Matthew Fritz1,2, Caitlin M Quinn1,2, Mingzhang Wang1,2, Guangjin Hou1, Xingyu Lu1,2, Leonardus M I Koharudin2,3, Tatyana Polenova1,2, Angela M Gronenborn2,3. 1. Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States. 2. Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States. 3. Department of Structural Biology, University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States.
Abstract
NMR chemical shifts are exquisitely sensitive probes for conformation and dynamics in molecules and supramolecular assemblies. Although isotropic chemical shifts are easily measured with high accuracy and precision in conventional NMR experiments, they remain challenging to calculate quantum mechanically, particularly in inherently dynamic biological systems. Using a model benchmark protein, the 133-residue agglutinin from Oscillatoria agardhii (OAA), which has been extensively characterized by us previously, we have explored the integration of X-ray crystallography, solution NMR, MAS NMR, and quantum mechanics/molecular mechanics (QM/MM) calculations for analysis of 13Cα and 15NH isotropic chemical shifts. The influence of local interactions, quaternary contacts, and dynamics on the accuracy of calculated chemical shifts is analyzed. Our approach is broadly applicable and expected to be beneficial in chemical shift analysis and chemical-shift-based structure refinement for proteins and protein assemblies.
NMR chemical shifts are exquisitely sensitive probes for conformation and dynamics in molecules and supramolecular assemblies. Although isotropic chemical shifts are easily measured with high accuracy and precision in conventional NMR experiments, they remain challenging to calculate quantum mechanically, particularly in inherently dynamic biological systems. Using a model benchmark protein, the 133-residue agglutinin from Oscillatoria agardhii (n class="Species">OAA), which has been extensively characterized by us previously, we have explored the integration of X-ray crystallography, solution NMR, MAS NMR, and quantum mechanics/molecular mechanics (QM/MM) calculations for analysis of 13Cα and 15NH isotropic chemical shifts. The influence of local interactions, quaternary contacts, and dynamics on the accuracy of calculated chemical shifts is analyzed. Our approach is broadly applicable and expected to be beneficial in chemical shift analysis and chemical-shift-based structure refinement for proteins and protein assemblies.
Authors: Frank H Schumann; Hubert Riepl; Till Maurer; Wolfram Gronwald; Klaus-Peter Neidig; Hans Robert Kalbitzer Journal: J Biomol NMR Date: 2007-10-23 Impact factor: 2.835
Authors: Marta G Carneiro; Leonardus M I Koharudin; Christian Griesinger; Angela M Gronenborn; Donghan Lee Journal: Biomol NMR Assign Date: 2015-02-14 Impact factor: 0.746