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Correlating protein function and stability through the analysis of single amino acid substitutions

Yana Bromberg, Burkhard Rost
2009 BMC Bioinformatics  
Single amino acid substitutions as caused by nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) often disrupt function by altering protein structure and/or stability, but can also wreak havoc by directly  ...  In fact, such methods consistently outperform approaches that predict functional change through the application of binary thresholds to stability change.  ...  The authors were supported by the grants R02-LM07329 from the National Library of Medicine (NLM) and U54-GM074958-01 to the Northeast Structural Genomics consortium (NESG) from the Protein Structure Initiative  ... 
doi:10.1186/1471-2105-10-s8-s8 pmid:19758472 pmcid:PMC2745590 fatcat:bktgdmk7j5dx7ktzongd5spk2u

Evolutionary patterns of amino acid substitutions in 12 Drosophila genomes

Lev Y Yampolsky, Michael A Bouzinier
2010 BMC Genomics  
We present a tool for the genome-wide analysis of frequencies and patterns of amino acid substitutions in multiple alignments of genes' coding regions, and a database of amino acid substitutions in the  ...  These patterns differ among protein families of different functionality, with genes coding for RNA-binding proteins differing from most other functional groups in terms of amino acid substitution patterns  ...  Hahn for providing alignments and useful discussion and to A. Kondrashov, Y. Wolf and three anonymous reviewers for helpful suggestions on improving the analysis and the manuscript.  ... 
doi:10.1186/1471-2164-11-s4-s10 pmid:21143793 pmcid:PMC3005911 fatcat:g2ztyaipkrghpn2bhiconan73y

Computational Methods to Work as First-Pass Filter in Deleterious SNP Analysis of Alkaptonuria

R. Magesh, C. George Priya Doss
2012 The Scientific World Journal  
The prediction of phenotype of nsSNPs by computational analysis may provide a good way to explore the function of nsSNPs and its relationship with susceptibility to disease.  ...  In this context, we surveyed and compared variation databases along within silicoprediction programs to assess the effects of deleterious functional variants on protein functions.  ...  Acknowledgment The authors thank the management of VIT University for providing the facilities to carry out this work.  ... 
doi:10.1100/2012/738423 pmid:22606059 pmcid:PMC3349151 fatcat:yxkhqhqb3nfwdmnfxypxz5r6oi

In Silico profiling of deleterious amino acid substitutions of potential pathological importance in haemophlia A and haemophlia B

George Priya Doss C
2012 Journal of Biomedical Science  
In this study, instead of current biochemical methods, the effects of deleterious amino acid substitutions in F8 and F9 gene upon protein structure and function were assayed by means of computational methods  ...  Furthermore, we modeled mutant proteins and compared them with the native protein for analysis of protein structure stability.  ...  Acknowledgements The authors thank the management of VIT University for providing the facilities to carry out this work.  ... 
doi:10.1186/1423-0127-19-30 pmid:22423892 pmcid:PMC3361463 fatcat:spxhcwk4c5gzzjcczsxuukoagy

Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates [article]

Christoffer Norn, Ingemar André
2022 bioRxiv   pre-print
amino acid substitutions.  ...  By evolving proteins under different fitness functions, we can study how the fitness function affects the distribution of proposed and accepted mutations, site-specific rates, and the prevalence of correlated  ...  Theobald for helpful discussions on the implementation of RosettaEvolve.  ... 
doi:10.1101/2022.06.01.494278 fatcat:mj7tmdzgbbf7pmhfsvvcyyyjgq

Prediction of a highly deleterious mutation E17K in AKT-1 gene: An in silico approach

Imran Khan, Irfan A. Ansari
2017 Biochemistry and Biophysics Reports  
The insight of the structural attribute was gained through analysis of, secondary structures, solvent accessibility and intermolecular hydrogen bond analysis which confirmed one missense mutation (E17K  ...  In conclusion, the investigated gene AKT1 has twenty nine SNPs in the coding region and through progressive analysis using different bioinformatics tools one highly deleterious SNP with rs121434592 was  ...  Acknowledgments The authors thank the management of the Integral University for providing the facilities to carry out this study.  ... 
doi:10.1016/j.bbrep.2017.04.013 pmid:29114575 pmcid:PMC5637233 fatcat:m4tamsguj5bltkmnxtor3h4nh4

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene

Tikam Chand Dakal, Deepak Kala, Gourav Dhiman, Vinod Yadav, Andrey Krokhotin, Nikolay V. Dokholyan
2017 Scientific Reports  
This study, for the first time, provided in-depth insights on the effects of amino acid substitutions on IL-8 protein structure, function and disease association.  ...  In step 2, based on conservation of amino acid residues, stability analysis, structural superimposition, RSMD and docking analysis, the possible structural-functional relationship was ascertained for high-confidence  ...  Acknowledgements T.C.D. acknowledges all faculty members and the research scholars of the Biosciences Department for their support and encouragement.  ... 
doi:10.1038/s41598-017-06575-4 pmid:28747718 pmcid:PMC5529537 fatcat:cebfh6p46vhsrct3d6dia3a3hu

Rational Design of Adenylate Kinase Thermostability through Coevolution and Sequence Divergence Analysis

