10.1021/ja068336h.s001
Hans-Jürgen Sass
Hans-Jürgen
Sass
Franziska Fang-Fang Schmid
Franziska Fang-Fang
Schmid
Stephan Grzesiek
Stephan
Grzesiek
Correlation of Protein Structure and Dynamics to Scalar
Couplings across Hydrogen Bonds
American Chemical Society
2007
water models
protein G
h 3JNC values
h 3JNC
h 3JNC data
SMN Tudor domain
MD simulations
hydrogen bonds
backbone hydrogen bonds
GB 1 domain
2007-05-09 00:00:00
Journal contribution
https://acs.figshare.com/articles/journal_contribution/Correlation_of_Protein_Structure_and_Dynamics_to_Scalar_Couplings_across_Hydrogen_Bonds/3008665
NMR-observable scalar couplings across hydrogen bonds in nucleic acids and proteins present
a quantitative measure for the geometry and by the implicit experimental time averaging dynamics of
hydrogen bonds. We have carried out in-depth molecular dynamics (MD) simulations with various force
fields on three proteins: ubiquitin, the GB1 domain of protein G, and the SMN Tudor domain, for which
experimental <sup>h3</sup><i>J</i><sub>NC</sub><sub>‘</sub> scalar couplings of backbone hydrogen bonds and various high-resolution X-ray
structures are available. Theoretical average values for <sup>h3</sup><i>J</i><sub>NC</sub><sub>‘</sub> were calculated from the snapshots of these
MD simulations either by density functional theory or by a geometric parametrization (Barfield, M. <i>J. Am.
Chem. Soc.</i> <b>2002</b>, <i>124</i>, 4158−4168). No significant difference was found between the two methods. The
results indicate that time-averaging using explicit water solvation in the MD simulations improves significantly
the agreement between experimental and theoretical values for the lower resolution structures ubiquitin
(1.8 Å), Tudor domain (1.8 Å), and protein G (2.1 Å). Only marginal improvement is found for the high-resolution structure (1.1 Å) of protein G. Hence, experimental <sup>h3</sup><i>J</i><sub>NC</sub><sub>‘</sub> values are compatible with a static,
high-resolution structural model. The MD averaging of the low-resolution structures moves the averages
of the <i>r</i><sub>HO</sub> distance and the H···OC angle θ closer to their respective values in the high-resolution structures,
thereby improving the agreement using experimental <sup>h3</sup><i>J</i><sub>NC</sub><sub>‘</sub> data. In contrast, MD averaging with implicit
water models deteriorates the agreement with experiment for all proteins. The differing behavior can be
explained by an artifactual lengthening of H-bonds caused by the implicit water models.