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For: Sánchez IE, Tejero J, Gómez-Moreno C, Medina M, Serrano L. Point mutations in protein globular domains: contributions from function, stability and misfolding. J Mol Biol 2006;363:422-32. [PMID: 16978645 DOI: 10.1016/j.jmb.2006.08.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 07/25/2006] [Accepted: 08/08/2006] [Indexed: 11/25/2022]
Number Cited by Other Article(s)
1
Sánchez IE, Galpern EA, Garibaldi MM, Ferreiro DU. Molecular Information Theory Meets Protein Folding. J Phys Chem B 2022;126:8655-8668. [PMID: 36282961 DOI: 10.1021/acs.jpcb.2c04532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
2
Houben B, Rousseau F, Schymkowitz J. Protein structure and aggregation: a marriage of necessity ruled by aggregation gatekeepers. Trends Biochem Sci 2021;47:194-205. [PMID: 34561149 DOI: 10.1016/j.tibs.2021.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/25/2021] [Accepted: 08/31/2021] [Indexed: 12/27/2022]
3
Pacheco-García JL, Cano-Muñoz M, Sánchez-Ramos I, Salido E, Pey AL. Naturally-Occurring Rare Mutations Cause Mild to Catastrophic Effects in the Multifunctional and Cancer-Associated NQO1 Protein. J Pers Med 2020;10:E207. [PMID: 33153185 PMCID: PMC7711955 DOI: 10.3390/jpm10040207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022]  Open
4
Yang Y, Ding X, Zhu G, Niroula A, Lv Q, Vihinen M. ProTstab - predictor for cellular protein stability. BMC Genomics 2019;20:804. [PMID: 31684883 PMCID: PMC6830000 DOI: 10.1186/s12864-019-6138-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/24/2019] [Indexed: 01/10/2023]  Open
5
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
6
Foy SG, Wilson BA, Bertram J, Cordes MHJ, Masel J. A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution. Genetics 2019;211:1345-1355. [PMID: 30692195 PMCID: PMC6456324 DOI: 10.1534/genetics.118.301719] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/25/2019] [Indexed: 01/06/2023]  Open
7
Local frustration around enzyme active sites. Proc Natl Acad Sci U S A 2019;116:4037-4043. [PMID: 30765513 DOI: 10.1073/pnas.1819859116] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
8
Buß O, Rudat J, Ochsenreither K. FoldX as Protein Engineering Tool: Better Than Random Based Approaches? Comput Struct Biotechnol J 2018;16:25-33. [PMID: 30275935 PMCID: PMC6158775 DOI: 10.1016/j.csbj.2018.01.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/21/2017] [Accepted: 01/20/2018] [Indexed: 02/04/2023]  Open
9
Buß O, Muller D, Jager S, Rudat J, Rabe KS. Improvement in the Thermostability of a β-Amino Acid Converting ω-Transaminase by Using FoldX. Chembiochem 2017;19:379-387. [PMID: 29120530 DOI: 10.1002/cbic.201700467] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 12/19/2022]
10
Knies JL, Cai F, Weinreich DM. Enzyme Efficiency but Not Thermostability Drives Cefotaxime Resistance Evolution in TEM-1 β-Lactamase. Mol Biol Evol 2017;34:1040-1054. [PMID: 28087769 PMCID: PMC5400381 DOI: 10.1093/molbev/msx053] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
11
Porebski BT, Conroy PJ, Drinkwater N, Schofield P, Vazquez-Lombardi R, Hunter MR, Hoke DE, Christ D, McGowan S, Buckle AM. Circumventing the stability-function trade-off in an engineered FN3 domain. Protein Eng Des Sel 2016;29:541-550. [PMID: 27578887 PMCID: PMC5081044 DOI: 10.1093/protein/gzw046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 08/05/2016] [Accepted: 08/05/2016] [Indexed: 01/10/2023]  Open
12
Childers MC, Towse CL, Daggett V. The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design. Protein Eng Des Sel 2016;29:271-80. [PMID: 27284086 DOI: 10.1093/protein/gzw023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 01/30/2023]  Open
