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For: Ferrer-Costa C, Orozco M, de la Cruz X. Characterization of compensated mutations in terms of structural and physico-chemical properties. J Mol Biol 2006;365:249-56. [PMID: 17059831 DOI: 10.1016/j.jmb.2006.09.053] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Revised: 09/14/2006] [Accepted: 09/21/2006] [Indexed: 11/29/2022]
Number Cited by Other Article(s)
1
Hoehe MR, Herwig R. Analysis of 1276 Haplotype-Resolved Genomes Allows Characterization of Cis- and Trans-Abundant Genes. Methods Mol Biol 2023;2590:237-272. [PMID: 36335503 DOI: 10.1007/978-1-0716-2819-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
2
Azbukina N, Zharikova A, Ramensky V. Intragenic compensation through the lens of deep mutational scanning. Biophys Rev 2022;14:1161-1182. [PMID: 36345285 PMCID: PMC9636336 DOI: 10.1007/s12551-022-01005-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/26/2022] [Indexed: 12/20/2022]  Open
3
Fu T, Li F, Zhang Y, Yin J, Qiu W, Li X, Liu X, Xin W, Wang C, Yu L, Gao J, Zheng Q, Zeng S, Zhu F. VARIDT 2.0: structural variability of drug transporter. Nucleic Acids Res 2021;50:D1417-D1431. [PMID: 34747471 PMCID: PMC8728241 DOI: 10.1093/nar/gkab1013] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/08/2021] [Accepted: 11/04/2021] [Indexed: 12/20/2022]  Open
4
Serrano C, Teixeira CSS, Cooper DN, Carneiro J, Lopes-Marques M, Stenson PD, Amorim A, Prata MJ, Sousa SF, Azevedo L. Compensatory epistasis explored by molecular dynamics simulations. Hum Genet 2021;140:1329-1342. [PMID: 34173867 DOI: 10.1007/s00439-021-02307-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/20/2021] [Indexed: 11/24/2022]
5
Sharma V, Hiller M. Losses of human disease-associated genes in placental mammals. NAR Genom Bioinform 2019;2:lqz012. [PMID: 33575564 PMCID: PMC7671337 DOI: 10.1093/nargab/lqz012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/24/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023]  Open
6
Hoehe MR, Herwig R, Mao Q, Peters BA, Drmanac R, Church GM, Huebsch T. Significant abundance of cis configurations of coding variants in diploid human genomes. Nucleic Acids Res 2019;47:2981-2995. [PMID: 30698752 PMCID: PMC6451136 DOI: 10.1093/nar/gkz031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/05/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022]  Open
7
Marín Ò, Aguirre J, de la Cruz X. Compensated pathogenic variants in coagulation factors VIII and IX present complex mapping between molecular impact and hemophilia severity. Sci Rep 2019;9:9538. [PMID: 31267011 PMCID: PMC6606640 DOI: 10.1038/s41598-019-45916-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 06/18/2019] [Indexed: 01/07/2023]  Open
8
Storz JF. Compensatory mutations and epistasis for protein function. Curr Opin Struct Biol 2018;50:18-25. [PMID: 29100081 PMCID: PMC5936477 DOI: 10.1016/j.sbi.2017.10.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/05/2017] [Accepted: 10/12/2017] [Indexed: 01/09/2023]
9
Tiberti M, Pandini A, Fraternali F, Fornili A. In silico identification of rescue sites by double force scanning. Bioinformatics 2018;34:207-214. [PMID: 28961796 PMCID: PMC5860198 DOI: 10.1093/bioinformatics/btx515] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/23/2017] [Accepted: 08/10/2017] [Indexed: 01/03/2023]  Open
10
Starr TN, Thornton JW. Epistasis in protein evolution. Protein Sci 2016;25:1204-18. [PMID: 26833806 PMCID: PMC4918427 DOI: 10.1002/pro.2897] [Citation(s) in RCA: 317] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 01/18/2023]
11
Storz JF. Causes of molecular convergence and parallelism in protein evolution. Nat Rev Genet 2016;17:239-50. [PMID: 26972590 PMCID: PMC5482790 DOI: 10.1038/nrg.2016.11] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
12
