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For: Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, Shen T. Mapping allostery through computational glycine scanning and correlation analysis of residue-residue contacts. Biochemistry 2015;54:1534-41. [PMID: 25658131 DOI: 10.1021/bi501152d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Number Cited by Other Article(s)
1
Mukhaleva E, Ma N, van der Velden WJC, Gogoshin G, Branciamore S, Bhattacharya S, Rodin AS, Vaidehi N. Bayesian network models identify cooperative GPCR:G protein interactions that contribute to G protein coupling. J Biol Chem 2024;300:107362. [PMID: 38735478 PMCID: PMC11176750 DOI: 10.1016/j.jbc.2024.107362] [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: 11/03/2023] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/14/2024]  Open
2
Kumar A, Vashisth H. Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface. J Chem Inf Model 2024;64:2068-2076. [PMID: 38460144 DOI: 10.1021/acs.jcim.3c01933] [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: 03/11/2024]
3
Muhammed Aziz D, Hassan SA, Amin AAM, Abdullah MN, Qurbani K, Aziz SB. A synergistic investigation of azo-thiazole derivatives incorporating thiazole moieties: a comprehensive exploration of their synthesis, characterization, computational insights, solvatochromism, and multimodal biological activity assessment. RSC Adv 2023;13:34534-34555. [PMID: 38024963 PMCID: PMC10668576 DOI: 10.1039/d3ra06469g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]  Open
4
Mukhaleva E, Ma N, van der Velden WJC, Gogoshin G, Branciamore S, Bhattacharya S, Rodin AS, Vaidehi N. Bayesian network models identify co-operative GPCR:G protein interactions that contribute to G protein coupling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561618. [PMID: 37873104 PMCID: PMC10592737 DOI: 10.1101/2023.10.09.561618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
5
Ray Chaudhuri N, Ghosh Dastidar S. Allosteric Boost by TAB1 on the TAK1 Kinase Favorably Sculpts the Thermodynamic Landscape of Activation. J Chem Inf Model 2023;63:224-239. [PMID: 36374995 DOI: 10.1021/acs.jcim.2c00778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
6
Remote communication between unstructured and structured regions of Bcl-2 tunes its ligand binding capacity: Mechanistic insights. Comput Biol Chem 2022;100:107736. [DOI: 10.1016/j.compbiolchem.2022.107736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/05/2022] [Accepted: 07/16/2022] [Indexed: 11/23/2022]
7
Bai F, Puk KM, Liu J, Zhou H, Tao P, Zhou W, Wang S. Sparse group selection and analysis of function-related residue for protein-state recognition. J Comput Chem 2022;43:1342-1354. [PMID: 35656889 PMCID: PMC9248267 DOI: 10.1002/jcc.26937] [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: 11/05/2021] [Revised: 03/23/2022] [Accepted: 05/08/2022] [Indexed: 11/08/2022]
8
Pham B, Cheng Z, Lopez D, Lindsay RJ, Foutch D, Majors RT, Shen T. Statistical Analysis of Protein-Ligand Interaction Patterns in Nuclear Receptor RORγ. Front Mol Biosci 2022;9:904445. [PMID: 35782874 PMCID: PMC9240913 DOI: 10.3389/fmolb.2022.904445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/16/2022] [Indexed: 11/21/2022]  Open
9
Yao XQ, Hamelberg D. From Distinct to Differential Conformational Dynamics to Map Allosteric Communication Pathways in Proteins. J Phys Chem B 2022;126:2612-2620. [PMID: 35319195 DOI: 10.1021/acs.jpcb.2c00199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
10
Hidden electrostatic energy contributions define dynamic allosteric communications within p53 during molecular recognition. Biophys J 2021;120:4512-4524. [PMID: 34478701 DOI: 10.1016/j.bpj.2021.08.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/03/2021] [Accepted: 08/26/2021] [Indexed: 12/15/2022]  Open
11
Lim JPL, Braza MKE, Nellas RB. The effect of ligand affinity to the contact dynamics of the ligand binding domain of thyroid hormone receptor - retinoid X receptor. J Mol Graph Model 2021;104:107829. [PMID: 33450664 DOI: 10.1016/j.jmgm.2020.107829] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 11/19/2022]
12
Liu Q, Zhou J, Gao J, Ma W, Wang S, Xing L. Rational design of EGFR dimerization-disrupting peptides: A new strategy to combat drug resistance in targeted lung cancer therapy. Biochimie 2020;176:128-137. [DOI: 10.1016/j.biochi.2020.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/13/2020] [Accepted: 07/18/2020] [Indexed: 12/24/2022]
13
Zhang W, Liu J, Shan H, Yin F, Zhong B, Zhang C, Yu X. Machine learning-guided evolution of BMP-2 knuckle Epitope-Derived osteogenic peptides to target BMP receptor II. J Drug Target 2020;28:802-810. [PMID: 32354236 DOI: 10.1080/1061186x.2020.1757100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
14
Surpeta B, Sequeiros-Borja CE, Brezovsky J. Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering. Int J Mol Sci 2020;21:E2713. [PMID: 32295283 PMCID: PMC7215530 DOI: 10.3390/ijms21082713] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/10/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022]  Open
15
Bordelon T, Bobay B, Murphy A, Reese H, Shanahan C, Odeh F, Broussard A, Kormos C, Menegatti S. Translating antibody-binding peptides into peptoid ligands with improved affinity and stability. J Chromatogr A 2019;1602:284-299. [DOI: 10.1016/j.chroma.2019.05.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/03/2019] [Accepted: 05/24/2019] [Indexed: 12/18/2022]
