Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms

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题名:	Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms
作者:	賴山強;Hsu, P. J.;Cheong, S. A.;Lai, S. K.
贡献者:	理學院物理學系
关键词:	ATOMS;Computer simulation;Correlation analysis;FLUCTUATIONS;Folding;INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY;MATHEMATICAL METHODS AND COMPUTING;Molecular dynamics;MOLECULAR DYNAMICS METHOD;Molecular Dynamics Simulation;Nuclear Magnetic Resonance, Biomolecular;Protein Folding;Protein Structure, Secondary;Protein Unfolding;PROTEINS;Proteins - chemistry;Sequences;Shape recognition;Signatures;SIMULATION;Thermodynamics;Time series;Variations
日期:	2014-05-28
上传时间:	2026-04-23 12:40:45 (UTC+8)
出版者:	American Institute of Physics;United States: American Institute of Physics
摘要:	摘要： Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1) ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with α helix and β hairpin, but also the important role played by weaker correlations in such protein folding dynamics. 其他題名： J Chem Phys 出版者： United States: American Institute of Physics 出版日期： 2014-05-28 出處： The Journal of chemical physics, 2014-05, Vol.140 (20), p.204905 資源來源： AIP Journals (American Institute of Physics) 版權： 2014 AIP Publishing LLC. 識別號： ISSN: 0021-9606 識別號： ISSN: 1089-7690 識別號： ISSN: 1520-9032 識別號： EISSN: 1089-7690 識別號： DOI: 10.1063/1.4875802 識別號： PMID: 24880323
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