Conformation dependence of the C(alpha)D(alpha) stretch mode in peptides. II. explicitly hydrated alanine peptide structures.
Our previous studies of the potential utility of the C(alpha)D(alpha) stretch frequency, nu(CD), as a tool for determining conformation in peptide systems (Mirkin and Krimm, J Phys Chem A 2004, 108, 10923-10924; 2007, 111, 5300-5303) dealt with the spectroscopic characteristics of isolated alanine peptides with alpha(R), beta, and polyproline II structures. We have now extended these ab initio calculations to include various explicit-water environments interacting with such conformers. We find that the structure-discriminating feature of this technique is in fact enhanced as a result of the conformation-specific interactions of the bonding waters, in part due to our finding (Mirkin and Krimm, J Phys Chem B 2008, 112, 15268) that C(alpha)--D(alpha)...O(water) hydrogen bonds can be present in addition to those expected between water and the CO and NH of the peptide groups. In fact, nu(CD) is hardly affected by the latter bonding but can be shifted by up to 70 cm(-1) by the former hydrogen bonds. We also discuss the factors that will have to be considered in developing the molecular dynamics (MD) treatment needed to satisfactorily take account of the influence of outer water layers on the structure of the first-layer water molecules that hydrogen bond to the peptide backbone.
LSA Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA.
Noemi G
NG
Mirkin
Samuel
S
Krimm
D000409:Alanine / Q000737:chemistry*; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000235:genetics; D011487:Protein Conformation; D013057:Spectrum Analysis / Q000379:methods; D014867:Water / Q000737:chemistry
D010455:Peptides; D014867:Water; D000409:Alanine