16
Lindsay RJ, Pham B, Shen T, McCord RP. Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework. Nucleic Acids Res 2019;46:8143-8152. [PMID: 29992238 PMCID: PMC6144818 DOI: 10.1093/nar/gky604] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/25/2018] [Indexed: 11/13/2022]  Open
17
Pham B, Lindsay RJ, Shen T. Effector-Binding-Directed Dimerization and Dynamic Communication between Allosteric Sites of Ribonucleotide Reductase. Biochemistry 2019;58:697-705. [PMID: 30571104 DOI: 10.1021/acs.biochem.8b01131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
18
Lindsay RJ, Siess J, Lohry DP, McGee TS, Ritchie JS, Johnson QR, Shen T. Characterizing protein conformations by correlation analysis of coarse-grained contact matrices. J Chem Phys 2018;148:025101. [PMID: 29331124 DOI: 10.1063/1.5004141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
19
Fernandez EJ. Allosteric pathways in nuclear receptors - Potential targets for drug design. Pharmacol Ther 2018;183:152-159. [PMID: 29080700 PMCID: PMC5817003 DOI: 10.1016/j.pharmthera.2017.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
20
Johnson QR, Lindsay RJ, Shen T. CAMERRA: An analysis tool for the computation of conformational dynamics by evaluating residue-residue associations. J Comput Chem 2018;39:1568-1578. [PMID: 29464733 DOI: 10.1002/jcc.25192] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/04/2018] [Accepted: 01/29/2018] [Indexed: 12/20/2022]
21
Sinha S, Maity A, Ghosh Dastidar S. BIM Binding Remotely Regulates BAX Activation: Insights from the Free Energy Landscapes. J Chem Inf Model 2018;58:370-382. [PMID: 29278499 DOI: 10.1021/acs.jcim.7b00628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
22
Hidden electrostatic basis of dynamic allostery in a PDZ domain. Proc Natl Acad Sci U S A 2017. [PMID: 28634294 DOI: 10.1073/pnas.1705311114] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
23
Fernandez EJ, Gahlot V, Rodriguez C, Amburn J. DNA-induced unfolding of the thyroid hormone receptor α A/B domain through allostery. FEBS Open Bio 2017;7:854-864. [PMID: 28593140 PMCID: PMC5458466 DOI: 10.1002/2211-5463.12229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 01/22/2023]  Open
24
Sayyed-Ahmad A, Prakash P, Gorfe AA. Distinct dynamics and interaction patterns in H- and K-Ras oncogenic P-loop mutants. Proteins 2017;85:1618-1632. [PMID: 28498561 DOI: 10.1002/prot.25317] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 04/27/2017] [Accepted: 05/05/2017] [Indexed: 12/31/2022]
25
Sridhar J, Liu J, Komati R, Schroeder R, Jiang Q, Tram P, Riley K, Foroozesh M. Ortho-Methylarylamines as Time-Dependent Inhibitors of Cytochrome P450 1A1 Enzyme. Drug Metab Lett 2017;10:270-277. [PMID: 28000546 PMCID: PMC6697106 DOI: 10.2174/1872312810666161220155226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 12/01/2016] [Accepted: 12/01/2016] [Indexed: 11/22/2022]
26
Barman A, Hamelberg D. Coupled Dynamics and Entropic Contribution to the Allosteric Mechanism of Pin1. J Phys Chem B 2016;120:8405-15. [DOI: 10.1021/acs.jpcb.6b02123] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
27
Kalescky R, Zhou H, Liu J, Tao P. Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery. PLoS Comput Biol 2016;12:e1004893. [PMID: 27115535 PMCID: PMC4846164 DOI: 10.1371/journal.pcbi.1004893] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 04/01/2016] [Indexed: 12/22/2022]  Open
28
Clark AK, Wilder JH, Grayson AW, Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, Shen T. The Promiscuity of Allosteric Regulation of Nuclear Receptors by Retinoid X Receptor. J Phys Chem B 2016;120:8338-45. [PMID: 27110634 DOI: 10.1021/acs.jpcb.6b02057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
29
Johnson QR, Lindsay RJ, Nellas RB, Shen T. Pressure-induced conformational switch of an interfacial protein. Proteins 2016;84:820-7. [DOI: 10.1002/prot.25031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 02/04/2016] [Accepted: 03/01/2016] [Indexed: 12/14/2022]
30
Dynamical network of residue-residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation. Proc Natl Acad Sci U S A 2016;113:4735-40. [PMID: 27071107 DOI: 10.1073/pnas.1523573113] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
31
Guarnera E, Berezovsky IN. Allosteric sites: remote control in regulation of protein activity. Curr Opin Struct Biol 2016;37:1-8. [DOI: 10.1016/j.sbi.2015.10.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/19/2015] [Accepted: 10/22/2015] [Indexed: 01/22/2023]
32
Lang EJM, Heyes LC, Jameson GB, Parker EJ. Calculated pKa Variations Expose Dynamic Allosteric Communication Networks. J Am Chem Soc 2016;138:2036-45. [DOI: 10.1021/jacs.5b13134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
33
Ribeiro AAST, Ortiz V. A Chemical Perspective on Allostery. Chem Rev 2016;116:6488-502. [DOI: 10.1021/acs.chemrev.5b00543] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
34
Johnson QR, Lindsay RJ, Petridis L, Shen T. Investigation of Carbohydrate Recognition via Computer Simulation. Molecules 2015;20:7700-18. [PMID: 25927900 PMCID: PMC6272577 DOI: 10.3390/molecules20057700] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/15/2015] [Accepted: 04/15/2015] [Indexed: 12/11/2022]  Open
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