Jian Chang, Chengxin Zhang, Huaqiang Cheng, Yan-Wen Tan
2021 International Journal of Molecular Sciences  
most of the catalytic function at ambient temperatures.  ...  Single- and double-point mutants constructed based on this method increase the thermal denaturation temperature of the mesophilic Escherichia coli (E. coli) ADK by 5.5 and 8.3 °C, respectively, while preserving  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/ijms22052768 pmid:33803409 fatcat:aggr7ovss5gq7gddtd23bawnym

Path to Facilitate the Prediction of Functional Amino Acid Substitutions in Red Blood Cell Disorders – A Computational Approach

Rajith B, George Priya Doss C, Reiner Albert Veitia
2011 PLoS ONE  
Single Nucleotide Polymorphisms (SNPs) are amino acid substitutions that currently account for approximately half of the known gene lesions responsible for human inherited diseases.  ...  Furthermore, we modeled mutant proteins and compared them with the native protein for evaluation of protein structure stability.  ...  Acknowledgments The authors take this opportunity to thank the management of Vellore Institute of Technology University for providing the facilities and encouragement to carry out this work.  ... 
doi:10.1371/journal.pone.0024607 pmid:21931771 pmcid:PMC3172254 fatcat:za37pyfcibdo7h5c3wv5ozkbi4

Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes

Álvarez-Machancoses, De Andrés-Galiana, Fernández-Martínez, Kloczkowski
2019 Biomolecules  
Accurate prediction of protein stability changes resulting from amino acid substitutions is of utmost importance in medicine to better understand which mutations are deleterious, leading to diseases, and  ...  The Holdout Random Sampler is utilized to analysis the energy change, the corresponding uncertainty, and to obtain a set of admissible energy changes, expressed as a cumulative distribution function.  ...  The understanding of the mechanisms that determine protein stability is one of the forefront challenges in proteomics and transcriptomics, since even a single amino acid substitution can be the cause of  ... 
doi:10.3390/biom10010067 pmid:31906171 pmcid:PMC7023245 fatcat:idm3x6cbefedfgeptkong6etji

Mutations in a CCHC zinc-binding motif of the reovirus sigma 3 protein decrease its intracellular stability

T Mabrouk, G Lemay
1994 Journal of Virology  
Further analysis revealed that zinc-binding capability, as measured by retention on a zinc chelate affinity adsorbent, correlates with stability.  ...  To further understand the role of the amino-terminal portion of the cr3 protein, encompassing the zinc-binding region, we performed individual amino acid substitutions in this region.  ...  T.M. is the recipient of a studentship from the Agence Canadienne de Developpement International, and G.L. is the recipient of a Chercheur-boursier award from the Fonds de la Recherche en Sante du Quebec  ... 
doi:10.1128/jvi.68.8.5287-5290.1994 fatcat:6msiiakiyrbntck24hailg6ytm

Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness [article]

Martin Schwersensky, Marianne Rooman, Fabrizio Pucci
2020 bioRxiv   pre-print
At the nucleobase level, single base substitutions were shown to yield on average less destabilizing amino acid mutations than multiple base substitutions.  ...  At the amino acid level, we found the protein surface to be more robust to mutations than the core, in a protein length-dependent manner.  ...  Acknowledgments We thank the FNRS -Fund for Scientific Research for its financial support through a PDR research project.  ... 
doi:10.1101/2020.02.05.935809 fatcat:imxl7w47c5h4zpehfs7chmdqta

How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme

Luciano A. Abriata, Timothy Palzkill, Matteo Dal Peraro, Vladimir N. Uversky
2015 PLoS ONE  
Substitution patterns in over one third of the residues can be quantitatively modeled by monotonic dependencies on amino acid descriptors and predictions of changes in folding stability.  ...  Here we present a quantitative, structure-based analysis of a high-resolution map describing the tolerance to all substitutions in all positions of a functional enzyme, namely a TEM lactamase previously  ...  Introduction The amino acid sequence of a protein defines its structure and function, but also a number of other entangled traits such as stability, water solubility/membrane integration, potential for  ... 
doi:10.1371/journal.pone.0118684 pmid:25706742 pmcid:PMC4338278 fatcat:hcf7wjllirhl3jxggjq3jndnru

A Novel Methodology for Structural, Functional and Toxicological Analysis of Mutant Angiogenin Protein in Human

Basit Haidar, Muhammad Asif Nawaz, Rabbia Mumtaz, Muhammad Aamir Hassan, Simon Manzoor, Aqib Zafar Khan
2017 Journal of Proteomics & Bioinformatics  
DDG value of Q36L and H138R were positive while DDG values of all the other mutations were negative representing the decreased stability of protein with single amino acid substitution.  ...  Mutation3D is an online tool used for functional analysis and visualization of amino acid substitutions on three-dimensional structure of protein.  ... 
doi:10.4172/jpb.1000450 fatcat:rk6j6tddmnbpng476e3orhc7um

Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness

Martin Schwersensky, Marianne Rooman, Fabrizio Pucci
2020 BMC Biology  
than 20,000 protein structures, as well as through available experimental stability and fitness data.  ...  Results At the amino acid level, we found the protein surface to be more robust against random mutations than the core, this difference being stronger for small proteins.  ...  Funding We acknowledge financial support from the FNRS -Fund for Scientific Research through a PDR research project.  ... 
doi:10.1186/s12915-020-00870-9 pmid:33081759 fatcat:io5hrbnyvvc5vkpex2ry4kcw6q
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