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For: Wheeler LC, Lim SA, Marqusee S, Harms MJ. The thermostability and specificity of ancient proteins. Curr Opin Struct Biol 2016;38:37-43. [PMID: 27288744 DOI: 10.1016/j.sbi.2016.05.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/18/2016] [Accepted: 05/24/2016] [Indexed: 11/16/2022]
Number Cited by Other Article(s)
1
Koch NG, Budisa N. Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion. Chem Rev 2024. [PMID: 38953775 DOI: 10.1021/acs.chemrev.4c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
2
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]
3
Johnson SR, Fu X, Viknander S, Goldin C, Monaco S, Zelezniak A, Yang KK. Computational scoring and experimental evaluation of enzymes generated by neural networks. Nat Biotechnol 2024:10.1038/s41587-024-02214-2. [PMID: 38653796 DOI: 10.1038/s41587-024-02214-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
4
Tripp A, Braun M, Wieser F, Oberdorfer G, Lechner H. Click, Compute, Create: A Review of Web-based Tools for Enzyme Engineering. Chembiochem 2024:e202400092. [PMID: 38634409 DOI: 10.1002/cbic.202400092] [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: 01/31/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
5
Sennett MA, Theobald DL. Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation. J Mol Evol 2024;92:181-206. [PMID: 38502220 PMCID: PMC10978691 DOI: 10.1007/s00239-024-10162-3] [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: 07/12/2023] [Accepted: 02/20/2024] [Indexed: 03/21/2024]
6
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
7
Fujikawa T, Sasamoto T, Zhao F, Yamagishi A, Akanuma S. Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat. Sci Rep 2024;14:398. [PMID: 38172176 PMCID: PMC10764835 DOI: 10.1038/s41598-023-50828-4] [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: 05/22/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024]  Open
8
Chisholm LO, Orlandi KN, Phillips SR, Shavlik MJ, Harms MJ. Ancestral Reconstruction and the Evolution of Protein Energy Landscapes. Annu Rev Biophys 2023;53:10.1146/annurev-biophys-030722-125440. [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
9
Muellers SN, Allen KN, Whitty A. MEnTaT: A machine-learning approach for the identification of mutations to increase protein stability. Proc Natl Acad Sci U S A 2023;120:e2309884120. [PMID: 38039271 PMCID: PMC10710055 DOI: 10.1073/pnas.2309884120] [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: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023]  Open
10
Ji Z, Belfield EJ, Zhang S, Bouvier J, Li S, Schnell J, Fu X, Harberd NP. Evolution of a plant growth-regulatory protein interaction specificity. NATURE PLANTS 2023;9:2059-2070. [PMID: 37903985 PMCID: PMC10724065 DOI: 10.1038/s41477-023-01556-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/27/2023] [Indexed: 11/01/2023]
11
Romero-Romero S, Lindner S, Ferruz N. Exploring the Protein Sequence Space with Global Generative Models. Cold Spring Harb Perspect Biol 2023;15:a041471. [PMID: 37848247 PMCID: PMC10626256 DOI: 10.1101/cshperspect.a041471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
12
Nicoll CR, Massari M, Fraaije MW, Mascotti ML, Mattevi A. Impact of ancestral sequence reconstruction on mechanistic and structural enzymology. Curr Opin Struct Biol 2023;82:102669. [PMID: 37544113 DOI: 10.1016/j.sbi.2023.102669] [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: 03/29/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023]
13
Wijayanti SD, Tsvik L, Haltrich D. Recent Advances in Electrochemical Enzyme-Based Biosensors for Food and Beverage Analysis. Foods 2023;12:3355. [PMID: 37761066 PMCID: PMC10529900 DOI: 10.3390/foods12183355] [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: 08/09/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]  Open
14
Buda K, Miton CM, Fan XC, Tokuriki N. Molecular determinants of protein evolvability. Trends Biochem Sci 2023;48:751-760. [PMID: 37330341 DOI: 10.1016/j.tibs.2023.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/19/2023]
15
Dishman AF, Volkman BF. Metamorphic protein folding as evolutionary adaptation. Trends Biochem Sci 2023;48:665-672. [PMID: 37270322 PMCID: PMC10526677 DOI: 10.1016/j.tibs.2023.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/12/2023] [Accepted: 05/04/2023] [Indexed: 06/05/2023]
16
Li S, Li Z, Tan GY, Xin Z, Wang W. In vitro allosteric transcription factor-based biosensing. Trends Biotechnol 2023;41:1080-1095. [PMID: 36967257 DOI: 10.1016/j.tibtech.2023.03.001] [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: 01/03/2023] [Revised: 02/15/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
17
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: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
18
