Research Paper on Dissecting Several Pathways in the Helix’s Relaxation Dynamics == Optimal dimension-reduction coil transitions

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Title: Dissecting Several Pathways in the Helix’s Relaxation Dynamics == Optimal dimension-reduction coil transitions

Abstract: Understanding the fundamental processes in protein folding pathways involving the formation of a-helices and b-hairpins, contact formation, and overall collapse of the peptide chain has benefited greatly from fast kinetic experiments with dramatically improved time resolution. The key to this understanding was the application of a straightforward statistical mechanical model to the interpretation of experimental results. It was difficult to describe all of the events that were seen in the experimental results atomically. An atomically precise description of kinetics, examining folding pathways, validating experimental findings, and reporting new findings for a wide range of molecular processes in biophysical chemistry were made possible by recent theoretical advances, more complex algorithms, and a true long-term trajectory. This review explains how optimum dimensionality reduction theory can create a low-dimensional, simplified coarse-grained model with a kinetic matrix that captures brand-new information about folding pathways. Following transition pathway analysis, a set of metastable states from molecular dynamics analysis creates an optimally reduced dimensionality rate matrix. The validity of the combined approach is confirmed by analysis of the actual long-term simulation trajectory, which yields a relaxation time that is directly comparable to the experimental findings. Several examples of helix ==> coil transition pathways are used to discuss and illustrate how the theory is applied. Our ongoing research is the main focus of this paper, which combines time-resolved experiments and long-term molecular dynamics simulation.

Keywords: laser temperature jump; molecular dynamics; dimensionality reduction; kinetics

Paper Quality: SCOPUS / Web of Science Level Research Paper

Subject: Biomolecules

Writer Experience: 20+ Years

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