Mueller SC, Sommer B, Backes C, Haas J, Meder B, Meese E, Keller A. From Single Variants to Protein Cascades: MULTISCALE MODELING OF SINGLE NUCLEOTIDE VARIANT SETS IN GENETIC DISORDERS. J Biol Chem 2016;291:1582-1590. [PMID: 26601959 DOI: 10.1074/jbc.m115.695247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Indexed: 01/18/2023]  Open
13
Barešić A, Martin ACR. Compensated pathogenic deviations. Biomol Concepts 2015;2:281-92. [PMID: 25962036 DOI: 10.1515/bmc.2011.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
14
Identification of cis-suppression of human disease mutations by comparative genomics. Nature 2015;524:225-9. [PMID: 26123021 DOI: 10.1038/nature14497] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 04/23/2015] [Indexed: 11/08/2022]
15
Sikosek T, Chan HS. Biophysics of protein evolution and evolutionary protein biophysics. J R Soc Interface 2015;11:20140419. [PMID: 25165599 DOI: 10.1098/rsif.2014.0419] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
16
Riera C, Lois S, Domínguez C, Fernandez-Cadenas I, Montaner J, Rodríguez-Sureda V, de la Cruz X. Molecular damage in Fabry disease: characterization and prediction of alpha-galactosidase A pathological mutations. Proteins 2014;83:91-104. [PMID: 25382311 DOI: 10.1002/prot.24708] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/25/2014] [Accepted: 10/18/2014] [Indexed: 12/12/2022]
17
Ivankov DN, Finkelstein AV, Kondrashov FA. A structural perspective of compensatory evolution. Curr Opin Struct Biol 2014;26:104-12. [PMID: 24981969 PMCID: PMC4141909 DOI: 10.1016/j.sbi.2014.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/11/2014] [Accepted: 05/16/2014] [Indexed: 11/25/2022]
18
Xu J, Zhang J. Why human disease-associated residues appear as the wild-type in other species: genome-scale structural evidence for the compensation hypothesis. Mol Biol Evol 2014;31:1787-92. [PMID: 24723421 DOI: 10.1093/molbev/msu130] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
19
Riera C, Lois S, de la Cruz X. Prediction of pathological mutations in proteins: the challenge of integrating sequence conservation and structure stability principles. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
20
Soylemez O, Kondrashov FA. Estimating the rate of irreversibility in protein evolution. Genome Biol Evol 2013;4:1213-22. [PMID: 23132897 PMCID: PMC3542581 DOI: 10.1093/gbe/evs096] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
21
Wang C, Huang R, He B, Du Q. Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis. BMC Bioinformatics 2012;13:263. [PMID: 23057711 PMCID: PMC3478181 DOI: 10.1186/1471-2105-13-263] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 09/11/2012] [Indexed: 11/12/2022]  Open
22
Current challenges in genome annotation through structural biology and bioinformatics. Curr Opin Struct Biol 2012;22:594-601. [PMID: 22884875 DOI: 10.1016/j.sbi.2012.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 06/29/2012] [Accepted: 07/09/2012] [Indexed: 01/25/2023]
23
Zhang G, Pei Z, Ball EV, Mort M, Kehrer-Sawatzki H, Cooper DN. Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations. Hum Genomics 2012;5:453-84. [PMID: 21807602 PMCID: PMC3525967 DOI: 10.1186/1479-7364-5-5-453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
24
Kumar S, Dudley JT, Filipski A, Liu L. Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. Trends Genet 2011;27:377-86. [PMID: 21764165 PMCID: PMC3272884 DOI: 10.1016/j.tig.2011.06.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 06/10/2011] [Accepted: 06/13/2011] [Indexed: 12/30/2022]
25
Gong S, Worth CL, Cheng TMK, Blundell TL. Meet Me Halfway: When Genomics Meets Structural Bioinformatics. J Cardiovasc Transl Res 2011;4:281-303. [DOI: 10.1007/s12265-011-9259-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 02/08/2011] [Indexed: 01/08/2023]
26
Zhang G, Pei Z, Krawczak M, Ball EV, Mort M, Kehrer-Sawatzki H, Cooper DN. Triangulation of the human, chimpanzee, and Neanderthal genome sequences identifies potentially compensated mutations. Hum Mutat 2010;31:1286-93. [DOI: 10.1002/humu.21389] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
