A molecular dynamics simulation of bovine calbindin D9k. Molecular structure an dynamics

A molecular dynamics simulation of the Ca2+-binding protein calbindin D9k is reported. The calcium-saturated protein is simulated in an aqueous environment with an X-ray diffraction structure as the starting point. The simulation, which lasted 39 + 124 ps, was performed with the molecular dynamics program MUMOD. Structural and dynamic properties were investigated and compared with experiment. The protein contracts compared to the crystal form during the equilibration. The major contribution to the electrostatic part of the Ca2+-binding energy arises from the amino acids of the Ca2+-binding loops with only marginal contributions from the flanking helices. The estimated global rotational diffusion is faster than in experimental studies. From the simulation a characteristic time for a local reorientation process of the single tyrosine (Tyr 13) is estimated to 0.02-0.06 ns. More long-lived processes are present, but poor sampling precludes comparison with the experimental characteristic time of 0.36 ns obtained from fluorescence depolarization measurements. The simulated relaxation rates for 43Ca in the two binding sites are in qualitative agreement with and corroborate the assignments made in a recent experimental study