Probing multiple effects on 15N, 13Cα, 13Cβ, and 13C′ chemical shifts in peptides using density functional theory

Xiao‐Ping Xu; David A. Case

doi:10.1002/bip.10276

journal article Oct 29, 2002

Probing multiple effects on 15N, 13Cα, 13Cβ, and 13C′ chemical shifts in peptides using density functional theory

Xiao‐Ping Xu David A. Case

Biopolymers Vol. 65 No. 6 pp. 408-423 · Wiley

View at Publisher Save 10.1002/bip.10276

Abstract

AbstractWe have used density functional calculations on model peptides to study conformational effects on 15N, 13Cα, 13Cβ, and 13C′ chemical shifts, associated with hydrogen bonding, backbone conformation, and side‐chain orientation. The results show a significant dependence on the backbone torsion angles of the nearest three residues. Contributions to 15N chemical shifts from hydrogen bonding (up to 8 ppm), backbone conformation (up to 13 ppm), side‐chain orientation and neighborhood residue effects (up to 22 ppm) are significant, and a unified theory will be required to account for their behavior in proteins. In contrast to this, the dependence on sequence and hydrogen bonding is much less for 13Cα and 13Cβ chemical shifts (<0.5 ppm), and moderate for carbonyl carbon shifts (<2 ppm). The effects of side‐chain orientation are mainly limited to the residue itself for both nitrogen and carbon, but the χ1 effect is also significant for the nitrogen shift of the following residue and for the 13C′ shift of the preceding residue. The calculated results are used, in conjunction with an additive model of chemical shift contributions, to create an algorithm for prediction of 15N and 13C shifts in proteins from their structure; this includes a model to extrapolate results to regions of torsion angle space that have not been explicitly studied by density functional theory (DFT) calculations. Crystal structures of 20 proteins with measured shifts have been used to test the prediction scheme. Root mean square deviations between calculated and experimental shifts 2.71, 1.22, 1.31, and 1.28 ppm for N, Cα, Cβ, and C′, respectively. This prediction algorithm should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 408–423, 2002

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Details

Published: Oct 29, 2002
Vol/Issue: 65(6)
Pages: 408-423
License: View

Authors

Rutgers, The State University of New Jersey

Cite This Article

Xiao‐Ping Xu, David A. Case (2002). Probing multiple effects on 15N, 13Cα, 13Cβ, and 13C′ chemical shifts in peptides using density functional theory. Biopolymers, 65(6), 408-423. https://doi.org/10.1002/bip.10276

Probing multiple effects on 15N, 13Cα, 13Cβ, and 13C′ chemical shifts in peptides using density functional theory

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