TY - JOUR
T1 - Effect of macromolecular crowding on reaction rates
T2 - A computational and theoretical study
AU - Jun, Soo Kim
AU - Yethiraj, Arun
N1 - Funding Information:
This material is based upon work supported by the National Science Foundation under grant No. CHE-0717569.
PY - 2009/2/18
Y1 - 2009/2/18
N2 - The effect of macromolecular crowding on the rates of association reactions are investigated using theory and computer simulations. Reactants and crowding agents are both hard spheres, and when two reactants collide they form product with a reaction probability, prxn. A value of prxn < 1 crudely mimics the fact that proteins must be oriented properly for an association reaction to occur. The simulations show that the dependence of the reaction rate on the volume fraction of crowding agents varies with the reaction probability. For reaction probabilities close to unity where most of encounters between reactants lead to a reaction, the reaction rate always decreases as the volume fraction of crowding agents is increased due to the reduced diffusion coefficient of reactants. On the other hand, for very small reaction probabilities where, in most of encounters, the reaction does not occur, the reaction rate increases with the volume fraction of crowding agents - in this case, due to the increase probability of a recollision. The Smoluchowski theory refined with the radiation boundary condition and the radial distribution function at contact is in quantitative agreement with simulations for the reaction rate constant and allows the quantitative analysis of both effects separately.
AB - The effect of macromolecular crowding on the rates of association reactions are investigated using theory and computer simulations. Reactants and crowding agents are both hard spheres, and when two reactants collide they form product with a reaction probability, prxn. A value of prxn < 1 crudely mimics the fact that proteins must be oriented properly for an association reaction to occur. The simulations show that the dependence of the reaction rate on the volume fraction of crowding agents varies with the reaction probability. For reaction probabilities close to unity where most of encounters between reactants lead to a reaction, the reaction rate always decreases as the volume fraction of crowding agents is increased due to the reduced diffusion coefficient of reactants. On the other hand, for very small reaction probabilities where, in most of encounters, the reaction does not occur, the reaction rate increases with the volume fraction of crowding agents - in this case, due to the increase probability of a recollision. The Smoluchowski theory refined with the radiation boundary condition and the radial distribution function at contact is in quantitative agreement with simulations for the reaction rate constant and allows the quantitative analysis of both effects separately.
UR - http://www.scopus.com/inward/record.url?scp=62649161932&partnerID=8YFLogxK
U2 - 10.1016/j.bpj.2008.11.030
DO - 10.1016/j.bpj.2008.11.030
M3 - Article
C2 - 19217851
AN - SCOPUS:62649161932
SN - 0006-3495
VL - 96
SP - 1333
EP - 1340
JO - Biophysical Journal
JF - Biophysical Journal
IS - 4
ER -