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Title: Entropy and enthalpy of interaction between amino acid side chains in nanopores

Abstract

Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between the side chain pairs ALA-PHE, SER-ASN, and LYS-GLU in bulk water and in water-filled nanopores. The temperature dependence of the bulk solvent potentials of mean force and the interaction free energies in cylindrical and spherical nanopores is used to identify the corresponding entropic and enthalpic components. The entropically stabilized hydrophobic interaction between ALA and PHE in bulk water is enthalpically dominated upon confinement depending on the relative orientations between the side chains. In the case of SER-ASN, hydrogen bonded configurations that are similar in bulk water are thermodynamically distinct in a cylindrical pore, thus making rotamer distributions different from those in the bulk. Remarkably, salt bridge formation between LYS-GLU is stabilized by entropy in contrast to the bulk. Implications of our findings for confinement-induced alterations in protein stability are briefly outlined.

Authors:
 [1];  [1];  [2]
  1. Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742 (United States)
  2. (United States)
Publication Date:
OSTI Identifier:
22413314
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 141; Journal Issue: 22; Other Information: (c) 2014 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; AMINO ACIDS; ENTHALPY; ENTROPY; FREE ENERGY; INTERACTIONS; MOLECULAR DYNAMICS METHOD; SIMULATION; SOLVENTS; STABILITY; TEMPERATURE DEPENDENCE; WATER

Citation Formats

Vaitheeswaran, S., E-mail: vaithee05@gmail.com, Thirumalai, D., and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742. Entropy and enthalpy of interaction between amino acid side chains in nanopores. United States: N. p., 2014. Web. doi:10.1063/1.4901204.
Vaitheeswaran, S., E-mail: vaithee05@gmail.com, Thirumalai, D., & Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742. Entropy and enthalpy of interaction between amino acid side chains in nanopores. United States. doi:10.1063/1.4901204.
Vaitheeswaran, S., E-mail: vaithee05@gmail.com, Thirumalai, D., and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742. 2014. "Entropy and enthalpy of interaction between amino acid side chains in nanopores". United States. doi:10.1063/1.4901204.
@article{osti_22413314,
title = {Entropy and enthalpy of interaction between amino acid side chains in nanopores},
author = {Vaitheeswaran, S., E-mail: vaithee05@gmail.com and Thirumalai, D. and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742},
abstractNote = {Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between the side chain pairs ALA-PHE, SER-ASN, and LYS-GLU in bulk water and in water-filled nanopores. The temperature dependence of the bulk solvent potentials of mean force and the interaction free energies in cylindrical and spherical nanopores is used to identify the corresponding entropic and enthalpic components. The entropically stabilized hydrophobic interaction between ALA and PHE in bulk water is enthalpically dominated upon confinement depending on the relative orientations between the side chains. In the case of SER-ASN, hydrogen bonded configurations that are similar in bulk water are thermodynamically distinct in a cylindrical pore, thus making rotamer distributions different from those in the bulk. Remarkably, salt bridge formation between LYS-GLU is stabilized by entropy in contrast to the bulk. Implications of our findings for confinement-induced alterations in protein stability are briefly outlined.},
doi = {10.1063/1.4901204},
journal = {Journal of Chemical Physics},
number = 22,
volume = 141,
place = {United States},
year = 2014,
month =
}
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