Protein-protein diffusional encounter
نویسندگان
چکیده
منابع مشابه
Brownian dynamics simulation of protein-protein diffusional encounter.
Protein association events are ubiquitous in biological systems. Some protein associations and subsequent responses are diffusion controlled in vivo. Hence, it is important to be able to compute bimolecular diffusional association rates for proteins. The Brownian dynamics simulation methodology may be used to simulate protein-protein encounter, compute association rates, and examine their depen...
متن کاملRole of anisotropy for protein-protein encounter.
Protein-protein interactions comprise both transport and reaction steps. During the transport step, anisotropy of proteins and their complexes is important both for hydrodynamic diffusion and accessibility of the binding site. Using a Brownian dynamics approach and extensive computer simulations, we quantify the effect of anisotropy on the encounter rate of ellipsoidal particles covered with sp...
متن کاملEncounter complexes and dimensionality reduction in protein–protein association
An outstanding challenge has been to understand the mechanism whereby proteins associate. We report here the results of exhaustively sampling the conformational space in protein-protein association using a physics-based energy function. The agreement between experimental intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE profiles calculated from the docked structures show...
متن کاملFree energy landscapes of encounter complexes in protein-protein association.
We report the computer generation of a high-density map of the thermodynamic properties of the diffusion-accessible encounter conformations of four receptor-ligand protein pairs, and use it to study the electrostatic and desolvation components of the free energy of association. Encounter complex conformations are generated by sampling the translational/rotational space of the ligand around the ...
متن کاملReplica exchange simulations of transient encounter complexes in protein-protein association.
Recent paramagnetic relaxation enhancement (PRE) studies on several weakly interacting protein complexes have unequivocally demonstrated the existence of transient encounter complexes. Here, we present a computational method to study protein-protein binding by creating equilibrium ensembles that include both specific and nonspecific protein complexes. In a joint analysis of simulation and exper...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 1997
ISSN: 0006-3495
DOI: 10.1016/s0006-3495(97)78837-4