Title

Are Density Functional Theory Predictions Of The Raman Spectra Accurate Enough To Distinguish Conformational Transitions During Amyloid Formation?

Keywords

Amide vibrational band; Assignment of raman spectra; Densityfunction theory conformational transition; Peptide conformational change; Polyglutamic acid

Abstract

We report density functional theory (DFT) calculations of the Raman spectra for hexapepetides of glutamic acid and lysine in three different conformations (a, β 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. © Springer-Verlag 2009.

Publication Date

6-1-2010

Publication Title

Journal of Molecular Modeling

Volume

16

Issue

6

Number of Pages

1093-1101

Document Type

Article

Personal Identifier

scopus

DOI Link

https://doi.org/10.1007/s00894-009-0610-2

Socpus ID

77955096647 (Scopus)

Source API URL

https://api.elsevier.com/content/abstract/scopus_id/77955096647

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