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For: Leander M, Liu Z, Cui Q, Raman S. Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins. eLife 2022;11:e79932. [PMID: 36226916 PMCID: PMC9662819 DOI: 10.7554/elife.79932] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/13/2022] [Indexed: 01/29/2023]  Open
Number Cited by Other Article(s)
1
Colom MS, Vučinić J, Adolf‐Bryfogle J, Bowman JW, Verel S, Moczygemba I, Schiex T, Simoncini D, Bahl CD. Complete combinatorial mutational enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity. Protein Sci 2024;33:e5109. [PMID: 38989563 PMCID: PMC11237556 DOI: 10.1002/pro.5109] [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: 02/17/2024] [Revised: 05/20/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024]
2
Wu Y, Zhang S, York DM, Wang L. Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions. J Phys Chem B 2024;128:6529-6541. [PMID: 38935925 DOI: 10.1021/acs.jpcb.4c02303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
3
Liu Z, Gillis TG, Raman S, Cui Q. A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery. eLife 2024;12:RP92262. [PMID: 38836839 PMCID: PMC11152574 DOI: 10.7554/elife.92262] [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: 06/06/2024]  Open
4
Rao J, Xin R, Macdonald C, Howard MK, Estevam GO, Yee SW, Wang M, Fraser JS, Coyote-Maestas W, Pimentel H. Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage. Genome Biol 2024;25:138. [PMID: 38789982 PMCID: PMC11127319 DOI: 10.1186/s13059-024-03279-7] [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: 10/31/2023] [Accepted: 05/14/2024] [Indexed: 05/26/2024]  Open
5
Nishikawa KK, Chen J, Acheson JF, Harbaugh SV, Huss P, Frenkel M, Novy N, Sieren HR, Lodewyk EC, Lee DH, Chávez JL, Fox BG, Raman S. Highly multiplexed design of an allosteric transcription factor to sense novel ligands. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583947. [PMID: 38496486 PMCID: PMC10942455 DOI: 10.1101/2024.03.07.583947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
6
Billerbeck S, Walker RSK, Pretorius IS. Killer yeasts: expanding frontiers in the age of synthetic biology. Trends Biotechnol 2024:S0167-7799(24)00067-2. [PMID: 38575438 DOI: 10.1016/j.tibtech.2024.03.003] [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: 01/24/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 04/06/2024]
7
Swint-Kruse L, Fenton AW. Rheostats, toggles, and neutrals, Oh my! A new framework for understanding how amino acid changes modulate protein function. J Biol Chem 2024;300:105736. [PMID: 38336297 PMCID: PMC10914490 DOI: 10.1016/j.jbc.2024.105736] [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: 11/15/2023] [Revised: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]  Open
8
Liu Z, Gillis T, Raman S, Cui Q. A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allostery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.06.552196. [PMID: 37662419 PMCID: PMC10473640 DOI: 10.1101/2023.08.06.552196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
9
Deng J, Yuan Y, Cui Q. Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR. J Am Chem Soc 2024;146:2757-2768. [PMID: 38231868 PMCID: PMC10843641 DOI: 10.1021/jacs.3c12494] [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] [Indexed: 01/19/2024]
10
Jardón-Valadez E, Ulloa-Aguirre A. Tracking conformational transitions of the gonadotropin hormone receptors in a bilayer of (SDPC) poly-unsaturated lipids from all-atom molecular dynamics simulations. PLoS Comput Biol 2024;20:e1011415. [PMID: 38206994 PMCID: PMC10807830 DOI: 10.1371/journal.pcbi.1011415] [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: 08/08/2023] [Revised: 01/24/2024] [Accepted: 12/15/2023] [Indexed: 01/13/2024]  Open
11
Deng J, Yuan Y, Cui Q. Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555381. [PMID: 37905112 PMCID: PMC10614727 DOI: 10.1101/2023.08.29.555381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
12
Nussinov R, Liu Y, Zhang W, Jang H. Protein conformational ensembles in function: roles and mechanisms. RSC Chem Biol 2023;4:850-864. [PMID: 37920394 PMCID: PMC10619138 DOI: 10.1039/d3cb00114h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/02/2023] [Indexed: 11/04/2023]  Open
13
Swint-Kruse L, Dougherty LL, Page B, Wu T, O’Neil PT, Prasannan CB, Timmons C, Tang Q, Parente DJ, Sreenivasan S, Holyoak T, Fenton AW. PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes. Database (Oxford) 2023;2023:baad030. [PMID: 37171062 PMCID: PMC10176505 DOI: 10.1093/database/baad030] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
14
Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. From Deep Mutational Mapping of Allosteric Protein Landscapes to Deep Learning of Allostery and Hidden Allosteric Sites: Zooming in on "Allosteric Intersection" of Biochemical and Big Data Approaches. Int J Mol Sci 2023;24:7747. [PMID: 37175454 PMCID: PMC10178073 DOI: 10.3390/ijms24097747] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023]  Open
15
Xiao S, Verkhivker GM, Tao P. Machine learning and protein allostery. Trends Biochem Sci 2023;48:375-390. [PMID: 36564251 PMCID: PMC10023316 DOI: 10.1016/j.tibs.2022.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/16/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022]
16
Agajanian S, Alshahrani M, Bai F, Tao P, Verkhivker GM. Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. J Chem Inf Model 2023;63:1413-1428. [PMID: 36827465 PMCID: PMC11162550 DOI: 10.1021/acs.jcim.2c01634] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
17
Wei H, Li X. Deep mutational scanning: A versatile tool in systematically mapping genotypes to phenotypes. Front Genet 2023;14:1087267. [PMID: 36713072 PMCID: PMC9878224 DOI: 10.3389/fgene.2023.1087267] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023]  Open
18
Krishnan K, Tian H, Tao P, Verkhivker GM. Probing conformational landscapes and mechanisms of allosteric communication in the functional states of the ABL kinase domain using multiscale simulations and network-based mutational profiling of allosteric residue potentials. J Chem Phys 2022;157:245101. [PMID: 36586979 PMCID: PMC11184971 DOI: 10.1063/5.0133826] [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: 11/06/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]  Open
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