Determination of Conformational Preferences of Dipeptides Using Vibrational Spectroscopy
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- 作者：Jo<img src="http ; //pubs.acs.org/images/entities/zcaron.gif" border="0">e Grdadolnik ; Simona Goli<img src="http ; //pubs.acs.org/images/entities/ccaron.gif" border="0"> Grdadolnik ; Franc Avbelj
- 刊名：Journal of Physical Chemistry B
- 出版年：2008
- 出版时间：March 6, 2008
- 年：2008
- 卷：112
- 期：9
- 页码：2712 - 2718
- 全文大小：269K
- 年卷期：v.112,no.9(March 6, 2008)
- ISSN：1520-5207
文摘
The NMR coupling constants (3J(HN, H<IMG SRC="/images/gifchars/alpha.gif" BORDER=0>)) of dipeptides indicate that the backbone conformational preferencesvary strikingly among dipeptides. These preferences are similar to those of residues in small peptides, denaturedproteins, and the coil regions of native proteins. Detailed characterization of the conformational preferencesof dipeptides is therefore of fundamental importance for understanding protein structure and folding. Here,we studied the conformational preferences of 13 dipeptides using infrared and Raman spectroscopy. Themain advantage of vibrational spectroscopy over NMR spectroscopy is in its much shorter time scale, whichenables the determination of the conformational preferences of short-lived states. Accuracy of structuredetermination using vibrational spectroscopy depends critically on identification of the vibrational parametersthat are sensitive to changes in conformation. We show that the frequencies of the amide I band and the A12ratio of the amide I components of dipeptides correlate with the 3J(HN, H
). These two infrared vibrationalparameters are thus analogous to 3J(HN, H), indicators for the preference for the dihedral angle 
. We alsoshow that the intensities of the components of the amide III bands in infrared spectra and the intensities ofthe skeletal vibrations in Raman spectra are indicators of populations of the PII, 
, and R conformations.The results show that alanine dipeptide adopts predominantly a PII conformation. The population of the conformation increases in valine dipeptides. The populations of the R conformation are generally small.These data are in accord with the electrostatic screening model of conformational preferences.
). These two infrared vibrationalparameters are thus analogous to 3J(HN, H), indicators for the preference for the dihedral angle . We alsoshow that the intensities of the components of the amide III bands in infrared spectra and the intensities ofthe skeletal vibrations in Raman spectra are indicators of populations of the PII, , and R conformations.The results show that alanine dipeptide adopts predominantly a PII conformation. The population of the conformation increases in valine dipeptides. The populations of the R conformation are generally small.These data are in accord with the electrostatic screening model of conformational preferences.