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For: Okafor CD, Pathak MC, Fagan CE, Bauer NC, Cole MF, Gaucher EA, Ortlund EA. Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus. Structure 2018;26:118-129.e3. [PMID: 29276038 PMCID: PMC5785943 DOI: 10.1016/j.str.2017.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/18/2017] [Accepted: 11/27/2017] [Indexed: 01/07/2023]
Number Cited by Other Article(s)
1
Gholampour-Faroji N, Hemmat J, Haddad-Mashadrizeh A, Asoodeh A. Characterization, structural, and evolutionary analysis of an extremophilic GH5 endoglucanase from Bacillus sp. G131: Insights from ancestral sequence reconstruction. Int J Biol Macromol 2024:134311. [PMID: 39094869 DOI: 10.1016/j.ijbiomac.2024.134311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 07/16/2024] [Accepted: 07/28/2024] [Indexed: 08/04/2024]
2
Chisholm LO, Orlandi KN, Phillips SR, Shavlik MJ, Harms MJ. Ancestral Reconstruction and the Evolution of Protein Energy Landscapes. Annu Rev Biophys 2024;53:127-146. [PMID: 38134334 PMCID: PMC11192866 DOI: 10.1146/annurev-biophys-030722-125440] [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] [Indexed: 12/24/2023]
3
Fang N, Wu L, Duan S, Li J. The Structural and Molecular Mechanisms of Mycobacterium tuberculosis Translational Elongation Factor Proteins. Molecules 2024;29:2058. [PMID: 38731549 PMCID: PMC11085428 DOI: 10.3390/molecules29092058] [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: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024]  Open
4
Sucharski F, Gallo G, Coelho C, Hardy L, Würtele M. Modeling the role of charged residues in thermophilic proteins by rotamer and dynamic cross correlation analysis. J Mol Model 2023;29:132. [PMID: 37036538 DOI: 10.1007/s00894-023-05490-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/24/2023] [Indexed: 04/11/2023]
5
Clifton BE, Kozome D, Laurino P. Efficient Exploration of Sequence Space by Sequence-Guided Protein Engineering and Design. Biochemistry 2023;62:210-220. [PMID: 35245020 DOI: 10.1021/acs.biochem.1c00757] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
6
Rational Design of a Thermostable 2'-Deoxyribosyltransferase for Nelarabine Production by Prediction of Disulfide Bond Engineering Sites. Int J Mol Sci 2022;23:ijms231911806. [PMID: 36233108 PMCID: PMC9570332 DOI: 10.3390/ijms231911806] [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: 08/03/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022]  Open
7
Fer E, McGrath KM, Guy L, Hockenberry AJ, Kaçar B. Early divergence of translation initiation and elongation factors. Protein Sci 2022;31:e4393. [PMID: 36250475 PMCID: PMC9601768 DOI: 10.1002/pro.4393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 11/18/2022]
8
Engineering functional thermostable proteins using ancestral sequence reconstruction. J Biol Chem 2022;298:102435. [PMID: 36041629 PMCID: PMC9525910 DOI: 10.1016/j.jbc.2022.102435] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022]  Open
9
Rahban M, Zolghadri S, Salehi N, Ahmad F, Haertlé T, Rezaei-Ghaleh N, Sawyer L, Saboury AA. Thermal stability enhancement: Fundamental concepts of protein engineering strategies to manipulate the flexible structure. Int J Biol Macromol 2022;214:642-654. [DOI: 10.1016/j.ijbiomac.2022.06.154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 01/28/2023]
10
Gonzalez NA, Li BA, McCully ME. The stability and dynamics of computationally designed proteins. Protein Eng Des Sel 2022;35:6529794. [PMID: 35174855 DOI: 10.1093/protein/gzac001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022]  Open
11
Akanuma S, Yamaguchi M, Yamagishi A. Comprehensive mutagenesis to identify amino acid residues contributing to the difference in thermostability between two originally thermostable ancestral proteins. PLoS One 2021;16:e0258821. [PMID: 34673819 PMCID: PMC8530338 DOI: 10.1371/journal.pone.0258821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022]  Open
12
Spence MA, Kaczmarski JA, Saunders JW, Jackson CJ. Ancestral sequence reconstruction for protein engineers. Curr Opin Struct Biol 2021;69:131-141. [PMID: 34023793 DOI: 10.1016/j.sbi.2021.04.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/22/2021] [Accepted: 04/07/2021] [Indexed: 12/11/2022]
13
Modi T, Campitelli P, Kazan IC, Ozkan SB. Protein folding stability and binding interactions through the lens of evolution: a dynamical perspective. Curr Opin Struct Biol 2020;66:207-215. [PMID: 33388636 DOI: 10.1016/j.sbi.2020.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/02/2020] [Accepted: 11/26/2020] [Indexed: 01/06/2023]
14
Sternke M, Tripp KW, Barrick D. The use of consensus sequence information to engineer stability and activity in proteins. Methods Enzymol 2020;643:149-179. [PMID: 32896279 DOI: 10.1016/bs.mie.2020.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
15
Babkova P, Dunajova Z, Chaloupkova R, Damborsky J, Bednar D, Marek M. Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics. Comput Struct Biotechnol J 2020;18:1497-1508. [PMID: 32637047 PMCID: PMC7327271 DOI: 10.1016/j.csbj.2020.06.021] [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: 04/07/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 12/30/2022]  Open
16
Noh D, Bower RL, Hay DL, Zhyvoloup A, Raleigh DP. Analysis of Amylin Consensus Sequences Suggests That Human Amylin Is Not Optimized to Minimize Amyloid Formation and Provides Clues to Factors That Modulate Amyloidogenicity. ACS Chem Biol 2020;15:1408-1416. [PMID: 32364695 DOI: 10.1021/acschembio.9b01050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
17
Girodat D, Blanchard SC, Wieden HJ, Sanbonmatsu KY. Elongation Factor Tu Switch I Element is a Gate for Aminoacyl-tRNA Selection. J Mol Biol 2020;432:3064-3077. [PMID: 32061931 DOI: 10.1016/j.jmb.2020.01.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/15/2020] [Accepted: 01/24/2020] [Indexed: 12/16/2022]
18
Timr S, Madern D, Sterpone F. Protein thermal stability. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020;170:239-272. [PMID: 32145947 DOI: 10.1016/bs.pmbts.2019.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
19
Thomas A, Cutlan R, Finnigan W, van der Giezen M, Harmer N. Highly thermostable carboxylic acid reductases generated by ancestral sequence reconstruction. Commun Biol 2019;2:429. [PMID: 31799431 PMCID: PMC6874671 DOI: 10.1038/s42003-019-0677-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/04/2019] [Indexed: 12/19/2022]  Open
20
Nussinov R, Tsai CJ, Jang H. Protein ensembles link genotype to phenotype. PLoS Comput Biol 2019;15:e1006648. [PMID: 31220071 PMCID: PMC6586255 DOI: 10.1371/journal.pcbi.1006648] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
21
Trudeau DL, Tawfik DS. Protein engineers turned evolutionists-the quest for the optimal starting point. Curr Opin Biotechnol 2019;60:46-52. [PMID: 30611116 DOI: 10.1016/j.copbio.2018.12.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/22/2018] [Accepted: 12/03/2018] [Indexed: 12/12/2022]
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