Lei L, Zhao L, Hou Y, Yue C, Liu P, Zheng Y, Peng W, Yang J. An Inferred Ancestral CotA Laccase with Improved Expression and Kinetic Efficiency. Int J Mol Sci 2023;24:10901. [PMID: 37446078 DOI: 10.3390/ijms241310901] [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: 05/22/2023] [Revised: 06/17/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]  Open
19
Chiang CH, Wymore T, Rodríguez Benítez A, Hussain A, Smith JL, Brooks CL, Narayan ARH. Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction. Proc Natl Acad Sci U S A 2023;120:e2218248120. [PMID: 37014851 PMCID: PMC10104550 DOI: 10.1073/pnas.2218248120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/06/2023] [Indexed: 04/05/2023]  Open
20
Livada J, Vargas AM, Martinez CA, Lewis RD. Ancestral Sequence Reconstruction Enhances Gene Mining Efforts for Industrial Ene Reductases by Expanding Enzyme Panels with Thermostable Catalysts. ACS Catal 2023. [DOI: 10.1021/acscatal.2c03859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
21
Mingarro G, Del Olmo ML. Improvements in the genetic editing technologies: CRISPR-Cas and beyond. Gene 2023;852:147064. [PMID: 36435506 DOI: 10.1016/j.gene.2022.147064] [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: 08/22/2022] [Revised: 10/31/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022]
22
Zhao F, Akanuma S. Ancestral Sequence Reconstruction of the Ribosomal Protein uS8 and Reduction of Amino Acid Usage to a Smaller Alphabet. J Mol Evol 2023;91:10-23. [PMID: 36396786 DOI: 10.1007/s00239-022-10078-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022]
23
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]
24
Verma A, Åberg-Zingmark E, Sparrman T, Mushtaq AU, Rogne P, Grundström C, Berntsson R, Sauer UH, Backman L, Nam K, Sauer-Eriksson E, Wolf-Watz M. Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases. SCIENCE ADVANCES 2022;8:eabm4089. [PMID: 36332013 PMCID: PMC9635829 DOI: 10.1126/sciadv.abm4089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
25
Ayuso-Fernández I, Molpeceres G, Camarero S, Ruiz-Dueñas FJ, Martínez AT. Ancestral sequence reconstruction as a tool to study the evolution of wood decaying fungi. FRONTIERS IN FUNGAL BIOLOGY 2022;3:1003489. [PMID: 37746217 PMCID: PMC10512382 DOI: 10.3389/ffunb.2022.1003489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/22/2022] [Indexed: 09/26/2023]
26
Hobbs HT, Shah NH, Shoemaker SR, Amacher JF, Marqusee S, Kuriyan J. Saturation mutagenesis of a predicted ancestral Syk-family kinase. Protein Sci 2022;31:e4411. [PMID: 36173161 PMCID: PMC9601881 DOI: 10.1002/pro.4411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/27/2022] [Accepted: 07/25/2022] [Indexed: 11/08/2022]
27
Tang QY, Ren W, Wang J, Kaneko K. The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database. Mol Biol Evol 2022;39:6701686. [PMID: 36108094 PMCID: PMC9550990 DOI: 10.1093/molbev/msac197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
28
Harris KL, Thomson RES, Gumulya Y, Foley G, Carrera-Pacheco SE, Syed P, Janosik T, Sandinge AS, Andersson S, Jurva U, Bodén M, Gillam EMJ. Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defence reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates. Mol Biol Evol 2022;39:6593376. [PMID: 35639613 PMCID: PMC9185370 DOI: 10.1093/molbev/msac116] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
29
Karlsson E, Sorgenfrei FA, Andersson E, Dogan J, Jemth P, Chi CN. The dynamic properties of a nuclear coactivator binding domain are evolutionarily conserved. Commun Biol 2022;5:286. [PMID: 35354917 PMCID: PMC8967867 DOI: 10.1038/s42003-022-03217-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/02/2022] [Indexed: 12/21/2022]  Open
30
Sinnott‐Armstrong MA, Deanna R, Pretz C, Liu S, Harris JC, Dunbar‐Wallis A, Smith SD, Wheeler LC. How to approach the study of syndromes in macroevolution and ecology. Ecol Evol 2022;12:e8583. [PMID: 35342598 PMCID: PMC8928880 DOI: 10.1002/ece3.8583] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/23/2021] [Accepted: 12/31/2021] [Indexed: 11/12/2022]  Open
31
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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
32
Unusual commonality in active site structural features of substrate promiscuous and specialist enzymes. J Struct Biol 2022;214:107835. [DOI: 10.1016/j.jsb.2022.107835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/26/2021] [Accepted: 01/23/2022] [Indexed: 11/21/2022]
33
Lichman BR. Ancestral Sequence Reconstruction for Exploring Alkaloid Evolution. Methods Mol Biol 2022;2505:165-179. [PMID: 35732944 DOI: 10.1007/978-1-0716-2349-7_12] [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: 06/15/2023]
34
Structural dynamics in the evolution of a bilobed protein scaffold. Proc Natl Acad Sci U S A 2021;118:2026165118. [PMID: 34845009 PMCID: PMC8694067 DOI: 10.1073/pnas.2026165118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2021] [Indexed: 11/18/2022]  Open
