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For: McLoughlin SY, Copley SD. A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities. Proc Natl Acad Sci U S A 2008;105:13497-502. [PMID: 18757760 DOI: 10.1073/pnas.0804804105] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Fritts RK, Ebmeier CC, Copley SD. Transcriptomic and proteomic ramifications of segmental amplification in Escherichia coli. Proc Natl Acad Sci U S A 2025;122:e2422424122. [PMID: 40372434 PMCID: PMC12107188 DOI: 10.1073/pnas.2422424122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Accepted: 04/17/2025] [Indexed: 05/16/2025]  Open
2
Truong DP, Dharmatti R, Suriadinata D, Huddleston J, Skouby R, Owusu Addo G, Zhu M, Acharige AD, Sankari Bayana R, Davila C, Fults SC, Raushel FM, Hull KG, Romo D, Glasner ME. Intramolecular epistasis correlates with divergence of specificity in promiscuous and bifunctional NSAR/OSBS enzymes. Protein Sci 2025;34:e70113. [PMID: 40247822 PMCID: PMC12006748 DOI: 10.1002/pro.70113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Revised: 03/10/2025] [Accepted: 03/18/2025] [Indexed: 04/19/2025]
3
Schmutzer M, Dasmeh P, Wagner A. Frustration can Limit the Adaptation of Promiscuous Enzymes Through Gene Duplication and Specialisation. J Mol Evol 2024;92:104-120. [PMID: 38470504 PMCID: PMC10978624 DOI: 10.1007/s00239-024-10161-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/16/2024] [Indexed: 03/14/2024]
4
Medina-Carmona E, Gutierrez-Rus LI, Manssour-Triedo F, Newton MS, Gamiz-Arco G, Mota AJ, Reiné P, Cuerva JM, Ortega-Muñoz M, Andrés-León E, Ortega-Roldan JL, Seelig B, Ibarra-Molero B, Sanchez-Ruiz JM. Cell Survival Enabled by Leakage of a Labile Metabolic Intermediate. Mol Biol Evol 2023;40:7036845. [PMID: 36788592 PMCID: PMC9989741 DOI: 10.1093/molbev/msad032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 01/19/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023]  Open
5
Copley SD, Newton MS, Widney KA. How to Recruit a Promiscuous Enzyme to Serve a New Function. Biochemistry 2023;62:300-308. [PMID: 35729117 PMCID: PMC9881647 DOI: 10.1021/acs.biochem.2c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
6
Perchat N, Dubois C, Mor-Gautier R, Duquesne S, Lechaplais C, Roche D, Fouteau S, Darii E, Perret A. Characterization of a novel β-alanine biosynthetic pathway consisting of promiscuous metabolic enzymes. J Biol Chem 2022;298:102067. [PMID: 35623386 PMCID: PMC9213253 DOI: 10.1016/j.jbc.2022.102067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/19/2022] [Accepted: 05/22/2022] [Indexed: 10/28/2022]  Open
7
Gade M, Tan LL, Damry AM, Sandhu M, Brock JS, Delaney A, Villar-Briones A, Jackson CJ, Laurino P. Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases. JACS AU 2021;1:2349-2360. [PMID: 34977903 PMCID: PMC8715544 DOI: 10.1021/jacsau.1c00464] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 05/14/2023]
8
Khan MS, Gargiulo S, Soumillion P. Promiscuous activity of 3-isopropylmalate dehydrogenase produced at physiological level affords Escherichia coli growth on d-malate. FEBS Lett 2020;594:2421-2430. [PMID: 32412093 DOI: 10.1002/1873-3468.13814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 11/08/2022]
9
Copley SD. The physical basis and practical consequences of biological promiscuity. Phys Biol 2020;17:10.1088/1478-3975/ab8697. [PMID: 32244231 PMCID: PMC9291633 DOI: 10.1088/1478-3975/ab8697] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
10
Morgenthaler AB, Kinney WR, Ebmeier CC, Walsh CM, Snyder DJ, Cooper VS, Old WM, Copley SD. Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome. eLife 2019;8:53535. [PMID: 31815667 PMCID: PMC6941894 DOI: 10.7554/elife.53535] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/02/2019] [Indexed: 11/13/2022]  Open
