Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions

Eight 100-ns molecular dynamics simulations of a β-heptapeptide in methanol at 340 K (within cubic periodic computational boxes of about 6-nm edge) are reported and compared. These simulations were performed with three different charge-state combinations at the peptide termini, one of them with or w...

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Veröffentlicht in:The journal of physical chemistry. B 2009-03, Vol.113 (10), p.3112-3128
Hauptverfasser: Reif, Maria M, Kräutler, Vincent, Kastenholz, Mika A, Daura, Xavier, Hünenberger, Philippe H
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container_end_page 3128
container_issue 10
container_start_page 3112
container_title The journal of physical chemistry. B
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creator Reif, Maria M
Kräutler, Vincent
Kastenholz, Mika A
Daura, Xavier
Hünenberger, Philippe H
description Eight 100-ns molecular dynamics simulations of a β-heptapeptide in methanol at 340 K (within cubic periodic computational boxes of about 6-nm edge) are reported and compared. These simulations were performed with three different charge-state combinations at the peptide termini, one of them with or without a neutralizing chloride counterion, and using either the lattice-sum (LS) or reaction-field (RF) scheme to handle electrostatic interactions. The choice of the electrostatic scheme has essentially no influence on the folding−unfolding equilibrium when the peptide termini are uncharged and only a small influence when the peptide is positively charged at its N-terminus (with or without inclusion of a neutralizing chloride counterion). However, when the peptide is zwitterionic, the LS scheme leads to preferential sampling of the high-dipole folded helical state, whereas the RF scheme leads to preferential sampling of a low-dipole unfolded salt-bridged state. A continuum electrostatics analysis based on the sampled configurations (zwitterionic case) suggests that the LS scheme stabilizes the helical state through artificial periodicity, but that the magnitude of this perturbation is essentially negligible (compared to the thermal energy) for the large box size and relatively polar solvent considered. The results thus provide clear evidence (continuum electrostatics analysis) for the absence of LS artifacts and some indications (still not definitive because of the limited sampling of the folding−unfolding transition) for the presence of RF artifacts in this specific system.
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subjects B: Biophysical Chemistry
Computational Biology - methods
Computer Simulation
Ions
Magnetic Resonance Spectroscopy
Methanol - chemistry
Models, Molecular
Models, Statistical
Molecular Conformation
Peptides - chemistry
Protein Folding
Protein Structure, Tertiary
Solvents
Static Electricity
Thermodynamics
title Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions
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