Theoretical investigation of the kinetics and thermodynamics of conformational equilibrium in crowded medium
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Date
2017
Authors
Iqbal, Muhammad Sajid
University of Lethbridge. Faculty of Arts and Science
Journal Title
Journal ISSN
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Publisher
Lethbridge, Alta : University of Lethbridge, Dept. of Chemistry and Biochemistry
Abstract
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.
Description
Keywords
conformational equilibrium , excluded volume effect , kinetics , macromolecular crowding , macromolecular solutes , thermodynamic activies