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For: Lim SA, Bolin ER, Marqusee S. Tracing a protein's folding pathway over evolutionary time using ancestral sequence reconstruction and hydrogen exchange. eLife 2018;7:38369. [PMID: 30204082 PMCID: PMC6158009 DOI: 10.7554/elife.38369] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/09/2018] [Indexed: 12/15/2022]  Open
Number Cited by Other Article(s)
1
Mallimadugula UL, Cruz MA, Vithani N, Zimmerman MI, Bowman GR. Opening and closing of a cryptic pocket in VP35 toggles it between two different RNA-binding modes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.22.609218. [PMID: 39229186 PMCID: PMC11370563 DOI: 10.1101/2024.08.22.609218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
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
Nixon C, Lim SA, Sternke M, Barrick D, Harms MJ, Marqusee S. The importance of input sequence set to consensus-derived proteins and their relationship to reconstructed ancestral proteins. Protein Sci 2024;33:e5011. [PMID: 38747388 PMCID: PMC11094778 DOI: 10.1002/pro.5011] [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: 06/29/2023] [Revised: 04/02/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
4
Li ZL, Sun CQ, Qing ZL, Li ZM, Liu HL. Engineering the thermal stability of a polyphosphate kinase by ancestral sequence reconstruction to expand the temperature boundary for an industrially applicable ATP regeneration system. Appl Environ Microbiol 2024;90:e0157423. [PMID: 38236018 PMCID: PMC10880597 DOI: 10.1128/aem.01574-23] [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: 09/09/2023] [Accepted: 12/06/2023] [Indexed: 01/19/2024]  Open
5
Bhatia S, Udgaonkar JB. Understanding the heterogeneity intrinsic to protein folding. Curr Opin Struct Biol 2024;84:102738. [PMID: 38041993 DOI: 10.1016/j.sbi.2023.102738] [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] [Received: 09/19/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 12/04/2023]
6
Nixon C, Lim SA, Sternke M, Barrick D, Harms M, Marqusee S. The importance of input sequence set to consensus-derived proteins and their relationship to reconstructed ancestral proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547063. [PMID: 37425932 PMCID: PMC10327145 DOI: 10.1101/2023.06.29.547063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
7
Kaur U, Kihn KC, Ke H, Kuo W, Gierasch LM, Hebert DN, Wintrode PL, Deredge D, Gershenson A. The conformational landscape of a serpin N-terminal subdomain facilitates folding and in-cell quality control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.537978. [PMID: 37163105 PMCID: PMC10168285 DOI: 10.1101/2023.04.24.537978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
8
Mascotti ML. Resurrecting Enzymes by Ancestral Sequence Reconstruction. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022;2397:111-136. [PMID: 34813062 DOI: 10.1007/978-1-0716-1826-4_7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
9
Opening of a cryptic pocket in β-lactamase increases penicillinase activity. Proc Natl Acad Sci U S A 2021;118:2106473118. [PMID: 34799442 PMCID: PMC8617505 DOI: 10.1073/pnas.2106473118] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2021] [Indexed: 11/18/2022]  Open
10
Appel M, Longwell SA, Morri M, Neff N, Herschlag D, Fordyce PM. uPIC-M: Efficient and Scalable Preparation of Clonal Single Mutant Libraries for High-Throughput Protein Biochemistry. ACS OMEGA 2021;6:30542-30554. [PMID: 34805683 PMCID: PMC8600632 DOI: 10.1021/acsomega.1c04180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
11
Romero-Romero S, Kordes S, Michel F, Höcker B. Evolution, folding, and design of TIM barrels and related proteins. Curr Opin Struct Biol 2021;68:94-104. [PMID: 33453500 PMCID: PMC8250049 DOI: 10.1016/j.sbi.2020.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/16/2022]
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: 69] [Impact Index Per Article: 17.3] [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
Zou T, Woodrum BW, Halloran N, Campitelli P, Bobkov AA, Ghirlanda G, Ozkan SB. Local Interactions That Contribute Minimal Frustration Determine Foldability. J Phys Chem B 2021;125:2617-2626. [PMID: 33687216 DOI: 10.1021/acs.jpcb.1c00364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
14
Ando N, Barquera B, Bartlett DH, Boyd E, Burnim AA, Byer AS, Colman D, Gillilan RE, Gruebele M, Makhatadze G, Royer CA, Shock E, Wand AJ, Watkins MB. The Molecular Basis for Life in Extreme Environments. Annu Rev Biophys 2021;50:343-372. [PMID: 33637008 DOI: 10.1146/annurev-biophys-100120-072804] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
15
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: 29] [Impact Index Per Article: 5.8] [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]
16
Bhunia A, Ilyas H, Bhattacharjya S. Salt Dependence Conformational Stability of the Dimeric SAM Domain of MAPKKK Ste11 from Budding Yeast: A Native-State H/D Exchange NMR Study. Biochemistry 2020;59:2849-2858. [PMID: 32667811 DOI: 10.1021/acs.biochem.0c00522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
17
Oltrogge LM, Chaijarasphong T, Chen AW, Bolin ER, Marqusee S, Savage DF. Multivalent interactions between CsoS2 and Rubisco mediate α-carboxysome formation. Nat Struct Mol Biol 2020;27:281-287. [PMID: 32123388 PMCID: PMC7337323 DOI: 10.1038/s41594-020-0387-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/24/2020] [Indexed: 11/23/2022]
18
Guin D, Gruebele M. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Chem Rev 2019;119:10691-10717. [PMID: 31356058 DOI: 10.1021/acs.chemrev.8b00753] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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