13
Romero-Romero ML, Risso VA, Martinez-Rodriguez S, Gaucher EA, Ibarra-Molero B, Sanchez-Ruiz JM. Selection for Protein Kinetic Stability Connects Denaturation Temperatures to Organismal Temperatures and Provides Clues to Archaean Life. PLoS One 2016;11:e0156657. [PMID: 27253436 PMCID: PMC4890807 DOI: 10.1371/journal.pone.0156657] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/17/2016] [Indexed: 01/24/2023]  Open
14
De Laet M, Gilis D, Rooman M. Stability strengths and weaknesses in protein structures detected by statistical potentials: Application to bovine seminal ribonuclease. Proteins 2015;84:143-58. [DOI: 10.1002/prot.24962] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 10/27/2015] [Accepted: 11/09/2015] [Indexed: 11/10/2022]
15
Computational Approaches to Identification of Aggregation Sites and the Mechanism of Amyloid Growth. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015;855:213-39. [DOI: 10.1007/978-3-319-17344-3_9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
16
Sukenik S, Boyarski Y, Harries D. Effect of salt on the formation of salt-bridges in β-hairpin peptides. Chem Commun (Camb) 2014;50:8193-6. [DOI: 10.1039/c4cc03195d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
17
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]
18
Neutral and weakly nonneutral sequence variants may define individuality. Proc Natl Acad Sci U S A 2013;110:14255-60. [PMID: 23940345 DOI: 10.1073/pnas.1216613110] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
19
Evolutionary selection for protein aggregation. Biochem Soc Trans 2013;40:1032-7. [PMID: 22988860 DOI: 10.1042/bst20120160] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
20
Li Y, Fang J. PROTS-RF: a robust model for predicting mutation-induced protein stability changes. PLoS One 2012;7:e47247. [PMID: 23077576 PMCID: PMC3471942 DOI: 10.1371/journal.pone.0047247] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 09/11/2012] [Indexed: 11/19/2022]  Open
21
Bardwell JCA, Jakob U. Conditional disorder in chaperone action. Trends Biochem Sci 2012;37:517-25. [PMID: 23018052 DOI: 10.1016/j.tibs.2012.08.006] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/17/2012] [Accepted: 08/29/2012] [Indexed: 11/18/2022]
22
Arodź T, Płonka PM. Effects of point mutations on protein structure are nonexponentially distributed. Proteins 2012;80:1780-90. [DOI: 10.1002/prot.24073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 02/02/2012] [Accepted: 03/12/2012] [Indexed: 11/07/2022]
23
Binolfi A, Fernández CO, Sica MP, Delfino JM, Santos J. Recognition between a short unstructured peptide and a partially folded fragment leads to the thioredoxin fold sharing native-like dynamics. Proteins 2012;80:1448-64. [DOI: 10.1002/prot.24043] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 12/27/2011] [Accepted: 01/11/2012] [Indexed: 11/09/2022]
24
Dehouck Y, Kwasigroch JM, Gilis D, Rooman M. PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality. BMC Bioinformatics 2011;12:151. [PMID: 21569468 PMCID: PMC3113940 DOI: 10.1186/1471-2105-12-151] [Citation(s) in RCA: 367] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 05/13/2011] [Indexed: 12/31/2022]  Open
25
Shortridge MD, Triplet T, Revesz P, Griep MA, Powers R. Bacterial protein structures reveal phylum dependent divergence. Comput Biol Chem 2011;35:24-33. [PMID: 21315656 DOI: 10.1016/j.compbiolchem.2010.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 12/28/2010] [Accepted: 12/29/2010] [Indexed: 01/26/2023]
26
Chen P, Shakhnovich EI. Thermal adaptation of viruses and bacteria. Biophys J 2010;98:1109-18. [PMID: 20371310 DOI: 10.1016/j.bpj.2009.11.048] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 11/10/2009] [Accepted: 11/30/2009] [Indexed: 01/24/2023]  Open
