Simulations of oligopeptide vibrational CD: Effects of isotopic labeling

Simulated ir absorption and vibrational CD (VCD) spectra of four alanine‐based octapeptides, each having its main chain constrained to a different secondary structure conformation, were analyzed and compared with experimental results for several different peptides. The octapeptide simulations were b...

Full description

Saved in:
Bibliographic Details
Published in:Biopolymers 2000-04, Vol.53 (5), p.380-395
Main Authors: Bour, Petr, Kubelka, Jan, Keiderling, Timothy A.
Format: Article
Language:English
Subjects:
Alanine - chemistry
Biopolymers - chemistry
Carbon Isotopes
Circular Dichroism
ir absorption
isotope labeling
oligopeptide
Oligopeptides - chemistry
Protein Structure, Secondary
Spectrophotometry, Infrared
theoretical simulation
vibrational CD
Citations: Items that this one cites
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Simulated ir absorption and vibrational CD (VCD) spectra of four alanine‐based octapeptides, each having its main chain constrained to a different secondary structure conformation, were analyzed and compared with experimental results for several different peptides. The octapeptide simulations were based on transfer of property tensors from a series of ab initio calculations for a short L‐alanine based segment containing 3 peptide bonds with relative ϕ, ψ angles fixed to those appropriate for α‐helix, 310‐helix, ProII‐like helix, and β‐sheet‐like strand. The tripeptide force field (FF) and atomic polar tensors were obtained with density functional theory techniques at the BPW91/6‐31G** level and the atomic axial tensor at the mixed BPW91/6‐31G**/HF/6‐31G level. Allowing for frequency correction due to the FF limitations, the octapeptide results obtained are qualitatively consistent with experimental observations for ir and VCD spectra of polypeptides and oligopeptides in established conformations. In all cases, the correct VCD sign patterns for the amide I and II bands were predicted, but the intensities did have some variation from the experimental patterns. Predicted VCD changes upon deuteration of either the peptide or side‐chains as well as for 13C isotopic labeling of the amide CO at specific sites in the peptide chain were computed for analysis of experimental observations. A combination of theoretical modeling with experimental data for labeled compounds leads both to enhanced resolution of component transitions and added conformational applicability of the VCD spectra. © 2000 John Wiley & Sons, Inc. Biopoly 53: 380–395, 2000
ISSN:0006-3525
1097-0282
DOI:10.1002/(SICI)1097-0282(20000415)53:5<380::AID-BIP3>3.0.CO;2-R