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Peptide secondary structure folding reaction coordinate: Correlation between UV Raman amide III frequency, ψ Ramachandran angle, and hydrogen bonding

Mikhonin, AV and Bykov, SV and Myshakina, NS and Asher, SA (2006) Peptide secondary structure folding reaction coordinate: Correlation between UV Raman amide III frequency, ψ Ramachandran angle, and hydrogen bonding. Journal of Physical Chemistry B, 110 (4). 1928 - 1943. ISSN 1520-6106

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Abstract

We used UV resonance Raman (UVRR) spectroscopy to quantitatively correlate the peptide bond AmIII3 frequency to its ψ Ramachandran angle and to the number and types of amide hydrogen bonds at different temperatures. This information allows us to develop a family of relationships to directly estimate the ψ Ramachandran angle from measured UVRR AmIII3 frequencies for peptide bonds (PBs) with known hydrogen bonding (HB). These relationships ignore the more modest Φ Ramachandran angle dependence and allow determination of the ψ angle with a standard error of ±8°, if the HB state of a PB is known. This is normally the case if a known secondary structure motif is studied. Further, if the HB state of a PB in water is unknown, the extreme alterations in such a state could additionally bias the ψ angle by ±6°. The resulting ability to measure ψ spectroscopically will enable new incisive protein conformational studies, especially in the field of protein folding. This is because any attempt to understand reaction mechanisms requires elucidation of the relevant reaction coordinate(s). The ψ angle is precisely the reaction coordinate that determines secondary structure changes. As shown elsewhere (Mikhonin et al. J. Am. Chem. Soc. 2005, 727, 7712), this correlation can be used to determine portions of the energy landscape along the ψ reaction coordinate. © 2006 American Chemical Society.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Mikhonin, AV
Bykov, SV
Myshakina, NS
Asher, SAasher@pitt.eduASHER
Date: 2 February 2006
Date Type: Publication
Journal or Publication Title: Journal of Physical Chemistry B
Volume: 110
Number: 4
Page Range: 1928 - 1943
DOI or Unique Handle: 10.1021/jp054593h
Schools and Programs: Dietrich School of Arts and Sciences > Chemistry
Refereed: Yes
ISSN: 1520-6106
MeSH Headings: Amides--chemistry; Carbon--chemistry; Hydrogen Bonding; Models, Molecular; Nitrogen--chemistry; Peptides--chemistry; Protein Folding; Protein Structure, Secondary; Spectrophotometry, Ultraviolet--methods; Spectrum Analysis, Raman--methods
PubMed ID: 16471764
Date Deposited: 08 Feb 2013 21:12
Last Modified: 02 Feb 2019 15:59
URI: http://d-scholarship.pitt.edu/id/eprint/17214

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