BROWNIAN DYNAMICS SIMULATIONS OF ACTINS WITH ALDOLASE

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The proposed study will employ theoretical methods to investigate the interactions between actin and two glycolytic enzymes, aldolase and GAPDH, in order to better understand the nature of their associations. Brownian dynamics (BD) will be employed to study the diffusive dynamics and electrostatic interactions between the glycolytic enzymes and actin, the various kinds of complexes between actin and glycolytic enzymes, and their relative stabilities. This work will initiate adding hydrophobic forces to the existing electrostatic forces during the simulation so that combined free energies can be used to approximate binding constants. The Brownian dynamics (BD) simulation method will be applied to both equilibrium and dynamical aspects of the association of the proteins, with special attention to the electrostatics that affect association. The study will begin with simulations of aldolase interacting with F-actin and F-actin mutants, and subsequently be extended to a large number of BD-docked complexes which provide dynamic snapshots of binding. BD simulations will be used to compute the protein-protein potential of mean force versus the docking coordinate and obtain a free energy curve for the docking between the two proteins. The specific questions to be addressed include a) how do the complexes predicted for aldolase with G- or F-actin compare with the complexes predicted for GAPDH and G- or F-actin? b) Are the predicted energetics for the two glycolytic enzymes comparable? c) Do any of the predicted interactions correspond with experimental observations? d)When F-actin is mutated, how do the energetics and predicted interactions change? e) Is quaternary structure of the glycolytic enzyme important? f) Does a dimer of aldolase bind as effectively to F-actin as the intact tetrameric form of the enzyme? g) Do isolated peptides of pieces of an aldolase or a GAPDH bind in the same fashion as the intact enzyme? Can hydrophobic forces be included so that reasonable predictions of a binding constant can be made? Do the intact enzymes when bound to F-actin exhibit the same affinity for their substrate as they do when they are not bound to F-actin?