A practical implicit solvent potential for NMR structure calculation. J Magn Reson 2014 Jun;243:54-64
Date
04/22/2014Pubmed ID
24747742Pubmed Central ID
PMC4037354DOI
10.1016/j.jmr.2014.03.011Scopus ID
2-s2.0-84898953449 (requires institutional sign-in at Scopus site) 38 CitationsAbstract
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 List
Tian Y, Schwieters CD, Opella SJ, Marassi FMAuthor
Francesca M. Marassi PhD Chair, Professor in the Biophysics department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
AlgorithmsAmino Acid Sequence
Computer Simulation
Magnetic Resonance Spectroscopy
Models, Chemical
Models, Molecular
Molecular Sequence Data
Protein Conformation
Proteins
Solvents
Water