11
Zhao J, Zhang H, Qin B, Nikolay R, He QY, Spahn CMT, Zhang G. Multifaceted Stoichiometry Control of Bacterial Operons Revealed by Deep Proteome Quantification. Front Genet 2019;10:473. [PMID: 31178895 PMCID: PMC6544118 DOI: 10.3389/fgene.2019.00473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/01/2019] [Indexed: 12/03/2022]  Open
12
Kassen R. Experimental Evolution of Innovation and Novelty. Trends Ecol Evol 2019;34:712-722. [PMID: 31027838 DOI: 10.1016/j.tree.2019.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/19/2019] [Accepted: 03/27/2019] [Indexed: 12/14/2022]
13
Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions. Methods Enzymol 2019;620:315-347. [PMID: 31072492 DOI: 10.1016/bs.mie.2019.03.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
14
Harnessing Underground Metabolism for Pathway Development. Trends Biotechnol 2019;37:29-37. [DOI: 10.1016/j.tibtech.2018.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/17/2018] [Accepted: 08/06/2018] [Indexed: 01/13/2023]
15
Pontrelli S, Fricke RCB, Teoh ST, Laviña WA, Putri SP, Fitz-Gibbon S, Chung M, Pellegrini M, Fukusaki E, Liao JC. Metabolic repair through emergence of new pathways in Escherichia coli. Nat Chem Biol 2018;14:1005-1009. [DOI: 10.1038/s41589-018-0149-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/13/2018] [Indexed: 01/12/2023]
16
Kristofich J, Morgenthaler AB, Kinney WR, Ebmeier CC, Snyder DJ, Old WM, Cooper VS, Copley SD. Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme. PLoS Genet 2018;14:e1007615. [PMID: 30148850 PMCID: PMC6128649 DOI: 10.1371/journal.pgen.1007615] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 09/07/2018] [Accepted: 08/07/2018] [Indexed: 01/26/2023]  Open
17
Copp JN, Akiva E, Babbitt PC, Tokuriki N. Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks. Biochemistry 2018;57:4651-4662. [PMID: 30052428 DOI: 10.1021/acs.biochem.8b00473] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
18
Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset. Proc Natl Acad Sci U S A 2018;115:E7293-E7302. [PMID: 30012610 DOI: 10.1073/pnas.1607817115] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
19
Schniete JK, Cruz-Morales P, Selem-Mojica N, Fernández-Martínez LT, Hunter IS, Barona-Gómez F, Hoskisson PA. Expanding Primary Metabolism Helps Generate the Metabolic Robustness To Facilitate Antibiotic Biosynthesis in Streptomyces. mBio 2018;9:e02283-17. [PMID: 29437921 PMCID: PMC5801464 DOI: 10.1128/mbio.02283-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 01/09/2018] [Indexed: 02/04/2023]  Open
20
Copley SD. Shining a light on enzyme promiscuity. Curr Opin Struct Biol 2017;47:167-175. [DOI: 10.1016/j.sbi.2017.11.001] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 08/14/2017] [Accepted: 11/02/2017] [Indexed: 11/16/2022]
21
Landry Z, Swan BK, Herndl GJ, Stepanauskas R, Giovannoni SJ. SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter. mBio 2017;8:e00413-17. [PMID: 28420738 PMCID: PMC5395668 DOI: 10.1128/mbio.00413-17] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 01/09/2023]  Open
22
Baier F, Copp JN, Tokuriki N. Evolution of Enzyme Superfamilies: Comprehensive Exploration of Sequence–Function Relationships. Biochemistry 2016;55:6375-6388. [DOI: 10.1021/acs.biochem.6b00723] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
23
Kaltenbach M, Emond S, Hollfelder F, Tokuriki N. Functional Trade-Offs in Promiscuous Enzymes Cannot Be Explained by Intrinsic Mutational Robustness of the Native Activity. PLoS Genet 2016;12:e1006305. [PMID: 27716796 PMCID: PMC5065130 DOI: 10.1371/journal.pgen.1006305] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/17/2016] [Indexed: 11/19/2022]  Open
