Experimentally Verifying Molecular Dynamics Simulations through Fluorescence Anisotropy Measurements

The fluorescence anisotropy decay of the single tryptophan residue in phospholipase A₂ was studied by use of differential polarized phase fluorometry and computer simulations of protein dynamics. The results enable the verification of a simulated dynamic event by direct experimental measurement on the same time scale. When all hydrogen atoms are modeled explicitly, the simulations agree well with the experimental measurements. However, the measurements contradict simulations in which nonpolar hydrogens are incorporated into “extended” or “united” atoms. These simulations predict an anisotropy decay in excess of measured values and appear to seriously underestimate the electrostatic interactions occurring between water and aromatic side chains. The results support the general validity of studying protein dynamics with the molecular-mechanics approach and illustrate a potentially serious deficiency of simulations which do not explicitly model all hydrogen atoms.