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For: Lou SC, Wetzel S, Zhang H, Crone EW, Lee YT, Jackson SE, Hsu STD. The Knotted Protein UCH-L1 Exhibits Partially Unfolded Forms under Native Conditions that Share Common Structural Features with Its Kinetic Folding Intermediates. J Mol Biol 2016;428:2507-2520. [PMID: 27067109 DOI: 10.1016/j.jmb.2016.04.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/22/2016] [Accepted: 04/02/2016] [Indexed: 10/22/2022]
Number Cited by Other Article(s)
1
Lai CH, Ko KT, Fan PJ, Yu TA, Chang CF, Draczkowski P, Hsu STD. Structural insight into the ZFAND1-p97 interaction involved in stress granule clearance. J Biol Chem 2024;300:107230. [PMID: 38537699 PMCID: PMC11047754 DOI: 10.1016/j.jbc.2024.107230] [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: 12/22/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]  Open
2
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]
3
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
4
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: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023]
5
Salicari L, Baiesi M, Orlandini E, Trovato A. Folding kinetics of an entangled protein. PLoS Comput Biol 2023;19:e1011107. [PMID: 37956216 PMCID: PMC10681328 DOI: 10.1371/journal.pcbi.1011107] [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: 04/16/2023] [Revised: 11/27/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023]  Open
6
Doyle LA, Takushi B, Kibler RD, Milles LF, Orozco CT, Jones JD, Jackson SE, Stoddard BL, Bradley P. De novo design of knotted tandem repeat proteins. Nat Commun 2023;14:6746. [PMID: 37875492 PMCID: PMC10598012 DOI: 10.1038/s41467-023-42388-y] [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: 04/17/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]  Open
7
Kumar P, Kumar P, Mandal D, Velayutham R. The emerging role of Deubiquitinases (DUBs) in parasites: A foresight review. Front Cell Infect Microbiol 2022;12:985178. [PMID: 36237424 PMCID: PMC9552668 DOI: 10.3389/fcimb.2022.985178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022]  Open
8
Puri S, Chiu YH, Draczkowski P, Ko KT, Yang TJ, Wang YS, Uchiyama S, Danny Hsu ST. Impacts of cancer-associated mutations on the structure-activity relationship of BAP1. J Mol Biol 2022;434:167553. [DOI: 10.1016/j.jmb.2022.167553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/24/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
9
Puri S, Hsu STD. Elucidation of folding pathways of knotted proteins. Methods Enzymol 2022;675:275-297. [DOI: 10.1016/bs.mie.2022.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
10
Nguyen TT, Marzolf DR, Seffernick JT, Heinze S, Lindert S. Protein structure prediction using residue-resolved protection factors from hydrogen-deuterium exchange NMR. Structure 2021;30:313-320.e3. [PMID: 34739840 DOI: 10.1016/j.str.2021.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/04/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022]
11
Fonseka HYY, Javidi A, Oliveira LFL, Micheletti C, Stan G. Unfolding and Translocation of Knotted Proteins by Clp Biological Nanomachines: Synergistic Contribution of Primary Sequence and Topology Revealed by Molecular Dynamics Simulations. J Phys Chem B 2021;125:7335-7350. [PMID: 34110163 DOI: 10.1021/acs.jpcb.1c00898] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
12
Hsu STD, Lee YTC, Mikula KM, Backlund SM, Tascón I, Goldman A, Iwaï H. Tying up the Loose Ends: A Mathematically Knotted Protein. Front Chem 2021;9:663241. [PMID: 34109153 PMCID: PMC8182377 DOI: 10.3389/fchem.2021.663241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022]  Open
13
