Mechanical stability of helical beta-peptides and a comparison of explicit and implicit solvent models.
Synthetic beta-peptide oligomers have been shown to form stable folded structures analogous to those encountered in naturally occurring proteins. Literature studies have speculated that the conformational stability of beta-peptides is greater than that of alpha-peptides. Direct measurements of that stability, however, are not available. Molecular simulations are used in this work to quantify the mechanical stability of four helical beta-peptides. This is achieved by subjecting the molecules to tension. The potential of mean force associated with the resulting unfolding process is determined using both an implicit and an explicit solvent model. It is found that all four molecules exhibit a highly stable helical structure. It is also found that the energetic contributions to the potential of mean force do not change appreciably when the molecules are stretched in explicit water. In contrast, the entropic contributions decrease significantly. As the peptides unfold, a loss of intramolecular energy is compensated by the formation of additional water-peptide hydrogen bonds. These entropic effects lead in some cases to a loss of stability upon cooling the peptides, a phenomenon akin to the cold denaturing of some proteins. While the location of the free energy minimum and the structural helicity of the peptides are comparable in the implicit-solvent and explicit-water cases, it is found that, in general, the helical structure of the molecules is more stable in the implicit solvent model than in explicit water.
Miller
Clark A
CA
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, USA.
Gellman
Samuel H
SH
Abbott
Nicholas L
NL
de Pablo
Juan J
JJ
D000595:Amino Acid Sequence; D001696:Biomechanical Phenomena; D003198:Computer Simulation; D019277:Entropy; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D016014:Linear Models; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011489:Protein Denaturation / Q000187:drug effects; D017433:Protein Structure, Secondary / Q000187:drug effects; D012997:Solvents / Q000494:pharmacology*; D055672:Static Electricity; D013696:Temperature; D014867:Water / Q000494:pharmacology
D010455:Peptides; D012997:Solvents; D014867:Water