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Structural assessment of the effects of Amino Acid Substitutions on protein stability and protein protein interaction

Shaolei Teng, Anand K. Srivastava, Charles E. Schwartz, Emil Alexov, Liangjiang Wang
2010 International Journal of Computational Biology and Drug Design  
Folding and binding energy differences between wild-type and mutant structures were computed to quantitatively assess the effects of amino acid substitutions on protein stability and protein-protein interaction  ...  A structure-based approach is described for predicting the effects of amino acid substitutions on protein function. Structures were predicted using a homology modelling method.  ...  Acknowledgments This work is supported by the CSREES/USDA, under project number SC-1700355. EA acknowledges the support from NIH/NLM, grant number R03 LM009748.  ... 
doi:10.1504/ijcbdd.2010.038396 pmid:21297231 pmcid:PMC3319068 fatcat:rrg2yz3gebduxndztodardj5hm

D76V, L161R, and C117S are the most pathogenic amino acid substitutions with several dangerous consequences on leptin structure, function, and stability

Mohammed Baqur S. Al-Shuhaib
2019 Egyptian Journal of Medical Human Genetics  
on the protein structure, function, and stability.  ...  The exploration of these missense mutations may present novel perspectives for various deleterious consequences originated from such amino acids substitutions.  ...  Predicting amino acid mutation effect on protein stability through CUPSAT To get a better view to the stability of the mutant human leptin, amino acids substitutions were analyzed using CUPSAT, an automatic  ... 
doi:10.1186/s43042-019-0033-2 fatcat:46vtbr5imjca3a7khrpg5ngqam

IN-SILICO BASED PREDICTION OF DELETERIOUS NON-SYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISMS IN THE HUMAN CDK1 GENE

Shikha Suman, Ashutosh Mishra, GyanPrakash Tiwari, Anurag Kulshrestha
2016 International Journal of Advanced Research  
Using structure, function and evolution based bioinformatics approaches, most damaging single nucleotide polymorphisms (SNPs) in CDK1 gene and their impact on the structure and function of CDK1 protein  ...  I136N and R275Q were predicted to be highly damaging and hence affecting the structure, function and stability of CDK1 protein, which were further crosschecked using I-Mutant and DUET tools.  ...  Acknowledgments:- Computing amenities of IIIT Allahabad is greatly acknowledged.  ... 
doi:10.21474/ijar01/1337 fatcat:ibnctddyszfnzjizqlxrknavdq

Using Knowledge of Protein Structural Constraints to Predict the Evolution of HIV-1

Simon G. Williams, Rachit Madan, Matthew G.S. Norris, John Archer, Kenji Mizuguchi, David L. Robertson, Simon C. Lovell
2011 Journal of Molecular Biology  
Our approach is based on the identification of likely amino acid changes in the context of these structural constraints using environmentspecific substitution matrices as well as considering the physical  ...  The high levels of sequence diversity and rapid rates of evolution of HIV-1 represent the main challenges for developing effective therapies.  ...  The prediction of protein sequence evolution based on structural templates relies heavily on amino acid side-chain packing analysis and interpretation of interactions at the atomic level.  ... 
doi:10.1016/j.jmb.2011.04.037 pmid:21763504 fatcat:bcbkxhdiejgdzdjkrsabrkpna4

Single Amino Acid Change Mutation in the Hydrophobic Core of the N-terminal Domain of P22 TSP affects the Proteins Stability [article]

Joseph A Ayariga, Robert Villafane
2021 bioRxiv   pre-print
stability of the N-terminal domain of the P22 TSP.  ...  In this process, the valine patch (triple valine residues that formed a hydrophobic core) was replaced with charged amino acids (Asp or lysine) or hydrophobic amino acids (Leucine or isoleucine).  ...  We are grateful to Alabama State University and the College of Science, Mathematics and Technology for their continuous support.  ... 
doi:10.1101/2021.12.16.472976 fatcat:t5is6hkq3vb3jditz4jmf2ls7q

