Assessing backbone solvation effects in the conformational propensities of amino acid residues in unfolded peptides

Physical Chemistry Chemical Physics : PCCP
Niranjan V IlaweBryan M Wong

Abstract

Conformational ensembles of individual amino acid residues within model GxG peptides (x representing different amino acid residues) are dominated by a mixture of polyproline II (pPII) and β-strand like conformations. We recently discovered rather substantial differences between the enthalpic and entropic contributions to this equilibrium for different amino acid residues. Isoleucine and valine exceed all other amino acid residues in terms of their rather large enthalpic stabilization and entropic destabilization of polyproline II. In order to shed light on these underlying physical mechanisms, we performed high-level DFT calculations to explore the energetics of four representative GxG peptides where x = alanine (A), leucine (L), valine (V), and isoleucine (I) in explicit water (10 H2O molecules with a polarizable continuum water model) and in vacuo. We found that the large energetic contributions to the stabilization of pPII result, to a major extent, from peptide-water, water-water interactions, and changes of the solvent self-energy. Differences between the peptide-solvent interaction energies of hydration in pPII and β-strand peptides are particularly important for the pPII ⇌ β equilibria of the more aliphatic peptides GIG ...Continue Reading

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Citations

Dec 23, 2015·The Journal of Physical Chemistry. B·Adolfo BastidaMiguel A Soler
Feb 27, 2016·Journal of Chemical Theory and Computation·M Belén Oviedo, Bryan M Wong
Oct 22, 2016·The Journal of Physical Chemistry. B·Giuseppe Lanza, Maria A Chiacchio
Jan 4, 2017·Physical Chemistry Chemical Physics : PCCP·Masakazu FurutaMasashi Unno
Apr 4, 2017·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Giuseppe Lanza, Maria A Chiacchio
May 22, 2018·Chemical Communications : Chem Comm·Yan ZhangZhengshuang Shi
Nov 23, 2017·Journal of Molecular Modeling·Roksana Wałęsa, Małgorzata A Broda
Apr 27, 2018·Physical Chemistry Chemical Physics : PCCP·Niranjan V IlaweBryan M Wong
Nov 12, 2015·SpringerPlus·Robert P Bywater, Valera Veryazov
Aug 6, 2020·Biomolecules·Brian AndrewsBrigita Urbanc
Mar 16, 2017·Physical Chemistry Chemical Physics : PCCP·Rakesh S SinghDavid Tiemessen
Mar 15, 2018·Biophysical Journal·Reinhard Schweitzer-Stenner, Siobhan E Toal
Mar 28, 2018·The Journal of Physical Chemistry. B·Giuseppe Lanza, Maria A Chiacchio
Jan 5, 2019·The Journal of Physical Chemistry. B·Reinhard Schweitzer-StennerCunlan Guo

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