Jump to main content
Jump to site search

Issue 35, 2012
Previous Article Next Article

Rapid calculation of protein chemical shifts using bond polarization theory and its application to protein structure refinement

Author affiliations

Abstract

Although difficult to analyze, NMR chemical shifts provide detailed information on protein structure. We have adapted the semi-empirical bond polarization theory (BPT) to protein chemical shift calculation and chemical shift driven protein structure refinement. A new parameterization for BPT amide nitrogen chemical shift calculation has been derived from MP2 ab initio calculations and successfully evaluated using crystalline tripeptides. We computed the chemical shifts of the small globular protein ubiquitin, demonstrating that BPT calculations can match the results obtained at the DFT level of theory at very low computational cost. In addition to the calculation of chemical shift tensors, BPT allows the calculation of chemical shift gradients and consequently chemical shift driven geometry optimizations. We applied chemical shift driven protein structure refinement to the conformational analysis of a set of Trypanosoma brucei (the causative agent of African sleeping sickness) tryparedoxin peroxidase Px III structures. We found that the interaction of Px III with its reaction partner Tpx seems to be governed by conformational selection rather than by induced fit.

Graphical abstract: Rapid calculation of protein chemical shifts using bond polarization theory and its application to protein structure refinement

Back to tab navigation

Supplementary files

Publication details

The article was received on 25 May 2012, accepted on 11 Jul 2012 and first published on 12 Jul 2012


Article type: Paper
DOI: 10.1039/C2CP41726J
Phys. Chem. Chem. Phys., 2012,14, 12263-12276

  •   Request permissions

    Rapid calculation of protein chemical shifts using bond polarization theory and its application to protein structure refinement

    I. Jakovkin, M. Klipfel, C. Muhle-Goll, A. S. Ulrich, B. Luy and U. Sternberg, Phys. Chem. Chem. Phys., 2012, 14, 12263
    DOI: 10.1039/C2CP41726J

Search articles by author

Spotlight

Advertisements