Epistasis in protein evolution

Tyler N. Starr, Joseph W. Thornton
2016 Protein Science  
The structure, function, and evolution of proteins depend on physical and genetic interactions among amino acids.  ...  dramatically; it therefore makes evolution more contingent on low-probability historical events and leaves stronger marks on the sequences, structures, and functions of protein families.  ...  Acknowledgments The authors thank members of the Thornton laboratory past and present for insightful comments. The authors declare no conflict of interest.  ... 
doi:10.1002/pro.2897 pmid:26833806 pmcid:PMC4918427 fatcat:myrgp3f7lzgwdelbc4eqjljkmi

In silico prediction of the functional and structural consequences of the non-synonymous single nucleotide polymorphism A122V in bovine CXC chemokine receptor type 1

A. F. Guzzi, F. S. L. Oliveira, M. M. S. Amaro, P. F. Tavares-Filho, J. E. Gabriel
2019 Brazilian Journal of Biology  
CXCR1 sequences were submitted as input to different Bioinformatics' tools to examine the effects of this polymorphism on functional and structural stabilities, to predict eventual alterations in the 3  ...  The current study aimed to assess whether the A122V causal polymorphism promotes alterations in the functional and structural proprieties of the CXC chemokine receptor type 1 protein (CXCR1) of cattle  ...  Acknowledgements This research was supported by the Bioinformatics and Computational Biology Group, designated "BIO in BYTES".  ... 
doi:10.1590/1519-6984.188655 pmid:31017232 fatcat:m5kgmoy5svb5pfyouf74hm3l5q

Comprehensive Analysis of rsSNPs Associated with Hypertension Using In-Silico Bioinformatics Tools

Alsadig Gassoum, Nahla E. Abdelraheem, Nehad Elsadig
2016 OALib  
Results: SNPs were evaluated for their deleterious effect on the protein function and stability, in the present study, 7 SNPs were predicted deleterious (A288S, M731T, R172C, R50Q, G460W, K197N, G75V).  ...  However, the genetic analysis of hypertension produced complex, inconsistent and nonreproducible results, which makes it difficult to draw conclusions about the association between specific genes and hypertension  ...  PROVEAN (Protein Variation Effect Analyzer) Is a soft ware that predict the amino acid substitution has any impact on the biological function of the protein, the assessment is based on PROVEAN score, where  ... 
doi:10.4236/oalib.1102839 fatcat:iozfocqfzrecfmmczao3y7goci

Protein Destabilization as a Common Factor in Diverse Inherited Disorders

Rachel L. Redler, Jhuma Das, Juan R. Diaz, Nikolay V. Dokholyan
2015 Journal of Molecular Evolution  
To test this hypothesis, we computationally evaluate the effects on protein stability of all possible amino acid substitutions in 20 disease-associated proteins with multiple identified pathogenic missense  ...  This finding supports the notion that destabilization of native protein structure underlies the pathogenicity of broad set of missense mutations, even in cases where reduced protein stability and/or aggregation  ...  R.L.R. was supported by the National Institutes of Health Predoctoral Fellowship F31NS073435 from the National Institute of Neurological Disorders and Stroke.  ... 
doi:10.1007/s00239-015-9717-5 pmid:26584803 pmcid:PMC4712097 fatcat:heurr2jgzjfhjlkefi3d22n7fi

Proteome-wide identification of amino acid substitutions deleterious for protein function [article]

Ricard A. Rodriguez-Mias, Kyle N. Hess, Bianca Y. Ruiz, Ian R. Smith, Anthony S. Barente, Stephanie M. Zimmerman, Yang Y. Lu, William S. Noble, Stanley Fields, Judit Villen
2022 bioRxiv   pre-print
We apply this technology to the proteome of yeast to reveal amino acid substitutions that impact protein structure, ligand binding, protein-protein interactions, protein post-translational modifications  ...  , and protein thermal stability.  ...  ., and W.S.N.). This work is supported in part by the University of Washington's Proteomics Resource (UWPR95794).  ... 
doi:10.1101/2022.04.06.487405 fatcat:dpv3wgbqzfg5nm6s5dxfxq5df4

