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Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction
dc.contributor.author | Jas, Gouri S. | |
dc.contributor.author | Childs, Ed W. | |
dc.contributor.author | Middaugh, C. Russell | |
dc.contributor.author | Kuczera, Krzysztof | |
dc.date.accessioned | 2021-12-01T22:21:41Z | |
dc.date.available | 2021-12-01T22:21:41Z | |
dc.date.issued | 2021-09-12 | |
dc.identifier.citation | Jas, G.S.; Childs, E.W.; Middaugh, C.R.; Kuczera, K. Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction. Biomolecules 2021, 11, 1351. https://doi.org/10.3390/biom11091351 | en_US |
dc.identifier.uri | http://hdl.handle.net/1808/32234 | |
dc.description.abstract | Fast kinetic experiments with dramatically improved time resolution have contributed significantly to understanding the fundamental processes in protein folding pathways involving the formation of a-helices and b-hairpin, contact formation, and overall collapse of the peptide chain. Interpretation of experimental results through application of a simple statistical mechanical model was key to this understanding. Atomistic description of all events observed in the experimental findings was challenging. Recent advancements in theory, more sophisticated algorithms, and a true long-term trajectory made way for an atomically detailed description of kinetics, examining folding pathways, validating experimental results, and reporting new findings for a wide range of molecular processes in biophysical chemistry. This review describes how optimum dimensionality reduction theory can construct a simplified coarse-grained model with low dimensionality involving a kinetic matrix that captures novel insights into folding pathways. A set of metastable states derived from molecular dynamics analysis generate an optimally reduced dimensionality rate matrix following transition pathway analysis. Analysis of the actual long-term simulation trajectory extracts a relaxation time directly comparable to the experimental results and confirms the validity of the combined approach. The application of the theory is discussed and illustrated using several examples of helix <==> coil transition pathways. This paper focuses primarily on a combined approach of time-resolved experiments and long-term molecular dynamics simulation from our ongoing work. | en_US |
dc.publisher | MDPI | en_US |
dc.rights | Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This work is licensed under a Creative Commons Attribution 4.0 International License. | en_US |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | en_US |
dc.subject | Laser temperature jump | en_US |
dc.subject | Molecular dynamics | en_US |
dc.subject | Dimensionality reduction | en_US |
dc.subject | Kinetics | en_US |
dc.title | Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction | en_US |
dc.type | Article | en_US |
kusw.kuauthor | Jas, Gouri S. | |
kusw.kuauthor | Middaugh, C. Russell | |
kusw.kuauthor | Kuczera, Krzysztof | |
kusw.kudepartment | Pharmaceutical Chemistry | en_US |
kusw.kudepartment | Chemistry | en_US |
kusw.kudepartment | Molecular Biosciences | en_US |
dc.identifier.doi | 10.3390/biom11091351 | en_US |
dc.identifier.orcid | https://orcid.org/ 0000-0002-0774-012X | en_US |
dc.identifier.orcid | https://orcid.org/ 0000-0003-2358-1349 | en_US |
kusw.oaversion | Scholarly/refereed, publisher version | en_US |
kusw.oapolicy | This item meets KU Open Access policy criteria. | en_US |
dc.identifier.pmid | PMC8471320 | en_US |
dc.rights.accessrights | openAccess | en_US |