Dissecting Protein Configurational Entropy into Conformational and Vibrational Contributions

The Journal of Physical Chemistry. B
Song-Ho Chong, Sihyun Ham

Abstract

Quantifying how the rugged nature of the underlying free-energy landscape determines the entropic cost a protein must incur upon folding and ligand binding is a challenging problem. Here, we present a novel computational approach that dissects the protein configurational entropy on the basis of the classification of protein dynamics on the landscape into two separate components: short-term vibrational dynamics related to individual free-energy wells and long-term conformational dynamics associated with transitions between wells. We apply this method to separate the configurational entropy of the protein villin headpiece subdomain into its conformational and vibrational components. We find that the change in configurational entropy upon folding is dominated by the conformational entropy despite the fact that the magnitude of the vibrational entropy is the significantly larger component in each of the folded and unfolded states, which is in accord with the previous empirical estimations. The straightforward applicability of our method to unfolded proteins promises a wide range of applications, including those related to intrinsically disordered proteins.

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Citations

May 7, 2016·Journal of Chemical Theory and Computation·Song-Ho Chong, Sihyun Ham
Dec 21, 2016·Journal of Chemical Information and Modeling·Ido Y Ben-ShalomHolger Gohlke
Mar 30, 2017·Journal of Chemical Theory and Computation·Holger GohlkeKarl-Heinz Baringhaus
Feb 23, 2017·Annual Review of Physical Chemistry·Song-Ho ChongSihyun Ham
Jun 1, 2016·Physical Chemistry Chemical Physics : PCCP·Kaushik ChakrabortySanjoy Bandyopadhyay
Oct 24, 2017·Soft Matter·Fernando Vargas-LaraJack F Douglas
Oct 19, 2019·Scientific Reports·Song-Ho Chong, Sihyun Ham
May 10, 2018·Scientific Reports·Song-Ho Chong, Sihyun Ham
May 5, 2021·The Journal of Physical Chemistry. B·Tawny N Fajardo, Matthias Heyden
Jun 25, 2021·The Journal of Physical Chemistry. B·Myung Keun ChoSihyun Ham
Dec 9, 2020·Journal of Chemical Theory and Computation·Changwon YangYoungshang Pak
Sep 22, 2020·Journal of Chemical Information and Modeling·Arghya ChakravortyRichard H Henchman

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