35
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
36
Kropp C, Bruckmann A, Babinger P. Controlling Enzymatic Activity by Modulating the Oligomerization State via Chemical Rescue and Optical Control. Chembiochem 2021;23:e202100490. [PMID: 34633135 PMCID: PMC9298306 DOI: 10.1002/cbic.202100490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/08/2021] [Indexed: 12/22/2022]
37
Pinto GP, Corbella M, Demkiv AO, Kamerlin SCL. Exploiting enzyme evolution for computational protein design. Trends Biochem Sci 2021;47:375-389. [PMID: 34544655 DOI: 10.1016/j.tibs.2021.08.008] [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: 06/29/2021] [Revised: 08/18/2021] [Accepted: 08/24/2021] [Indexed: 11/15/2022]
38
Wheeler LC, Harms MJ. Were Ancestral Proteins Less Specific? Mol Biol Evol 2021;38:2227-2239. [PMID: 33528559 PMCID: PMC8136485 DOI: 10.1093/molbev/msab019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
39
Kozuka K, Nakano S, Asano Y, Ito S. Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations. Biochemistry 2021;60:2309-2319. [PMID: 34254784 DOI: 10.1021/acs.biochem.1c00309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
40
Khan RT, Musil M, Stourac J, Damborsky J, Bednar D. Fully Automated Ancestral Sequence Reconstruction using FireProtASR. Curr Protoc 2021;1:e30. [PMID: 33524240 DOI: 10.1002/cpz1.30] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
41
Laursen L, Čalyševa J, Gibson TJ, Jemth P. Divergent Evolution of a Protein-Protein Interaction Revealed through Ancestral Sequence Reconstruction and Resurrection. Mol Biol Evol 2021;38:152-167. [PMID: 32750125 PMCID: PMC7782867 DOI: 10.1093/molbev/msaa198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
42
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]
43
Ngo K, Bruno da Silva F, Leite VBP, Contessoto VG, Onuchic JN. Improving the Thermostability of Xylanase A from Bacillus subtilis by Combining Bioinformatics and Electrostatic Interactions Optimization. J Phys Chem B 2021;125:4359-4367. [PMID: 33887137 DOI: 10.1021/acs.jpcb.1c01253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
44
A meta-analysis of the activity, stability, and mutational characteristics of temperature-adapted enzymes. Biosci Rep 2021;41:228416. [PMID: 33871022 PMCID: PMC8150157 DOI: 10.1042/bsr20210336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/29/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022]  Open
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Irumagawa S, Kobayashi K, Saito Y, Miyata T, Umetsu M, Kameda T, Arai R. Rational thermostabilisation of four-helix bundle dimeric de novo proteins. Sci Rep 2021;11:7526. [PMID: 33824364 PMCID: PMC8024369 DOI: 10.1038/s41598-021-86952-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/22/2021] [Indexed: 11/29/2022]  Open
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Wang CK, Craik DJ. Linking molecular evolution to molecular grafting. J Biol Chem 2021;296:100425. [PMID: 33600801 PMCID: PMC8005815 DOI: 10.1016/j.jbc.2021.100425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/01/2022]  Open
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Crippa M, Andreghetti D, Capelli R, Tiana G. Evolution of frustrated and stabilising contacts in reconstructed ancient proteins. EUROPEAN BIOPHYSICS JOURNAL 2021;50:699-712. [PMID: 33569610 PMCID: PMC8260555 DOI: 10.1007/s00249-021-01500-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/14/2020] [Accepted: 01/13/2021] [Indexed: 11/30/2022]
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Perez-Garcia P, Kobus S, Gertzen CGW, Hoeppner A, Holzscheck N, Strunk CH, Huber H, Jaeger KE, Gohlke H, Kovacic F, Smits SHJ, Streit WR, Chow J. A promiscuous ancestral enzyme´s structure unveils protein variable regions of the highly diverse metallo-β-lactamase family. Commun Biol 2021;4:132. [PMID: 33514861 PMCID: PMC7846560 DOI: 10.1038/s42003-021-01671-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023]  Open
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Musil M, Khan RT, Beier A, Stourac J, Konegger H, Damborsky J, Bednar D. FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction. Brief Bioinform 2020;22:6042664. [PMID: 33346815 PMCID: PMC8294521 DOI: 10.1093/bib/bbaa337] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/12/2020] [Indexed: 12/13/2022]  Open
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Motoyama T, Hiramatsu N, Asano Y, Nakano S, Ito S. Protein Sequence Selection Method That Enables Full Consensus Design of Artificial l-Threonine 3-Dehydrogenases with Unique Enzymatic Properties. Biochemistry 2020;59:3823-3833. [PMID: 32945652 DOI: 10.1021/acs.biochem.0c00570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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