Dynamics of the Streptavidin−Biotin Complex in Solution and in Its Crystal Lattice: Distinct Behavior Revealed by Molecular Simulations

Abstract

We present a 250 ns simulation of the wild-type, biotin-liganded streptavidin tetramer in the solution phase and compare the trajectory to two previously published simulations of the protein in its crystal lattice. By performing both types of simulations, we are able to interpret the protein's behavior in solution in the context of its X-ray structure. We find that the rate of conformational sampling is increased in solution over the lattice environment, although the relevant conformational space in solution is also much larger, as indicated by overall fluctuations in the positions of backbone atoms. We also compare the distributions of chi1 angles sampled by side chains exposed to solvent in the lattice and in the solution phase, obtaining overall good agreement between the distributions obtained in our most rigorous lattice simulation and the crystallographic chi1 angles. We observe changes in the chi1 distributions in the solution phase, and note an apparent progression of the distributions as the environment changes from a tightly packed lattice filled with crystallization media to a bath of pure water. Finally, we examine the interaction of biotin and streptavidin in each simulation, uncovering a possible alternate conformation of the biotin carboxylate tail. We also note that a hydrogen bond observed to break transiently in previous solution-phase simulations is predominantly broken in this much longer solution-phase trajectory; in the lattice simulations, the lattice environment appears to help maintain the hydrogen bond, but more sampling will be needed to confirm whether the simulation model truly gives good agreement with the X-ray data in the lattice simulations. We expect that pairing solution-phase biomolecular simulations with crystal lattice simulations will help to validate simulation models and improve the interpretation of experimentally determined structures.