Theoretical investigation of the kinetics and thermodynamics of conformational equilibrium in crowded medium

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Iqbal, Muhammad Sajid
University of Lethbridge. Faculty of Arts and Science
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Lethbridge, Alta : University of Lethbridge, Dept. of Chemistry and Biochemistry
Macromolecular crowding alters the thermodynamic activities and kinetics of biochemical processes through an excluded volume effect. A theoretical framework, comprised of the Monte Carlo, extended scaled particle theory, and the transition state theory models is employed to compute the thermodynamic activities of three systems in virtually crowded media filled with polyethylene glycol molecules chosen from appropriately constructed conformational ensembles. The theoretical framework covers all the key steps required to prepare the equilibrated crowded medium and subsequently calculate the thermodynamic activities and kinetics. The thermodynamic activity depends on the geometrical parameters of all fluid particles and the model extracts the geometrical parameters by generating a convex hull from atomic coordinates. Moreover, it considers the nonideal contributions of crowder aggregates. This model predicts low to moderate crowding effects consistently with experimental findings with an enhancement in the stability of folded conformations from -0:2 to -2:0kT over open conformations due to crowding.
conformational equilibrium , excluded volume effect , kinetics , macromolecular crowding , macromolecular solutes , thermodynamic activies