Regular Article
| Simulations of oligopeptide vibrational CD: Effects of isotopic labeling |
| Petr Bour 1, Jan Kubelka 2, Timothy A. Keiderling 2 * |
| 1Institute of Organic Chemistry and
Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám.
2, 16610, Praha 6, Czech Republic 2Department of Chemistry (M/C 111), University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061, USA |
| email: Timothy A. Keiderling (tak@uic.edu) |
*Correspondence to Timothy A. Keiderling, Department of Chemistry (M/C 111), University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061, USA
Funded by:
Grant
Agency of the Czech Republic (CR); Grant Number: 203/97/P002 (CR) NIH; Grant Number: CGM30147
(NIH)
| Keywords |
| oligopeptide; vibrational CD; isotope labeling; ir absorption; theoretical simulation |
| Abstract |
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  ,  angles fixed to those appropriate for  -helix, 310-helix,
ProII-like helix, and  -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 |
Received: 23 July 1999; Accepted: 29 October 1999