however,quite a number of non-histones lysine acetylation have been brought to light,largely due to the maturation of detection technologies such as high-resolution mass spectrometry and label-free quantification (LFQ). Although the molecular mechanisms underlying cellular regulation of lysine acetylation remain elusive and the detection of highly dynamic lysine acetylation is still a challenge,mounting documented evidence has demonstrated that lysine acetylation is widely involved in such cellular biological activities as cell growth,apoptosis,cytokinetics and cell metabolisms. In this review,we present the progression in this field as well as our current understanding of this modification,starting with the developing detection technologies of lysine acetylation. We also highlight the function of lysine acetylation in the regulation of gene transcription,energy metabolism,cancer development as well as its therapeutic implications.%蛋白质赖氨酸残基上的乙酰化修饰,包括非组蛋白赖氨酸的乙酰化修饰,是一种普遍存在的可逆性翻译后修饰作用,然而检测技术上的限制一直阻碍着赖氨酸乙酰化修饰在细胞中的功能解析和研究.随着赖氨酸乙酰化检测技术的不断成熟,现已发现大量的非组蛋白存在赖氨酸乙酰化修饰的现象.目前,调控细胞内赖氨酸乙酰化的分子机制还不十分清楚,对于活体内高度动态的赖氨酸乙酰化修饰的捕捉尚存困难,但已有越来越多的证据表明,赖氨酸乙酰化修饰广泛地参与细胞的生长、凋亡、动力学、能量代谢等生理活动过程.本文以不断发展的赖氨酸检测技术为出发点,介绍非组蛋白

  8. Structural definition of the lysine swing in Arabidopsis thaliana PDX1: Intermediate channeling facilitating vitamin B6 biosynthesis.

    Science.gov (United States)

    Robinson, Graham C; Kaufmann, Markus; Roux, Céline; Fitzpatrick, Teresa B

    2016-10-04

    Vitamin B6 is indispensible for all organisms, notably as the coenzyme form pyridoxal 5'-phosphate. Plants make the compound de novo using a relatively simple pathway comprising pyridoxine synthase (PDX1) and pyridoxine glutaminase (PDX2). PDX1 is remarkable given its multifaceted synthetic ability to carry out isomerization, imine formation, ammonia addition, aldol-type condensation, cyclization, and aromatization, all in the absence of coenzymes or recruitment of specialized domains. Two active sites (P1 and P2) facilitate the plethora of reactions, but it is not known how the two are coordinated and, moreover, if intermediates are tunneled between active sites. Here we present X-ray structures of PDX1.3 from Arabidopsis thaliana, the overall architecture of which is a dodecamer of (β/α)8 barrels, similar to the majority of its homologs. An apoenzyme structure revealed that features around the P1 active site in PDX1.3 have adopted inward conformations consistent with a catalytically primed state and delineated a substrate accessible cavity above this active site, not noted in other reported structures. Comparison with the structure of PDX1.3 with an intermediate along the catalytic trajectory demonstrated that a lysine residue swings from the distinct P2 site to the P1 site at this stage of catalysis and is held in place by a molecular catch and pin, positioning it for transfer of serviced substrate back to P2. The study shows that a simple lysine swinging arm coordinates use of chemically disparate sites, dispensing with the need for additional factors, and provides an elegant example of solving complex chemistry to generate an essential metabolite.

  9. Global analysis of lysine acetylation in strawberry leaves

    Directory of Open Access Journals (Sweden)

    Xianping eFang

    2015-09-01

    Full Text Available Protein lysine acetylation is a reversible and dynamic post-translational modification. It plays an important role in regulating diverse cellular processes including chromatin dynamic, metabolic pathways and transcription in both prokaryotes and eukaryotes. Although studies of lysine acetylome in plants have been reported, the throughput was not high enough, hindering the deep understanding of lysine acetylation in plant physiology and pathology. In this study, taking advantages of anti-acetyllysine-based enrichment and high-sensitive-mass spectrometer, we applied an integrated proteomic approach to comprehensively investigate lysine acetylome in strawberry. In total, we identified 1392 acetylation sites in 684 proteins, representing the largest dataset of acetylome in plants to date. To reveal the functional impacts of lysine acetylation in strawberry, intensive bioinformatic analysis was performed. The results significantly expanded our current understanding of plant acetylome and demonstrated that lysine acetylation is involved in multiple cellular metabolism and cellular processes. More interestingly, nearly 50% of all acetylated proteins identified in this work were localized in chloroplast and the vital role of lysine acetylation in photosynthesis was also revealed. Taken together, this study not only established the most extensive lysine acetylome in plants to date, but also systematically suggests the significant and unique roles of lysine acetylation in plants.

  10. Histone H4 Lysine 20 methylation

    DEFF Research Database (Denmark)

    Jørgensen, Stine; Schotta, Gunnar; Sørensen, Claus Storgaard

    2013-01-01

    of histones have emerged as key regulators of genomic integrity. Intense research during the past few years has revealed histone H4 lysine 20 methylation (H4K20me) as critically important for the biological processes that ensure genome integrity, such as DNA damage repair, DNA replication and chromatin...... instability, demonstrating the important functions of H4K20 methylation in genome maintenance. In this review, we explain molecular mechanisms underlying these defects and discuss novel ideas for furthering our understanding of genome maintenance in higher eukaryotes....

  11. Optimization of lysine metabolism in Corynebacterium glutamicum

    DEFF Research Database (Denmark)

    Rytter, Jakob Vang

    the project intends to eliminate. PGI catalyzes the conversion of alpha-D-glucose-6-phosphate to fructose-6-phosphate just downstream of the branch in the glycolysis, but it also catalyzes the reverse reaction. It is unknown whether up- or down-regulation of the pgi is required to increase the flux through......, and increased NADPH availability is therefore a potential way to enhance lysine production. The generation of NADPH is mainly located in the pentose phosphate pathway (PPP). Using the genome scale model the phosphoglucoisomerase enzyme (PGI) has been identified as a possible bottleneck in the metabolism, which...

  12. Biological function and regulation of histone and non-histone lysine methylation in response to DNA damage

    Institute of Scientific and Technical Information of China (English)

    Yongcan Chen; Wei-Guo Zhu

    2016-01-01

    DNA damage response (DDR) signaling network is initiated to protect cells from various exogenous and endogenous damage resources.Timely and accurate regulation of DDR proteins is required for distinct DNA damage repair pathways.Post-translational modifications of histone and non-histone proteins play a vital role in the DDR factor foci formation and signaling pathway.Phosphorylation,ubiquitylation,SUMOylation,neddylation,poly(ADP-ribosyl)ation,acetylation,and methylation are all involved in the spatial-temporal regulation of DDR,among which phosphorylation and ubiquitylation are well studied.Studies in the past decade also revealed extensive roles of lysine methylation in response to DNA damage.Lysine methylation is finely regulated by plenty of lysine methyltransferases,lysine demethylases,and can be recognized by proteins with chromodomain,plant homeodomain,Tudor domain,malignant brain tumor domain,or prolinetryptophan-tryptophan-proline domain.In this review,we outline the dynamics and regulation of histone lysine methylation at canonical (H3K4,H3K9,H3K27,H3K36,H3K79,and H4K20) and non-canonical sites after DNA damage,and discuss their context-specific functions in DDR protein recruitment or extraction,chromatin environment establishment,and transcriptional regulation.We also present the emerging advances of lysine methylation in non-histone proteins during DDR.

  13. Progress in biogas. Biogas production from agricultural biomass and organic residues. Pt. 1 and 2. Proceedings (oral presentations and poster presentations); Fortschritt beim Biogas. Biogas aus landwirtschaftlicher Biomasse and organischen Reststoffen. T. 1 und 2. Tagungsband. Vortraege and Poster

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2007-07-01

    Within the International Conference ''Progress in Biogas - Biogas production from agricultural biomass and organic residues'' at the University Hohenheim (Stuttgart, Federal Republic of Germany) from 18th to 21st September, 2007, the following lectures were held: (1) Global relevance and potential of bioenergy for regional development; (2) Biogas electricity for France feed-in tariff and some other things to know before entering French market; (3) Policy drivers and future prospects for on-farm anaerobic digestion in Northern Ireland; (4) Biogas in Belgium, a swot analysis; (5) Status and prospects of biogas energy use in Ukraine; (6) Recent developments in Chinese agricultural biogas production; (7) Opportunities for agricultural based biogas systems in the province of Ontario, Canada; (8) Pre-treatment and digestion of separated collected household waste in Sweden; (9) To the problem of monitoring measures and prophylaxis measures with the utilization of organic residual substances in biological gas facilities from hygienic view; (10) Fermenting residues from biological gas facilities - nutrients and pollutants, possibilities of application in the agriculture; (11) Treatment and utilization of fermentation residues; (12) Potential of residual gas of NaWaRo feeded biogas plants in Baden-Wuerttemberg; (13) Operating analytics of biogas plants to improve efficiency and to ensure process stability; (14) The potential of biogas and electric power production from subproducts in the sugar and alcohol industries by the application of anaerobic digestion; (15) Co-digestion plant in dairy cattle farm in Emilia Romagna region (Italy); (16) Facing operational problems in a biodigeser in Yuvientsa - Amazonian Region of Ecuador; (17) Biogas plant instead of milk cow - payment and occupation with the use of grassilage; (18) Biogas in ecologic agriculture - experiences from 3 years of fermentation of grass-clover ley; (19) Combined solar-biogas basis for the

  14. Chromosomal protein HMGN1 enhances the acetylation of lysine 14 in histone H3

    OpenAIRE

    Lim, Jae-Hwan; West, Katherine L.; Rubinstein, Yaffa; Bergel, Michael; Postnikov, Yuri V.; Bustin, Michael

    2005-01-01

    The acetylation levels of lysine residues in nucleosomes, which are determined by the opposing activities of histone acetyltransferases (HATs) and deacetylases, play an important role in regulating chromatin-related processes, including transcription. We report that HMGN1, a nucleosomal binding protein that reduces the compaction of the chromatin fiber, increases the levels of acetylation of K14 in H3. The levels of H3K14ac in Hmgn1−/− cells are lower than in Hmgn1+/+ cells. Induced expressio...

  15. Prediction of carbamylated lysine sites based on the one-class k-nearest neighbor method.

    Science.gov (United States)

    Huang, Guohua; Zhou, You; Zhang, Yuchao; Li, Bi-Qing; Zhang, Ning; Cai, Yu-Dong

    2013-11-01

    Protein carbamylation is one of the important post-translational modifications, which plays a pivotal role in a number of biological conditions, such as diseases, chronic renal failure and atherosclerosis. Therefore, recognition and identification of protein carbamylated sites are essential for disease treatment and prevention. Yet the mechanism of action of carbamylated lysine sites is still not realized. Thus it remains a largely unsolved challenge to uncover it, whether experimentally or theoretically. To address this problem, we have presented a computational framework for theoretically predicting and analyzing carbamylated lysine sites based on both the one-class k-nearest neighbor method and two-stage feature selection. The one-class k-nearest neighbor method requires no negative samples in training. Experimental results showed that by using 280 optimal features the presented method achieved promising performances of SN=82.50% for the jackknife test on the training set, and SN=66.67%, SP=100.00% and MCC=0.8097 for the independent test on the testing set, respectively. Further analysis of the optimal features provided insights into the mechanism of action of carbamylated lysine sites. It is anticipated that our method could be a potentially useful and essential tool for biologists to theoretically investigate carbamylated lysine sites.

  16. Triple therapy with pyridoxine, arginine supplementation and dietary lysine restriction in pyridoxine-dependent epilepsy: Neurodevelopmental outcome.

    Science.gov (United States)

    Coughlin, Curtis R; van Karnebeek, Clara D M; Al-Hertani, Walla; Shuen, Andrew Y; Jaggumantri, Sravan; Jack, Rhona M; Gaughan, Sommer; Burns, Casey; Mirsky, David M; Gallagher, Renata C; Van Hove, Johan L K

    2015-01-01

    Pyridoxine-dependent epilepsy (PDE) is an epileptic encephalopathy characterized by response to pharmacologic doses of pyridoxine. PDE is caused by deficiency of α-aminoadipic semialdehyde dehydrogenase resulting in impaired lysine degradation and subsequent accumulation of α-aminoadipic semialdehyde. Despite adequate seizure control with pyridoxine monotherapy, 75% of individuals with PDE have significant developmental delay and intellectual disability. We describe a new combined therapeutic approach to reduce putative toxic metabolites from impaired lysine metabolism. This approach utilizes pyridoxine, a lysine-restricted diet to limit the substrate that leads to neurotoxic metabolite accumulation and L-arginine to compete for brain lysine influx and liver mitochondrial import. We report the developmental and biochemical outcome of six subjects who were treated with this triple therapy. Triple therapy reduced CSF, plasma, and urine biomarkers associated with neurotoxicity in PDE. The addition of arginine supplementation to children already treated with dietary lysine restriction and pyridoxine further reduced toxic metabolites, and in some subjects appeared to improve neurodevelopmental outcome. Dietary lysine restriction was associated with improved seizure control in one subject, and the addition of arginine supplementation increased the objective motor outcome scale in two twin siblings, illustrating the contribution of each component of this treatment combination. Optimal results were noted in the individual treated with triple therapy early in the course of the disease. Residual disease symptoms could be related to early injury suggested by initial MR imaging prior to initiation of treatment or from severe epilepsy prior to diagnosis. This observational study reports the use of triple therapy, which combines three effective components in this rare condition, and suggests that early diagnosis and treatment with this new triple therapy may ameliorate the

  17. File list: Oth.Unc.50.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Unc.50.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Unclassified ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Unc.50.Crotonyl_lysine.AllCell.bed ...

  18. File list: Oth.Pan.05.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  19. File list: Oth.Plc.20.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  20. File list: Oth.Unc.10.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  1. File list: Oth.Unc.20.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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  3. File list: Oth.Plc.50.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  4. File list: Oth.Prs.10.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  5. File list: Oth.Prs.05.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  6. File list: Oth.Prs.20.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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  8. File list: Oth.Pan.10.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  9. File list: Oth.Plc.10.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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  12. Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH).

    Science.gov (United States)

    Meyer, Jesse G; D'Souza, Alexandria K; Sorensen, Dylan J; Rardin, Matthew J; Wolfe, Alan J; Gibson, Bradford W; Schilling, Birgit

    2016-11-01

    Post-translational modification of lysine residues by NƐ-acylation is an important regulator of protein function. Many large-scale protein acylation studies have assessed relative changes of lysine acylation sites after antibody enrichment using mass spectrometry-based proteomics. Although relative acylation fold-changes are important, this does not reveal site occupancy, or stoichiometry, of individual modification sites, which is critical to understand functional consequences. Recently, methods for determining lysine acetylation stoichiometry have been proposed based on ratiometric analysis of endogenous levels to those introduced after quantitative per-acetylation of proteins using stable isotope-labeled acetic anhydride. However, in our hands, we find that these methods can overestimate acetylation stoichiometries because of signal interferences when endogenous levels of acylation are very low, which is especially problematic when using MS1 scans for quantification. In this study, we sought to improve the accuracy of determining acylation stoichiometry using data-independent acquisition (DIA). Specifically, we use SWATH acquisition to comprehensively collect both precursor and fragment ion intensity data. The use of fragment ions for stoichiometry quantification not only reduces interferences but also allows for determination of site-level stoichiometry from peptides with multiple lysine residues. We also demonstrate the novel extension of this method to measurements of succinylation stoichiometry using deuterium-labeled succinic anhydride. Proof of principle SWATH acquisition studies were first performed using bovine serum albumin for both acetylation and succinylation occupancy measurements, followed by the analysis of more complex samples of E. coli cell lysates. Although overall site occupancy was low (<1%), some proteins contained lysines with relatively high acetylation occupancy. Graphical Abstract ᅟ.

