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• W3199698544 endingPage "1351" @default.
• W3199698544 startingPage "1351" @default.
• W3199698544 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." @default.
• W3199698544 created "2021-09-27" @default.
• W3199698544 creator A5016207344 @default.
• W3199698544 creator A5060120854 @default.
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• W3199698544 creator A5069970299 @default.
• W3199698544 date "2021-09-12" @default.
• W3199698544 modified "2023-10-11" @default.
• W3199698544 title "Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction" @default.
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• W3199698544 doi "https://doi.org/10.3390/biom11091351" @default.
• W3199698544 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/8471320" @default.
• W3199698544 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/34572564" @default.
• W3199698544 hasPublicationYear "2021" @default.
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