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

    Authors

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

    Comments

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    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

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