27
Protein kinetic stability. Biophys Chem 2010;148:1-15. [DOI: 10.1016/j.bpc.2010.02.004] [Citation(s) in RCA: 274] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2010] [Accepted: 02/06/2010] [Indexed: 01/23/2023]
28
Foit L, Morgan GJ, Kern MJ, Steimer LR, von Hacht AA, Titchmarsh J, Warriner SL, Radford SE, Bardwell JC. Optimizing protein stability in vivo. Mol Cell 2009;36:861-71. [PMID: 20005848 PMCID: PMC2818778 DOI: 10.1016/j.molcel.2009.11.022] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 08/04/2009] [Accepted: 10/24/2009] [Indexed: 11/23/2022]
29
Bloom JD, Glassman MJ. Inferring stabilizing mutations from protein phylogenies: application to influenza hemagglutinin. PLoS Comput Biol 2009;5:e1000349. [PMID: 19381264 PMCID: PMC2664478 DOI: 10.1371/journal.pcbi.1000349] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 03/05/2009] [Indexed: 01/08/2023]  Open
30
Woycechowsky KJ, Choutko A, Vamvaca K, Hilvert D. Relative tolerance of an enzymatic molten globule and its thermostable counterpart to point mutation. Biochemistry 2009;47:13489-96. [PMID: 19053245 DOI: 10.1021/bi801108a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
31
Aggregation propensity of the human proteome. PLoS Comput Biol 2008;4:e1000199. [PMID: 18927604 PMCID: PMC2557143 DOI: 10.1371/journal.pcbi.1000199] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 09/04/2008] [Indexed: 11/19/2022]  Open
32
Kelly RM, Leemhuis H, Gätjen L, Dijkhuizen L. Evolution toward Small Molecule Inhibitor Resistance Affects Native Enzyme Function and Stability, Generating Acarbose-insensitive Cyclodextrin Glucanotransferase Variants. J Biol Chem 2008;283:10727-34. [DOI: 10.1074/jbc.m709287200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
33
Pey AL, Rodriguez-Larrea D, Bomke S, Dammers S, Godoy-Ruiz R, Garcia-Mira MM, Sanchez-Ruiz JM. Engineering proteins with tunable thermodynamic and kinetic stabilities. Proteins 2008;71:165-74. [DOI: 10.1002/prot.21670] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
34
Tokuriki N, Stricher F, Serrano L, Tawfik DS. How protein stability and new functions trade off. PLoS Comput Biol 2008;4:e1000002. [PMID: 18463696 PMCID: PMC2265470 DOI: 10.1371/journal.pcbi.1000002] [Citation(s) in RCA: 406] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Accepted: 01/22/2008] [Indexed: 12/27/2022]  Open
35
Monsellier E, Chiti F. Prevention of amyloid-like aggregation as a driving force of protein evolution. EMBO Rep 2007;8:737-42. [PMID: 17668004 PMCID: PMC1978086 DOI: 10.1038/sj.embor.7401034] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Accepted: 06/18/2007] [Indexed: 12/16/2022]  Open
36
Zeldovich KB, Chen P, Shakhnovich EI. Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci U S A 2007;104:16152-7. [PMID: 17913881 PMCID: PMC2042177 DOI: 10.1073/pnas.0705366104] [Citation(s) in RCA: 187] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Indexed: 01/18/2023]  Open
37
Monsellier E, Ramazzotti M, de Laureto PP, Tartaglia GG, Taddei N, Fontana A, Vendruscolo M, Chiti F. The distribution of residues in a polypeptide sequence is a determinant of aggregation optimized by evolution. Biophys J 2007;93:4382-91. [PMID: 17766358 PMCID: PMC2098718 DOI: 10.1529/biophysj.107.111336] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
38
Bloom JD, Raval A, Wilke CO. Thermodynamics of neutral protein evolution. Genetics 2006;175:255-66. [PMID: 17110496 PMCID: PMC1775007 DOI: 10.1534/genetics.106.061754] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
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