| Abstract
| - NMR biomolecular structure calculations exploit simulated annealing methods for conformationalsampling and require a relatively high level of redundancy in the experimental restraints to determine qualitythree-dimensional structures. Recent advances in generalized Born (GB) implicit solvent models shouldmake it possible to combine information from both experimental measurements and accurate empiricalforce fields to improve the quality of NMR-derived structures. In this paper, we study the influence of implicitsolvent on the refinement of protein NMR structures and identify an optimal protocol of utilizing theseimproved force fields. To do so, we carry out structure refinement experiments for model proteins withpublished NMR structures using full NMR restraints and subsets of them. We also investigate the applicationof advanced sampling techniques to NMR structure refinement. Similar to the observations of Xia et al. (J.Biomol. NMR2002, 22, 317−331), we find that the impact of implicit solvent is rather small when there isa sufficient number of experimental restraints (such as in the final stage of NMR structure determination),whether implicit solvent is used throughout the calculation or only in the final refinement step. The applicationof advanced sampling techniques also seems to have minimal impact in this case. However, when theexperimental data are limited, we demonstrate that refinement with implicit solvent can substantially improvethe quality of the structures. In particular, when combined with an advanced sampling technique, the replicaexchange (REX) method, near-native structures can be rapidly moved toward the native basin. The REXmethod provides both enhanced sampling and automatic selection of the most native-like (lowest energy)structures. An optimal protocol based on our studies first generates an ensemble of initial structures thatmaximally satisfy the available experimental data with conventional NMR software using a simplified forcefield and then refines these structures with implicit solvent using the REX method. We systematically examinethe reliability and efficacy of this protocol using four proteins of various sizes ranging from the 56-residueB1 domain of Streptococcal protein G to the 370-residue Maltose-binding protein. Significant improvementin the structures was observed in all cases when refinement was based on low-redundancy restraint data.The proposed protocol is anticipated to be particularly useful in early stages of NMR structure determinationwhere a reliable estimate of the native fold from limited data can significantly expedite the overall process.This refinement procedure is also expected to be useful when redundant experimental data are not readilyavailable, such as for large multidomain biomolecules and in solid-state NMR structure determination.
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