  13. Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH)

    Science.gov (United States)

    Meyer, Jesse G.; D'Souza, Alexandria K.; Sorensen, Dylan J.; Rardin, Matthew J.; Wolfe, Alan J.; Gibson, Bradford W.; Schilling, Birgit

    2016-09-01

    Post-translational modification of lysine residues by NƐ-acylation is an important regulator of protein function. Many large-scale protein acylation studies have assessed relative changes of lysine acylation sites after antibody enrichment using mass spectrometry-based proteomics. Although relative acylation fold-changes are important, this does not reveal site occupancy, or stoichiometry, of individual modification sites, which is critical to understand functional consequences. Recently, methods for determining lysine acetylation stoichiometry have been proposed based on ratiometric analysis of endogenous levels to those introduced after quantitative per-acetylation of proteins using stable isotope-labeled acetic anhydride. However, in our hands, we find that these methods can overestimate acetylation stoichiometries because of signal interferences when endogenous levels of acylation are very low, which is especially problematic when using MS1 scans for quantification. In this study, we sought to improve the accuracy of determining acylation stoichiometry using data-independent acquisition (DIA). Specifically, we use SWATH acquisition to comprehensively collect both precursor and fragment ion intensity data. The use of fragment ions for stoichiometry quantification not only reduces interferences but also allows for determination of site-level stoichiometry from peptides with multiple lysine residues. We also demonstrate the novel extension of this method to measurements of succinylation stoichiometry using deuterium-labeled succinic anhydride. Proof of principle SWATH acquisition studies were first performed using bovine serum albumin for both acetylation and succinylation occupancy measurements, followed by the analysis of more complex samples of E. coli cell lysates. Although overall site occupancy was low (<1%), some proteins contained lysines with relatively high acetylation occupancy.

  14. Quantification of Nε-(2-Furoylmethyl)-L-lysine (furosine), Nε-(Carboxymethyl)-L-lysine (CML), Nε-(Carboxyethyl)-L-lysine (CEL) and total lysine through stable isotope dilution assay and tandem mass spectrometry

    NARCIS (Netherlands)

    Troise, A.D.; Fiore, A.; Wiltafsky, M.; Fogliano, V.

    2015-01-01

    The control of Maillard reaction (MR) is a key point to ensure processed foods quality. Due to the presence of a primary amino group on its side chain, lysine is particularly prone to chemical modifications with the formation of Amadori products (AP), Nε-(Carboxymethyl)-L-lysine (CML),

  15. STUDY OF LYSINE AND ALANINE DELIVERANCE THROUGH POLYPYRROLE MEMBRANE

    Directory of Open Access Journals (Sweden)

    Adhitasari Suratman

    2010-06-01

    Full Text Available Electropolymerization processes of pyrrole and the usage of polypyrrole membrane as lysine and alanine deliverance have been studied by cyclic voltammetry technique. Polypyrrole membrane was prepared by electropolymerization processes of pyrrole in water based solvent containing sodium perchlorate as supporting electrolyte. Electropolymerization processes were carried out within potential range of 0-1100 mV vs Ag/AgCl reference electrode and at the scanning rate of 100 mV/s. In this study, lysine and alanine have been used as molecules which could easily be loaded on and released from polypyrrole membrane. The presence of lysine or alanine during electropolymerization process reduced the rate of electropolymerization of polypyrrole. In lysine or alanine transfer processes into polypyrrole membrane, the interaction between polypyrrole and lysine or alanine showed by the curve of E½ oxidation in respect of - log C. It proved that the E½ oxidation shifted to more positive potential showed by the increasing of concentration of lysine or alanine. Beside that, voltammetric responses of lysine and alanine transfered into polypyrrole membrane were found to be Nernstian. The results indicated that polypyrrole could be used as a sensor of lysine and alanine.   Keywords: Electropolymerization, polypyrrole membrane, voltammetry technique

  16. Digestible lysine levels in diets supplemented with ractopamine

    Directory of Open Access Journals (Sweden)

    Evelar de Oliveira Souza

    2011-10-01

    Full Text Available In order evaluate digestible lysine levels in diets supplemented with 20 ppm of ractopamine on the performance and carcass traits, 64 barrows with high genetic potential at finishing phase were allotted in a completely randomized block design with four digestible lysine levels (0.80, 0.90, 1.00, and 1.10%, eight replicates and two pigs per experimental unit. Initial body weight and pigs' kinship were used as criteria in the blocks formation. Diets were mainly composed of corn and soybean meal supplemented with minerals, vitamins and amino acids to meet pigs' nutritional requirements at the finishing phase, except for digestible lysine. No effect of digestible lysine levels was observed in animal performance. The digestible lysine intake increased linearly by increasing the levels of digestible lysine in the diets. Carcass traits were not influenced by the dietary levels of digestible lysine. The level of 0.80% of digestible lysine in diets supplemented with 20 ppm ractopamine meets the nutritional requirements of castrated male pigs during the finishing phase.

  17. The Tale of Protein Lysine Acetylation in the Cytoplasm

    Directory of Open Access Journals (Sweden)

    Karin Sadoul

    2011-01-01

    Full Text Available Reversible posttranslational modification of internal lysines in many cellular or viral proteins is now emerging as part of critical signalling processes controlling a variety of cellular functions beyond chromatin and transcription. This paper aims at demonstrating the role of lysine acetylation in the cytoplasm driving and coordinating key events such as cytoskeleton dynamics, intracellular trafficking, vesicle fusion, metabolism, and stress response.

  18. 我国残膜回收机研究现状及建议%Present Situation of Research on Plastic Film Residue Collector in China and Some Suggestions

    Institute of Scientific and Technical Information of China (English)

    李明洋; 马少辉

    2014-01-01

    Plastic film covers are important in the Chinese agricultural production .The coverage area has reached over ten millions hectares .Plastic film covers application greatly improves the production of crops , With the increase of plastic film application amounts , the residue of mulching plastic film in the field become more and more .These residual film has caused serious white pollution on cultivated land and villages .In order to recover the remnant film better and reduce the white pollution .This paper describes the present situation of plastic film residue collector in China and the working prin -ciple of several typical plastic film residue collector .At last put forward some suggestions on the future development of plastic film residue collector .%地膜已成为我国农业生产中广泛应用的物质材料之一,我国应用地膜技术的土地多达1000万 hm2多。地膜的应用大大提高了农作物的产量,但是随着废膜越来越多的残留,对耕地、村庄造成了严重的白色污染。为此,阐述了我国残膜回收机研究的现状和几种典型残膜回收机的工作原理,并对未来残膜回收机的发展提出了建议。

  19. Residuation theory

    CERN Document Server

    Blyth, T S; Sneddon, I N; Stark, M

    1972-01-01

    Residuation Theory aims to contribute to literature in the field of ordered algebraic structures, especially on the subject of residual mappings. The book is divided into three chapters. Chapter 1 focuses on ordered sets; directed sets; semilattices; lattices; and complete lattices. Chapter 2 tackles Baer rings; Baer semigroups; Foulis semigroups; residual mappings; the notion of involution; and Boolean algebras. Chapter 3 covers residuated groupoids and semigroups; group homomorphic and isotone homomorphic Boolean images of ordered semigroups; Dubreil-Jacotin and Brouwer semigroups; and loli

  20. Lysine acetylation is a common post-translational modification of key metabolic pathway enzymes of the anaerobe Porphyromonas gingivalis.

    Science.gov (United States)

    Butler, Catherine A; Veith, Paul D; Nieto, Matthew F; Dashper, Stuart G; Reynolds, Eric C

    2015-10-14

    production in this bacterium were acetylated on certain lysine residues. These enzymes were often found catalysing sequential reactions within the same catabolic pathway. The results suggest that lysine acetylation is an important mechanism of metabolic regulation in P. gingivalis vital for its adaptation and proliferation to produce disease.

  1. Residuos de insecticidas organoclorados presentes en leche cruda comercializada en el departamento de Córdoba, Colombia Organochlorine insecticide residues present in raw milk sold in the Department Córdoba, Colombia

    Directory of Open Access Journals (Sweden)

    2012-01-01

    Full Text Available En el estudio se determinaron residuos de plaguicidas organoclorados en leche cruda proveniente de hatos lecheros del departamento de Córdoba, Colombia. Durante el procedimiento de extracción se utilizó una columna de tierra de diatomeas y como sistema eluyente una mezcla de n-hexano-acetonaacetato de etilo (4:2:1, seguida de metanol al 5% en hexano. Para la determinación se usó un cromatógrafo de gases Perkin Elmer, Autosystem XL con detector captura de electrones, en modo de inyección ‘splitless', una columna capilar Rtx-5 30 m, 0.25 mm di y 0.25 µm de espesor de película. El porcentaje de recuperación para los plaguicidas determinados se encontró entre 88.5 y 96%, los límites de detección se definieron entre 0.01 y 0.04 ng/g con desviaciones estándar In this investigation organochlorine pesticide residues in raw milk from Dairy herds in the Cordoba department were determined. During the extraction procedure using a column of diatomaceous earth as eluting system a mixture of n-hexane-acetone-ethyl acetate (4:2:1, followed by 5% methanol in hexane. For the determination we used a gas Chromatograph Perkin Elmer, Autosystem XL with electron capture detector, split less injection mode, a capillary column Rtx-5 30m, 0.25 mm id and 0.25 um film thickness. The recovery rate for certain pesticides were between 88.5 and 96%, the detection limits were defined between 0.01 and 0.04 ng/g, relative standard deviations less than 6%. In the 63 samples tested p, p'-DDT, a-HCH, d-HCH, aldrin, dieldrin, endrin, heptachlor, heptachlor epoxide and g-chlordane were determined, establishing concentrations between 27.1 and 469.6 ng/g. The frequencies of occurrence ranged between 1.6 and 65.1% for heptachlor and p, p'-DDT, respectively. The older population that lives in the sub-regions: Middle Sinú, San Jorge and Savannas were exposed to high health risk associated with the concentration a-HCH, aldrin and dieldrin in raw milk.

  2. Lysine Acetylation and Deacetylation in Brain Development and Neuropathies

    Directory of Open Access Journals (Sweden)

    Alicia Tapias

    2017-02-01

    Full Text Available Embryonic development is critical for the final functionality and maintenance of the adult brain. Brain development is tightly regulated by intracellular and extracellular signaling. Lysine acetylation and deacetylation are posttranslational modifications that are able to link extracellular signals to intracellular responses. A wealth of evidence indicates that lysine acetylation and deacetylation are critical for brain development and functionality. Indeed, mutations of the enzymes and cofactors responsible for these processes are often associated with neurodevelopmental and psychiatric disorders. Lysine acetylation and deacetylation are involved in all levels of brain development, starting from neuroprogenitor survival and proliferation, cell fate decisions, neuronal maturation, migration, and synaptogenesis, as well as differentiation and maturation of astrocytes and oligodendrocytes, to the establishment of neuronal circuits. Hence, fluctuations in the balance between lysine acetylation and deacetylation contribute to the final shape and performance of the brain. In this review, we summarize the current basic knowledge on the specific roles of lysine acetyltransferase (KAT and lysine deacetylase (KDAC complexes in brain development and the different neurodevelopmental disorders that are associated with dysfunctional lysine (deacetylation machineries.

  3. Mutation of aspartic acid-351, lysine-352, and lysine-515 alters the Ca2+ transport activity of the Ca2+-ATPase expressed in COS-1 cells.

    Science.gov (United States)

    Maruyama, K; MacLennan, D H

    1988-01-01

    Full-length cDNAs encoding neonatal and adult isoforms of the Ca2+-ATPase of rabbit fast-twitch skeletal muscle sarcoplasmic reticulum were expressed transiently in COS-1 cells. The microsomal fraction isolated from transfected COS-1 cells contained immunoreactive Ca2+-ATPase and catalyzed Ca2+ transport at rates at least 15-fold above controls. No differences were observed in either the rates or Ca2+ dependency of Ca2+ transport catalyzed by the two isoforms. Aspartic acid-351, the site of formation of the catalytic acyl phosphate in the enzyme, was mutated to asparagine, glutamic acid, serine, threonine, histidine, or alanine. In every case, Ca2+ transport activity and Ca2+-dependent phosphorylation were eliminated. Ca2+ transport was also eliminated by mutation of lysine-352 to arginine, glutamine, or glutamic acid or by mutation of Asp351-Lys352 to Lys351-Asp352. Mutation of lysine-515, the site of fluorescein isothiocyanate modification in the enzyme, resulted in diminished Ca2+ transport activity as follows: arginine, 60%; glutamine, 25%; glutamic acid, 5%. These results demonstrate the absolute requirement of acylphosphate formation for the Ca2+ transport function and define a residue important for ATP binding. They also demonstrate the feasibility of a thorough analysis of active sites in the Ca2+-ATPase by expression and site-specific mutagenesis. Images PMID:2966962

  4. HDAC inhibitors induce global changes in histone lysine and arginine methylation and alter expression of lysine demethylases.

    Science.gov (United States)

    Lillico, Ryan; Sobral, Marina Gomez; Stesco, Nicholas; Lakowski, Ted M

    2016-02-01

    Histone deacetylase (HDAC) inhibitors are cancer treatments that inhibit the removal of the epigenetic modification acetyllysine on histones, resulting in altered gene expression. Such changes in expression may influence other histone epigenetic modifications. We describe a validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to quantify lysine acetylation and methylation and arginine methylation on histones extracted from cultured cells treated with HDAC inhibitors. The HDAC inhibitors vorinostat, mocetinostat and entinostat induced 400-600% hyperacetylation in HEK 293 and K562 cells. All HDAC inhibitors decreased histone methylarginines in HEK 293 cells but entinostat produced dose dependent reductions in asymmetric dimethylarginine, not observed in K562 cells. Vorinostat produced increases in histone lysine methylation and decreased expression of some lysine demethylases (KDM), measured by quantitative PCR. Entinostat had variable effects on lysine methylation and decreased expression of some KDM while increasing expression of others. Mocetinostat produced dose dependent increases in histone lysine methylation by LC-MS/MS. This was corroborated with a multiplex colorimetric assay showing increases in histone H3 lysine 4, 9, 27, 36 and 79 methylation. Increases in lysine methylation were correlated with dose dependent decreases in the expression of seven KDM. Mocetinostat functions as an HDAC inhibitor and a de facto KDM inhibitor.

  5. pSuc-Lys: Predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach.

    Science.gov (United States)

    Jia, Jianhua; Liu, Zi; Xiao, Xuan; Liu, Bingxiang; Chou, Kuo-Chen

    2016-04-07

    Being one type of post-translational modifications (PTMs), protein lysine succinylation is important in regulating varieties of biological processes. It is also involved with some diseases, however. Consequently, from the angles of both basic research and drug development, we are facing a challenging problem: for an uncharacterized protein sequence having many Lys residues therein, which ones can be succinylated, and which ones cannot? To address this problem, we have developed a predictor called pSuc-Lys through (1) incorporating the sequence-coupled information into the general pseudo amino acid composition, (2) balancing out skewed training dataset by random sampling, and (3) constructing an ensemble predictor by fusing a series of individual random forest classifiers. Rigorous cross-validations indicated that it remarkably outperformed the existing methods. A user-friendly web-server for pSuc-Lys has been established at http://www.jci-bioinfo.cn/pSuc-Lys, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved. It has not escaped our notice that the formulation and approach presented here can also be used to analyze many other problems in computational proteomics.

  6. Lysine nutritional requirements of broilers reared in clean and dirty environments during the pre-starter and starter phases

    Directory of Open Access Journals (Sweden)

    Rodrigo Santana Toledo

    2011-10-01

    Full Text Available A total of 3,760 Ross male broiler chicks were used in two trials, one in the pre-starter (1-11 days phase and the other in the starter (12-22 days phase. Birds were distributed in a completely randomized experimental design with a factorial arrangement of 5 digestible lysine levels × 2 environments (clean and dirty environment, with eight replicates per treatment. The following dietary digestible lysine levels used were: 1.06, 1.12, 1.18, 1.24 and 1.30% in the pre-starter phase, and 1.00, 1.06, 1.12, 1.18 and 1.24% in the starter phase. Minimal relation of digestible lysine:digestible methionine + cystine, threonine, tryptophan and arginine (72, 67, 19 and 108%, respectively were maintained, as well as 2.088 and 2.002% of glycine+serine in the pre-starter and starter diets, respectively. Weight gain, feed intake and feed conversion were evaluated. In all phases, dietary digestible lysine levels significantly influenced broiler performance, and broilers reared in the clean environment presented better performance than those reared in the dirty environment. The recommended digestible lysine levels during the pre-starter and starter phases are 1.30 and 1.24% when broilers are reared in the clean enviroment and 1.26 and 1.165% in the dirty enviroment, respectively.

  7. Duplicate abalone egg coat proteins bind sperm lysin similarly, but evolve oppositely, consistent with molecular mimicry at fertilization.

