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Structure-Based Function Prediction of Functionally Unannotated Structures in the PDB: Prediction of ATP, GTP, Sialic Acid, Retinoic Acid and Heme-bound and -Unbound (Free) Nitric Oxide Protein Binding Sites [article]

Vicente M. Reyes
2015 arXiv   pre-print
Computational prediction of ligand binding sites (LBS) is a well-established protein function assignment method.  ...  taken as a further validation of the predicted LBSs.  ...  He also acknowledges the Division of Research Computing at RIT, and computing resources from the Dept. of Biological Sciences, College of Science, at RIT.  ... 
arXiv:1505.01143v1 fatcat:u5chxg5qizexzkxqnsgormzqki

In silico analysis of Myoglobin in Channa striata

Farzana Parveen, Vineet Kumar Mishra
2014 Bioinformation  
The active sites were predicted in the model with further ASA analysis of active site residues.  ...  Functionally, myoglobin is well accepted as an O2- storage protein in muscle, capable of releasing O2 during periods of hypoxia or anoxia.  ...  Prediction of active site One of the keenest areas in the bioinformatics is the active sites of the protein and its residual identification.  ... 
doi:10.6026/97320630010019 pmid:24516321 pmcid:PMC3916814 fatcat:hjlv2g2b3ndhvhrvlgtoxuw2zu

Unraveling Oxidative Stress Resistance: Molecular Properties Govern Proteome Vulnerability [article]

Roger L. Chang, Julian A. Stanley, Matthew C. Robinson, Joel W. Sher, Zhanwen Li, Yujia A. Chan, Ashton R. Omdahl, Ruddy Wattiez, Adam Godzik, Sabine Matallana-Surget
2020 bioRxiv   pre-print
to oxidation, a mode of evolutionary adaptation for stress tolerance in bacteria.  ...  Our model predicts proteome maintenance machinery and proteins protecting against ROS are more resistant in D. radiodurans.  ...  We also evaluated performance of our model for predicting protein-scale vulnerability to oxidation (Fig. 5B ) by calculating an oxidation site enrichment metric.  ... 
doi:10.1101/2020.03.09.983213 fatcat:7gf773mv6va25ivenmf5enifza

Rules Governing Selective Protein Carbonylation

Etienne Maisonneuve, Adrien Ducret, Pierre Khoueiry, Sabrina Lignon, Sonia Longhi, Emmanuel Talla, Sam Dukan, Andreas Hofmann
2009 PLoS ONE  
We used these rules to design an in silico model (available at, allowing an effective and accurate prediction of sites and of proteins more prone to carbonylation in the  ...  Conclusions/Significance: We observed that proteins evolve to either selectively maintain or lose predicted hot spots of carbonylation depending on their biological function.  ...  Rechsteiner (University of Utah, Salt Lake City, USA) for helpful comments on the manuscript. We thank D. Moinier and R. Lebrun for their technical assistance with mass spectrometry analysis.  ... 
doi:10.1371/journal.pone.0007269 pmid:19802390 pmcid:PMC2751825 fatcat:kz66u6zi25fsrpwxzjkgkcifvm

Computer Simulation of Native Epidermal Enzyme Structures in the Presence and Absence of Hydrogen Peroxide (H2O2): Potential and Pitfalls

Nicholas C.J. Gibbons, John M. Wood, Hartmut Rokos, Karin U. Schallreuter
2006 Journal of Investigative Dermatology  
Molecular dynamic computer modelling is a new powerful tool to predict or confirm oxidative stress-mediated structural changes consequently altering the function of enzymes/proteins/peptides.  ...  The human epidermis is especially vulnerable to oxidative stress, which in turn leads to oxidation of important antioxidant enzymes, other proteins, and peptides.  ...  (c) The model predicts oxidation of the enzyme substrate-binding site. The conversion of Trp 84 (dark blue) to 5-OH-Trp 84 (yellow) disrupts the Ach-substrate binding site predicting deactivation.  ... 
doi:10.1038/sj.jid.5700612 pmid:17108904 fatcat:fhgvct3gsbg4rlts63yue55wdq

