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Dahlstrom TJ, Capraro DT, Jennings PA, Finke JM. Knotting Optimization and Folding Pathways of a Go-Model with a Deep Knot. J Phys Chem B 2022; 126:10221-10236. [PMID: 36424347 DOI: 10.1021/acs.jpcb.2c05588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Formation of protein knots is an intriguing offshoot of the protein folding problem. Since experimental resolution on knot formation is limited, theoretical methods currently provide the most detailed insights into the knotting process. While suitable for shallow knots, molecular dynamics simulations have faced challenges capturing the formation of deep knots in proteins such as the minimally tied trefoil α/β methyltransferase from Thermotoga maritima (MTTTM). To improve the efficiency of MTTTM knotting in Cα Go-model simulations, mutant variants of the MTTTM Go-model were investigated. Through a structure-based analysis of knotted and unknotted states, four residues (K71, R72, E75, V76) were identified to increase the knotting efficiency from 2% to 83% when their contact energies were doubled and dihedral strength around the knot loop increased. The key features of this model are (i) a C-terminal slipknot intermediate that threads the knot in a highly unstructured intermediate, (ii) the inability to knot in native-like intermediate states, and (iii) a minor population in a long-lived trap that cannot knot. Examination of residue 71-76 contacts provides a small set of potential mutants that can directly test the model's validity. In addition, the knotting optimization process developed here has broad applicability in generating knotting-efficient models of other knotted proteins.
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Affiliation(s)
- Thomas J Dahlstrom
- Division of Sciences and Mathematics, Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, Washington98402, United States
| | - Dominique T Capraro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California92093, United States
| | - Particia A Jennings
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California92093, United States
| | - John M Finke
- Division of Sciences and Mathematics, Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, Washington98402, United States
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Piana S, Lindorff-Larsen K, Shaw DE. Atomistic Description of the Folding of a Dimeric Protein. J Phys Chem B 2013; 117:12935-42. [DOI: 10.1021/jp4020993] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefano Piana
- D. E. Shaw Research, New York, New York
10036, United States
| | | | - David E. Shaw
- D. E. Shaw Research, New York, New York
10036, United States
- Center
for Computational Biology
and Bioinformatics, Columbia University, New York, New York 10032, United States
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Zhang P, Li G. Structural relaxation behavior of strain hardened shape memory polymer fibers for self-healing applications. ACTA ACUST UNITED AC 2013. [DOI: 10.1002/polb.23295] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Pengfei Zhang
- Department of Mechanical and Industrial Engineering; Louisiana State University; Baton Rouge Louisiana 70803
| | - Guoqiang Li
- Department of Mechanical and Industrial Engineering; Louisiana State University; Baton Rouge Louisiana 70803
- Department of Mechanical Engineering; Southern University; Baton Rouge Louisiana 70813
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Larriva M, Prieto L, Bruscolini P, Rey A. A simple simulation model can reproduce the thermodynamic folding intermediate of apoflavodoxin. Proteins 2009; 78:73-82. [DOI: 10.1002/prot.22521] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Tellez LA, Blancas-Mejia LM, Carrillo-Nava E, Mendoza-Hernández G, Cisneros DA, Fernández-Velasco DA. Thermal Unfolding of Triosephosphate Isomerase from Entamoeba histolytica: Dimer Dissociation Leads to Extensive Unfolding. Biochemistry 2008; 47:11665-73. [DOI: 10.1021/bi801360k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luis A. Tellez
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - Luis M. Blancas-Mejia
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - Ernesto Carrillo-Nava
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - Guillermo Mendoza-Hernández
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - David A. Cisneros
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - D. Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
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Gu Z, Rao MK, Forsyth WR, Finke JM, Matthews CR. Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Gō model simulation. J Mol Biol 2007; 374:528-46. [PMID: 17942114 DOI: 10.1016/j.jmb.2007.09.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 09/06/2007] [Accepted: 09/07/2007] [Indexed: 10/22/2022]
Abstract
The structures of partially folded states appearing during the folding of a (betaalpha)(8) TIM barrel protein, the indole-3-glycerol phosphate synthase from Sulfolobus solfataricus (sIGPS), was assessed by hydrogen exchange mass spectrometry (HX-MS) and Gō model simulations. HX-MS analysis of the peptic peptides derived from the pulse-labeled product of the sub-millisecond folding reaction from the urea-denatured state revealed strong protection in the (betaalpha)(4) region, modest protection in the neighboring (betaalpha)(1-3) and (betaalpha)(5)beta(6) segments and no significant protection in the remaining N and C-terminal segments. These results demonstrate that this species is not a collapsed form of the unfolded state under native-favoring conditions nor is it the native state formed via fast-track folding. However, the striking contrast of these results with the strong protection observed in the (betaalpha)(2-5)beta(6) region after 5 s of folding demonstrates that these species represent kinetically distinct folding intermediates that are not identical as previously thought. A re-examination of the kinetic folding mechanism by chevron analysis of fluorescence data confirmed distinct roles for these two species: the burst-phase intermediate is predicted to be a misfolded, off-pathway intermediate, while the subsequent 5 s intermediate corresponds to an on-pathway equilibrium intermediate. Comparison with the predictions using a C(alpha) Gō model simulation of the kinetic folding reaction for sIGPS shows good agreement with the core of the structure offering protection against exchange in the on-pathway intermediate(s). Because the native-centric Gō model simulations do not explicitly include sequence-specific information, the simulation results support the hypothesis that the topology of TIM barrel proteins is a primary determinant of the folding free energy surface for the productive folding reaction. The early misfolding reaction must involve aspects of non-native structure not detected by the Gō model simulation.
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Affiliation(s)
- Zhenyu Gu
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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