    Directory of Open Access Journals (Sweden)

    Jan E Aagaard

    Full Text Available Sperm and egg proteins constitute a remarkable paradigm in evolutionary biology: despite their fundamental role in mediating fertilization (suggesting stasis, some of these molecules are among the most rapidly evolving ones known, and their divergence can lead to reproductive isolation. Because of strong selection to maintain function among interbreeding individuals, interacting fertilization proteins should also exhibit a strong signal of correlated divergence among closely related species. We use evidence of such molecular co-evolution to target biochemical studies of fertilization in North Pacific abalone (Haliotis spp., a model system of reproductive protein evolution. We test the evolutionary rates (d(N/d(S of abalone sperm lysin and two duplicated egg coat proteins (VERL and VEZP14, and find a signal of co-evolution specific to ZP-N, a putative sperm binding motif previously identified by homology modeling. Positively selected residues in VERL and VEZP14 occur on the same face of the structural model, suggesting a common mode of interaction with sperm lysin. We test this computational prediction biochemically, confirming that the ZP-N motif is sufficient to bind lysin and that the affinities of VERL and VEZP14 are comparable. However, we also find that on phylogenetic lineages where lysin and VERL evolve rapidly, VEZP14 evolves slowly, and vice versa. We describe a model of sexual conflict that can recreate this pattern of anti-correlated evolution by assuming that VEZP14 acts as a VERL mimic, reducing the intensity of sexual conflict and slowing the co-evolution of lysin and VERL.

  8. protein, tryptophan and lysine contents in quality protien maize ...

    African Journals Online (AJOL)

    owner

    for human nutrition recommended by Food and Agriculture Organization in ... METHODS: The protein, tryptophan and lysine contents of improved ... This study revealed the fact that genetic factor influences the protein, ... Ethiop J Health Sci.

  9. 蔬菜农药残留现状及其潜在风险分析%Present Status of Pesticide Residue in Vegetables and Its Potential Risk Analysis

    Institute of Scientific and Technical Information of China (English)

    叶雪珠; 赵燕申; 王强; 蒋玉根

    2012-01-01

    By detecting the pesticide use and 94 kinds pesticide residues in vegetable production in Zhejiang Province, major pesticide residue types at present and their risks in vegetable were analyzed. The results showed that 78 kinds of pesticides mainly used in vegetable production, including insecticide, fungicide, growth regulator and herbicide were mostly pesticides with high effective and low toxic. The detection of pesticide residues revealed that 28 pesticides got high detectable rate in vegetables, including acetamiprid, carbendazim, dursban, imidacloprid, morpholine, triazophos, propamocarb, pyridaben, etc.. The results also indicated that 46.4% of the detected pesticides with residual in vegetables were not found in using. But methamidophos and other highly toxic pesticides were still checked out. One of the main risks is some pesticide products without label and their component is unclear to customer. In addition, a unified standard testing method has not been established for 28 kinds of pesticides frequently used in vegetable production. Pesticide residue is still a security risk for vegetable consumption.%通过对浙江省蔬菜生产中使用农药情况调查和94种农药的残留检测,分析了目前蔬菜中主要残留农药品种及其潜在风险.结果发现,目前蔬菜生产中主要使用78种农药,包括杀虫剂、杀菌剂、生长调节剂和除草剂,以低毒农药品种为主;蔬菜中主要残留28种农药,检出频率较高的农药依次为啶虫脒、多菌灵、毒死蜱、吡虫啉、烯酰吗啉、三唑磷、霜霉威和哒螨灵等,检出的残留农药品种中,有46.4%在调查中未发现有使用,甲胺磷等高毒农药仍有检出.农药产品标识和农药成分不明是主要风险之一.此外,蔬菜中使用的28种农药尚未建立统一的标准检测方法,蔬菜食用仍存在农药残留安全风险.

  10. Digestible lysine levels in diets for laying Japanese quails

    Directory of Open Access Journals (Sweden)

    Cleverson Luís Nascimento Ribeiro

    2013-07-01

    Full Text Available The objective of this study was to estimate the digestible lysine requirement of Japanese quails in the egg-laying phase. A total of 336 female Japanese quails (Coturnix coturnix japonica of average initial age of 207 days were distributed in a completely randomized experimental design, composed of 6 treatments (lysine levels with 7 replicates and 8 birds per experimental unit, with duration of 84 days. Experimental diets were formulated from a basal diet, with corn and soybean meal, with 2.800 kcal ME/kg and 203.70 g/kg crude protein, showing levels of 9.50; 10.00; 10.50; 11.00; 11.50; and 12.00 g/kg digestible lysine; diets remained isoprotein and isocaloric. The following variables were studied: feed intake (FI; lysine intake (LI; egg production per bird per day (EPBD; egg production per bird housed (EPBH; production of marketable eggs (PME; egg weight (EW; egg mass (EM; utilization efficiency of lysine for egg mass production (UELEM; feed conversion per mass (FCEM; feed conversion per dozen eggs (FCDZ; bird availability (BA; percentages of yolk (Y, albumen (A and shell (S; specific egg weight (SW; nitrogen ingested (NI; nitrogen excreted (NE; and nitrogen balance (NB. Significant effect was only observed for LI, EW, EM, UELEM, FCEM, Y, A and SW. The digestible lysine level estimated in diets for laying Japanese quails is 11.20 g digestible lysine/kg diet, corresponding to an average daily intake of 272.23 mg lysine.

  11. H3 lysine 4 is acetylated at active gene promoters and is regulated by H3 lysine 4 methylation.

    Directory of Open Access Journals (Sweden)

    Benoit Guillemette

    2011-03-01

    Full Text Available Methylation of histone H3 lysine 4 (H3K4me is an evolutionarily conserved modification whose role in the regulation of gene expression has been extensively studied. In contrast, the function of H3K4 acetylation (H3K4ac has received little attention because of a lack of tools to separate its function from that of H3K4me. Here we show that, in addition to being methylated, H3K4 is also acetylated in budding yeast. Genetic studies reveal that the histone acetyltransferases (HATs Gcn5 and Rtt109 contribute to H3K4 acetylation in vivo. Whilst removal of H3K4ac from euchromatin mainly requires the histone deacetylase (HDAC Hst1, Sir2 is needed for H3K4 deacetylation in heterochomatin. Using genome-wide chromatin immunoprecipitation (ChIP, we show that H3K4ac is enriched at promoters of actively transcribed genes and located just upstream of H3K4 tri-methylation (H3K4me3, a pattern that has been conserved in human cells. We find that the Set1-containing complex (COMPASS, which promotes H3K4me2 and -me3, also serves to limit the abundance of H3K4ac at gene promoters. In addition, we identify a group of genes that have high levels of H3K4ac in their promoters and are inadequately expressed in H3-K4R, but not in set1Δ mutant strains, suggesting that H3K4ac plays a positive role in transcription. Our results reveal a novel regulatory feature of promoter-proximal chromatin, involving mutually exclusive histone modifications of the same histone residue (H3K4ac and H3K4me.

  12. A lysine-to-arginine mutation on NEDD8 markedly reduces the activity of cullin RING E3 ligase through the impairment of neddylation cascades

    Energy Technology Data Exchange (ETDEWEB)

    Sui, Yiyan; Liu, Yaobin; Xu, Guoqiang, E-mail: gux2002@suda.edu.cn

    2015-06-12

    Neural-precursor-cell-expressed developmentally down-regulated 8 (NEDD8) is a ubiquitin-like modifier, which forms covalent conjugates on lysines of its substrates. This post-translational modification, neddylation, plays important roles in tumor cell proliferation and viability. Ubiquitin can form diverse polyubiquitin chains, on its seven lysines, which play important functions in various biological processes. However, the roles of lysines in NEDD8 have not been explored. Here, we generated nine NEDD8 point mutants, each with one lysine replaced by an arginine, to study the putative function of lysines in NEDD8. Our experiments discover that Lys27 in NEDD8 is a critical residue for protein neddylation. Replacement of this residue with arginine almost completely eliminates the conjugation of NEDD8 to its substrates. Furthermore, we find that the K27R mutant impairs NEDD8 conjugation to the E2 enzyme, which normally forms thioester bonds for further transferring NEDD8 to its ligases and substrates. Therefore, this mutation completely inhibits global protein neddylation, including neddylation of cullin family proteins, resulting in decreased activity of cullin-RING E3 ligases. This work sheds new light on the roles of NEDD8 lysines on neddylation cascades and provides a dominant negative mutant for the study of neddylation and its biological functions. - Highlights: • Lys27 in NEDD8 is critical for protein neddylation. • NEDD8 K27R mutant impairs the NEDD8 conjugation. • NEDD8 K27R mutant significantly reduces the activity of cullin-RING E3 ligases.

  13. Maintenance requirement and deposition efficiency of lysine in pigs

    Directory of Open Access Journals (Sweden)

    Marcos Speroni Ceron

    2013-09-01

    Full Text Available The objective of this work was to determine the maintenance requirement and the deposition efficiency of lysine in growing pigs. It was used the incomplete changeover experimental design, with replicates over time. Twelve castrated pigs with average body weight (BW of 52±2 kg were kept in metabolism crates with a controlled temperature of 22ºC. The diets were formulated to supply 30, 50, 60, and 70% of the expected requirements of standardized lysine, and provided at 2.6 times the energy requirements for maintenance. The trial lasted 24 days and was divided into two periods of 12 days: seven days for animal adaptation to the diet and five days for sample collection. The increasing content of lysine in the diet did not affect dry matter intake of the pigs. The amount of nitrogen excreted was 47% of the nitrogen intake, of which 35% was excreted through feces and 65% through urine. The estimated endogenous losses of lysine were 36.4 mg kg-1 BW0.75. The maintenance requirement of lysine for pigs weighing around 50 kg is 40.4 mg kg-1 BW0.75, and the deposition efficiency of lysine is 90%.

  14. Targeting protein lysine methylation and demethylation in cancers

    Institute of Scientific and Technical Information of China (English)

    Yunlong He; Ilia Korboukh; Jian Jin; Jing Huang

    2012-01-01

    During the last decade,we saw an explosion of studies investigating the role of lysine methylation/demethylation of histones and non-histone proteins,such as p53,NF-kappaB,and E2F1.These ‘Ying-Yang' post-translational modifications are important to fine-tuning the activity of these proteins. Lysine methylation and demethylation are catalyzed by protein lysine methyltransferases (PKMTs) and protein lysine demethylases (PKDMs).PKMTs,PKDMs,and their substrates have been shown to play important roles in cancers.Although the underlying mechanisms of tumorigenesis are still largely unknown,growing evidence is starting to link aberrant regulation of methylation to tumorigenesis.This review focuses on summarizing the recent progress in understanding of the function of protein lysine methylation,and in the discovery of small molecule inhibitors for PKMTs and PKDMs.We also discuss the potential and the caveats of targeting protein lysine methylation for the treatment of cancer.

  15. Enzymic and chemical synthesis of epilson-N-(L-propionyl-2)-L-lysine.

    Science.gov (United States)

    Fujioka, M; Tanaka, M

    1978-10-01

    Pyruvate was shown to act as an oxo acid substrate in the reverse direction of saccharopine dehydrogenase [epsilon N-(L-glutaryl-2)-L-lysine: NAD oxidoreductase (L-lysine-forming)] reaction. The enzymic condensation product of lysine and pyruvate was isolated and identified as epsilon-N-(L-propionyl-2)-L-lysine by comparison with the synthetic compound. A method for the chemical preparation of diastereoisomers of epsilon-N-(propionyl-2)-L-lysine is also described.

  16. Affecting proton mobility in activated peptide and whole protein ions via lysine guanidination.

    Science.gov (United States)

    Pitteri, Sharon J; Reid, Gavin E; McLuckey, Scott A

    2004-01-01

    We have evaluated the effect of lysine guanidination in peptides and proteins on the dissociation of protonated ions in the gas phase. The dissociation of guanidinated model peptide ions compared to their unmodified forms showed behavior consistent with concepts of proton mobility as a major factor in determining favored fragmentation channels. Reduction of proton mobility associated with lysine guanidination was reflected by a relative increase in cleavages occurring C-terminal to aspartic acid residues as well as increases in small molecule losses. To evaluate the effect of guanidination on the dissociation behavior of whole protein ions, bovine ubiquitin was selected as a model. Essentially, all of the amide bond cleavages associated with the +10 charge state of fully guanidinated ubiquitin were observed to occur C-terminal to aspartic acid residues, unlike the dissociation behavior of the +10 ion of the unmodified protein, where competing cleavage N-terminal to proline and nonspecific amide bond cleavages were also observed. The +8 and lower charge states of the guanidinated protein showed prominent losses of small neutral molecules. This overall fragmentation behavior is consistent with current hypotheses regarding whole protein dissociation that consider proton mobility and intramolecular charge solvation as important factors in determining favored dissociation channels, and are also consistent with the fragmentation behaviors observed for the guanidinated model peptide ions. Further evaluation of the utility of condensed phase guanidination of whole proteins is necessary but the results described here confirm that guanidination can be an effective strategy for enhancing C-terminal aspartic acid cleavages. Gas phase dissociation exclusively at aspartic acid residues, especially for whole protein ions, could be useful in identifying and characterizing proteins via tandem mass spectrometry of whole protein ions.

  17. Lysine acetylation stoichiometry and proteomics analyses reveal pathways regulated by sirtuin 1 in human cells.

    Science.gov (United States)

    Gil, Jeovanis; Ramírez-Torres, Alberto; Chiappe, Diego; Luna-Peñaloza, Juan; Fernandez-Reyes, Francis C; Arcos-Encarnación, Bolivar; Contreras, Sandra; Encarnación-Guevara, Sergio

    2017-09-11

    Lysine acetylation is a widespread posttranslational modification (PTM) affecting many biological pathways. Recent studies indicate that acetylated lysine residues mainly exhibit low acetylation occupancy, but challenges in sample preparation and analysis make it difficult to confidently assign these numbers, limiting understanding of their biological significance. Here, we tested three common sample preparation methods to determine their suitability for assessing acetylation stoichiometry in three human cell lines, identifying the acetylation occupancy in more than 1,300 proteins from each cell line. The stoichiometric analysis in combination with quantitative proteomics also enabled us to explore their functional roles. We found that higher abundance of the deacetylase sirtuin 1 (SIRT1) correlated with lower acetylation occupancy and lower levels of ribosomal proteins including those involved in ribosome biogenesis and rRNA processing. Treatment with the SIRT1 inhibitor EX-527 confirmed SIRT1's role in the regulation of pre-rRNA synthesis and processing. Specifically, proteins involved in pre-rRNA transcription, including subunits of the Pol 1 and SL1 complexes and the RNA polymerase I specific transcription initiation factor RRN3 were up-regulated after SIRT1 inhibition. Moreover, many protein effectors and regulators of pre-rRNA processing needed for rRNA maturation were also up-regulated after EX-527 treatment, with the outcome that pre-rRNA and 28S rRNA levels also increased. More generally, we found that SIRT1 inhibition down-regulates metabolic pathways including glycolysis and pyruvate metabolism. Together, these results provide the largest dataset thus far of lysine acetylation stoichiometry (available via ProteomeXchange with identifier PXD005903) and set the stage for further biological investigations of this central PTM. Copyright © 2017, The American Society for Biochemistry and Molecular Biology.

  18. Converting the yeast arginine can1 permease to a lysine permease.

    Science.gov (United States)

    Ghaddar, Kassem; Krammer, Eva-Maria; Mihajlovic, Natalija; Brohée, Sylvain; André, Bruno; Prévost, Martine

    2014-03-01

    Amino acid uptake in yeast cells is mediated by about 16 plasma membrane permeases, most of which belong to the amino acid-polyamine-organocation (APC) transporter family. These proteins display various substrate specificity ranges. For instance, the general amino acid permease Gap1 transports all amino acids, whereas Can1 and Lyp1 catalyze specific uptake of arginine and lysine, respectively. Although Can1 and Lyp1 have different narrow substrate specificities, they are close homologs. Here we investigated the molecular rules determining the substrate specificity of the H(+)-driven arginine-specific permease Can1. Using a Can1-Lyp1 sequence alignment as a guideline and a three-dimensional Can1 structural model based on the crystal structure of the bacterial APC family arginine/agmatine antiporter, we introduced amino acid substitutions liable to alter Can1 substrate specificity. We show that the single substitution T456S results in a Can1 variant transporting lysine in addition to arginine and that the combined substitutions T456S and S176N convert Can1 to a Lyp1-like permease. Replacement of a highly conserved glutamate in the Can1 binding site leads to variants (E184Q and E184A) incapable of any amino acid transport, pointing to a potential role for this glutamate in H(+) coupling. Measurements of the kinetic parameters of arginine and lysine uptake by the wild-type and mutant Can1 permeases, together with docking calculations for each amino acid in their binding site, suggest a model in which residues at positions 176 and 456 confer substrate selectivity at the ligand-binding stage and/or in the course of conformational changes required for transport.

