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Cosolvent effects on the growth of protein aggregates formed by a single domain globular protein and an intrinsically disordered protein

Mondal, B and Reddy, G (2019) Cosolvent effects on the growth of protein aggregates formed by a single domain globular protein and an intrinsically disordered protein. In: Journal of Physical Chemistry B .

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Official URL: https://doi.org/10.1021/acs.jpcb.8b11128

Abstract

Cosolvents modulate the stability of protein conformations and exhibit contrasting effects on the kinetics of aggregation by globular proteins and intrinsically disordered proteins (IDPs). The growth of ordered protein aggregates after the initial nucleation step is believed to proceed through a dock-lock mechanism. We have studied the effect of two denaturants guanidinium chloride (GdmCl) and urea and four protective osmolytes (trimethylamine N-oxide (TMAO), sucrose, sarcosine, and sorbitol) on the free energy surface (FES) of the dock-lock growth step of protein aggregation using a coarse-grained protein model and metadynamics simulations. We have used the proteins cSrc-SH3 and Aβ 9-40 as model systems representing globular proteins and IDPs, respectively. The effect of cosolvents on protein conformations is taken into account using the molecular transfer model (MTM). The computed FES shows that protective osmolytes stabilize the compact aggregates, while denaturants destabilize them for both cSrc-SH3 and Aβ 9-40 . However, protective osmolytes increase the effective energy barrier for the multistep domain-swapped dimerization of cSrc-SH3, which is critical to the growth of protein aggregates by globular proteins, thus slowing down the overall aggregation rate. Contrastingly, denaturants decrease the effective barrier height for cSrc-SH3 dimerization and hence enhance the aggregation rate in globular proteins. The simulations further show that cSrc-SH3 monomers unfold before dimerization and the barrier to monomer unfolding regulates the effective rate of aggregation. In the case of IDP, Aβ 9-40 , protective osmolytes decrease and denaturants increase the effective barriers in the dock-lock mechanism of fibril growth, leading to faster and slower growth kinetics, respectively. © 2019 American Chemical Society.

Item Type: Journal Article
Additional Information: Copyright for this article belongs to American Chemical Society.
Keywords: Aggregates; Chlorine compounds; Conformations; Dimerization; Docks; Free energy; Growth kinetics; Hydraulic structures; Locks (fasteners); Monomers; Proteins; Urea, Effective barrier heights; Free energy surface; Guanidinium chlorides; Intrinsically disordered proteins; Metadynamics simulations; Protein aggregation; Protein conformation; Trimethylamine N oxides, Agglomeration
Department/Centre: Division of Chemical Sciences > Solid State & Structural Chemistry Unit
Depositing User: Id for Latest eprints
Date Deposited: 08 Apr 2019 11:51
Last Modified: 08 Apr 2019 11:51
URI: http://eprints.iisc.ac.in/id/eprint/62028

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