27
Cooper DN, Chen JM, Ball EV, Howells K, Mort M, Phillips AD, Chuzhanova N, Krawczak M, Kehrer-Sawatzki H, Stenson PD. Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Hum Mutat 2010;31:631-55. [PMID: 20506564 DOI: 10.1002/humu.21260] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
28
Liang Z, Xu M, Teng M, Niu L, Wu J. Coevolution is a short-distance force at the protein interaction level and correlates with the modular organization of protein networks. FEBS Lett 2010;584:4237-40. [DOI: 10.1016/j.febslet.2010.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Revised: 09/04/2010] [Accepted: 09/08/2010] [Indexed: 11/17/2022]
29
Talavera D, Taylor MS, Thornton JM. The (non)malignancy of cancerous amino acidic substitutions. Proteins 2010;78:518-29. [PMID: 19787769 DOI: 10.1002/prot.22574] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
30
Gong S, Blundell TL. Structural and functional restraints on the occurrence of single amino acid variations in human proteins. PLoS One 2010;5:e9186. [PMID: 20169194 PMCID: PMC2820541 DOI: 10.1371/journal.pone.0009186] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 01/24/2010] [Indexed: 11/19/2022]  Open
31
Chakrabarti S, Panchenko AR. Structural and functional roles of coevolved sites in proteins. PLoS One 2010;5:e8591. [PMID: 20066038 PMCID: PMC2797611 DOI: 10.1371/journal.pone.0008591] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 10/19/2009] [Indexed: 01/09/2023]  Open
32
Baresić A, Hopcroft LEM, Rogers HH, Hurst JM, Martin ACR. Compensated pathogenic deviations: analysis of structural effects. J Mol Biol 2009;396:19-30. [PMID: 19900462 DOI: 10.1016/j.jmb.2009.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 10/29/2009] [Accepted: 11/03/2009] [Indexed: 10/20/2022]
33
Azevedo L, Carneiro J, van Asch B, Moleirinho A, Pereira F, Amorim A. Epistatic interactions modulate the evolution of mammalian mitochondrial respiratory complex components. BMC Genomics 2009;10:266. [PMID: 19523237 PMCID: PMC2711975 DOI: 10.1186/1471-2164-10-266] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 06/13/2009] [Indexed: 11/22/2022]  Open
34
Jakubowska A, Korona R. Lack of evolutionary conservation at positions important for thermal stability in the yeast ODCase protein. Mol Biol Evol 2009;26:1431-4. [PMID: 19349645 DOI: 10.1093/molbev/msp066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
35
Pazos F, Valencia A. Protein co-evolution, co-adaptation and interactions. EMBO J 2008;27:2648-55. [PMID: 18818697 PMCID: PMC2556093 DOI: 10.1038/emboj.2008.189] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 08/28/2008] [Indexed: 01/28/2023]  Open
36
Juan D, Pazos F, Valencia A. Co-evolution and co-adaptation in protein networks. FEBS Lett 2008;582:1225-30. [DOI: 10.1016/j.febslet.2008.02.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Accepted: 02/08/2008] [Indexed: 10/22/2022]
37
Musumeci MA, Arakaki AK, Rial DV, Catalano-Dupuy DL, Ceccarelli EA. Modulation of the enzymatic efficiency of ferredoxin-NADP(H) reductase by the amino acid volume around the catalytic site. FEBS J 2008;275:1350-66. [PMID: 18279389 DOI: 10.1111/j.1742-4658.2008.06298.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
38
Paulander W, Maisnier-Patin S, Andersson DI. Multiple mechanisms to ameliorate the fitness burden of mupirocin resistance in Salmonella typhimurium. Mol Microbiol 2007;64:1038-48. [PMID: 17501926 DOI: 10.1111/j.1365-2958.2007.05713.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
39
Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome. BMC Genomics 2006;7:306. [PMID: 17144929 PMCID: PMC1702542 DOI: 10.1186/1471-2164-7-306] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Accepted: 12/05/2006] [Indexed: 02/02/2023]  Open
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