  19. Towards the development of activity-based probes for detection of lysine-specific demethylase-1 activity

    NARCIS (Netherlands)

    Ourailidou, Maria E.; Lenoci, Alessia; Zwergel, Clemens; Rotili, Dante; Mai, Antonello; Dekker, Frank J

    2017-01-01

    The implications of lysine-specific demethylase-1 (LSD1) in tumorigenesis have urged scientists to develop diagnostic tools in order to explore the function of this enzyme. In this work, we present our efforts on the development of tranylcypromine (TCP)-based functionalized probes for activity-based

  20. Crystal Structure of the Lysine Riboswitch Regulatory mRNA Element

    Energy Technology Data Exchange (ETDEWEB)

    Garst, A.; Heroux, A; Rambo, R; Batey, R

    2008-01-01

    Riboswitches are metabolite-sensitive elements found in mRNAs that control gene expression through a regulatory secondary structural switch. Along with regulation of lysine biosynthetic genes, mutations within the lysine-responsive riboswitch (L-box) play a role in the acquisition of resistance to antimicrobial lysine analogs. To understand the structural basis for lysine binding, we have determined the 2.8{angstrom} resolution crystal structure of lysine bound to the Thermotoga maritima asd lysine riboswitch ligand-binding domain. The structure reveals a complex architecture scaffolding a binding pocket completely enveloping lysine. Mutations conferring antimicrobial resistance cluster around this site as well as highly conserved long range interactions, indicating that they disrupt lysine binding or proper folding of the RNA. Comparison of the free and bound forms by x-ray crystallography, small angle x-ray scattering, and chemical probing reveals almost identical structures, indicating that lysine induces only limited and local conformational changes upon binding.

  1. Lysine methylation-dependent binding of 53BP1 to the pRb tumor suppressor.

    Science.gov (United States)

    Carr, Simon M; Munro, Shonagh; Zalmas, Lykourgos-Panagiotis; Fedorov, Oleg; Johansson, Catrine; Krojer, Tobias; Sagum, Cari A; Bedford, Mark T; Oppermann, Udo; La Thangue, Nicholas B

    2014-08-01

    The retinoblastoma tumor suppressor protein pRb is a key regulator of cell cycle progression and mediator of the DNA damage response. Lysine methylation at K810, which occurs within a critical Cdk phosphorylation motif, holds pRb in the hypophosphorylated growth-suppressing state. We show here that methyl K810 is read by the tandem tudor domain containing tumor protein p53 binding protein 1 (53BP1). Structural elucidation of 53BP1 in complex with a methylated K810 pRb peptide emphasized the role of the 53BP1 tandem tudor domain in recognition of the methylated lysine and surrounding residues. Significantly, binding of 53BP1 to methyl K810 occurs on E2 promoter binding factor target genes and allows pRb activity to be effectively integrated with the DNA damage response. Our results widen the repertoire of cellular targets for 53BP1 and suggest a previously unidentified role for 53BP1 in regulating pRb tumor suppressor activity.

  2. The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3

    DEFF Research Database (Denmark)

    Cloos, Paul A C; Christensen, Jesper; Agger, Karl;

    2006-01-01

    Methylation of lysine and arginine residues on histone tails affects chromatin structure and gene transcription. Tri- and dimethylation of lysine 9 on histone H3 (H3K9me3/me2) is required for the binding of the repressive protein HP1 and is associated with heterochromatin formation...... and transcriptional repression in a variety of species. H3K9me3 has long been regarded as a 'permanent' epigenetic mark. In a search for proteins and complexes interacting with H3K9me3, we identified the protein GASC1 (gene amplified in squamous cell carcinoma 1), which belongs to the JMJD2 (jumonji domain containing...... 2) subfamily of the jumonji family, and is also known as JMJD2C. Here we show that three members of this subfamily of proteins demethylate H3K9me3/me2 in vitro through a hydroxylation reaction requiring iron and alpha-ketoglutarate as cofactors. Furthermore, we demonstrate that ectopic expression...

  3. Design and synthesis of benzodiazepine analogs as isoform-selective human lysine deacetylase inhibitors.

    Science.gov (United States)

    Reddy, D Rajasekhar; Ballante, Flavio; Zhou, Nancy J; Marshall, Garland R

    2017-02-15

    A comprehensive investigation was performed to identify new benzodiazepine (BZD) derivatives as potent and selective human lysine deacetylase inhibitors (hKDACis). A total of 108 BZD compounds were designed, synthesized and from that 104 compounds were biologically evaluated against human lysine deacetylases (hKDACs) 1, 3 and 8 (class I) and 6 (class IIb). The most active compounds showed mid-nanomolar potencies against hKDACs 1, 3 and 6 and micromolar activity against hKDAC8, while a promising compound (6q) showed selectivity towards hKDAC3 among the different enzyme isoforms. An hKDAC6 homology model, refined by molecular dynamics simulation was generated, and molecular docking studies performed to rationalize the dominant ligand-residue interactions as well as to define structure-activity-relationships. Experimental results confirmed the usefulness of the benzodiazepine moiety as capping group when pursuing hKDAC isoform-selectivity inhibition, suggesting its continued use when designing new hKDACis.

  4. Chemoselective small molecules that covalently modify one lysine in a non-enzyme protein in plasma

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Sungwook; Connelly, Stephen; Reixach, Natàlia; Wilson, Ian A.; Kelly, Jeffery W. (Scripps)

    2010-02-19

    A small molecule that could bind selectively to and then react chemoselectively with a non-enzyme protein in a complex biological fluid, such as blood, could have numerous practical applications. Herein, we report a family of designed stilbenes that selectively and covalently modify the prominent plasma protein transthyretin in preference to more than 4,000 other human plasma proteins. They react chemoselectively with only one of eight lysine {epsilon}-amino groups within transthyretin. The crystal structure confirms the expected binding orientation of the stilbene substructure and the anticipated conjugating amide bond. These covalent transthyretin kinetic stabilizers exhibit superior amyloid inhibition potency compared to their noncovalent counterparts, and they prevent cytotoxicity associated with amyloidogenesis. Though there are a few prodrugs that, upon metabolic activation, react with a cysteine residue inactivating a specific non-enzyme, we are unaware of designed small molecules that react with one lysine {epsilon}-amine within a specific non-enzyme protein in a complex biological fluid.

  5. A new anaplerotic respiratory pathway involving lysine biosynthesis in isocitrate dehydrogenase-deficient Arabidopsis mutants.

    Science.gov (United States)

    Boex-Fontvieille, Edouard R A; Gauthier, Paul P G; Gilard, Françoise; Hodges, Michael; Tcherkez, Guillaume G B

    2013-08-01

    The cornerstone of carbon (C) and nitrogen (N) metabolic interactions - respiration - is presently not well understood in plant cells: the source of the key intermediate 2-oxoglutarate (2OG), to which reduced N is combined to yield glutamate and glutamine, remains somewhat unclear. We took advantage of combined mutations of NAD- and NADP-dependent isocitrate dehydrogenase activity and investigated the associated metabolic effects in Arabidopsis leaves (the major site of N assimilation in this genus), using metabolomics and (13)C-labelling techniques. We show that a substantial reduction in leaf isocitrate dehydrogenase activity did not lead to changes in the respiration efflux rate but respiratory metabolism was reorchestrated: 2OG production was supplemented by a metabolic bypass involving both lysine synthesis and degradation. Although the recycling of lysine has long been considered important in sustaining respiration, we show here that lysine neosynthesis itself participates in an alternative respiratory pathway. Lys metabolism thus contributes to explaining the metabolic flexibility of plant leaves and the effect (or the lack thereof) of respiratory mutations.

  6. Mass Spectrometry Analysis of Lysine Posttranslational Modifications of Tau Protein from Alzheimer's Disease Brain.

    Science.gov (United States)

    Thomas, Stefani N; Yang, Austin J

    2017-01-01

    Recent advances in mass spectrometry (MS)-based proteomics have greatly facilitated the robust identification and quantification of posttranslational modifications (PTMs), including those that are present at substoichiometric site occupancies. The abnormal posttranslational modification and accumulation of the microtubule-associated protein tau has been implicated in the pathogenesis of Alzheimer's disease (AD), and it is thought that the primary mode of regulation of tau occurs through PTMs. Several studies have been published regarding tau phosphorylation; however, other tau PTMs such as ubiquitylation, acetylation, methylation, oxidation, sumoylation, nitration, and glycosylation have not been analyzed as extensively. The comprehensive detection and delineation of these PTMs is critical for drug target discovery and validation. Lysine-directed PTMs including ubiquitylation, acetylation, and methylation play key regulatory roles with respect to the rates of tau turnover and aggregation. MS-based analytical approaches have been used to gain insight into the tau lysine-directed PTM signature that is most closely associated with neurofibrillary lesion formation. This chapter provides details pertaining to the liquid chromatography tandem mass spectrometry (LC-MS/MS)-based analysis of the lysine-directed posttranslational modification of tau.

  7. Dichotomy in the Epigenetic Mark Lysine Acetylation is Critical for the Proliferation of Prostate Cancer Cells

    Energy Technology Data Exchange (ETDEWEB)

    Pathak, Ravi [Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Ave, New York, NY 10029 (United States); Philizaire, Marc [Medgar Evers College, City University of New York, 1638 Bedford Ave, 403D, Brooklyn, NY 11225 (United States); Mujtaba, Shiraz, E-mail: smujtaba@mec.cuny.edu [Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Ave, New York, NY 10029 (United States); Medgar Evers College, City University of New York, 1638 Bedford Ave, 403D, Brooklyn, NY 11225 (United States)

    2015-08-19

    The dynamics of lysine acetylation serve as a major epigenetic mark, which regulates cellular response to inflammation, DNA damage and hormonal changes. Microarray assays reveal changes in gene expression, but cannot predict regulation of a protein function by epigenetic modifications. The present study employs computational tools to inclusively analyze microarray data to understand the potential role of acetylation during development of androgen-independent PCa. The data revealed that the androgen receptor interacts with 333 proteins, out of which at least 92 proteins were acetylated. Notably, the number of cellular proteins undergoing acetylation in the androgen-dependent PCa was more as compared to the androgen-independent PCa. Specifically, the 32 lysine-acetylated proteins in the cellular models of androgen-dependent PCa were mainly involved in regulating stability as well as pre- and post-processing of mRNA. Collectively, the data demonstrate that protein lysine acetylation plays a crucial role during the transition of androgen-dependent to -independent PCa, which importantly, could also serve as a functional axis to unravel new therapeutic targets.

  8. Human borna disease virus infection impacts host proteome and histone lysine acetylation in human oligodendroglia cells

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xia [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 (China); Department of Neurology, The Fifth People' s Hospital of Shanghai, School of Medicine, Fudan University, Shanghai, 200240 (China); Zhao, Libo [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 (China); Department of Neurology, The Third People' s Hospital of Chongqing, 400014 (China); Yang, Yongtao [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 (China); Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016 (China); Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016 (China); Bode, Liv [Bornavirus Research Group affiliated to the Free University of Berlin, Berlin (Germany); Huang, Hua [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 (China); Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016 (China); Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016 (China); Liu, Chengyu [Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016 (China); Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016 (China); Huang, Rongzhong [Department of Rehabilitative Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010 (China); Zhang, Liang [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 (China); Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016 (China); Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016 (China); and others

    2014-09-15

    Background: Borna disease virus (BDV) replicates in the nucleus and establishes persistent infections in mammalian hosts. A human BDV strain was used to address the first time, how BDV infection impacts the proteome and histone lysine acetylation (Kac) of human oligodendroglial (OL) cells, thus allowing a better understanding of infection-driven pathophysiology in vitro. Methods: Proteome and histone lysine acetylation were profiled through stable isotope labeling for cell culture (SILAC)-based quantitative proteomics. The quantifiable proteome was annotated using bioinformatics. Histone acetylation changes were validated by biochemistry assays. Results: Post BDV infection, 4383 quantifiable differential proteins were identified and functionally annotated to metabolism pathways, immune response, DNA replication, DNA repair, and transcriptional regulation. Sixteen of the thirty identified Kac sites in core histones presented altered acetylation levels post infection. Conclusions: BDV infection using a human strain impacted the whole proteome and histone lysine acetylation in OL cells. - Highlights: • A human strain of BDV (BDV Hu-H1) was used to infect human oligodendroglial cells (OL cells). • This study is the first to reveal the host proteomic and histone Kac profiles in BDV-infected OL cells. • BDV infection affected the expression of many transcription factors and several HATs and HDACs.

  9. Effects of lysine-induced acute renal failure in dogs.

    Science.gov (United States)

    Asanuma, Kentaro; Adachi, Kenji; Sugimoto, Tetsuro; Chiba, Shuichi

    2006-05-01

    This study investigates the effects of lysine-induced acute renal failure. Female dogs received a lysine hydrochloride (lysine) of 4500 mg/kg/day (3.75 ml/kg/hr) for 3 consecutive days. The dogs were observed for clinical signs. Body weights were recorded, food consumption and water consumption calculated, and urinalysis and blood biochemistry were performed daily. Plasma samples for amino acid determinations were obtained from all dogs, which were necropsied on Day 3. Histopathological examinations were done on all test animals. Compound-related findings include the following. Blood biochemistry results showed increases in ammonia, blood urea nitrogen, blood urea nitrogen/creatinine ratio, and creatinine. Urinary changes consisted of increases in urine volume, total protein, albumin, gamma-glutamyl transpeptidase, and N-acetyl-beta-D-glucosaminidase. In addition, macroscopic findings consisted of pale, congested capsule; microscopic findings consisted of hypertrophy of proximal convoluted tubule (mainly S1 segment), and degeneration/desquamation of urinary tubule (mainly S3 segment with hyaline casts) in the kidney. From these findings, it can be concluded that lysine is nephrotoxic in dogs. Nephrotoxicity of lysine may relate to direct tubular toxicity and to tubular obstruction.

  10. Seed-Specific Expression of a Lysine-Rich Protein Gene, GhLRP, from Cotton Significantly Increases the Lysine Content in Maize Seeds

    Directory of Open Access Journals (Sweden)

    Jing Yue

    2014-03-01

    Full Text Available Maize seed storage proteins are a major source of human and livestock consumption. However, these proteins have poor nutritional value, because they are deficient in lysine and tryptophan. Much research has been done to elevate the lysine content by reducing zein content or regulating the activities of key enzymes in lysine metabolism. Using the naturally lysine-rich protein genes, sb401 and SBgLR, from potato, we previously increased the lysine and protein contents of maize seeds. Here, we examined another natural lysine-rich protein gene, GhLRP, from cotton, which increased the lysine content of transgenic maize seeds at levels varying from 16.2% to 65.0% relative to the wild-type. The total protein content was not distinctly different, except in the six transgenic lines. The lipid and starch levels did not differ substantially in Gossypium hirsutum L. lysine-rich protein (GhLRP transgenic kernels when compared to wild-type. The agronomic characteristics of all the transgenic maize were also normal. GhLRP is a high-lysine protein candidate gene for increasing the lysine content of maize. This study provided a valuable model system for improving maize lysine content.

  11. Seed-specific expression of a lysine-rich protein gene, GhLRP, from cotton significantly increases the lysine content in maize seeds.

