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For: Biddle JW, Martinez-Corral R, Wong F, Gunawardena J. Allosteric conformational ensembles have unlimited capacity for integrating information. eLife 2021;10:65498. [PMID: 34106049 PMCID: PMC8189718 DOI: 10.7554/elife.65498] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/30/2021] [Indexed: 12/24/2022]  Open
Number Cited by Other Article(s)
1
Martinez-Corral R, Nam KM, DePace AH, Gunawardena J. The Hill function is the universal Hopfield barrier for sharpness of input-output responses. Proc Natl Acad Sci U S A 2024;121:e2318329121. [PMID: 38787881 PMCID: PMC11145184 DOI: 10.1073/pnas.2318329121] [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: 10/20/2023] [Accepted: 04/25/2024] [Indexed: 05/26/2024]  Open
2
Martinez-Corral R, Nam KM, DePace AH, Gunawardena J. The Hill function is the universal Hopfield barrier for sharpness of input-output responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587054. [PMID: 38585761 PMCID: PMC10996692 DOI: 10.1101/2024.03.27.587054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
3
Nussinov R, Liu Y, Zhang W, Jang H. Cell phenotypes can be predicted from propensities of protein conformations. Curr Opin Struct Biol 2023;83:102722. [PMID: 37871498 PMCID: PMC10841533 DOI: 10.1016/j.sbi.2023.102722] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
4
Nam KM, Gunawardena J. The linear framework II: using graph theory to analyse the transient regime of Markov processes. Front Cell Dev Biol 2023;11:1233808. [PMID: 38020901 PMCID: PMC10656611 DOI: 10.3389/fcell.2023.1233808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023]  Open
5
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
6
Djemili R, Adrouche S, Durot S, Heitz V. Allosterically Driven Assembly of a Multisite Cage-Based [2]Semirotaxane. J Org Chem 2023;88:14760-14766. [PMID: 37812736 DOI: 10.1021/acs.joc.3c01381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
7
Richardson K. Misguided model of human behavior: Comment on C. H. Burt: "Challenging the utility of polygenic scores for social science…". Behav Brain Sci 2023;46:e225. [PMID: 37695003 DOI: 10.1017/s0140525x22002333] [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: 09/12/2023]
8
Martinez-Corral R, Park M, Biette KM, Friedrich D, Scholes C, Khalil AS, Gunawardena J, DePace AH. Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology. Cell Syst 2023;14:324-339.e7. [PMID: 37080164 PMCID: PMC10472254 DOI: 10.1016/j.cels.2023.02.003] [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: 11/30/2021] [Revised: 08/22/2022] [Accepted: 02/10/2023] [Indexed: 04/22/2023]
9
Sikorski V, Selberg S, Lalowski M, Karelson M, Kankuri E. The structure and function of YTHDF epitranscriptomic m6A readers. Trends Pharmacol Sci 2023;44:335-353. [PMID: 37069041 DOI: 10.1016/j.tips.2023.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 04/19/2023]
10
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]
11
Competing constraints shape the nonequilibrium limits of cellular decision-making. Proc Natl Acad Sci U S A 2023;120:e2211203120. [PMID: 36862689 PMCID: PMC10013869 DOI: 10.1073/pnas.2211203120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]  Open
12
Çetiner U, Gunawardena J. Reformulating nonequilibrium steady states and generalized Hopfield discrimination. Phys Rev E 2022;106:064128. [PMID: 36671125 DOI: 10.1103/physreve.106.064128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022]
13
Schay G, Fidy J, Herenyi L. Slow dynamics measured by phosphorescence lifetime reveals global conformational changes in human adult hemoglobin induced by allosteric effectors. PLoS One 2022;17:e0278417. [PMID: 36454779 PMCID: PMC9714750 DOI: 10.1371/journal.pone.0278417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]  Open
14
Richter WF, Nayak S, Iwasa J, Taatjes DJ. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 2022;23:732-749. [PMID: 35725906 PMCID: PMC9207880 DOI: 10.1038/s41580-022-00498-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 02/08/2023]
15
Nussinov R, Zhang M, Maloney R, Liu Y, Tsai CJ, Jang H. Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs. J Mol Biol 2022;434:167569. [PMID: 35378118 PMCID: PMC9398924 DOI: 10.1016/j.jmb.2022.167569] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/11/2022] [Accepted: 03/25/2022] [Indexed: 01/12/2023]
16
Iorio A, Brochier-Armanet C, Mas C, Sterpone F, Madern D. Protein Conformational Space at the Edge of Allostery: Turning a Non-allosteric Malate Dehydrogenase into an "Allosterized" Enzyme using Evolution Guided Punctual Mutations. Mol Biol Evol 2022;39:6691310. [PMID: 36056899 PMCID: PMC9486893 DOI: 10.1093/molbev/msac186] [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] [Indexed: 11/20/2022]  Open
17
Lavrinenko IA, Vashanov GA, Hernández Cáceres JL, Buchelnikov AS, Nechipurenko YD. A New Model of Hemoglobin Oxygenation. ENTROPY (BASEL, SWITZERLAND) 2022;24:1214. [PMID: 36141103 PMCID: PMC9498255 DOI: 10.3390/e24091214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 06/16/2023]
18
Nussinov R, Zhang M, Liu Y, Jang H. AlphaFold, Artificial Intelligence (AI), and Allostery. J Phys Chem B 2022;126:6372-6383. [PMID: 35976160 PMCID: PMC9442638 DOI: 10.1021/acs.jpcb.2c04346] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
19
Nam KM, Martinez-Corral R, Gunawardena J. The linear framework: using graph theory to reveal the algebra and thermodynamics of biomolecular systems. Interface Focus 2022;12:20220013. [PMID: 35860006 PMCID: PMC9184966 DOI: 10.1098/rsfs.2022.0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/25/2022] [Indexed: 12/25/2022]  Open
20
Cellular sentience as the primary source of biological order and evolution. Biosystems 2022;218:104694. [PMID: 35595194 DOI: 10.1016/j.biosystems.2022.104694] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/17/2022]
21
Allosteric transitions of rabbit skeletal muscle lactate dehydrogenase induced by pH-dependent dissociation of the tetrameric enzyme. Biochimie 2022;199:23-35. [DOI: 10.1016/j.biochi.2022.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/23/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023]
22
Richardson K. Genes and knowledge: Response to Baverstock, K. the gene an appraisal. https://doi.org/10.1016/j.pbiomolbio.2021.04.005. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021;167:12-17. [PMID: 34736965 DOI: 10.1016/j.pbiomolbio.2021.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/21/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
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