High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.

摘要: Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, environments and under conditions that closely mimic those encountered vivo. For example, advances solid-state methods enable structure membrane detergent-free lipid bilayers, large soluble prepared sedimentation, while parallel solution optimization nanodiscs are rapidly pushing the envelope size limit for both proteins. These experimental advantages, however, partially squandered during calculation, because commonly used force fields purely repulsive neglect solvation, Van der Waals forces electrostatic energy. Here we describe a new field, updated energy functions, protein calculations with EEFx implicit electrostatics, Lennard-Jones forces, widely program Xplor-NIH. The field based primarily on CHARMM22, facilitating wider range biomolecules. function has been rewritten OpenMP parallelism, optimized enhance computation efficiency. It implements terms together, thus ensuring more consistent efficient complete nonbonded lists. Updates related python module allow detailed analysis interaction energies associated parameters. work proteins, including cofactors or engineered tags, effective situations where there sparse restraints. Results obtained NMR-restrained set five show structures calculated have significant improvements accuracy, precision, conformation, refinement can be short relaxation obtain these key metrics. developments broaden biomolecular high fidelity from