Brownian Dynamics Simulations of Actins with Aldolase

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DESCRIPTION (provided by applicant): The cytoskeletal structure, F-actin, plays an important role in cellular metabolism by providing conditions for the high specificity of reactions within various metabolic pathways. Many glycolytic enzymes including fructose-1,6-bisphophsate aldolase (aldolase), glycerladehyde-3-phosphate dehydrogenase (GAPDH), and lactate dehydrogenase (LDH) bind actin reversibly. Other enzymes such as triose phosphate isomerase (TIM) bind indirectly through interactions with the enzymes that bind. The proposed study will use and enhance existing theoretical methods to better investigate the interaction of F-actin with glycolytic enzymes. The method of Brownian dynamics (BD) predicts the various kinds of complexes between F-actin and the glycolytic enzymes; BD also provides the relative stability of complexes by performing an automated forceguided exhaustive search. BD simulates the protein-protein associations in water as influenced by the ionic effects that mediate molecular interactions in physiological complexes. The simulations provide free energies of protein-protein associations. This work will expand the enzymes studied and continue to enhance the existing method as found in the program package MacroDox. The goals are: (1) to examine LDH and TIM interactions with F-actin and compare them to predictions for aldolase and GAPDH; (2) to reproduce experimentally observed factors on binding such as ionic strength, pH, and relative binding affinities; and (3) to treat enzyme-enzyme/F-actin complex interactions. The importance of the proposed study relates to the hypothesis that F-actin creates a structure in the cell cytoplasm upon which glycolytic enzymes associate and dissociate dynamically. These dynamic associations may be important to organizing the reactions in the glycolytic pathway and assembling an extensive complex of glycolytic enzymes. The outcome of the research would be an improved understanding of protein association with actin in solution. It will be a theoretical test for F-actin forming a framework for glycolytic enzymes to function in cells. It will further the understanding of the theory behind assembly of structures in the cytoplasmic matrix. Thus, the outcome of this research should have far-reaching implications for cytoplasmic structure and metabolic regulation.