Outer Cell Surface Components Essential for Fe(III) Oxide Reduction by Geobacter metallireducens

Jessica A. Smith, Derek R. Lovley, Pier-Luc Tremblay
2012 Applied and Environmental Microbiology  
Other genes essential for Fe(III) oxide reduction included a gene predicted to encode an NHL (Ncl-1–HT2A–Lin-41) repeat-containing protein and a gene potentially involved in pili glycosylation.  ...  Deletion of genes forc-type cytochromes that had higher transcript abundance during growth on Fe(III) oxides and/or were detected in the outer-surface protein fraction identified sixc-type cytochrome genes  ...  Gmet 0557 is predicted to have four heme binding sites, whereas Gmet 0558 is predicted to have between 23 and 27 heme binding sites.  ... 
doi:10.1128/aem.02954-12 pmid:23183974 pmcid:PMC3568551 fatcat:cbfaoyb62ffprm5jaq2afp6rvm

Prediction of DtxR regulon: identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae

Sailu Yellaboina, Sarita Ranjan, Prachee Chakhaiyar, Seyed Ehtesham Hasnain, Akash Ranjan
2004 BMC Microbiology  
In addition, DtxR-regulated operons were also identified taking into account the predicted DtxR regulatory sites and genome annotation.  ...  Few of the predicted motifs were experimentally validated by electrophoretic mobility shift assay.  ...  Prediction of DtxR-binding sites DtxR-binding site recognition profile was calculated by positional Shannon relative entropy method [23, 24] .  ... 
doi:10.1186/1471-2180-4-38 pmid:15447793 pmcid:PMC524172 fatcat:owj74nvkcng6tltwnt62pswcpy

Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes

Nathan Mih, Jonathan M. Monk, Xin Fang, Edward Catoiu, David Heckmann, Laurence Yang, Bernhard O. Palsson
2020 BMC Bioinformatics  
As proteins are one of the main targets of oxidative damage, understanding how the genetic changes of different strains of a species relates to its oxidative environment can reveal hypotheses as to why  ...  We computationally assess a strain's sensitivity to an oxidative environment, based on known chemical mechanisms of oxidative damage to protein groups, defined by their localization and functionality.  ...  Special thanks go to Chia-An Yen for helping with the conception of the research directions and Marc Abrams for proofreading of the manuscript.  ... 
doi:10.1186/s12859-020-3505-y pmid:32349661 fatcat:ykcq66rzdzd7fecdprmnx5u5j4

Proteome-wide Light/Dark Modulation of Thiol Oxidation in Cyanobacteria Revealed by Quantitative Site-specific Redox Proteomics

Jia Guo, Amelia Y. Nguyen, Ziyu Dai, Dian Su, Matthew J. Gaffrey, Ronald J. Moore, Jon M. Jacobs, Matthew E. Monroe, Richard D. Smith, David W. Koppenaal, Himadri B. Pakrasi, Wei-Jun Qian
2014 Molecular & Cellular Proteomics  
On-resin TMT 6-plex labeling; -sensitive proteins in important biological processes Site-specific redox sensitivity predicts functional cysteine sites Novel redox regulatory proteins Stoichiometry of Cys  ...  physiological conditions. • The redox sensitivity data for individual Cys-residues provides important predictive information for identifying functional sites of given proteins as supported by functional  ... 
doi:10.1074/mcp.m114.041160 pmid:25118246 pmcid:PMC4256482 fatcat:5zpgshx2eraononcfwpgf3bahe

Glutathione redox cycle enzymes as potential targets for heme-mediated oxidation under hemolysis: in silico analysis

