Simulating the dynamics and orientations of spin-labeled side chains in a protein-DNA complex.

ABSTRACT: Site-directed spin labeling, wherein a nitroxide side chain is introduced into a protein at a selected mutant site, is increasingly employed to investigate biological systems by electron spin resonance (ESR) spectroscopy. An understanding of the packing and dynamics of the spin label is needed to extract the biologically relevant information about the macromolecule from ESR measurements. In this work, molecular dynamics (MD) simulations were performed on the spin-labeled restriction endonuclease, EcoRI in complex with DNA. Mutants of this homodimeric enzyme were previously constructed, and distance measurements were performed using the double electron electron resonance experiment. These correlated distance constraints have been leveraged with MD simulations to learn about side chain packi

SUBMITTER: Sarver JL 

PROVIDER: S-EPMC3325110 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature