Internal dynamics of green fluorescent protein

A 1 ns molecular dynamics simulation was performed to study the dynamic beh avior of wild-type green fluorescent protein from Aequorea victoria. We fin d the protein to be remarkably rigid, both overall, because the cylindrical beta-barrel provides a stable framework, but also on an atomic level in th e immediate surrounding of the chromophore. Here, a tight H-bond network is formed mainly involving six internal water molecules. The perfect barrel i s interrupted only between beta-strands 7 and 8 where contact is made via s ide chain interactions, and we investigated the dynamic behavior of this re gion in detail. After ca. 320 ps of simulation, an arginine residue, initia lly 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 import ant for stabilization of the overall protein architecture.