On the Use of a Supramolecular Coarse‐Grained Model for the Solvent in Simulations of the Folding Equilibrium of an Octa‐β‐peptide in MeOH and H2O |
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| Authors: | Wei Huang Niels Hansen Wilfred F van Gunsteren |
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| Institution: | 1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH‐8093 Zürich;2. Present address: Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, DE‐70569 Stuttgart. |
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| Abstract: | Molecular dynamics (MD) simulation can give a detailed picture of conformational equilibria of biomolecules, but it is only reliable if the force field used in the simulation is accurate, and the sampling of the conformational space accessible to the biomolecule shows many (un)folding transitions to allow for precise averages of observable quantities. Here, the use of coarse‐grained (CG) solvent MeOH and H2O models to speed up the sampling of the conformational equilibria of an octa‐β‐peptide is investigated. This peptide is thought to predominantly adopt a 314‐helical fold when solvated in MeOH, and a hairpin fold when solvated in H2O on the basis of the NMR data. Various factors such as the chirality of a residue, a force‐field modification for the solute, coarse‐graining of the solvent model, and an extension of the nonbonded interaction cut‐off radius are shown to influence the simulated conformational equilibria and the agreement with the experimental NMR data for the octa‐β‐peptide. |
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| Keywords: | Octa‐β ‐peptide folding Peptides Coarse‐graining Molecular dynamics (MD) Force field Multi‐graining NMR Spectroscopy |
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