A practical implicit solvent potential for NMR structure calculation.

 In
by Ye Tian, Charles D Schwieters, Stanley J Opella, Francesca M Marassi
Abstract:
The benefits of protein structure refinement in water are well documented. However, performing structure refinement with explicit atomic representation of the solvent molecules is computationally expensive and impractical for NMR-restrained structure calculations that start from completely extended polypeptide templates. Here we describe a new implicit solvation potential, EEFx (Effective Energy Function for XPLOR-NIH), for NMR-restrained structure calculations of proteins in XPLOR-NIH. The key components of EEFx are an energy term for solvation energy that works together with other nonbonded energy functions, and a dedicated force field for conformational and nonbonded protein interaction parameters. The initial results obtained with EEFx show that significant improvements in structural quality can be obtained. EEFx is computationally efficient and can be used both to fold and refine structures. Overall, EEFx improves the quality of protein conformation and nonbonded atomic interactions. Moreover, such benefits are accompanied by enhanced structural precision and enhanced structural accuracy, reflected in improved agreement with the cross-validated dipolar coupling data. Finally, implementation of EEFx calculations is straightforward and computationally efficient. Overall, EEFx provides a useful method for the practical calculation of experimental protein structures in a physically realistic environment.
Reference:
A practical implicit solvent potential for NMR structure calculation. (Ye Tian, Charles D Schwieters, Stanley J Opella, Francesca M Marassi), In Journal of magnetic resonance (San Diego, Calif. : 1997), volume 243, 2014.
Bibtex Entry:
@article{Tian2014a,
abstract = {The benefits of protein structure refinement in water are well documented. However, performing structure refinement with explicit atomic representation of the solvent molecules is computationally expensive and impractical for NMR-restrained structure calculations that start from completely extended polypeptide templates. Here we describe a new implicit solvation potential, EEFx (Effective Energy Function for XPLOR-NIH), for NMR-restrained structure calculations of proteins in XPLOR-NIH. The key components of EEFx are an energy term for solvation energy that works together with other nonbonded energy functions, and a dedicated force field for conformational and nonbonded protein interaction parameters. The initial results obtained with EEFx show that significant improvements in structural quality can be obtained. EEFx is computationally efficient and can be used both to fold and refine structures. Overall, EEFx improves the quality of protein conformation and nonbonded atomic interactions. Moreover, such benefits are accompanied by enhanced structural precision and enhanced structural accuracy, reflected in improved agreement with the cross-validated dipolar coupling data. Finally, implementation of EEFx calculations is straightforward and computationally efficient. Overall, EEFx provides a useful method for the practical calculation of experimental protein structures in a physically realistic environment.},
author = {Tian, Ye and Schwieters, Charles D and Opella, Stanley J and Marassi, Francesca M},
doi = {10.1016/j.jmr.2014.03.011},
issn = {1096-0856},
journal = {Journal of magnetic resonance (San Diego, Calif. : 1997)},
keywords = {Calculation,EEFx,Implicit solvent,NMR,Protein structure,XPLOR-NIH},
month = {jun},
pages = {54--64},
pmid = {24747742},
title = {{A practical implicit solvent potential for NMR structure calculation.}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1090780714000998 http://www.ncbi.nlm.nih.gov/pubmed/24747742 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4037354},
volume = {243},
year = {2014}
}

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