2018 V N Karazin National University Series "Biology  
From one (in PGD) to three (GSR) cysteines susceptible to oxidation were found in each protein including cysteines that were predicted to bind heme.  ...  Free heme accumulation under hemolysis can affect proteins activity thereby in silico analysis of glutathione redox cycle enzymes structure was performed in order to reveal putative heme-binding sites  ...  (4,49 Å), Glu132, Glu133, Ala135 Active site area Table 6 . 6 Potentially oxidized cysteines in human proteins of the glutathione redox cycle predicted by Cy-Preds.  ... 
doi:10.26565/2075-5457-2018-30-1 fatcat:syvq5o4nbvadxkc2b4oj2db5ia

A computational method to predict carbonylation sites in yeast proteins

H.Q. Lv, J. Liu, J.Q. Han, J.G. Zheng, R.L. Liu
2016 Genetics and Molecular Research  
Among a variety of oxidative stressinduced PTM, protein carbonylation is considered a biomarker of oxidative stress.  ...  Furthermore, there is no bioinformational method to predict carbonylation sites in yeast proteins. Therefore, we propose a computational method to predict yeast carbonylation sites.  ...  Therefore, it is necessary to develop a computational method for prediction of carbonylation sites in yeast proteins.  ... 
doi:10.4238/gmr.15028006 pmid:27420944 fatcat:xp232hwhtrdxxfjxpcnxh3vqxa

Protein tyrosine nitration in plants: Present knowledge, computational prediction and future perspectives

Zsuzsanna Kolbert, Gábor Feigl, Ádám Bordé, Árpád Molnár, László Erdei
2017 Plant physiology and biochemistry (Paris)  
, and evolution of nitric oxide synthase-like proteins in the plant kingdom.  ...  Erdei, Protein tyrosine nitration in plants: Present knowledge, computational prediction and future perspectives, Plant Physiology et Biochemistry (2017), ABSTRACT Nitric oxide (NO) and related molecules  ...  FUNDING Table S1 Number of nitrated sites from experimentally identified nitrated proteins predicted by GPS-YNO 2 1.0.  ... 
doi:10.1016/j.plaphy.2017.01.028 pmid:28187345 fatcat:waxuzb7acbdntb5ctsyxtrz4je

Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation‐induced damage

Roger L Chang, Julian A Stanley, Matthew C Robinson, Joel W Sher, Zhanwen Li, Yujia A Chan, Ashton R Omdahl, Ruddy Wattiez, Adam Godzik, Sabine Matallana‐Surget
2020 EMBO Journal  
Our model predicts proteome maintenance machinery, and proteins protecting against ROS are more resistant in D. radiodurans.  ...  Deleterious effects of protein carbonylation by reactive oxygen species (ROS) make understanding molecular properties determining ROS susceptibility essential.  ...  Silver provided laboratory resources, feedback on the work, comments on the manuscript and full support of this independent publication. We also thank Dr.  ... 
doi:10.15252/embj.2020104523 pmid:33073387 fatcat:vwspyunzabgo5gbcukrlmpf4zu

A machine learning approach for predicting methionine oxidation sites

Juan C. Aledo, Francisco R. Cantón, Francisco J. Veredas
2017 BMC Bioinformatics  
The oxidation of protein-bound methionine to form methionine sulfoxide, has traditionally been regarded as an oxidative damage.  ...  Therefore, computational methods designed to predict methionine oxidation sites are an attractive alternative.  ...  The source code to extract features and carry out predictions can be obtained at  ... 
doi:10.1186/s12859-017-1848-9 pmid:28962549 pmcid:PMC5622526 fatcat:nus4ml35vfdkth2trr3w4rj2oy

Cysteine post-translational modifications: ten years from chemical proteomics to bioinformatics [article]

Yanzheng Meng, Lei Li
2021 arXiv   pre-print
We also discuss in silico approaches for the prediction of the different types of cysteine modified sites, giving directions for future study.  ...  These PTMs participate in a wide range of biological activities including the alteration of enzymatic reactions, protein-protein interactions and protein stability.  ...  Researchers can develop bioinformatics tools to predict specific PTMs sites based on a range of algorithms and identified PTM sites.  ... 
arXiv:2105.13582v1 fatcat:u4gmle62wbda3lvhazvurqzave
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