Computational Simulations Reveal How Calmodulin Methionine Oxidation Triggers Large-Scale Changes in Structural Dynamics

Abstract

We have examined the structural consequences of methionine (Met) oxidation in the calcium-sensing muscle regulatory protein calmodulin (CaM) using molecular dynamics simulations. Protein oxidation by reactive oxygen species (ROS), and subsequent reduction by the antioxidant enzyme methionine sulfoxide reductase, has emerged as a crucial cell regulatory mechanism. In the context of oxidative stress, protein oxidation is implicated in disease progression and biological aging. Our goal is to bridge our understanding of muscle dysfunction and protein oxidation with atomic-level insights into site-specific methionine oxidation and calmodulin structural dynamics.We have carried out multiple 50 ns molecular dynamics simulations of explicitly solvated calmodulin, starting from the calcium-bound (1cll) and apo (1cfd) structures. Simulations were performed using NAMD (University of Illinois) and the CHARMM27 force-field. Simulations suggest that Met oxidation alters the flexibility of calcium binding sites, the conformation of the linker helix connecting the lobes, and the relative orientation of the lobes. This work is a component of a larger study in which spectroscopic distance measurements and NMR experiments have been used to resolve the structural impact of site-specific CaM Met oxidation. We expect that our in silico results will bring atomic-level insight to spectroscopic measurements, and will be integral to creating a more complete model for oxidation-induced changes in CaM structural dynamics.This work is supported by a University of Wisconsin-La Crosse Faculty Research Grant to JC Klein, NIH grants to DD Thomas (R37AG026160), and the Minnesota Supercomputing Institute.