24
A Synonymous Mutation Upstream of the Gene Encoding a Weak-Link Enzyme Causes an Ultrasensitive Response in Growth Rate. J Bacteriol 2016;198:2853-63. [PMID: 27501982 DOI: 10.1128/jb.00262-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/22/2016] [Indexed: 12/21/2022]  Open
25
Newton MS, Arcus VL, Patrick WM. Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes. J R Soc Interface 2016;12:rsif.2015.0036. [PMID: 25926697 DOI: 10.1098/rsif.2015.0036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
26
Shimizu T, Tomita T, Kuzuyama T, Nishiyama M. Crystal Structure of the LysY·LysW Complex from Thermus thermophilus. J Biol Chem 2016;291:9948-59. [PMID: 26966182 DOI: 10.1074/jbc.m115.707034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 11/06/2022]  Open
27
Chakraborty M, Fry JD. Evidence that Environmental Heterogeneity Maintains a Detoxifying Enzyme Polymorphism in Drosophila melanogaster. Curr Biol 2015;26:219-223. [PMID: 26748852 DOI: 10.1016/j.cub.2015.11.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/09/2015] [Accepted: 11/11/2015] [Indexed: 11/28/2022]
28
Copley SD. An evolutionary biochemist's perspective on promiscuity. Trends Biochem Sci 2015;40:72-8. [PMID: 25573004 DOI: 10.1016/j.tibs.2014.12.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/08/2014] [Accepted: 12/08/2014] [Indexed: 12/31/2022]
29
Khanal A, Yu McLoughlin S, Kershner JP, Copley SD. Differential effects of a mutation on the normal and promiscuous activities of orthologs: implications for natural and directed evolution. Mol Biol Evol 2014;32:100-8. [PMID: 25246702 PMCID: PMC4271523 DOI: 10.1093/molbev/msu271] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
30
Vorobieva AA, Khan MS, Soumillion P. Escherichia coli D-malate dehydrogenase, a generalist enzyme active in the leucine biosynthesis pathway. J Biol Chem 2014;289:29086-96. [PMID: 25160617 DOI: 10.1074/jbc.m114.595363] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
31
Wang ZJ, Renata H, Peck NE, Farwell CC, Coelho PS, Arnold FH. Improved cyclopropanation activity of histidine-ligated cytochrome P450 enables the enantioselective formal synthesis of levomilnacipran. Angew Chem Int Ed Engl 2014;53:6810-3. [PMID: 24802161 PMCID: PMC4120663 DOI: 10.1002/anie.201402809] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Indexed: 02/03/2023]
32
Wang ZJ, Renata H, Peck NE, Farwell CC, Coelho PS, Arnold FH. Improved Cyclopropanation Activity of Histidine-Ligated Cytochrome P450 Enables the Enantioselective Formal Synthesis of Levomilnacipran. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402809] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
33
Kaltenbach M, Tokuriki N. Dynamics and constraints of enzyme evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014;322:468-87. [DOI: 10.1002/jez.b.22562] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/06/2014] [Indexed: 12/23/2022]
34
Employing directed evolution for the functional analysis of multi-specific proteins. Bioorg Med Chem 2013;21:3511-6. [DOI: 10.1016/j.bmc.2013.04.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/11/2013] [Accepted: 04/18/2013] [Indexed: 01/17/2023]
35
Yip SHC, Matsumura I. Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem. Mol Biol Evol 2013;30:2001-12. [PMID: 23728795 DOI: 10.1093/molbev/mst105] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
36
Wu CH, Chen YP, Mou CY, Cheng RP. Altering the Tat-derived peptide bioactivity landscape by changing the arginine side chain length. Amino Acids 2012;44:473-80. [DOI: 10.1007/s00726-012-1357-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 06/28/2012] [Indexed: 12/31/2022]
37
