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For: Inanami T, Terada TP, Sasai M. Folding pathway of a multidomain protein depends on its topology of domain connectivity. Proc Natl Acad Sci U S A 2014;111:15969-74. [PMID: 25267632 DOI: 10.1073/pnas.1406244111] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
Number Cited by Other Article(s)
1
Malagrinò F, Puglisi E, Pagano L, Travaglini-Allocatelli C, Toto A. GRB2: A dynamic adaptor protein orchestrating cellular signaling in health and disease. Biochem Biophys Rep 2024;39:101803. [PMID: 39175664 PMCID: PMC11340617 DOI: 10.1016/j.bbrep.2024.101803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 08/24/2024]  Open
2
Coleman T, Shin J, Silberg JJ, Shamoo Y, Atkinson JT. The Biochemical Impact of Extracting an Embedded Adenylate Kinase Domain Using Circular Permutation. Biochemistry 2024;63:599-609. [PMID: 38357768 DOI: 10.1021/acs.biochem.3c00605] [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: 02/16/2024]
3
Agam G, Barth A, Lamb DC. Folding pathway of a discontinuous two-domain protein. Nat Commun 2024;15:690. [PMID: 38263337 PMCID: PMC10805907 DOI: 10.1038/s41467-024-44901-3] [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: 05/25/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024]  Open
4
Ooka K, Arai M. Accurate prediction of protein folding mechanisms by simple structure-based statistical mechanical models. Nat Commun 2023;14:6338. [PMID: 37857633 PMCID: PMC10587348 DOI: 10.1038/s41467-023-41664-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/10/2023] [Indexed: 10/21/2023]  Open
5
Peng H, Wang M, Wang N, Yang C, Guo W, Li G, Huang S, Wei D, Liu D. Different N-Glycosylation Sites Reduce the Activity of Recombinant DSPAα2. Curr Issues Mol Biol 2022;44:3930-3947. [PMID: 36135182 PMCID: PMC9497888 DOI: 10.3390/cimb44090270] [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: 07/18/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 12/01/2022]  Open
6
Ooka K, Liu R, Arai M. The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics. Molecules 2022;27:molecules27144460. [PMID: 35889332 PMCID: PMC9319528 DOI: 10.3390/molecules27144460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022]  Open
7
Shityakov S, Skorb EV, Nosonovsky M. Topological bio-scaling analysis as a universal measure of protein folding. ROYAL SOCIETY OPEN SCIENCE 2022;9:220160. [PMID: 35845855 PMCID: PMC9277272 DOI: 10.1098/rsos.220160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/14/2022] [Indexed: 05/24/2023]
8
Liu Z, Thirumalai D. Cooperativity and Folding Kinetics in a Multidomain Protein with Interwoven Chain Topology. ACS CENTRAL SCIENCE 2022;8:763-774. [PMID: 35756371 PMCID: PMC9228575 DOI: 10.1021/acscentsci.2c00140] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Indexed: 06/15/2023]
9
The folding and misfolding mechanisms of multidomain proteins. MEDICINE IN DRUG DISCOVERY 2022. [DOI: 10.1016/j.medidd.2022.100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
10
Structural and Kinetic Views of Molecular Chaperones in Multidomain Protein Folding. Int J Mol Sci 2022;23:ijms23052485. [PMID: 35269628 PMCID: PMC8910466 DOI: 10.3390/ijms23052485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/10/2022]  Open
11
Naganathan AN, Kannan A. A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures. Curr Res Struct Biol 2021;3:257-267. [PMID: 34704074 PMCID: PMC8526763 DOI: 10.1016/j.crstbi.2021.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/08/2021] [Accepted: 09/30/2021] [Indexed: 12/22/2022]  Open
12
Nie QM, Sun LZ, Li HB, Chu X, Wang J. Effects of electrostatic interactions on global folding and local conformational dynamics of a multidomain Y-family DNA polymerase. Phys Chem Chem Phys 2021;23:20841-20847. [PMID: 34533560 DOI: 10.1039/d1cp02832d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
13
Chu X, Suo Z, Wang J. Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase. eLife 2020;9:60434. [PMID: 33079059 PMCID: PMC7641590 DOI: 10.7554/elife.60434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/16/2020] [Indexed: 01/01/2023]  Open
14
Hidden kinetic traps in multidomain folding highlight the presence of a misfolded but functionally competent intermediate. Proc Natl Acad Sci U S A 2020;117:19963-19969. [PMID: 32747559 PMCID: PMC7443948 DOI: 10.1073/pnas.2004138117] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
15
Chu X, Suo Z, Wang J. Confinement and Crowding Effects on Folding of a Multidomain Y-Family DNA Polymerase. J Chem Theory Comput 2020;16:1319-1332. [PMID: 31972079 PMCID: PMC7258223 DOI: 10.1021/acs.jctc.9b01146] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
