Title

Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation?

Authors

Authors

W. M. Berhanu; I. A. Mikhailov;A. E. Masunov

Comments

Authors: contact us about adding a copy of your work at STARS@ucf.edu

Abbreviated Journal Title

J. Mol. Model.

Keywords

Polyglutamic acid; Assignment of Raman spectra; Density function theory; Conformational transition; Amide vibrational band; Peptide; conformational change; UV RESONANCE RAMAN; PROTEIN SECONDARY STRUCTURE; POLYPROLINE-II; STRUCTURE; OPTICAL-ACTIVITY; ALPHA-HELIX; CIRCULAR-DICHROISM; GLOBULAR-PROTEINS; PEPTIDE; HYDRATION; RESIDUES; Biochemistry & Molecular Biology; Biophysics; Chemistry, ; Multidisciplinary; Computer Science, Interdisciplinary Applications

Abstract

We report density functional theory (DFT) calculations of the Raman spectra for hexapepetides of glutamic acid and lysine in three different conformations (alpha, beta and PPII). The wave numbers of amide I, amide II and amide III bands of all three conformations predicted at B3LYP/6-31G and B3LYP/6-31G* are in good agreement with previously reported experimental values of polyglutamic acid and polylysine. Agreement with experiment improves when polarization functions are included in the basis set. Explicit water molecules, H-bonded to the backbone amide groups were found to be absolutely necessary to obtain this agreement. Our results indicate that DFT is a promising tool for assignment of the spectral data on kinetics of conformational changes for peptides during amyloid formation.

Journal Title

Journal of Molecular Modeling

Volume

16

Issue/Number

6

Publication Date

1-1-2010

Document Type

Article

Language

English

First Page

1093

Last Page

1101

WOS Identifier

WOS:000277202700004

ISSN

1610-2940

Share

COinS