Fluorine: A new element in protein design

Benjamin C. Buer, E. Neil G. Marsh
2012 Protein Science  
Fluorination seems to be a general and effective strategy to enhance the stability of proteins, both soluble and membrane bound, against chemical and thermal denaturation, although retaining structure  ...  However, the development of various biosynthetic methods for introducing noncanonical amino acids into proteins promises to expand the utility of fluorinated amino acids in protein design.  ...  The position and pattern of the hFLeu substitutions also has an effect on the stability of the protein (Fig. 4) .  ... 
doi:10.1002/pro.2030 pmid:22274989 pmcid:PMC3375745 fatcat:kwf4vwyes5evxc7atpim3uvq24

In-silico structural, functional and immunogenic characterization of Taenia solium TS14 protein

Chitra Joshi, Siddharth Gautam
2017 Indian Journal of Animal Research  
Mutational analysis based on the single amino acid substitutions among six TS14 isolates demonstrated minor variations in structural stability; however, all the substitutions were well tolerated.  ...  However, the information on structure, function, stability and immunogenicity of TS14 derived from different isolates is primarily lacking.  ...  ACKNOWLEDGEMENT The authors are grateful to Director, Indian Veterinary Research Institute (IVRI), Izatnagar, India, and Dr. B.C.  ... 
doi:10.18805/ijar.b-3313 fatcat:kdubqmodqvcuzd5dmfkno7fmke

Neighbor Preferences of Amino Acids and Context-Dependent Effects of Amino Acid Substitutions in Human, Mouse, and Dog

Mingchuan Fu, Zhuoran Huang, Yuanhui Mao, Shiheng Tao
2014 International Journal of Molecular Sciences  
Among 20 amino acids, P elicited the greatest effect on amino acid substitutions.  ...  Using relative entropy, we investigated the neighbor preferences of 20 amino acids and the context-dependent effects of amino acid substitutions with protein sequences in human, mouse, and dog.  ...  This work was supported by the PhD Programs Foundation of the Ministry of Education of China (20100204110026) and project from National Science Foundation of China (31125007).  ... 
doi:10.3390/ijms150915963 pmid:25210846 pmcid:PMC4200849 fatcat:b5xrepoocrautdtzwuhzzeurg4

In silico analysis of Missense Variants in Human MPL Gene Associated with Essential Thrombocythemia [article]

Sahar G. Elbager, Abier A. Makkawi, Hadeel A. Mohamed, Fauzia A. Abdelrahman, Lamia H. Osman, Moroj F. Hameed, Asia M. Elrashid, Mohamed Y. Basher, Safinaz I. Khalil, Magdi Bayoumi
2019 bioRxiv   pre-print
RaptorX and Chimera were used to analyzing the effect of nsSNPs on functions and structure of the TPO-R. STRING and KEGG database were used for TPO-R protein-protein interaction.  ...  A total 5 nsSNPs (D295G, R257C, Y252H, R537W and D128Y) were predicted to have the most damaging effects on TPO-R structure and function.  ...  The effect of amino acid substitution on protein structure was assessed on the basis of degree of conservation of amino acids using sequence homology Substitution of an amino acid at each position with  ... 
doi:10.1101/830372 fatcat:h3feabkgr5autg63o4vm4mptgq

Identification and prediction of the consequences of nonsynonymous SNPs in glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene of zebrafish Danio rerio

Kiran Dashrath RASAL, Vemulawada CHAKRAPANI, Swagat Kumar PATRA, Sasmita JENA, Shibani Dutta MOHAPATRA, Swapnarani NAYAK, Jitendra Kumar SUNDARAY, Pallipuram JAYASANKAR, Hirak Kumar BARMAN
2016 Turkish Journal of Biology  
Altogether, this study demonstrated the impact of nsSNPs on the protein structure and function.  ...  The Procheck quality assessment in the Ramachandran plot showed that the incorporated mutation (p.W194R) led to a shifting of amino acid residues from the most favored regions towards the disallowed region  ...  Acknowledgment This work was supported by a grant from the Indian Council of Agricultural Research (ICAR), Ministry of Agriculture, India.  ... 
doi:10.3906/biy-1501-11 fatcat:6tqaumclnvhcjpbtmkq7qldvdu
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