Paissoni C, Puri S, Wang I, Chen SY, Camilloni C, Hsu STD. Converging experimental and computational views of the knotting mechanism of a small knotted protein. Biophys J 2021;120:2276-2286. [PMID: 33812848 PMCID: PMC8390826 DOI: 10.1016/j.bpj.2021.03.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/14/2021] [Accepted: 03/29/2021] [Indexed: 01/18/2023]  Open
14
Cross-over Loop Cysteine C152 Acts as an Antioxidant to Maintain the Folding Stability and Deubiquitinase Activity of UCH-L1 Under Oxidative Stress. J Mol Biol 2021;433:166879. [PMID: 33617897 DOI: 10.1016/j.jmb.2021.166879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/07/2021] [Accepted: 02/12/2021] [Indexed: 11/20/2022]
15
Molecular Mechanisms of DUBs Regulation in Signaling and Disease. Int J Mol Sci 2021;22:ijms22030986. [PMID: 33498168 PMCID: PMC7863924 DOI: 10.3390/ijms22030986] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023]  Open
16
Rivera M, Hao Y, Maillard RA, Baez M. Mechanical unfolding of a knotted protein unveils the kinetic and thermodynamic consequences of threading a polypeptide chain. Sci Rep 2020;10:9562. [PMID: 32533020 PMCID: PMC7292828 DOI: 10.1038/s41598-020-66258-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 05/12/2020] [Indexed: 12/21/2022]  Open
17
Sulkowska JI. On folding of entangled proteins: knots, lassos, links and θ-curves. Curr Opin Struct Biol 2020;60:131-141. [PMID: 32062143 DOI: 10.1016/j.sbi.2020.01.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/02/2020] [Accepted: 01/12/2020] [Indexed: 12/15/2022]
18
Perego C, Potestio R. Computational methods in the study of self-entangled proteins: a critical appraisal. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019;31:443001. [PMID: 31269476 DOI: 10.1088/1361-648x/ab2f19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
19
Sen S, Udgaonkar JB. Binding-induced folding under unfolding conditions: Switching between induced fit and conformational selection mechanisms. J Biol Chem 2019;294:16942-16952. [PMID: 31582563 DOI: 10.1074/jbc.ra119.009742] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/14/2019] [Indexed: 12/11/2022]  Open
20
Ko KT, Hu IC, Huang KF, Lyu PC, Hsu STD. Untying a Knotted SPOUT RNA Methyltransferase by Circular Permutation Results in a Domain-Swapped Dimer. Structure 2019;27:1224-1233.e4. [DOI: 10.1016/j.str.2019.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/01/2019] [Accepted: 04/05/2019] [Indexed: 11/28/2022]
21
Topological descriptions of protein folding. Proc Natl Acad Sci U S A 2019;116:9360-9369. [PMID: 31000594 PMCID: PMC6510998 DOI: 10.1073/pnas.1808312116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
22
He C, Li S, Gao X, Xiao A, Hu C, Hu X, Hu X, Li H. Direct observation of the fast and robust folding of a slipknotted protein by optical tweezers. NANOSCALE 2019;11:3945-3951. [PMID: 30762052 DOI: 10.1039/c8nr10070e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
23
Sivertsson EM, Jackson SE, Itzhaki LS. The AAA+ protease ClpXP can easily degrade a 31 and a 52-knotted protein. Sci Rep 2019;9:2421. [PMID: 30787316 PMCID: PMC6382783 DOI: 10.1038/s41598-018-38173-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 12/04/2018] [Indexed: 12/16/2022]  Open
24
Untying a Protein Knot by Circular Permutation. J Mol Biol 2019;431:857-863. [DOI: 10.1016/j.jmb.2019.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 01/13/2023]
25
Jarmolinska AI, Perlinska AP, Runkel R, Trefz B, Ginn HM, Virnau P, Sulkowska JI. Proteins' Knotty Problems. J Mol Biol 2018;431:244-257. [PMID: 30391297 DOI: 10.1016/j.jmb.2018.10.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/20/2022]
26
