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Default Parameterization of solvent–protein interaction and its use on NMR protein structure determination

Parameterization of solvent–protein interaction and its use on NMR protein structure determination

August 2012
Publication year: 2012
Source:Journal of Magnetic Resonance, Volume 221



NMR structure determination is frequently hindered by an insufficient amount of distance information for determining the correct fold of the protein in its early stages. In response we introduce a simple and general structure-based metric that can be used to incorporate NMR-based restraints on protein surface accessibility. This metric is inversely proportional to the sum of the inverse square distances to neighboring heavy atoms. We demonstrate the use of this restraint using a dataset from the water to protein magnetization transfer experiment on the protein Bax and the solvent paramagnetic relaxation enhancement experiment on the protein ubiquitin and Qua1 homodimer. The calculated solvent accessibility values using the new empirical function are well correlated with the experimental data. By incorporating an associated energy term into Xplor-NIH, we show that structure calculation with a limited number of additional experimental restraints, improves both the precision and accuracy of the resulting structures. This new empirical energy term will have general applicability to other types of solvent accessibility data.
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Highlights

? We formulated a new structural metric for solvent–protein interaction. ? We showed that this new metric correlated well with experimental NMR data. ? We developed a protocol to use this information in structure calculations. ? Addition of this new information improved precision and accuracy of the structures.





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