Probing the mutational interplay between primary and promiscuous protein functions: a computational-experimental approach. PLoS Comput Biol 2012;8:e1002558. [PMID: 22719242 PMCID: PMC3375227 DOI: 10.1371/journal.pcbi.1002558] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 04/29/2012] [Indexed: 12/16/2022]  Open
38
Allison SD. A trait-based approach for modelling microbial litter decomposition. Ecol Lett 2012;15:1058-70. [PMID: 22642621 DOI: 10.1111/j.1461-0248.2012.01807.x] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 01/15/2012] [Accepted: 04/26/2012] [Indexed: 11/29/2022]
39
Huang R, Hippauf F, Rohrbeck D, Haustein M, Wenke K, Feike J, Sorrelle N, Piechulla B, Barkman TJ. Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates. Proc Natl Acad Sci U S A 2012;109:2966-71. [PMID: 22315396 PMCID: PMC3286912 DOI: 10.1073/pnas.1019605109] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
40
ENVIRONMENTAL ROBUSTNESS AND THE ADAPTABILITY OF POPULATIONS. Evolution 2012;66:1598-612. [DOI: 10.1111/j.1558-5646.2011.01526.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
41
Copley SD. Toward a systems biology perspective on enzyme evolution. J Biol Chem 2012;287:3-10. [PMID: 22069330 PMCID: PMC3249082 DOI: 10.1074/jbc.r111.254714] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
42
The evolution of cefotaximase activity in the TEM β-lactamase. J Mol Biol 2011;415:205-20. [PMID: 22075446 DOI: 10.1016/j.jmb.2011.10.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/18/2011] [Accepted: 10/25/2011] [Indexed: 11/21/2022]
43
Lehner B. Molecular mechanisms of epistasis within and between genes. Trends Genet 2011;27:323-31. [PMID: 21684621 DOI: 10.1016/j.tig.2011.05.007] [Citation(s) in RCA: 214] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/11/2011] [Accepted: 05/11/2011] [Indexed: 11/19/2022]
44
Tawfik DS. Messy biology and the origins of evolutionary innovations. Nat Chem Biol 2010;6:692-6. [DOI: 10.1038/nchembio.441] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
45
Mutational effects and the evolution of new protein functions. Nat Rev Genet 2010;11:572-82. [PMID: 20634811 DOI: 10.1038/nrg2808] [Citation(s) in RCA: 307] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
46
Khersonsky O, Tawfik DS. Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem 2010;79:471-505. [PMID: 20235827 DOI: 10.1146/annurev-biochem-030409-143718] [Citation(s) in RCA: 986] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
47
Martí S, Andrés J, Moliner V, Silla E, Tuñón I, Bertrán J. Mechanism and plasticity of isochorismate pyruvate lyase: a computational study. J Am Chem Soc 2010;131:16156-61. [PMID: 19835359 DOI: 10.1021/ja905271g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wang X, Huang Y, Lavrov DV, Gu X. Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications. BMC Evol Biol 2009;9:275. [PMID: 19948060 PMCID: PMC2790464 DOI: 10.1186/1471-2148-9-275] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 11/30/2009] [Indexed: 11/10/2022]  Open
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The Conflict Between Horizontal Gene Transfer and the Safeguard of Identity: Origin of Meiotic Sexuality. J Mol Evol 2009;69:470-80. [DOI: 10.1007/s00239-009-9277-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Accepted: 09/08/2009] [Indexed: 02/05/2023]
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Tokuriki N, Tawfik DS. Chaperonin overexpression promotes genetic variation and enzyme evolution. Nature 2009;459:668-73. [PMID: 19494908 DOI: 10.1038/nature08009] [Citation(s) in RCA: 263] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 03/20/2009] [Indexed: 01/17/2023]
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