Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods.

ABSTRACT: Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) simulations constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine

SUBMITTER: Chakravorty DK 

PROVIDER: S-EPMC3773525 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature