PNNL

Abstract

A 1 ns molecular dynamics simulation was performed to study the dynamic behavior of wild-type green fluorescent protein from Aequorea Victoria. We find the protein to be remarkably rigid, both overall, because the cylindrical beta-barrel provides a stable framework, but also on an atomic level in the immediate surrounding of the chromophore. Here, a tight H-bond network is formed mainly involving six internal water molecules. The perfect barrel is interrupted only between beta-strands 7 and 8 where contact is made via side chain interactions, and we investigated the dynamic behavior of this region in detail. After ca. 320 ps of simulation, an arginine residue, initially sticking out into solution, folded over the cleft to form a H-bond with a backbone oxygen atom on the opposite strand. This contact appears important for stabilization of the overall protein architecture.