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For: Hsu STD. Folding and functions of knotted proteins. Curr Opin Struct Biol 2023;83:102709. [PMID: 37778185 DOI: 10.1016/j.sbi.2023.102709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023]
Number Cited by Other Article(s)
1
Thakuria S, Paul S. Discrepant Effects of Hydrated and Neat Reline on the Conformational Stability of a Knotted Protein. J Phys Chem B 2025;129:4629-4640. [PMID: 40310665 DOI: 10.1021/acs.jpcb.5c00148] [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: 05/02/2025]
2
Takezawa H, Tamura Y, Fujita M. Step-by-Step Self-Assembly of a Double-Walled Knotted Cage With Increasing Topological Complexity. Chemistry 2025;31:e202500009. [PMID: 40153241 PMCID: PMC12080300 DOI: 10.1002/chem.202500009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2025] [Revised: 03/27/2025] [Accepted: 03/28/2025] [Indexed: 03/30/2025]
3
Vatin M, Orlandini E, Locatelli E. Upsurge of Spontaneous Knotting in Polar Diblock Active Polymers. PHYSICAL REVIEW LETTERS 2025;134:168301. [PMID: 40344114 DOI: 10.1103/physrevlett.134.168301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 02/12/2025] [Accepted: 03/12/2025] [Indexed: 05/11/2025]
4
Begun AM, Korneev AA, Zorina AV. Effect of a Knot on the Thermal Stability of Protein MJ0366: Insights into Molecular Dynamics and Monte Carlo Simulations. J Phys Chem B 2025;129:3939-3947. [PMID: 40208585 DOI: 10.1021/acs.jpcb.4c07910] [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: 04/11/2025]
5
Zhang H, Jackson SE. Folding of a tandemly knotted protein: Evidence that a polypeptide chain can get out of deep kinetic traps. Protein Sci 2025;34:e70048. [PMID: 39969078 PMCID: PMC11837048 DOI: 10.1002/pro.70048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 01/15/2025] [Accepted: 01/20/2025] [Indexed: 02/20/2025]
6
Thakuria S, Paul S. Salt-bridge mediated conformational dynamics in the figure-of-eight knotted ketol acid reductoisomerase (KARI). Phys Chem Chem Phys 2024;26:24963-24974. [PMID: 39297222 DOI: 10.1039/d4cp02677b] [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: 10/03/2024]
7
Perlinska AP, Sikora M, Sulkowska JI. Everything AlphaFold tells us about protein knots. J Mol Biol 2024;436:168715. [PMID: 39029890 DOI: 10.1016/j.jmb.2024.168715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/29/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
8
Ferreira SGF, Sriramoju MK, Hsu STD, Faísca PFN, Machuqueiro M. Is There a Functional Role for the Knotted Topology in Protein UCH-L1? J Chem Inf Model 2024;64:6827-6837. [PMID: 39045738 PMCID: PMC11388461 DOI: 10.1021/acs.jcim.4c00880] [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: 07/25/2024]
9
Rubach P, Sikora M, Jarmolinska A, Perlinska A, Sulkowska J. AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models. Nucleic Acids Res 2024;52:W187-W193. [PMID: 38842945 PMCID: PMC11223836 DOI: 10.1093/nar/gkae443] [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: 03/16/2024] [Revised: 04/29/2024] [Accepted: 05/10/2024] [Indexed: 07/06/2024]  Open
10
Sikora M, Klimentova E, Uchal D, Sramkova D, Perlinska AP, Nguyen ML, Korpacz M, Malinowska R, Nowakowski S, Rubach P, Simecek P, Sulkowska JI. Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model. Protein Sci 2024;33:e4998. [PMID: 38888487 PMCID: PMC11184937 DOI: 10.1002/pro.4998] [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: 12/04/2023] [Revised: 03/14/2024] [Accepted: 04/09/2024] [Indexed: 06/20/2024]
11
Gren BA, Antczak M, Zok T, Sulkowska JI, Szachniuk M. Knotted artifacts in predicted 3D RNA structures. PLoS Comput Biol 2024;20:e1011959. [PMID: 38900780 PMCID: PMC11218946 DOI: 10.1371/journal.pcbi.1011959] [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: 03/08/2024] [Revised: 07/02/2024] [Accepted: 06/01/2024] [Indexed: 06/22/2024]  Open
12
Sriramoju MK, Ko KT, Hsu STD. Tying a true topological protein knot by cyclization. Biochem Biophys Res Commun 2024;696:149470. [PMID: 38244314 DOI: 10.1016/j.bbrc.2024.149470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024]
13
Hsu MF, Sriramoju MK, Lai CH, Chen YR, Huang JS, Ko TP, Huang KF, Hsu STD. Structure, dynamics, and stability of the smallest and most complex 71 protein knot. J Biol Chem 2024;300:105553. [PMID: 38072060 PMCID: PMC10840475 DOI: 10.1016/j.jbc.2023.105553] [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: 06/29/2023] [Revised: 11/21/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023]  Open
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