Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L

Maity, H and Reddy, G (2018) Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L. In: Journal of Chemical Physics, 148 (16).

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Abstract

Small single-domain globular proteins, which are believed to be dominantly two-state folders, played an important role in elucidating various aspects of the protein folding mechanism. However, recent single molecule fluorescence resonance energy transfer experiments H. Y. Aviram et al. J. Chem. Phys. 148, 123303 (2018) on a single-domain two-state folding protein L showed evidence for the population of an intermediate state and it was suggested that in this state, a β-hairpin present near the C-terminal of the native protein state is unfolded. We performed molecular dynamics simulations using a coarse-grained self-organized-polymer model with side chains to study the folding pathways of protein L. In agreement with the experiments, an intermediate is populated in the simulation folding pathways where the C-terminal β-hairpin detaches from the rest of the protein structure. The lifetime of this intermediate structure increased with the decrease in temperature. In low temperature conditions, we also observed a second intermediate state, which is globular with a significant fraction of the native-like tertiary contacts satisfying the features of a dry molten globule.

Item Type:	Journal Article
Publication:	Journal of Chemical Physics
Publisher:	American Institute of Physics Inc.
Additional Information:	The copyright for this article belongs to the American Institute of Physics Inc.
Keywords:	Bioinformatics; Energy transfer; Fluorescence; Molecular dynamics; Temperature, Intermediate state; Intermediate structures; Low temperature conditions; Molecular dynamics simulations; Protein folding mechanisms; Protein structures; Single molecule fluorescence; Transient intermediate, Proteins, protein, chemistry; molecular dynamics; protein domain; protein folding; temperature, Molecular Dynamics Simulation; Protein Domains; Protein Folding; Proteins; Temperature
Department/Centre:	Division of Chemical Sciences > Solid State & Structural Chemistry Unit
Date Deposited:	08 Aug 2022 06:29
Last Modified:	08 Aug 2022 06:29
URI:	https://eprints.iisc.ac.in/id/eprint/75571

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