Abstract We performed density functional calculations of backbone 15N shielding tensors in the regions of beta-sheet and turns of protein G. The calculations were carried out for all twenty-four beta-sheet residues and eight beta-turn residues in the protein GB3 and the results were compared with the available experimental data from solid-state and solution NMR measurements. Together with the alpha-helix data, our calculations cover 39 out of the 55 residues (or 71%) in GB3. The applicability of several computational models developed previously (Cai et al. in J Biomol NMR 45:245â??253, 2009) to compute 15N shielding tensors of alpha-helical residues is assessed. We show that the proposed quantum chemical computational model is capable of predicting isotropic 15N chemical shifts for an entire protein that are in good correlation with experimental data. However, the individual components of the predicted 15N shielding tensor agree with experiment less well: the computed values show much larger spread than the experimental data, and there is a profound difference in the behavior of the tensor components for alpha-helix/turns and beta-sheet residues. We discuss possible reasons for this.
Content Type Journal Article
Pages 1-15
DOI 10.1007/s10858-011-9474-8
Authors
Ling Cai, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
Daniel S. Kosov, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
David Fushman, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
Investigation of solvent effect and NMR shielding tensors of p53 tumor-suppressor gene in drug design.
Investigation of solvent effect and NMR shielding tensors of p53 tumor-suppressor gene in drug design.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Investigation of solvent effect and NMR shielding tensors of p53 tumor-suppressor gene in drug design.
Int J Nanomedicine. 2011;6:213-8
Authors: Irani S, Monajjemi M, Honarparvar B, Atyabi S, Sadeghizadeh M
Abstract
The p53 tumor-suppressor gene encodes a nuclear phosphoprotein with cancer- inhibiting properties. The...
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Addressing the Stereochemistry of Complex Organic Molecules by Density Functional Theory-NMR: Vannusal B in Retrospective
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Giacomo Saielli, K. C. Nicolaou, Adrian Ortiz, Hongjun Zhang and Alessandro Bagno
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja201108a/aop/images/medium/ja-2011-01108a_0003.gif
Journal of the American Chemical Society
DOI: 10.1021/ja201108a
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http://feeds.feedburner.com/~r/acs/jacsat/~4/hTB3xm5f79k
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At low ionic strength, apoplastocyanin forms an unfolded state under non-denaturing conditions. The refolding of this state is sufficiently slow to allow real-time NMR experiments to be performed. Folding of apoplastocyanin, initiated by the addition of salt and followed by real-time 2D 1H-15N...
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Authors: Stone MJ, Gupta S, Snyder N, Regan L
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Cross-correlated relaxation rates involving the Calpha-Halpha dipolar interaction and the carbonyl (C') chemical shift anisotropy (CSA) have been measured using two complementary 3D experiments. We show that the protein backbone angle psi can be directly refined...
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Density functional calculations of 15N chemical shifts in solvated dipeptides
Density functional calculations of 15N chemical shifts in solvated dipeptides
Ling Cai, David Fushman and Daniel S. Kosov
Journal of Biomolecular NMR; 2008; 41(2) pp 77 - 88
Abstract:
We performed density functional calculations to examine the effects of solvation, hydrogen bonding, backbone conformation, and the side chain on 15N chemical shielding in proteins. We used N-methylacetamide (NMA) and N-formyl-alanyl-X (with X being one of the 19 naturally occurring amino acids excluding proline) as model systems. In addition, calculations were performed for selected fragments from...