    Science.gov (United States)

    Yue, Jing; Li, Cong; Zhao, Qian; Zhu, Dengyun; Yu, Jingjuan

    2014-03-27

    Maize seed storage proteins are a major source of human and livestock consumption. However, these proteins have poor nutritional value, because they are deficient in lysine and tryptophan. Much research has been done to elevate the lysine content by reducing zein content or regulating the activities of key enzymes in lysine metabolism. Using the naturally lysine-rich protein genes, sb401 and SBgLR, from potato, we previously increased the lysine and protein contents of maize seeds. Here, we examined another natural lysine-rich protein gene, GhLRP, from cotton, which increased the lysine content of transgenic maize seeds at levels varying from 16.2% to 65.0% relative to the wild-type. The total protein content was not distinctly different, except in the six transgenic lines. The lipid and starch levels did not differ substantially in Gossypium hirsutum L. lysine-rich protein (GhLRP) transgenic kernels when compared to wild-type. The agronomic characteristics of all the transgenic maize were also normal. GhLRP is a high-lysine protein candidate gene for increasing the lysine content of maize. This study provided a valuable model system for improving maize lysine content.

  12. How modification of accessible lysines to phenylalanine modulates the structural and functional properties of horseradish peroxidase: a simulation study.

    Directory of Open Access Journals (Sweden)

    Leila Navapour

    Full Text Available Horseradish Peroxidase (HRP is one of the most studied peroxidases and a great number of chemical modifications and genetic manipulations have been carried out on its surface accessible residues to improve its stability and catalytic efficiency necessary for biotechnological applications. Most of the stabilized derivatives of HRP reported to date have involved chemical or genetic modifications of three surface-exposed lysines (K174, K232 and K241. In this computational study, we altered these lysines to phenylalanine residues to model those chemical modifications or genetic manipulations in which these positively charged lysines are converted to aromatic hydrophobic residues. Simulation results implied that upon these substitutions, the protein structure becomes less flexible. Stability gains are likely to be achieved due to the increased number of stable hydrogen bonds, improved heme-protein interactions and more integrated proximal Ca2+ binding pocket. We also found a new persistent hydrogen bond between the protein moiety (F174 and the heme prosthetic group as well as two stitching hydrogen bonds between the connecting loops GH and F'F″ in mutated HRP. However, detailed analysis of functionally related structural properties and dynamical features suggests reduced reactivity of the enzyme toward its substrates. Molecular dynamics simulations showed that substitutions narrow the bottle neck entry of peroxide substrate access channel and reduce the surface accessibility of the distal histidine (H42 and heme prosthetic group to the peroxide and aromatic substrates, respectively. Results also demonstrated that the area and volume of the aromatic-substrate binding pocket are significantly decreased upon modifications. Moreover, the hydrophobic patch functioning as a binding site or trap for reducing aromatic substrates is shrunk in mutated enzyme. Together, the results of this simulation study could provide possible structural clues to explain

  13. How modification of accessible lysines to phenylalanine modulates the structural and functional properties of horseradish peroxidase: a simulation study.

    Science.gov (United States)

    Navapour, Leila; Mogharrab, Navid; Amininasab, Mehriar

    2014-01-01

    Horseradish Peroxidase (HRP) is one of the most studied peroxidases and a great number of chemical modifications and genetic manipulations have been carried out on its surface accessible residues to improve its stability and catalytic efficiency necessary for biotechnological applications. Most of the stabilized derivatives of HRP reported to date have involved chemical or genetic modifications of three surface-exposed lysines (K174, K232 and K241). In this computational study, we altered these lysines to phenylalanine residues to model those chemical modifications or genetic manipulations in which these positively charged lysines are converted to aromatic hydrophobic residues. Simulation results implied that upon these substitutions, the protein structure becomes less flexible. Stability gains are likely to be achieved due to the increased number of stable hydrogen bonds, improved heme-protein interactions and more integrated proximal Ca2+ binding pocket. We also found a new persistent hydrogen bond between the protein moiety (F174) and the heme prosthetic group as well as two stitching hydrogen bonds between the connecting loops GH and F'F″ in mutated HRP. However, detailed analysis of functionally related structural properties and dynamical features suggests reduced reactivity of the enzyme toward its substrates. Molecular dynamics simulations showed that substitutions narrow the bottle neck entry of peroxide substrate access channel and reduce the surface accessibility of the distal histidine (H42) and heme prosthetic group to the peroxide and aromatic substrates, respectively. Results also demonstrated that the area and volume of the aromatic-substrate binding pocket are significantly decreased upon modifications. Moreover, the hydrophobic patch functioning as a binding site or trap for reducing aromatic substrates is shrunk in mutated enzyme. Together, the results of this simulation study could provide possible structural clues to explain those experimental

  14. Dissecting the functional role of key residues in triheme cytochrome PpcA: a path to rational design of G. sulfurreducens strains with enhanced electron transfer capabilities.

    Science.gov (United States)

    Morgado, Leonor; Lourenço, Sílvia; Londer, Yuri Y; Schiffer, Marianne; Pokkuluri, P Raj; Salgueiro, Carlos A

    2014-01-01

    PpcA is the most abundant member of a family of five triheme cytochromes c7 in the bacterium Geobacter sulfurreducens (Gs) and is the most likely carrier of electrons destined for outer surface during respiration on solid metal oxides, a process that requires extracellular electron transfer. This cytochrome has the highest content of lysine residues (24%) among the family, and it was suggested to be involved in e-/H(+) energy transduction processes. In the present work, we investigated the functional role of lysine residues strategically located in the vicinity of each heme group. Each lysine was replaced by glutamine or glutamic acid to evaluate the effects of a neutral or negatively charged residue in each position. The results showed that replacing Lys9 (located near heme IV), Lys18 (near heme I) or Lys22 (between hemes I and III) has essentially no effect on the redox properties of the heme groups and are probably involved in redox partner recognition. On the other hand, Lys43 (near heme IV), Lys52 (between hemes III and IV) and Lys60 (near heme III) are crucial in the regulation of the functional mechanism of PpcA, namely in the selection of microstates that allow the protein to establish preferential e-/H(+) transfer pathways. The results showed that the preferred e-/H(+) transfer pathways are only established when heme III is the last heme to oxidize, a feature reinforced by a higher difference between its reduction potential and that of its predecessor in the order of oxidation. We also showed that K43 and K52 mutants keep the mechanistic features of PpcA by establishing preferential e-/H+ transfer pathways at lower reduction potential values than the wild-type protein, a property that can enable rational design of Gs strains with optimized extracellular electron transfer capabilities.

  15. Dissecting the Functional Role of Key Residues in Triheme Cytochrome PpcA: A Path to Rational Design of G. sulfurreducens Strains with Enhanced Electron Transfer Capabilities

    Science.gov (United States)

    Morgado, Leonor; Lourenço, Sílvia; Londer, Yuri Y.; Schiffer, Marianne; Pokkuluri, P. Raj; Salgueiro, Carlos A.

    2014-01-01

    PpcA is the most abundant member of a family of five triheme cytochromes c7 in the bacterium Geobacter sulfurreducens (Gs) and is the most likely carrier of electrons destined for outer surface during respiration on solid metal oxides, a process that requires extracellular electron transfer. This cytochrome has the highest content of lysine residues (24%) among the family, and it was suggested to be involved in e−/H+ energy transduction processes. In the present work, we investigated the functional role of lysine residues strategically located in the vicinity of each heme group. Each lysine was replaced by glutamine or glutamic acid to evaluate the effects of a neutral or negatively charged residue in each position. The results showed that replacing Lys9 (located near heme IV), Lys18 (near heme I) or Lys22 (between hemes I and III) has essentially no effect on the redox properties of the heme groups and are probably involved in redox partner recognition. On the other hand, Lys43 (near heme IV), Lys52 (between hemes III and IV) and Lys60 (near heme III) are crucial in the regulation of the functional mechanism of PpcA, namely in the selection of microstates that allow the protein to establish preferential e−/H+ transfer pathways. The results showed that the preferred e−/H+ transfer pathways are only established when heme III is the last heme to oxidize, a feature reinforced by a higher difference between its reduction potential and that of its predecessor in the order of oxidation. We also showed that K43 and K52 mutants keep the mechanistic features of PpcA by establishing preferential e−/H+ transfer pathways at lower reduction potential values than the wild-type protein, a property that can enable rational design of Gs strains with optimized extracellular electron transfer capabilities. PMID:25153891

  16. Dissecting the functional role of key residues in triheme cytochrome PpcA: a path to rational design of G. sulfurreducens strains with enhanced electron transfer capabilities.

    Directory of Open Access Journals (Sweden)

    Leonor Morgado

    Full Text Available PpcA is the most abundant member of a family of five triheme cytochromes c7 in the bacterium Geobacter sulfurreducens (Gs and is the most likely carrier of electrons destined for outer surface during respiration on solid metal oxides, a process that requires extracellular electron transfer. This cytochrome has the highest content of lysine residues (24% among the family, and it was suggested to be involved in e-/H(+ energy transduction processes. In the present work, we investigated the functional role of lysine residues strategically located in the vicinity of each heme group. Each lysine was replaced by glutamine or glutamic acid to evaluate the effects of a neutral or negatively charged residue in each position. The results showed that replacing Lys9 (located near heme IV, Lys18 (near heme I or Lys22 (between hemes I and III has essentially no effect on the redox properties of the heme groups and are probably involved in redox partner recognition. On the other hand, Lys43 (near heme IV, Lys52 (between hemes III and IV and Lys60 (near heme III are crucial in the regulation of the functional mechanism of PpcA, namely in the selection of microstates that allow the protein to establish preferential e-/H(+ transfer pathways. The results showed that the preferred e-/H(+ transfer pathways are only established when heme III is the last heme to oxidize, a feature reinforced by a higher difference between its reduction potential and that of its predecessor in the order of oxidation. We also showed that K43 and K52 mutants keep the mechanistic features of PpcA by establishing preferential e-/H+ transfer pathways at lower reduction potential values than the wild-type protein, a property that can enable rational design of Gs strains with optimized extracellular electron transfer capabilities.

  17. Identification of structural determinants of NAD(P)H selectivity and lysine binding in lysine N(6)-monooxygenase.

    Science.gov (United States)

    Abdelwahab, Heba; Robinson, Reeder; Rodriguez, Pedro; Adly, Camelia; El-Sohaimy, Sohby; Sobrado, Pablo

    2016-09-15

    l-lysine (l-Lys) N(6)-monooxygenase (NbtG), from Nocardia farcinica, is a flavin-dependent enzyme that catalyzes the hydroxylation of l-Lys in the presence of oxygen and NAD(P)H in the biosynthetic pathway of the siderophore nocobactin. NbtG displays only a 3-fold preference for NADPH over NADH, different from well-characterized related enzymes, which are highly selective for NADPH. The structure of NbtG with bound NAD(P)(+) or l-Lys is currently not available. Herein, we present a mutagenesis study targeting M239, R301, and E216. These amino acids are conserved and located in either the NAD(P)H binding domain or the l-Lys binding pocket. M239R resulted in high production of hydrogen peroxide and little hydroxylation with no change in coenzyme selectivity. R301A caused a 300-fold decrease on kcat/Km value with NADPH but no change with NADH. E216Q increased the Km value for l-Lys by 30-fold with very little change on the kcat value or in the binding of NAD(P)H. These results suggest that R301 plays a major role in NADPH selectivity by interacting with the 2'-phosphate of the adenine-ribose moiety of NADPH, while E216 plays a role in l-Lys binding.

  18. Amine oxidation mediated by lysine-specific demethylase 1: quantum mechanics/molecular mechanics insights into mechanism and role of lysine 661.

    Science.gov (United States)

    Karasulu, Bora; Patil, Mahendra; Thiel, Walter

    2013-09-11

    We report classical molecular dynamics (MD) simulations and combined quantum mechanics/molecular mechanics (QM/MM) calculations to elucidate the catalytic mechanism of the rate-determining amine oxidation step in the lysine-specific demethylase 1 (LSD1)-catalyzed demethylation of the histone tail lysine (H3K4), with flavin adenine dinucleotide (FAD) acting as cofactor. The oxidation of substrate lysine (sLys) involves the cleavage of an α-CH bond accompanied by the transfer of a hydride ion equivalent to FAD, leading to an imine intermediate. This hydride transfer pathway is shown to be clearly favored for sLys oxidation over other proposed mechanisms, including the radical (or single-electron transfer) route as well as carbanion and polar-nucleophilic mechanisms. MD simulations on six NVT ensembles (covering different protonation states of sLys and K661 as well as the K661M mutant) identify two possible orientations of the reacting sLys and FAD subunits (called "downward" and "upward"). Calculations at the QM(B3LYP-D/6-31G*)/CHARMM22 level provide molecular-level insights into the mechanism, helping to understand how LSD1 achieves the activation of the rather inert methyl-CH bond in a metal-free environment. Factors such as proper alignment of sLys (downward orientation), transition-state stabilization (due to the protein environment and favorable orbital interactions), and product stabilization via adduct formation are found to be crucial for facilitating the oxidative α-CH bond cleavage. The current study also sheds light on the role of important active-site residues (Y761, K661, and W695) and of the conserved water-bridge motif. The steric influence of Y761 helps to position the reaction partners properly, K661 is predicted to get deprotonated prior to substrate binding and to act as an active-site base that accepts a proton from sLys to enable the subsequent amine oxidation, and the water bridge that is stabilized by K661 and W695 mediates this proton

  19. Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines

    DEFF Research Database (Denmark)

    Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.;

    2011-01-01

    Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation....... This method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously and can directly calculate the geometrical difference induced by H/D isotope effects. The calculations show that the one-bond deuterium isotope effects on 15N nuclear shielding, 1Δ15N......(D), in ammonium and amines decrease as a counterion or water molecule moves closer to the nitrogen. 1Δ15N(D) and 2Δ1H(D) of the NH3+ groups of lysine residues in the B1 domain of protein G have been calculated using truncated side chains and also determined experimentally by NMR. Comparisons show...

  20. Androgen receptor and histone lysine demethylases in ovine placenta.

    Directory of Open Access Journals (Sweden)

    Ellane R Cleys

    Full Text Available Sex steroid hormones regulate developmental programming in many tissues, including programming gene expression during prenatal development. While estradiol is known to regulate placentation, little is known about the role of testosterone and androgen signaling in placental development despite the fact that testosterone rises in maternal circulation during pregnancy and in placenta-induced pregnancy disorders. We investigated the role of testosterone in placental gene expression, and focused on androgen receptor (AR. Prenatal androgenization decreased global DNA methylation in gestational day 90 placentomes, and increased placental expression of AR as well as genes involved in epigenetic regulation, angiogenesis, and growth. As AR complexes with histone lysine demethylases (KDMs to regulate AR target genes in human cancers, we also investigated if the same mechanism is present in the ovine placenta. AR co-immunoprecipitated with KDM1A and KDM4D in sheep placentomes, and AR-KDM1A complexes were recruited to a half-site for androgen response element (ARE in the promoter region of VEGFA. Androgenized ewes also had increased cotyledonary VEGFA. Finally, in human first trimester placental samples KDM1A and KDM4D immunolocalized to the syncytiotrophoblast, with nuclear KDM1A and KDM4D immunostaining also present in the villous stroma. In conclusion, placental androgen signaling, possibly through AR-KDM complex recruitment to AREs, regulates placental VEGFA expression. AR and KDMs are also present in first trimester human placenta. Androgens appear to be an important regulator of trophoblast differentiation and placental development, and aberrant androgen signaling may contribute to the development of placental disorders.

  1. Lysine-iron agar in the detection of Arizona cultures.

    Science.gov (United States)

    EDWARDS, P R; FIFE, M A

    1961-11-01

    A lysine-iron agar is described and recommended for the detection of Arizona strains which ferment lactose rapidly. Black colonies which appear on bismuth sulfite agar should be transferred to the medium. Salmonellae and Arizona cultures produce a distinctive reaction since they are the only recognized groups of enteric bacteria which regularly produce lysine decarboxylase rapidly and form large amounts of hydrogen sulfide. Use of the medium is particularly recommended in the examination of specimens from enteric infections in which shigellae and salmonellae are not detected.

  2. Sugar Substrates for l-Lysine Fermentation by Ustilago maydis

    Science.gov (United States)

    Sánchez-Marroquín, A.; Ledezma, M.; Carreño, R.

