TY - JOUR
T1 - Specificity and completion time distributions of biochemical processes
AU - Munsky, Brian
AU - Nemenman, Ilya
AU - Bel, Golan
N1 - Funding Information:
We thank N. Hengartner, J. Hopfield, and N. Sinitsyn for discussions during early stages of this work. We also thank B. Goldstein, R. Gutenkunst, M. Monine, and especially M. Savageau for helpful comments regarding this work. This work was partially funded by LANL LDRD program.
PY - 2009/12/1
Y1 - 2009/12/1
N2 - In order to produce specific complex structures from a large set of similar biochemical building blocks, many biochemical systems require high sensitivity to small molecular differences. The first and most common model used to explain this high specificity is kinetic proofreading, which has been extended to a variety of systems from detection of DNA mismatch to cell signaling processes. While the specification properties of kinetic proofreading models are well known and were studied in various contexts, very little is known about their temporal behavior. In this work, we study the dynamical properties of discrete stochastic two-branch kinetic proofreading schemes. Using the Laplace transform of the corresponding chemical master equation, we obtain an analytical solution for the completion time distribution. In particular we provide expressions for the specificity as well as the mean and variance of the process completion times. We also show that, for a wide range of parameters, a process distinguishing between two different products can be reduced to a much simpler three-point process. Our results allow for the systematic study of the interplay between specificity and completion times, as well as testing the validity of the kinetic proofreading model in biological systems.
AB - In order to produce specific complex structures from a large set of similar biochemical building blocks, many biochemical systems require high sensitivity to small molecular differences. The first and most common model used to explain this high specificity is kinetic proofreading, which has been extended to a variety of systems from detection of DNA mismatch to cell signaling processes. While the specification properties of kinetic proofreading models are well known and were studied in various contexts, very little is known about their temporal behavior. In this work, we study the dynamical properties of discrete stochastic two-branch kinetic proofreading schemes. Using the Laplace transform of the corresponding chemical master equation, we obtain an analytical solution for the completion time distribution. In particular we provide expressions for the specificity as well as the mean and variance of the process completion times. We also show that, for a wide range of parameters, a process distinguishing between two different products can be reduced to a much simpler three-point process. Our results allow for the systematic study of the interplay between specificity and completion times, as well as testing the validity of the kinetic proofreading model in biological systems.
UR - http://www.scopus.com/inward/record.url?scp=73449101497&partnerID=8YFLogxK
U2 - 10.1063/1.3274803
DO - 10.1063/1.3274803
M3 - Article
AN - SCOPUS:73449101497
SN - 0021-9606
VL - 131
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
IS - 23
M1 - 235103
ER -