Sriramoju MK, Chen Y, Lee YTC, Hsu STD. Topologically knotted deubiquitinases exhibit unprecedented mechanostability to withstand the proteolysis by an AAA+ protease. Sci Rep 2018;8:7076. [PMID: 29728659 PMCID: PMC5935755 DOI: 10.1038/s41598-018-25470-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/23/2018] [Indexed: 01/03/2023]  Open
27
Lee YTC, Hsu STD. A Natively Monomeric Deubiquitinase UCH-L1 Forms Highly Dynamic but Defined Metastable Oligomeric Folding Intermediates. J Phys Chem Lett 2018;9:2433-2437. [PMID: 29688017 DOI: 10.1021/acs.jpclett.8b00815] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
28
Zhao Y, Dabrowski-Tumanski P, Niewieczerzal S, Sulkowska JI. The exclusive effects of chaperonin on the behavior of proteins with 52 knot. PLoS Comput Biol 2018;14:e1005970. [PMID: 29547629 PMCID: PMC5874080 DOI: 10.1371/journal.pcbi.1005970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/28/2018] [Accepted: 01/12/2018] [Indexed: 02/05/2023]  Open
29
Soler MA, Rey A, Faísca PFN. Steric confinement and enhanced local flexibility assist knotting in simple models of protein folding. Phys Chem Chem Phys 2018;18:26391-26403. [PMID: 27722468 DOI: 10.1039/c6cp05086g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
30
Sulkowska JI, Sułkowski P. Entangled Proteins: Knots, Slipknots, Links, and Lassos. SPRINGER SERIES IN SOLID-STATE SCIENCES 2018. [DOI: 10.1007/978-3-319-76596-9_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
31
Dabrowski-Tumanski P, Sulkowska JI. To Tie or Not to Tie? That Is the Question. Polymers (Basel) 2017;9:E454. [PMID: 30965758 PMCID: PMC6418553 DOI: 10.3390/polym9090454] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 12/18/2022]  Open
32
Lactose Binding Induces Opposing Dynamics Changes in Human Galectins Revealed by NMR-Based Hydrogen-Deuterium Exchange. Molecules 2017;22:molecules22081357. [PMID: 28813004 PMCID: PMC6152064 DOI: 10.3390/molecules22081357] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 11/17/2022]  Open
33
Zhang H, Jackson SE. Characterization of the Folding of a 52-Knotted Protein Using Engineered Single-Tryptophan Variants. Biophys J 2017;111:2587-2599. [PMID: 28002735 DOI: 10.1016/j.bpj.2016.10.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 10/20/2016] [Accepted: 10/20/2016] [Indexed: 11/16/2022]  Open
34
Lee YTC, Chang CY, Chen SY, Pan YR, Ho MR, Hsu STD. Entropic stabilization of a deubiquitinase provides conformational plasticity and slow unfolding kinetics beneficial for functioning on the proteasome. Sci Rep 2017;7:45174. [PMID: 28338014 PMCID: PMC5364529 DOI: 10.1038/srep45174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/20/2017] [Indexed: 02/07/2023]  Open
35
Hsu STD. Protein knotting through concatenation significantly reduces folding stability. Sci Rep 2016;6:39357. [PMID: 27982106 PMCID: PMC5159899 DOI: 10.1038/srep39357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/22/2016] [Indexed: 12/24/2022]  Open
36
Jackson SE, Suma A, Micheletti C. How to fold intricately: using theory and experiments to unravel the properties of knotted proteins. Curr Opin Struct Biol 2016;42:6-14. [PMID: 27794211 DOI: 10.1016/j.sbi.2016.10.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/06/2016] [Accepted: 10/03/2016] [Indexed: 11/15/2022]
37
Folding analysis of the most complex Stevedore's protein knot. Sci Rep 2016;6:31514. [PMID: 27527519 PMCID: PMC4985754 DOI: 10.1038/srep31514] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/21/2016] [Indexed: 12/21/2022]  Open
38
Knotting and unknotting of a protein in single molecule experiments. Proc Natl Acad Sci U S A 2016;113:7533-8. [PMID: 27339135 DOI: 10.1073/pnas.1600614113] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
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