    1970-01-01

    The extracellular production of l-lysine in media with cane sugar, blackstrap molasses, or clarified sugar-cane juice by a previously obtained mutant of Ustilago maydis was studied. Enzymatically inverted clarified juice (medium J-3) gave 2.9 g of lysine per liter under the following conditions: inoculum, 5%; pH 5.8; temperature, 30 C; KLa in the fermentors, 0.41 mmoles of O2 per liter per min; fermentation time, 72 hr. The concentrate, obtained by direct evaporation and drying of the fermentation broth, could be used as a possible feed supplement because of its amino-acid and vitamin content. PMID:5485081

  3. Quadratic residues and non-residues selected topics

    CERN Document Server

    Wright, Steve

    2016-01-01

    This book offers an account of the classical theory of quadratic residues and non-residues with the goal of using that theory as a lens through which to view the development of some of the fundamental methods employed in modern elementary, algebraic, and analytic number theory. The first three chapters present some basic facts and the history of quadratic residues and non-residues and discuss various proofs of the Law of Quadratic Reciprosity in depth, with an emphasis on the six proofs that Gauss published. The remaining seven chapters explore some interesting applications of the Law of Quadratic Reciprocity, prove some results concerning the distribution and arithmetic structure of quadratic residues and non-residues, provide a detailed proof of Dirichlet’s Class-Number Formula, and discuss the question of whether quadratic residues are randomly distributed. The text is a valuable resource for graduate and advanced undergraduate students as well as for mathematicians interested in number theory.

  4. Effect of Selected Plant Extracts and D- and L-Lysine on the Cyanobacterium Microcystis aeruginosa

    National Research Council Canada - National Science Library

    Lurling, M; Van Oosterhout, F

    2014-01-01

    We tested extracts from Fructus mume, Salvia miltiorrhiza and Moringa oleifera as well as L-lysine and D-Lysine as curative measures to rapidly suppress the cyanobacterium Microcystis aeruginosa NIVA-CYA 43...

  5. Lysine-Grafted MCM-41 Silica as an Antibacterial Biomaterial

    Directory of Open Access Journals (Sweden)

    María F. Villegas

    2017-09-01

    Full Text Available This paper proposes a facile strategy for the zwitterionization of bioceramics that is based on the direct incorporation of l-lysine amino acid via the ε-amino group onto mesoporous MCM-41 materials. Fourier transform infrared (FTIR studies of lysine-grafted MCM-41 (MCM-LYS simultaneously showed bands at 3080 and 1540 cm−1 and bands at 1625 and 1415 cm−1 corresponding to -NH3+/COO− pairs, which demonstrate the incorporation of the amino acid on the material surface keeping its zwitterionic character. Both elemental and thermogravimetric analyses showed that the amount of grafted lysine was 8 wt. % based on the bioceramic total weight. Moreover, MCM-LYS exhibited a reduction of adhesion of S. aureus and E. coli bacteria in 33% and 50%, respectively at physiological pH, as compared with pristine MCM-41. Biofilm studies onto surfaces showed that lysine functionalization elicited a reduction of the area covered by S. aureus biofilm from 42% to only 5% (88%. This research shows a simple and effective approach to chemically modify bioceramics using single amino acids that provides zwitterionic functionality, which is useful to develop new biomaterials that are able to resist bacterial adhesion.

  6. [Modification of the lysine-iron agar (author's transl)].

    Science.gov (United States)

    Wauters, G

    1975-12-01

    The addition of L-phenylalanine to the lysine-iron agar described by Edwards and Fife ]1] allows a more valuable screening of the Proteus group based on its deamination properties. Some minor modifications of the indicator and thiosulfate content lead to improve and earlier recording of the results.

  7. Detection of salt bridges to lysines in solution in barnase

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Williamson, Michael P.; Hounslow, Andrea M.

    2013-01-01

    We show that salt bridges involving lysines can be detected by deuterium isotope effects on NMR chemical shifts of the sidechain amine. Lys27 in the ribonuclease barnase is salt bridged, and mutation of Arg69 to Lys retains a partially buried salt bridge. The salt bridges are functionally important....

  8. Requirement of the laying hen for apparent fecal digestible lysine

    NARCIS (Netherlands)

    Schutte, J.B.; Smink, W.

    1998-01-01

    A study was conducted to determine the requirement for lysine of a White Leghorn strain of hens with a body weight of approximately 1,600 g. Before starting the experiment, apparent fecal digestibility of amino acids of the basal diet was determined in an in vivo digestibility trial with six individ

  9. Predicting post-translational lysine acetylation using support vector machines

    DEFF Research Database (Denmark)

    Gnad, Florian; Ren, Shubin; Choudhary, Chunaram

    2010-01-01

    spectrometry to identify 3600 lysine acetylation sites on 1750 human proteins covering most of the previously annotated sites and providing the most comprehensive acetylome so far. This dataset should provide an excellent source to train support vector machines (SVMs) allowing the high accuracy in silico...

  10. effects of dietary chromium tripicolinate and lysine on growth ...

    African Journals Online (AJOL)

    AISA

    Six traitements ont été répétés quatre fois, avec quatre porcs par répétition. Au cours de cette ... The potential capability of lysine to improve ... (chromium picolinate) on animal productivity has ... cholesterol (Sigma, 1989a), and total proteins.

  11. Amino acid nutrition beyond methionine and lysine for milk protein

    Science.gov (United States)

    Amino acids are involved in many important physiological processes affecting the production, health, and reproduction of high-producing dairy cows. Most research and recommendations for lactating dairy cows has focused on methionine and lysine for increasing milk protein yield. This is because these...

  12. File list: Oth.Gon.50.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  20. File list: His.Bld.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bld.10.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation B...lood http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Bld.10.Pan_lysine_crotonylation.AllCell.bed ...

  1. File list: His.Liv.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Liv.05.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Li...ver http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Liv.05.Pan_lysine_crotonylation.AllCell.bed ...

  2. File list: His.Epd.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Epd.20.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Ep...idermis http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Epd.20.Pan_lysine_crotonylation.AllCell.bed ...

  3. File list: His.Kid.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Kid.50.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation K...idney http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Kid.50.Pan_lysine_crotonylation.AllCell.bed ...

  4. File list: His.Lng.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lng.50.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Lu...ng http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Lng.50.Pan_lysine_crotonylation.AllCell.bed ...

  5. File list: His.Lng.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lng.10.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation L...ung SRX099891 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Lng.10.Pan_lysine_crotonylation.AllCell.bed ...

  6. File list: His.PSC.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.PSC.10.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation P...luripotent stem cell http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.PSC.10.Pan_lysine_crotonylation.AllCell.bed ...

  7. File list: His.Emb.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Emb.10.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Em...bryo http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Emb.10.Pan_lysine_crotonylation.AllCell.bed ...

  8. File list: His.Kid.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Kid.05.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation K...idney http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Kid.05.Pan_lysine_crotonylation.AllCell.bed ...

  9. File list: His.Unc.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Unc.20.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Un...classified http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Unc.20.Pan_lysine_crotonylation.AllCell.bed ...

  10. File list: His.Unc.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Unc.50.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation U...nclassified http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Unc.50.Pan_lysine_crotonylation.AllCell.bed ...

  11. File list: His.Kid.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Kid.05.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Ki...dney http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Kid.05.Pan_lysine_crotonylation.AllCell.bed ...

  12. File list: His.Pan.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Pan.05.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation P...ancreas http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Pan.05.Pan_lysine_crotonylation.AllCell.bed ...

  13. File list: His.Adp.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Adp.10.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation A...dipocyte http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Adp.10.Pan_lysine_crotonylation.AllCell.bed ...

  14. File list: His.Prs.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Prs.05.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation P...rostate http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Prs.05.Pan_lysine_crotonylation.AllCell.bed ...

  15. File list: His.Utr.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Utr.50.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation U...terus http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Utr.50.Pan_lysine_crotonylation.AllCell.bed ...

  16. File list: His.Bld.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bld.05.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation B...lood http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Bld.05.Pan_lysine_crotonylation.AllCell.bed ...

  17. File list: Oth.Dig.05.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Dig.05.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Digestive tra...ct http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Dig.05.Crotonyl_lysine.AllCell.bed ...

  18. File list: His.Kid.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Kid.10.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation K...idney http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Kid.10.Pan_lysine_crotonylation.AllCell.bed ...

  19. File list: Oth.NoD.20.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.NoD.20.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine No descriptio...n http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.NoD.20.Crotonyl_lysine.AllCell.bed ...

  20. File list: Oth.EmF.05.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.EmF.05.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Embryonic fib...roblast http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.EmF.05.Crotonyl_lysine.AllCell.bed ...

  1. File list: His.CDV.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.CDV.20.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Ca...rdiovascular http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.CDV.20.Pan_lysine_crotonylation.AllCell.bed ...

  2. File list: His.Pan.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Pan.10.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Pa...ncreas http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Pan.10.Pan_lysine_crotonylation.AllCell.bed ...

  3. File list: His.PSC.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.PSC.20.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Pl...uripotent stem cell http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.PSC.20.Pan_lysine_crotonylation.AllCell.bed ...

  4. File list: His.Dig.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Dig.10.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Di...gestive tract http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Dig.10.Pan_lysine_crotonylation.AllCell.bed ...

  5. File list: His.Brs.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Brs.10.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation B...reast http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Brs.10.Pan_lysine_crotonylation.AllCell.bed ...

  6. File list: His.Bld.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bld.50.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation B...lood http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Bld.50.Pan_lysine_crotonylation.AllCell.bed ...

  7. File list: Oth.Dig.20.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Dig.20.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Digestive tra...ct http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Dig.20.Crotonyl_lysine.AllCell.bed ...

  8. File list: His.Myo.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Myo.05.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation M...uscle http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Myo.05.Pan_lysine_crotonylation.AllCell.bed ...

  9. File list: His.Adp.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Adp.50.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Ad...ipocyte http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Adp.50.Pan_lysine_crotonylation.AllCell.bed ...

  10. File list: His.Emb.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Emb.20.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Em...bryo http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Emb.20.Pan_lysine_crotonylation.AllCell.bed ...

  11. File list: His.Oth.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Oth.20.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation O...thers http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Oth.20.Pan_lysine_crotonylation.AllCell.bed ...

  12. File list: His.Plc.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Plc.20.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation P...lacenta http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Plc.20.Pan_lysine_crotonylation.AllCell.bed ...

  13. File list: His.Myo.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Myo.10.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation M...uscle http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Myo.10.Pan_lysine_crotonylation.AllCell.bed ...

  14. File list: Oth.CDV.20.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.CDV.20.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Cardiovascula...r http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.CDV.20.Crotonyl_lysine.AllCell.bed ...

  15. File list: His.Bon.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bon.05.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation B...one http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Bon.05.Pan_lysine_crotonylation.AllCell.bed ...

  16. File list: His.Dig.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Dig.50.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Diges...tive tract http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Dig.50.Pan_lysine_acetylation.AllCell.bed ...

  17. File list: His.Pan.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Pan.05.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Pancre...as http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Pan.05.Pan_lysine_acetylation.AllCell.bed ...

  18. File list: His.Unc.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Unc.10.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Uncla...ssified http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Unc.10.Pan_lysine_acetylation.AllCell.bed ...

  19. File list: His.Pan.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Pan.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Pancr...eas http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Pan.20.Pan_lysine_acetylation.AllCell.bed ...

  20. File list: His.Neu.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Neural... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Neu.20.Pan_lysine_acetylation.AllCell.bed ...

  1. File list: His.Epd.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Epd.05.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Epide...rmis http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Epd.05.Pan_lysine_acetylation.AllCell.bed ...

  2. File list: His.Brs.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Brs.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Breast... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Brs.20.Pan_lysine_acetylation.AllCell.bed ...

  3. File list: His.Dig.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Dig.05.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Diges...tive tract http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Dig.05.Pan_lysine_acetylation.AllCell.bed ...

  4. File list: His.Prs.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Prs.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Prosta...te http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Prs.20.Pan_lysine_acetylation.AllCell.bed ...

  5. File list: His.Liv.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Liv.50.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Liver ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Liv.50.Pan_lysine_acetylation.AllCell.bed ...

  6. File list: His.Myo.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Myo.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Muscle... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Myo.20.Pan_lysine_acetylation.AllCell.bed ...

  7. File list: His.ALL.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.ALL.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation All ce...ll types SRX099893,SRX099896 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.ALL.10.Pan_lysine_acetylation.AllCell.bed ...

  8. File list: His.Emb.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Emb.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Embryo... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Emb.10.Pan_lysine_acetylation.AllCell.bed ...

  9. File list: His.Pan.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Pan.10.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Pancr...eas http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Pan.10.Pan_lysine_acetylation.AllCell.bed ...

  10. File list: His.Unc.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Unc.05.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Unclas...sified http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Unc.05.Pan_lysine_acetylation.AllCell.bed ...

  11. File list: His.Adp.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Adp.50.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Adipo...cyte http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Adp.50.Pan_lysine_acetylation.AllCell.bed ...

  12. File list: His.Neu.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.10.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Neura...l http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Neu.10.Pan_lysine_acetylation.AllCell.bed ...

  13. File list: His.Utr.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Utr.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Uterus... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Utr.20.Pan_lysine_acetylation.AllCell.bed ...

  14. File list: His.ALL.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.ALL.50.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation All ce...ll types SRX099893,SRX099896 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.ALL.50.Pan_lysine_acetylation.AllCell.bed ...

  15. File list: His.Bld.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bld.10.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Blood... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Bld.10.Pan_lysine_acetylation.AllCell.bed ...

  16. File list: His.CDV.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.CDV.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Cardi...ovascular http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.CDV.20.Pan_lysine_acetylation.AllCell.bed ...

  17. File list: His.Bld.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bld.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Blood ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Bld.20.Pan_lysine_acetylation.AllCell.bed ...

  18. File list: His.Bld.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bld.50.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Blood ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Bld.50.Pan_lysine_acetylation.AllCell.bed ...

  19. File list: His.Dig.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Dig.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Diges...tive tract http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Dig.20.Pan_lysine_acetylation.AllCell.bed ...

  20. File list: His.Oth.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Oth.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Others... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Oth.10.Pan_lysine_acetylation.AllCell.bed ...

  1. File list: His.Prs.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Prs.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Prost...ate http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Prs.20.Pan_lysine_acetylation.AllCell.bed ...

  2. File list: His.Epd.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Epd.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Epider...mis http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Epd.20.Pan_lysine_acetylation.AllCell.bed ...

  3. File list: His.Neu.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Neural... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Neu.10.Pan_lysine_acetylation.AllCell.bed ...

  4. File list: His.Unc.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Unc.05.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Uncla...ssified http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Unc.05.Pan_lysine_acetylation.AllCell.bed ...

  5. File list: His.Brs.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Brs.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Breas...t http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Brs.20.Pan_lysine_acetylation.AllCell.bed ...

  6. File list: His.Lng.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lng.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Lung h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Lng.20.Pan_lysine_acetylation.AllCell.bed ...

  7. File list: His.Kid.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Kid.05.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Kidney... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Kid.05.Pan_lysine_acetylation.AllCell.bed ...

  8. File list: His.Adp.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Adp.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Adipo...cyte http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Adp.20.Pan_lysine_acetylation.AllCell.bed ...

  9. File list: His.Oth.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Oth.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Others... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Oth.20.Pan_lysine_acetylation.AllCell.bed ...

  10. File list: His.Bon.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bon.05.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Bone h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Bon.05.Pan_lysine_acetylation.AllCell.bed ...

  11. File list: His.Bld.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bld.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Blood ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Bld.10.Pan_lysine_acetylation.AllCell.bed ...

  12. File list: His.Adp.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Adp.10.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Adipo...cyte http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Adp.10.Pan_lysine_acetylation.AllCell.bed ...

  13. File list: His.Adp.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Adp.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Adipoc...yte http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Adp.10.Pan_lysine_acetylation.AllCell.bed ...

  14. File list: His.CDV.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.CDV.50.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Cardio...vascular http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.CDV.50.Pan_lysine_acetylation.AllCell.bed ...

  15. File list: His.Neu.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.50.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Neural... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Neu.50.Pan_lysine_acetylation.AllCell.bed ...

  16. File list: His.Lng.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lng.50.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Lung h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Lng.50.Pan_lysine_acetylation.AllCell.bed ...

  17. File list: His.PSC.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.PSC.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Plurip...otent stem cell http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.PSC.10.Pan_lysine_acetylation.AllCell.bed ...

  18. File list: His.Plc.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Plc.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Placen...ta http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Plc.20.Pan_lysine_acetylation.AllCell.bed ...

  19. File list: His.Oth.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Oth.50.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Others... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Oth.50.Pan_lysine_acetylation.AllCell.bed ...

