The complexes of phage T4 lysozyme L99A with noble gases have been studied by molecular dynamics simulation. In a long simulation of the complex with one Xe atom, the structure was found to undergo global conformation change involving a reversible opening and closing of the entrance to the substrate-binding site, during which the conformations of the N and C-terminal domains varied little. The distributions of Xe positions sampled in dynamics simulations were refined in terms of anisotropic Gaussian distributions via least-squares minimization of the difference between Fourier transforms. In addition, molecular transformation simulations have been applied in order to calculate the binding free energies of Xe, Kr and Ar relative to a standard state at a pressure of 1 bar. A single bound Xe is found to assume an equilibrium distribution over three adjacent preferred sites, while in a two-Xe complex, the two Xe atoms preferentially occupy two of these. The positions of the three sites agree closely with the positions of bound Xe determined in the refined crystal structure of a complex formed at a pressure of 8 bar Xe, and the calculated affinities agree well with the observed partial occupancies. At a pressure of 8 bar, a mixture of one-Xe and two-Xe complexes is present, and similarly for complexes with Kr and Ar, with single occupancy relatively more prevalent with Kr and Ar. (Binding of a third Xe atom is found to be quite unfavorable.) A comparison with simulation results for the binding of benzene to the same site leads to the conclusion that binding of Xe within cavities in proteins is common because of several favorable factors: (1) Xe has a large atomic polarizability; (2) Xe can be applied at a relatively high pressure, i.e. high chemical potential; (3) an unfavorable entropic term related to the need to orient the ligand in the binding site is absent. Finally, it is found that the model’s binding energy of a water molecule in the cavity is insufficient to overcome the unfavorable binding entropy.

A molecular dynamics simulation approximates the motion of atoms in a system of molecules over short intervals of simulated time, typically in the order of picoseconds to nanoseconds. Such simulations may run for days or weeks on a computer when used to investigate the dynamic behavior of small proteins in biological systems. By adding additional restraints, a simulation may be steered to observe the possibility of particular behaviors or to eliminate others over shorter timescales. We have developed the steered molecular dynamics (SMD) system to interactively place and observe the effects of restraints in a running dynamics simulation. In this article, we describe an application of SMD to the extraction of small ligands from proteins, and an immersive virtual 3D environment through which the SMD system can be operated. The virtual environment is constructed using the protein interactive theater (PIT) system, a head-tracked stereo workspace for two users.