The solvation interface is a determining factor in peptide conformational preferences.
The 21 residue polyalanine-based F(s) peptide was studied using thousands of long, explicit solvent, atomistic molecular dynamics simulations that reached equilibrium at the ensemble level. Peptide conformational preference as a function of hydrophobicity was examined using a spectrum of explicit solvent models, and the peptide length-dependence of the hydrophilic and hydrophobic components of solvent-accessible surface area for several ideal conformational types was considered. Our results demonstrate how the character of the solvation interface induces several conformational preferences, including a decrease in mean helical content with increased hydrophilicity, which occurs predominantly through reduced nucleation tendency and, to a lesser extent, destabilization of helical propagation. Interestingly, an opposing effect occurs through increased propensity for 3(10)-helix conformations, as well as increased polyproline structure. Our observations provide a framework for understanding previous reports of conformational preferences in polyalanine-based peptides including (i) terminal 3(10)-helix prominence, (ii) low pi-helix propensity, (iii) increased polyproline conformations in short and unfolded peptides, and (iv) membrane helix stability in the presence and absence of water. These observations provide physical insight into the role of water in peptide conformational equilibria at the atomic level, and expand our view of the complexity of even the most "simple" of biopolymers. Whereas previous studies have focused predominantly on hydrophobic effects with respect to tertiary structure, this work highlights the need for consideration of such effects at the secondary structural level.
Sorin
Eric J
EJ
Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.
Rhee
Young Min
YM
Shirts
Michael R
MR
Pande
Vijay S
VS
D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D012995:Solubility; D012997:Solvents / Q000737:chemistry*
D010446:Peptide Fragments; D010455:Peptides; D012997:Solvents; C019529:polyalanine