16
Ghosh C, Jana B. Intersubunit Assisted Folding of DNA Binding Domains in Dimeric Catabolite Activator Protein. J Phys Chem B 2020;124:1411-1423. [DOI: 10.1021/acs.jpcb.9b10941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
17
Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps. Proc Natl Acad Sci U S A 2020;117:1485-1495. [PMID: 31911473 DOI: 10.1073/pnas.1913207117] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
18
Gershenson A, Gosavi S, Faccioli P, Wintrode PL. Successes and challenges in simulating the folding of large proteins. J Biol Chem 2020;295:15-33. [PMID: 31712314 PMCID: PMC6952611 DOI: 10.1074/jbc.rev119.006794] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
19
Gopi S, Aranganathan A, Naganathan AN. Thermodynamics and folding landscapes of large proteins from a statistical mechanical model. Curr Res Struct Biol 2019;1:6-12. [PMID: 34235463 PMCID: PMC8244504 DOI: 10.1016/j.crstbi.2019.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/10/2019] [Accepted: 10/13/2019] [Indexed: 01/01/2023]  Open
20
Khor S. Folding with a protein's native shortcut network. Proteins 2019;86:924-934. [PMID: 29790602 DOI: 10.1002/prot.25524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 04/13/2018] [Accepted: 05/14/2018] [Indexed: 11/09/2022]
21
Narayan A, Naganathan AN. Switching Protein Conformational Substates by Protonation and Mutation. J Phys Chem B 2018;122:11039-11047. [PMID: 30048131 DOI: 10.1021/acs.jpcb.8b05108] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
22
Kumar V, Chaudhuri TK. Spontaneous refolding of the large multidomain protein malate synthase G proceeds through misfolding traps. J Biol Chem 2018;293:13270-13283. [PMID: 29959230 DOI: 10.1074/jbc.ra118.003903] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/28/2018] [Indexed: 11/06/2022]  Open
23
Arai M. Unified understanding of folding and binding mechanisms of globular and intrinsically disordered proteins. Biophys Rev 2018;10:163-181. [PMID: 29307002 PMCID: PMC5899706 DOI: 10.1007/s12551-017-0346-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/13/2017] [Indexed: 12/18/2022]  Open
24
Yeh YQ, Liao KF, Shih O, Shiu YJ, Wu WR, Su CJ, Lin PC, Jeng US. Probing the Acid-Induced Packing Structure Changes of the Molten Globule Domains of a Protein near Equilibrium Unfolding. J Phys Chem Lett 2017;8:470-477. [PMID: 28067527 DOI: 10.1021/acs.jpclett.6b02722] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
25
Sasai M, Chikenji G, Terada TP. Cooperativity and modularity in protein folding. Biophys Physicobiol 2016;13:281-293. [PMID: 28409080 PMCID: PMC5221511 DOI: 10.2142/biophysico.13.0_281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/05/2016] [Indexed: 12/01/2022]  Open
26
Wako H, Abe H. Characterization of protein folding by a Φ-value calculation with a statistical-mechanical model. Biophys Physicobiol 2016;13:263-279. [PMID: 28409079 PMCID: PMC5221509 DOI: 10.2142/biophysico.13.0_263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/20/2016] [Indexed: 12/01/2022]  Open
27
Biswas S, Chowdhury PK. Correlated and Anticorrelated Domain Movement of Human Serum Albumin: A Peek into the Complexity of the Crowded Milieu. J Phys Chem B 2016;120:4897-911. [DOI: 10.1021/acs.jpcb.6b01671] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
28
Single-Molecule Fluorescence Studies of Fast Protein Folding. Methods Enzymol 2016;581:417-459. [DOI: 10.1016/bs.mie.2016.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
29
Sinner C, Lutz B, Verma A, Schug A. Revealing the global map of protein folding space by large-scale simulations. J Chem Phys 2015;143:243154. [DOI: 10.1063/1.4938172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
30
Where the complex things are: single molecule and ensemble spectroscopic investigations of protein folding dynamics. Curr Opin Struct Biol 2015;36:1-9. [PMID: 26687767 DOI: 10.1016/j.sbi.2015.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 11/10/2015] [Indexed: 01/11/2023]
31
Gavrilov Y, Hagai T, Levy Y. Nonspecific yet decisive: Ubiquitination can affect the native-state dynamics of the modified protein. Protein Sci 2015;24:1580-92. [PMID: 25970168 DOI: 10.1002/pro.2688] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 04/05/2015] [Indexed: 11/10/2022]
32
A simple theoretical model goes a long way in explaining complex behavior in protein folding. Proc Natl Acad Sci U S A 2014;111:15863-4. [PMID: 25349434 DOI: 10.1073/pnas.1418039111] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
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