title: Free Energy Landscape of Protein-Protein Encounter Resulting from Brownian Dynamics Simulations of Barnase:Barstar.
abstract: Over the past years Brownian dynamics (BD) simulations have been proven to be a suitable tool for the analysis of protein-protein association. The computed rates and relative trends for protein mutants and different ionic strength are generally in good agreement with experimental results, e.g. see ref 1. By design, BD simulations correspond to an intensive sampling over energetically favorable states, rather than to a systematic sampling over all possible states which is feasible only at rather low resolution. On the example of barnase and barstar, a well characterized model system of electrostatically steered diffusional encounter, we report here the computation of the 6-dimensional free energy landscape for the encounter process of two proteins by a novel, careful analysis of the trajectories from BD simulations. The aim of these studies was the clarification of the encounter state. Along the trajectories, the individual positions and orientations of one protein (relative to the other) are recorded and stored in so-called occupancy maps. Since the number of simulated trajectories is sufficiently high, these occupancy maps can be interpreted as a probability distribution which allows the calculation of the entropy landscape by the use of a locally defined entropy function. Additionally, the configuration dependent electrostatic and desolvation energies are recorded in separate maps. The free energy landscape of protein-protein encounter is finally obtained by summing the energy and entropy contributions. In the free energy profile along the reaction path, which is defined as the path along the minima in the free energy landscape, a minimum shows up suggesting this to be used as the definition of the encounter state. This minimum describes a state of reduced diffusion velocity where the electrostatic attraction is compensated by the repulsion due to the unfavorable desolvation of the charged residues and the entropy loss due to the increasing restriction of the motional freedom. In the simulations the orientational degrees of freedom at the encounter state are found to be less restricted than the translational degrees of freedom. Therefore, the orientational alignment of the two binding partners seems to take place beyond this free energy minimum. The free energy profiles along the reaction pathway are compared for different ionic strength and temperature. This novel analysis technique facilitates mechanistic interpretation of protein-protein encounter pathways which should be useful for interpretation of experimental results as well.
authors.affiliation: Center for Bioinformatics, Saarland University, Im Stadtwald, D-66041 Saarbrücken, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Spaar
authors.affiliation: Center for Bioinformatics, Saarland University, Im Stadtwald, D-66041 Saarbrücken, Germany.
authors.forename: Volkhard
authors.initials: V
authors.lastname: Helms