  20. File list: His.Oth.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Oth.05.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Others... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Oth.05.Pan_lysine_acetylation.AllCell.bed ...

  1. File list: His.Lng.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lng.05.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Lung h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Lng.05.Pan_lysine_acetylation.AllCell.bed ...

  2. File list: His.Prs.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Prs.50.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Prost...ate http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Prs.50.Pan_lysine_acetylation.AllCell.bed ...

  3. File list: His.Myo.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Myo.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Muscl...e http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Myo.20.Pan_lysine_acetylation.AllCell.bed ...

  4. File list: His.Unc.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Unc.50.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Unclas...sified http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Unc.50.Pan_lysine_acetylation.AllCell.bed ...

  5. File list: His.Epd.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Epd.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Epide...rmis http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Epd.20.Pan_lysine_acetylation.AllCell.bed ...

  6. File list: His.Prs.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Prs.05.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Prosta...te http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Prs.05.Pan_lysine_acetylation.AllCell.bed ...

  7. File list: His.Bld.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bld.05.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Blood... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Bld.05.Pan_lysine_acetylation.AllCell.bed ...

  8. File list: His.ALL.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.ALL.05.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation All ce...ll types SRX099893,SRX099896 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.ALL.05.Pan_lysine_acetylation.AllCell.bed ...

  9. File list: His.Neu.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Neura...l http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Neu.20.Pan_lysine_acetylation.AllCell.bed ...

  10. File list: His.PSC.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.PSC.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Plurip...otent stem cell http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.PSC.20.Pan_lysine_acetylation.AllCell.bed ...

  11. File list: His.Pan.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Pan.05.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Pancr...eas http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Pan.05.Pan_lysine_acetylation.AllCell.bed ...

  12. File list: His.ALL.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.ALL.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation All c...ell types SRX099890 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.ALL.20.Pan_lysine_acetylation.AllCell.bed ...

  13. File list: His.Liv.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Liv.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Liver ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Liv.20.Pan_lysine_acetylation.AllCell.bed ...

  14. File list: His.Gon.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Gon.50.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Gonad... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Gon.50.Pan_lysine_acetylation.AllCell.bed ...

  15. File list: His.ALL.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.ALL.10.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation All c...ell types SRX099890 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.ALL.10.Pan_lysine_acetylation.AllCell.bed ...

  16. File list: His.PSC.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.PSC.50.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Pluri...potent stem cell http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.PSC.50.Pan_lysine_acetylation.AllCell.bed ...

  17. File list: His.Prs.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Prs.50.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Prosta...te http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Prs.50.Pan_lysine_acetylation.AllCell.bed ...

  18. File list: His.CDV.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.CDV.05.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Cardi...ovascular http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.CDV.05.Pan_lysine_acetylation.AllCell.bed ...

  19. File list: His.Gon.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Gon.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Gonad ...SRX099893,SRX099896 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Gon.10.Pan_lysine_acetylation.AllCell.bed ...

  20. File list: His.Bon.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bon.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Bone ...http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Bon.20.Pan_lysine_acetylation.AllCell.bed ...

  1. File list: His.Dig.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Dig.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Digest...ive tract http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Dig.10.Pan_lysine_acetylation.AllCell.bed ...

  2. File list: His.Bld.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bld.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Blood... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Bld.20.Pan_lysine_acetylation.AllCell.bed ...

  3. File list: His.Unc.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Unc.50.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Uncla...ssified http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Unc.50.Pan_lysine_acetylation.AllCell.bed ...

  4. File list: His.Utr.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Utr.05.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Uteru...s http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Utr.05.Pan_lysine_acetylation.AllCell.bed ...

  5. File list: His.Liv.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Liv.05.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Liver ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Liv.05.Pan_lysine_acetylation.AllCell.bed ...

  6. File list: His.Lng.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lng.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Lung h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Lng.10.Pan_lysine_acetylation.AllCell.bed ...

  7. File list: His.Liv.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Liv.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Liver ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Liv.10.Pan_lysine_acetylation.AllCell.bed ...

  8. File list: His.Bld.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bld.05.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Blood ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Bld.05.Pan_lysine_acetylation.AllCell.bed ...

  9. File list: His.Epd.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Epd.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Epider...mis http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Epd.10.Pan_lysine_acetylation.AllCell.bed ...

  10. File list: His.Pan.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Pan.50.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Pancr...eas http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Pan.50.Pan_lysine_acetylation.AllCell.bed ...

  11. File list: His.PSC.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.PSC.50.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Plurip...otent stem cell http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.PSC.50.Pan_lysine_acetylation.AllCell.bed ...

  12. File list: His.Plc.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Plc.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Placen...ta http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Plc.10.Pan_lysine_acetylation.AllCell.bed ...

  13. File list: His.Plc.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Plc.10.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Place...nta http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Plc.10.Pan_lysine_acetylation.AllCell.bed ...

  14. File list: His.Prs.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Prs.10.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Prost...ate http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Prs.10.Pan_lysine_acetylation.AllCell.bed ...

  15. File list: His.Bon.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bon.50.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Bone h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Bon.50.Pan_lysine_acetylation.AllCell.bed ...

  16. File list: His.Lng.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lng.20.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Lung ...SRX099890 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Lng.20.Pan_lysine_acetylation.AllCell.bed ...

  17. File list: His.Unc.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Unc.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Unclas...sified http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Unc.10.Pan_lysine_acetylation.AllCell.bed ...

  18. File list: His.Utr.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Utr.10.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Uteru...s http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Utr.10.Pan_lysine_acetylation.AllCell.bed ...

  19. File list: His.Adp.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Adp.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Adipoc...yte http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Adp.20.Pan_lysine_acetylation.AllCell.bed ...

  20. File list: His.Gon.50.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Gon.50.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Gonad ...SRX099893,SRX099896 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Gon.50.Pan_lysine_acetylation.AllCell.bed ...

  1. File list: His.Dig.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Dig.05.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Digest...ive tract http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Dig.05.Pan_lysine_acetylation.AllCell.bed ...

  2. File list: His.Dig.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Dig.10.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Diges...tive tract http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Dig.10.Pan_lysine_acetylation.AllCell.bed ...

  3. File list: His.Brs.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Brs.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Breast... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Brs.10.Pan_lysine_acetylation.AllCell.bed ...

  4. File list: His.Myo.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Myo.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Muscle... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Myo.10.Pan_lysine_acetylation.AllCell.bed ...

  5. File list: His.CDV.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.CDV.10.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Cardio...vascular http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.CDV.10.Pan_lysine_acetylation.AllCell.bed ...

  6. File list: His.Bon.20.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bon.20.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Bone h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Bon.20.Pan_lysine_acetylation.AllCell.bed ...

  7. File list: His.Epd.05.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Epd.05.Pan_lysine_acetylation.AllCell mm9 Histone Pan lysine acetylation Epider...mis http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Epd.05.Pan_lysine_acetylation.AllCell.bed ...

  8. File list: His.Oth.10.Pan_lysine_acetylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Oth.10.Pan_lysine_acetylation.AllCell hg19 Histone Pan lysine acetylation Other...s http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Oth.10.Pan_lysine_acetylation.AllCell.bed ...

  9. File list: Oth.Adp.50.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Adp.50.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Adipocyte htt...p://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Adp.50.Crotonyl_lysine.AllCell.bed ...

  10. File list: Oth.NoD.05.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.NoD.05.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine No descriptio...n http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.NoD.05.Crotonyl_lysine.AllCell.bed ...

  11. File list: Oth.PSC.50.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.PSC.50.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Pluripotent s...tem cell http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.PSC.50.Crotonyl_lysine.AllCell.bed ...

  12. File list: Oth.PSC.10.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.PSC.10.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Pluripotent s...tem cell http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.PSC.10.Crotonyl_lysine.AllCell.bed ...

  13. File list: His.Myo.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Myo.05.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Mu...scle http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Myo.05.Pan_lysine_crotonylation.AllCell.bed ...

  14. File list: His.Prs.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Prs.50.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Pr...ostate http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Prs.50.Pan_lysine_crotonylation.AllCell.bed ...

  15. File list: His.ALL.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.ALL.20.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation A...ll cell types SRX099891 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.ALL.20.Pan_lysine_crotonylation.AllCell.bed ...

  16. File list: His.Gon.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Gon.20.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Go...nad SRX099894,SRX099897 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Gon.20.Pan_lysine_crotonylation.AllCell.bed ...

  17. File list: His.Oth.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Oth.10.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation O...thers http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Oth.10.Pan_lysine_crotonylation.AllCell.bed ...

  18. File list: Oth.EmF.20.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.EmF.20.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Embryonic fib...roblast http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.EmF.20.Crotonyl_lysine.AllCell.bed ...

  19. File list: His.PSC.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.PSC.05.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation P...luripotent stem cell http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.PSC.05.Pan_lysine_crotonylation.AllCell.bed ...

  20. File list: His.Lng.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lng.10.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Lu...ng http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Lng.10.Pan_lysine_crotonylation.AllCell.bed ...

  1. File list: His.Emb.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Emb.05.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Em...bryo http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Emb.05.Pan_lysine_crotonylation.AllCell.bed ...

  2. File list: Oth.CDV.05.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.CDV.05.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Cardiovascula...r http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.CDV.05.Crotonyl_lysine.AllCell.bed ...

  3. File list: His.Epd.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Epd.10.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Ep...idermis http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Epd.10.Pan_lysine_crotonylation.AllCell.bed ...

  4. File list: His.Bon.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bon.10.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Bo...ne http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Bon.10.Pan_lysine_crotonylation.AllCell.bed ...

  5. File list: His.Bld.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bld.20.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation B...lood http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Bld.20.Pan_lysine_crotonylation.AllCell.bed ...

  6. File list: His.Spl.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Spl.20.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Sp...leen http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Spl.20.Pan_lysine_crotonylation.AllCell.bed ...

  7. File list: His.Liv.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Liv.50.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Li...ver http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Liv.50.Pan_lysine_crotonylation.AllCell.bed ...

  8. File list: His.Pan.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Pan.05.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Pa...ncreas http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Pan.05.Pan_lysine_crotonylation.AllCell.bed ...

  9. File list: His.Unc.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Unc.05.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Un...classified http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Unc.05.Pan_lysine_crotonylation.AllCell.bed ...

  10. Optimization of lysine production in Corynebacteriumglutamicum ATCC15032 by Response surface methodology

    Directory of Open Access Journals (Sweden)

    Mehrnaz Haghi

    2017-03-01

    Discussion and conclusion: According to the results, the proposed culture media by response surface methodology causes 1400 times increase in the lysine production compared with M9 culture media and methionine had an important role in the production of lysine, probably by inhibiting the other metabolic pathway which has common metabolic precursor with lysine production metabolic pathway.

  11. File list: Oth.Gon.10.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Gon.10.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Gonad SRX1060...567,SRX1060566,SRX1060557 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Gon.10.Crotonyl_lysine.AllCell.bed ...

  12. File list: Oth.Adp.10.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Adp.10.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Adipocyte htt...p://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Adp.10.Crotonyl_lysine.AllCell.bed ...

  13. File list: Oth.ALL.20.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.ALL.20.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine All cell type...s SRX1060566,SRX1060567,SRX1060557 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.ALL.20.Crotonyl_lysine.AllCell.bed ...

  14. File list: Oth.Epd.20.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Epd.20.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Epidermis htt...p://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Epd.20.Crotonyl_lysine.AllCell.bed ...

  15. File list: Oth.Epd.50.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Epd.50.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Epidermis htt...p://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Epd.50.Crotonyl_lysine.AllCell.bed ...

  16. File list: Oth.ALL.10.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.ALL.10.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine All cell type...s SRX1060567,SRX1060566,SRX1060557 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.ALL.10.Crotonyl_lysine.AllCell.bed ...

  17. File list: Oth.Adp.05.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Adp.05.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Adipocyte htt...p://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Adp.05.Crotonyl_lysine.AllCell.bed ...

  18. File list: Oth.Dig.10.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Dig.10.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Digestive tra...ct http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Dig.10.Crotonyl_lysine.AllCell.bed ...

  19. File list: Oth.EmF.50.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.EmF.50.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Embryonic fib...roblast http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.EmF.50.Crotonyl_lysine.AllCell.bed ...

  20. File list: Oth.CDV.50.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.CDV.50.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Cardiovascula...r http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.CDV.50.Crotonyl_lysine.AllCell.bed ...

  1. File list: Oth.Gon.05.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Gon.05.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Gonad SRX1060...566,SRX1060567,SRX1060557 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Gon.05.Crotonyl_lysine.AllCell.bed ...

  2. File list: Oth.NoD.10.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.NoD.10.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine No descriptio...n http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.NoD.10.Crotonyl_lysine.AllCell.bed ...

  3. File list: Oth.PSC.05.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.PSC.05.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Pluripotent s...tem cell http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.PSC.05.Crotonyl_lysine.AllCell.bed ...

  4. File list: Oth.Epd.10.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Epd.10.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Epidermis htt...p://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Epd.10.Crotonyl_lysine.AllCell.bed ...

  5. File list: Oth.ALL.05.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.ALL.05.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine All cell type...s SRX1060566,SRX1060567,SRX1060557 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.ALL.05.Crotonyl_lysine.AllCell.bed ...

  6. File list: Oth.PSC.20.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.PSC.20.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Pluripotent s...tem cell http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.PSC.20.Crotonyl_lysine.AllCell.bed ...

  7. File list: Oth.Epd.05.Crotonyl_lysine.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Epd.05.Crotonyl_lysine.AllCell mm9 TFs and others Crotonyl lysine Epidermis htt...p://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Epd.05.Crotonyl_lysine.AllCell.bed ...

  8. File list: His.Oth.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Oth.50.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation O...thers http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Oth.50.Pan_lysine_crotonylation.AllCell.bed ...

  9. File list: His.Bon.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Bon.20.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation B...one http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Bon.20.Pan_lysine_crotonylation.AllCell.bed ...

  10. File list: His.Plc.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Plc.10.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Pl...acenta http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Plc.10.Pan_lysine_crotonylation.AllCell.bed ...

  11. File list: His.Prs.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Prs.20.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Pr...ostate http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Prs.20.Pan_lysine_crotonylation.AllCell.bed ...

  12. File list: His.Epd.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Epd.05.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Ep...idermis http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Epd.05.Pan_lysine_crotonylation.AllCell.bed ...

  13. File list: His.PSC.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.PSC.20.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation P...luripotent stem cell http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.PSC.20.Pan_lysine_crotonylation.AllCell.bed ...

  14. File list: His.Plc.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Plc.10.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation P...lacenta http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Plc.10.Pan_lysine_crotonylation.AllCell.bed ...

  15. File list: His.Pan.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Pan.50.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Pa...ncreas http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Pan.50.Pan_lysine_crotonylation.AllCell.bed ...

  16. File list: His.Neu.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.10.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation N...eural http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Neu.10.Pan_lysine_crotonylation.AllCell.bed ...

  17. File list: His.Utr.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Utr.10.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation U...terus http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Utr.10.Pan_lysine_crotonylation.AllCell.bed ...

  18. File list: His.Spl.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Spl.05.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Sp...leen http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Spl.05.Pan_lysine_crotonylation.AllCell.bed ...

  19. File list: His.Utr.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Utr.10.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Ut...erus http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Utr.10.Pan_lysine_crotonylation.AllCell.bed ...

  20. File list: His.Epd.10.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Epd.10.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation E...pidermis http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Epd.10.Pan_lysine_crotonylation.AllCell.bed ...

  1. File list: His.Oth.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Oth.20.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Ot...hers http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Oth.20.Pan_lysine_crotonylation.AllCell.bed ...

  2. File list: His.Dig.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Dig.50.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation D...igestive tract http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Dig.50.Pan_lysine_crotonylation.AllCell.bed ...

  3. File list: His.Prs.05.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Prs.05.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Pr...ostate http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Prs.05.Pan_lysine_crotonylation.AllCell.bed ...

  4. File list: His.Spl.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Spl.50.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Sp...leen http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Spl.50.Pan_lysine_crotonylation.AllCell.bed ...

  5. File list: His.Gon.50.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Gon.50.Pan_lysine_crotonylation.AllCell mm9 Histone Pan lysine crotonylation Go...nad SRX099894,SRX099897 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Gon.50.Pan_lysine_crotonylation.AllCell.bed ...

