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Residual dipolar couplings in short peptides reveal systematic conformational preferences of individual amino acids

Dames, S. A. and Aregger, R. and Vajpai, N. and Bernado, P. and Blackledge, M. and Grzesiek, S.. (2006) Residual dipolar couplings in short peptides reveal systematic conformational preferences of individual amino acids. Journal of the American Chemical Society, Vol. 128, H. 41. pp. 13508-13514.

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Official URL: http://edoc.unibas.ch/dok/A5258775

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Abstract

Residual dipolar couplings (RDCs) observed by NMR in solution under weak alignment conditions can monitor average net orientations and order parameters of individual bonds. By their simple geometrical dependence, RDCs bear particular promise for the quantitative characterization of conformations in partially folded or unfolded proteins. We have systematically investigated the influence of amino acid substitutions X on the conformation of unfolded model peptides EGAAXAASS as monitored by their (1)H(Nu)-(15)N and (1)H(alpha)-(13)C(alpha) RDCs detected at natural abundance of (15)N and (13)C in strained polyacrylamide gels. In total, 14 single amino acid substitutions were investigated. The RDCs show a specific dependence on the substitution X that correlates to steric or hydrophobic interactions with adjacent amino acids. In particular, the RDCs for the glycine and proline substitutions indicate less or more order, respectively, than the other amino acids. The RDCs for aromatic substitutions tryptophane and tyrosine give evidence of a kink in the peptide backbone. This effect is also observable for orientation by Pf1 phages and corroborated by variations in (13)C(alpha) secondary shifts and (3)J(HNH)(alpha) scalar couplings in isotropic samples. RDCs for a substitution with the beta-turn sequence KNGE differ from single amino acid substitutions. Terminal effects and next neighbor effects could be demonstrated by further specific substitutions. The results were compared to statistical models of unfolded peptide conformations derived from PDB coil subsets, which reproduce overall trends for (1)H(Nu)-(15)N RDCs for most substitutions, but deviate more strongly for (1)H(alpha)-(13)C(alpha) RDCs. The outlined approach opens the possibility to obtain a systematic experimental characterization of the influence of individual amino acid/amino acid interactions on orientational preferences in polypeptides.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Structural Biology & Biophysics > Structural Biology (Grzesiek)
UniBasel Contributors:Grzesiek, Stephan
Item Type:Article, refereed
Article Subtype:Research Article
Bibsysno:Link to catalogue
ISSN:0002-7863
Note:Publication type according to Uni Basel Research Database: Journal article
Last Modified:22 Mar 2012 14:20
Deposited On:22 Mar 2012 13:21

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