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For: 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: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
Number Cited by Other Article(s)
1
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]
2
Deng S. The origin of genetic and metabolic systems: Evolutionary structuralinsights. Heliyon 2023;9:e14466. [PMID: 36967965 PMCID: PMC10036676 DOI: 10.1016/j.heliyon.2023.e14466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023]  Open
3
Jayaraman V, Toledo‐Patiño S, Noda‐García L, Laurino P. Mechanisms of protein evolution. Protein Sci 2022;31:e4362. [PMID: 35762715 PMCID: PMC9214755 DOI: 10.1002/pro.4362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 11/06/2022]
4
Nolte TM, Peijnenburg WJGM, Miguel ABR, Zhang YN, Hendriks AJ. Stoichiometric ratios for biotics and xenobiotics capture effective metabolic coupling to re(de)fine biodegradation. WATER RESEARCH 2022;217:118333. [PMID: 35421691 DOI: 10.1016/j.watres.2022.118333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/07/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
5
Hall KR, Robins KJ, Williams EM, Rich MH, Calcott MJ, Copp JN, Little RF, Schwörer R, Evans GB, Patrick WM, Ackerley DF. Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues. eLife 2020;9:59081. [PMID: 33185191 PMCID: PMC7738182 DOI: 10.7554/elife.59081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/12/2020] [Indexed: 11/17/2022]  Open
6
Rickaby REM, Eason Hubbard MR. Upper ocean oxygenation, evolution of RuBisCO and the Phanerozoic succession of phytoplankton. Free Radic Biol Med 2019;140:295-304. [PMID: 31075497 PMCID: PMC6856715 DOI: 10.1016/j.freeradbiomed.2019.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/10/2019] [Accepted: 05/02/2019] [Indexed: 12/13/2022]
7
A major role for noncoding regulatory mutations in the evolution of enzyme activity. Proc Natl Acad Sci U S A 2019;116:12383-12389. [PMID: 31152141 PMCID: PMC6589674 DOI: 10.1073/pnas.1904071116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
8
Schulte‐Sasse M, Pardo‐Ávila F, Pulido‐Mayoral NO, Vázquez‐Lobo A, Costas M, García‐Hernández E, Rodríguez‐Romero A, Fernández‐Velasco DA. Structural, thermodynamic and catalytic characterization of an ancestral triosephosphate isomerase reveal early evolutionary coupling between monomer association and function. FEBS J 2019;286:882-900. [DOI: 10.1111/febs.14741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 11/01/2018] [Accepted: 12/23/2018] [Indexed: 01/06/2023]
9
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: 3.8] [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]
10
Davidi D, Longo LM, Jabłońska J, Milo R, Tawfik DS. A Bird’s-Eye View of Enzyme Evolution: Chemical, Physicochemical, and Physiological Considerations. Chem Rev 2018;118:8786-8797. [DOI: 10.1021/acs.chemrev.8b00039] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
11
Noda-Garcia L, Liebermeister W, Tawfik DS. Metabolite–Enzyme Coevolution: From Single Enzymes to Metabolic Pathways and Networks. Annu Rev Biochem 2018;87:187-216. [DOI: 10.1146/annurev-biochem-062917-012023] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
12
Risso VA, Sanchez-Ruiz JM, Ozkan SB. Biotechnological and protein-engineering implications of ancestral protein resurrection. Curr Opin Struct Biol 2018;51:106-115. [PMID: 29660672 DOI: 10.1016/j.sbi.2018.02.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 02/18/2018] [Accepted: 02/20/2018] [Indexed: 10/17/2022]
13
.Newton MS, Arcus VL, Gerth ML, Patrick WM. Enzyme evolution: innovation is easy, optimization is complicated. Curr Opin Struct Biol 2018;48:110-116. [DOI: 10.1016/j.sbi.2017.11.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
14
Ślesak I, Ślesak H, Kruk J. RubisCO Early Oxygenase Activity: A Kinetic and Evolutionary Perspective. Bioessays 2017;39. [PMID: 28976010 DOI: 10.1002/bies.201700071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/10/2017] [Indexed: 11/09/2022]
15
Castro-Fernandez V, Herrera-Morande A, Zamora R, Merino F, Gonzalez-Ordenes F, Padilla-Salinas F, Pereira HM, Brandão-Neto J, Garratt RC, Guixe V. Reconstructed ancestral enzymes reveal that negative selection drove the evolution of substrate specificity in ADP-dependent kinases. J Biol Chem 2017;292:15598-15610. [PMID: 28726643 DOI: 10.1074/jbc.m117.790865] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/05/2017] [Indexed: 11/06/2022]  Open
16
Tadepalli S, Wang Z, Liu KK, Jiang Q, Slocik J, Naik RR, Singamaneni S. Influence of Surface Charge of the Nanostructures on the Biocatalytic Activity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017;33:6611-6619. [PMID: 28605903 DOI: 10.1021/acs.langmuir.6b04490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
17
Koç I, Caetano-Anollés G. The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data. PLoS One 2017;12:e0176129. [PMID: 28467492 PMCID: PMC5414959 DOI: 10.1371/journal.pone.0176129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 04/05/2017] [Indexed: 11/18/2022]  Open
18
Structural and functional innovations in the real-time evolution of new (βα)8 barrel enzymes. Proc Natl Acad Sci U S A 2017;114:4727-4732. [PMID: 28416687 DOI: 10.1073/pnas.1618552114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
19
Bai Y, Gangoiti J, Dijkstra BW, Dijkhuizen L, Pijning T. Crystal Structure of 4,6-α-Glucanotransferase Supports Diet-Driven Evolution of GH70 Enzymes from α-Amylases in Oral Bacteria. Structure 2017;25:231-242. [DOI: 10.1016/j.str.2016.11.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/03/2016] [Accepted: 11/28/2016] [Indexed: 10/20/2022]
20
Soo VWC, Yosaatmadja Y, Squire CJ, Patrick WM. Mechanistic and Evolutionary Insights from the Reciprocal Promiscuity of Two Pyridoxal Phosphate-dependent Enzymes. J Biol Chem 2016;291:19873-87. [PMID: 27474741 PMCID: PMC5025676 DOI: 10.1074/jbc.m116.739557] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Indexed: 11/06/2022]  Open
21
Boucher JI, Bolon DNA, Tawfik DS. Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature. Protein Sci 2016;25:1219-26. [PMID: 27010590 DOI: 10.1002/pro.2928] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 11/11/2022]
22
Co-occurrence of analogous enzymes determines evolution of a novel (βα)8-isomerase sub-family after non-conserved mutations in flexible loop. Biochem J 2016;473:1141-52. [PMID: 26929404 DOI: 10.1042/bj20151271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/29/2016] [Indexed: 12/15/2022]
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