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For: Komeiji Y, Fujita I, Honda N, Tsutsui M, Tamura T, Yamato I. Glycine 85 of the trp-repressor of E. coli is important in forming the hydrophobic tryptophan binding pocket: experimental and computational approaches. Protein Eng 1994;7:1239-47. [PMID: 7855139 DOI: 10.1093/protein/7.10.1239] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Number Cited by Other Article(s)
1
Affinity, Specificity, and Cooperativity of DNA Binding by Bacterial Gene Regulatory Proteins. Int J Mol Sci 2022;23:ijms23010562. [PMID: 35008987 PMCID: PMC8745587 DOI: 10.3390/ijms23010562] [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] [Received: 10/01/2021] [Revised: 12/14/2021] [Accepted: 12/22/2021] [Indexed: 12/04/2022]  Open
2
Pandey SK, Melichercik M, Řeha D, Ettrich RH, Carey J. Conserved Dynamic Mechanism of Allosteric Response to L-arg in Divergent Bacterial Arginine Repressors. Molecules 2020;25:molecules25092247. [PMID: 32397647 PMCID: PMC7248756 DOI: 10.3390/molecules25092247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 11/23/2022]  Open
3
Carey J, Benoff B, Harish B, Yuan L, Lawson CL. Environment-dependent long-range structural distortion in a temperature-sensitive point mutant. Protein Sci 2012;21:63-74. [PMID: 22057811 PMCID: PMC3323781 DOI: 10.1002/pro.759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 10/25/2011] [Accepted: 10/27/2011] [Indexed: 01/07/2023]
4
Strawn R, Melichercik M, Green M, Stockner T, Carey J, Ettrich R. Symmetric allosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues. PLoS Comput Biol 2010;6:e1000801. [PMID: 20532206 PMCID: PMC2880562 DOI: 10.1371/journal.pcbi.1000801] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 04/29/2010] [Indexed: 12/20/2022]  Open
5
Yuan Z, Hanks TW. A reversible colorimetric and fluorescent polydiacetylene vesicle sensor platform. POLYMER 2008. [DOI: 10.1016/j.polymer.2008.09.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
6
Carey J, Lindman S, Bauer M, Linse S. Protein reconstitution and three-dimensional domain swapping: benefits and constraints of covalency. Protein Sci 2007;16:2317-33. [PMID: 17962398 PMCID: PMC2211703 DOI: 10.1110/ps.072985007] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Revised: 07/30/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
7
Danelon C, Suenaga A, Winterhalter M, Yamato I. Molecular origin of the cation selectivity in OmpF porin: single channel conductances vs. free energy calculation. Biophys Chem 2003;104:591-603. [PMID: 12914905 DOI: 10.1016/s0301-4622(03)00062-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
8
Suenaga A, Yatsu C, Komeiji Y, Uebayasi M, Meguro T, Yamato I. Molecular dynamics simulation of trp-repressor/operator complex: analysis of hydrogen bond patterns of protein–DNA interaction. J Mol Struct 2000. [DOI: 10.1016/s0022-2860(00)00459-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
9
Tomic S, Nilsson L, Wade RC. Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis. J Med Chem 2000;43:1780-92. [PMID: 10794695 DOI: 10.1021/jm9911175] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
10
Samanta U, Pal D, Chakrabarti P. Environment of tryptophan side chains in proteins. Proteins 2000. [DOI: 10.1002/(sici)1097-0134(20000215)38:3<288::aid-prot5>3.0.co;2-7] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
11
Honda N, Komeiji Y, Uebayasi M, Yamato I. Computational design of a substrate specificity mutant of a protein. Proteins 1996;26:459-64. [PMID: 8990498 DOI: 10.1002/(sici)1097-0134(199612)26:4<459::aid-prot6>3.0.co;2-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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