Molecular dynamics simulations of a reversibly folding beta-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions.
Eight 100-ns molecular dynamics simulations of a beta-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.
Reif
Maria M
MM
Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland.
Kräutler
Vincent
V
Kastenholz
Mika A
MA
Daura
Xavier
X
Hünenberger
Philippe H
PH
D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D007477:Ions; D009682:Magnetic Resonance Spectroscopy; D000432:Methanol / Q000737:chemistry*; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D012997:Solvents; D055672:Static Electricity; D013816:Thermodynamics
D007477:Ions; D010455:Peptides; D012997:Solvents; D000432:Methanol