  6. File list: His.Neu.20.Pan_lysine_crotonylation.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.20.Pan_lysine_crotonylation.AllCell hg19 Histone Pan lysine crotonylation N...eural http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Neu.20.Pan_lysine_crotonylation.AllCell.bed ...

  7. The plasminogen binding site of the C-type lectin tetranectin is located in the carbohydrate recognition domain, and binding is sensitive to both calcium and lysine

    DEFF Research Database (Denmark)

    Graversen, Jonas Heilskov; Lorentsen, R H; Jacobsen, C

    1998-01-01

    Tetranectin, a homotrimeric protein belonging to the family of C-type lectins and structurally highly related to corresponding regions of the mannose-binding proteins, is known specifically to bind the plasminogen kringle 4 protein domain, an interaction sensitive to lysine. Surface plasmon...... resonance and isothermal calorimetry binding analyses using single-residue and deletion mutant tetranectin derivatives produced in Escherichia coli showed that the kringle 4 binding site resides in the carbohydrate recognition domain and includes residues of the putative carbohydrate binding site...

  8. Post-translational serine/threonine phosphorylation and lysine acetylation: a novel regulatory aspect of the global nitrogen response regulator GlnR in S. coelicolor M145.

    Directory of Open Access Journals (Sweden)

    Rafat Amin

    2016-08-01

    Full Text Available Soil-dwelling Streptomyces bacteria such as S. coelicolor have to constantly adapt to the nitrogen (N availability in their habitat. Thus, strict transcriptional and post-translational control of the N-assimilation is fundamental for survival of this species. GlnR is a global response regulator that controls transcription of the genes related to the N-assimilation in S. coelicolor and other members of the Actinomycetales. GlnR represents an atypical orphan response regulator that is not activated by the phosphorylation of the conserved aspartate residue (Asp 50. We have applied transcriptional analysis, LC-MS/MS analysis and electrophoretic mobility shift assays (EMSAs to understand the regulation of GlnR in S. coelicolor M145. The expression of glnR and GlnR-target genes was revisited under four different N-defined conditions and a complex N-rich condition. Although, the expression of selected GlnR-target genes was strongly responsive to changing N-concentrations, the glnR expression itself was independent of the N-availability. Using LC-MS/MSanalysis we demonstrated that GlnR was post-translationally modified. The post-translational modifications of GlnR comprise phosphorylation of the serine/threonine residues and acetylation of lysine residues. In the complex N-rich medium GlnR was phosphorylated on six serine/ threonine residues and acetylated on one lysine residue. Under defined N-excess conditions only two phosphorylated residues were detected whereas under defined N-limiting conditions no phosphorylation was observed. GlnR phosphorylation is thus clearly correlated with N-rich conditions. Furthermore, GlnR was acetylated on four lysine residues independently of the N-concentration in the defined media and on only one lysine residue in the complex N-rich medium. Using EMSAs we demonstrated that phosphorylation inhibited the binding of GlnR to its targets genes, whereas acetylation had little influence on the formation of GlnR-DNA complex

  9. Severe dietary lysine restriction affects growth and body composition and hepatic gene expression for nitrogen metabolism in growing rats.

    Science.gov (United States)

    Kim, J; Lee, K S; Kwon, D-H; Bong, J J; Jeong, J Y; Nam, Y S; Lee, M S; Liu, X; Baik, M

    2014-02-01

    Dietary lysine restriction may differentially affect body growth and lipid and nitrogen metabolism, depending on the degree of lysine restriction. This study was conducted to examine the effect of dietary lysine restriction on growth and lipid and nitrogen metabolism with two different degree of lysine restriction. Isocaloric amino acid-defined diets containing 1.4% lysine (adequate), 0.70% lysine (50% moderate lysine restriction) and 0.35% lysine (75% severe lysine restriction) were fed from the age of 52 to 77 days for 25 days in male Sprague-Dawley rats. The 75% severe lysine restriction increased (p muscle lipid contents and abdominal fat accumulation, increased (p  0.05) affect body growth and lipid and nitrogen metabolism. Our results demonstrate that severe 75% lysine restriction has detrimental effects on body growth and deregulate lipid and nitrogen metabolism.

  10. Residual-stress measurements

    Energy Technology Data Exchange (ETDEWEB)

    Ezeilo, A.N.; Webster, G.A. [Imperial College, London (United Kingdom); Webster, P.J. [Salford Univ. (United Kingdom)

    1997-04-01

    Because neutrons can penetrate distances of up to 50 mm in most engineering materials, this makes them unique for establishing residual-stress distributions non-destructively. D1A is particularly suited for through-surface measurements as it does not suffer from instrumental surface aberrations commonly found on multidetector instruments, while D20 is best for fast internal-strain scanning. Two examples for residual-stress measurements in a shot-peened material, and in a weld are presented to demonstrate the attractive features of both instruments. (author).

  11. Expression, Purification and Antibacterial Activity of NK-Lysin Mature Peptides from the Channel Catfish (Ictalurus punctatus

    Directory of Open Access Journals (Sweden)

    Shurui Cai

    2016-08-01

    Full Text Available Antimicrobial peptides (AMPs are small peptides and play important roles in host innate immune response against microbial invasion. Aquatic animals secrete different kinds of antimicrobial peptides which have antimicrobial activity towards microorganisms. NK-lysins, mature peptides produced by cytotoxic T lymphocytes and natural killer cells, are comprised of 74–78 amino acid residues, demonstrating broad-spectrum antimicrobial activity against bacteria, fungi, protozoa, and parasites. In this study, three distinct NK-lysin mature peptide (mNKLs, transcripts (76 amino acid residues cloned from the channel catfish (Ictalurus punctatus head kidney were ligated into plasmid vector pET-32a(+ to express the mNKLs fusion protein. The fusion protein was successfully expressed in E. coli Rosetta (DE3 under optimized conditions. After purification by affinity column chromatography, the fusion protein was successfully cleaved by enterokinase and released the peptide mNKLs. Tricine-SDS-PAGE results showed that mNKLs (approximately 8.6 kDa were successfully expressed. The purified peptide mNKLs exhibited antibacterial activity against Staphylococcus aureus and E. coli.

  12. Mechanistic analysis of Mycobacterium tuberculosis Rv1347c, a lysine Nepsilon-acyltransferase involved in mycobactin biosynthesis.

    Science.gov (United States)

    Frankel, Brenda A; Blanchard, John S

    2008-09-15

    Mycobactin acylation plays a crucial role in the ability of Mycobacterium tuberculosis to acquire intracellular iron during infection. M. tuberculosis Rv1347c, the lysine N(epsilon)-acyltransferase responsible for mycobactin acylation, represents a valid target for the development of novel anti-tubercular agents. Here we investigate the substrate specificity of Rv1347c, evaluate its kinetic mechanism and probe the contributions of active-site residues to catalysis. Our results confirm that Rv1347c demonstrates a preference for longer acyl-chains and suggest that mycobactin acylation occurs subsequent to mycobactin core assembly. Steady-state bisubstrate kinetics and dead-end inhibitor studies support a random sequential kinetic mechanism. Analysis of the pH dependence of k(cat)/K(m) revealed the presence of two groups that must be deprotonated for efficient catalysis. Mutagenesis of His(130) and Asp(168) indicated that both residues are critical for acyltransferase activity and suggests that His(130) is responsible for general base activation of the epsilon-amino group of lysine.

  13. Eradication of Burkholderia cepacia Using Inhaled Aztreonam Lysine in Two Patients with Bronchiectasis

    Directory of Open Access Journals (Sweden)

    A. Iglesias

    2014-01-01

    Full Text Available There are not many articles about the chronic bronchial infection/colonization in patients with underlying lung disease other than cystic fibrosis (CF, especially with non-CF bronchiectasis (NCFBQ. The prevalence of B. cepacia complex is not well known in NCFBQ. The vast majority of published clinical data on Burkholderia infection in individuals with CF is comprised of uncontrolled, anecdotal, and/or single center experiences, and no consensus has emerged regarding treatment. We present two cases diagnosed with bronchiectasis (BQ of different etiology, with early pulmonary infection by B. cepacia complex, which was eradicated with inhaled aztreonam lysine.

  14. One Approach for Dynamic L-lysine Modelling of Repeated Fed-batch Fermentation

    Directory of Open Access Journals (Sweden)

    Kalin Todorov

    2007-03-01

    Full Text Available This article deals with establishment of dynamic unstructured model of variable volume fed-batch fermentation process with intensive droppings for L-lysine production. The presented approach of the investigation includes the following main procedures: description of the process by generalized stoichiometric equations; preliminary data processing and calculation of specific rates for main kinetic variables; identification of the specific rates as a second-order non-linear dynamic models; establishment and optimisation of dynamic model of the process; simulation researches. MATLAB is used as a research environment.

  15. Lysine deacetylases are produced in pancreatic beta cells and are differentially regulated by proinflammatory cytokines

    DEFF Research Database (Denmark)

    Lundh, M; Christensen, D P; Rasmussen, D N;

    2010-01-01

    Cytokine-induced beta cell toxicity is abrogated by non-selective inhibitors of lysine deacetylases (KDACs). The KDAC family consists of 11 members, namely histone deacetylases HDAC1 to HDAC11, but it is not known which KDAC members play a role in cytokine-mediated beta cell death. The aim...... of the present study was to examine the KDAC gene expression profile of the beta cell and to investigate whether KDAC expression is regulated by cytokines. In addition, the protective effect of the non-selective KDAC inhibitor ITF2357 and interdependent regulation of four selected KDACs were investigated....

  16. Impact of dry heating on physicochemical properties of corn starch and lysine mixture.

    Science.gov (United States)

    Ji, Ying; Yu, Jicheng; Xu, Yongbin; Zhang, Yinghui

    2016-10-01

    Corn starch was modified with lysine by dry heat treatment and to investigate how they can affect the pasting and structural properties of the treated starches. Dry heating with lysine reduced the pasting temperature and resulting in viscosity increase. The particle size of heated starch-lysine mixture increased, suggesting that starch granules were cross-linked to lysine. After dry heating, the onset temperature, peak temperature and conclusion temperature of corn starch-lysine mixture were lower than those of other starches. The degree of crystallinity decreased for the starch after dry heat treatment while these heated starch samples still have the same X-ray diffraction types as the original starch.

  17. Effect of different levels of L-carnitine and lysine-methionine on broiler blood parameters

    Directory of Open Access Journals (Sweden)

    Babak Hosseintabar

    2015-09-01

    Full Text Available Objetive. In the present study a completely randomized 3×3 factorial design was used to analyze the effects of different levels of L-Carnitine, lysine(Lys and methionine (Met on the blood concentrations of energy, protein and lipid metabolites of male broiler chickens. Materials and methods. A total of 270 newly hatched male broiler chickens (Ross 308 were randomly assigned to 9 groups (ten broilers per replicate and three replicates per treatment. The control group was fed a basal diet, whereas the treatment groups were fed basal diets supplemented with L-Carnitine (0 mg/kg, 75 mg/kg and 150 mg/kg and lysine-methionine (0, 15 and 30% for 42 days. On day 42, one bird was randomly chosen per replication, a blood sample was taken and the blood concentrations of glucose (GLU, uric acid (UAc, triglyceride (TG, VLDL, HDL, LDL, total protein (TP, albumin (Alb and total cholesterol (TC were analyzed. Results. Dietary L-carnitine supplementation had a significant effect (p<0.05 on uric acid (UAc, HDL, LDL, and total cholesterol (TC. The birds feed L-carnitine plus Lys and Met presented the highest plasmatic UAc level and the lowest plasmatic TC and LDL level. Moreover, L-carnitine significantly reduced total cholesterol (TC when compared with both the control group and the birds feed Lys and Met without L-carnitine. Conclusions. A diet with 150 mg/kg L-carnitine plus 15% Lys and Met seems to be enough to sustain low plasmatic TC, LDL and HDL concentrations on male broiler.

  18. Nε-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity.

    Directory of Open Access Journals (Sweden)

    Sandy Thao

    Full Text Available Evidence suggesting that eukaryotes and archaea use reversible N(ε-lysine (N(ε-Lys acetylation to modulate gene expression has been reported, but evidence for bacterial use of N(ε-Lys acetylation for this purpose is lacking. Here, we report data in support of the notion that bacteria can control gene expression by modulating the acetylation state of transcription factors (TFs. We screened the E. coli proteome for substrates of the bacterial Gcn5-like protein acetyltransferase (Pat. Pat acetylated four TFs, including the RcsB global regulatory protein, which controls cell division, and capsule and flagellum biosynthesis in many bacteria. Pat acetylated residue Lys180 of RcsB, and the NAD(+-dependent Sir2 (sirtuin-like protein deacetylase (CobB deacetylated acetylated RcsB (RcsB(Ac, demonstrating that N(ε-Lys acetylation of RcsB is reversible. Analysis of RcsB(Ac and variant RcsB proteins carrying substitutions at Lys180 provided biochemical and physiological evidence implicating Lys180 as a critical residue for RcsB DNA-binding activity. These findings further the likelihood that reversible N(ε-Lys acetylation of transcription factors is a mode of regulation of gene expression used by all cells.

  19. Ornithine decarboxylase antizyme induces hypomethylation of genome DNA and histone H3 lysine 9 dimethylation (H3K9me2 in human oral cancer cell line.

    Directory of Open Access Journals (Sweden)

    Daisuke Yamamoto

    Full Text Available BACKGROUND: Methylation of CpG islands of genome DNA and lysine residues of histone H3 and H4 tails regulates gene transcription. Inhibition of polyamine synthesis by ornithine decarboxylase antizyme-1 (OAZ in human oral cancer cell line resulted in accumulation of decarboxylated S-adenosylmethionine (dcSAM, which acts as a competitive inhibitor of methylation reactions. We anticipated that accumulation of dcSAM impaired methylation reactions and resulted in hypomethylation of genome DNA and histone tails. METHODOLOGY/PRINCIPAL FINDINGS: Global methylation state of genome DNA and lysine residues of histone H3 and H4 tails were assayed by Methylation by Isoschizomers (MIAMI method and western blotting, respectively, in the presence or absence of OAZ expression. Ectopic expression of OAZ mediated hypomethylation of CpG islands of genome DNA and histone H3 lysine 9 dimethylation (H3K9me2. Protein level of DNA methyltransferase 3B (DNMT3B and histone H3K9me specific methyltransferase G9a were down-regulated in OAZ transfectant. CONCLUSIONS/SIGNIFICANCE: OAZ induced hypomethylation of CpG islands of global genome DNA and H3K9me2 by down-regulating DNMT3B and G9a protein level. Hypomethylation of CpG islands of genome DNA and histone H3K9me2 is a potent mechanism of induction of the genes related to tumor suppression and DNA double strand break repair.

  20. RUBI: rapid proteomic-scale prediction of lysine ubiquitination and factors influencing predictor performance.

    Science.gov (United States)

    Walsh, Ian; Di Domenico, Tomás; Tosatto, Silvio C E

    2014-04-01

    Post-translational modification of protein lysines was recently shown to be a common feature of eukaryotic organisms. The ubiquitin modification is regarded as a versatile regulatory mechanism with many important cellular roles. Large-scale datasets are becoming available for H. sapiens ubiquitination. However, using current experimental techniques the vast majority of their sites remain unidentified and in silico tools may offer an alternative. Here, we introduce Rapid UBIquitination (RUBI) a sequence-based ubiquitination predictor designed for rapid application on a genome scale. RUBI was constructed using an iterative approach. At each iteration, important factors which influenced performance and its usability were investigated. The final RUBI model has an AUC of 0.868 on a large cross-validation set and is shown to outperform other available methods on independent sets. Predicted intrinsic disorder is shown to be weakly anti-correlated to ubiquitination for the H. sapiens dataset and improves performance slightly. RUBI predicts the number of ubiquitination sites correctly within three sites for ca. 80% of the tested proteins. The average potentially ubiquitinated proteome fraction is predicted to be at least 25% across a variety of model organisms, including several thousand possible H. sapiens proteins awaiting experimental characterization. RUBI can accurately predict ubiquitination on unseen examples and has a signal across different eukaryotic organisms. The factors which influenced the construction of RUBI could also be tested in other post-translational modification predictors. One of the more interesting factors is the influence of intrinsic protein disorder on ubiquitinated lysines where residues with low disorder probability are preferred.