Specificity and Completion Time Distributions of Biochemical Processes

作者: Brian Munsky , Ilya Nemenman , Golan Bel

DOI: 10.1063/1.3274803

关键词:

摘要: In order to produce specific complex structures from a large set of similar biochemical building blocks, many systems require high sensitivity small molecular differences. The first and most common model used explain this specificity is kinetic proofreading, which has been extended variety detection DNA mismatch cell signaling processes. While the specification properties proofreading are well known were studied in various contexts, very little about its temporal behavior. work, we study dynamical discrete stochastic two branch schemes. Using Laplace transform corresponding chemical master equation, obtain an analytical solution for completion time distribution. particular provide expressions mean variance process times. We also show that, wide range parameters distinguishing between different products can be reduced much simpler three point process. Our results allow systematic interplay times as testing validity biological systems.

参考文章(43)
Jie Yan, Marcelo O. Magnasco, John F. Marko, A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases Nature. ,vol. 401, pp. 932- 935 ,(1999) , 10.1038/44872
A. Zilman, J. Pearson, G. Bel, Effects of jamming on nonequilibrium transport times in nanochannels. Physical Review Letters. ,vol. 103, pp. 128103- 128103 ,(2009) , 10.1103/PHYSREVLETT.103.128103
Michael A. Savageau, Accuracy of Proofreading with Zero Energy Cost Journal of Theoretical Biology. ,vol. 93, pp. 179- 195 ,(1981) , 10.1016/0022-5193(81)90063-1
Caridad Rosette, Guy Werlen, Mark A Daniels, Philmore O Holman, S.Munir Alam, Paul J Travers, Nicholas R.J Gascoigne, Ed Palmer, Stephen C Jameson, The impact of duration versus extent of TCR occupancy on T cell activation: a revision of the kinetic proofreading model. Immunity. ,vol. 15, pp. 59- 70 ,(2001) , 10.1016/S1074-7613(01)00173-X
Clark F. Springgate, Lawrence A. Loeb, On the fidelity of transcription by Escherichia coli ribonucleic acid polymerase. Journal of Molecular Biology. ,vol. 97, pp. 577- 591 ,(1975) , 10.1016/S0022-2836(75)80060-X
T. Lu, T. Shen, C. Zong, J. Hasty, P. G. Wolynes, Statistics of cellular signal transduction as a race to the nucleus by multiple random walkers in compartment/phosphorylation space Proceedings of the National Academy of Sciences of the United States of America. ,vol. 103, pp. 16752- 16757 ,(2006) , 10.1073/PNAS.0607698103
Christoph Dellago, Peter G. Bolhuis, Félix S. Csajka, David Chandler, Transition path sampling and the calculation of rate constants Journal of Chemical Physics. ,vol. 108, pp. 1964- 1977 ,(1998) , 10.1063/1.475562
Yueheng Lan, Peter G. Wolynes, Garegin A. Papoian, A variational approach to the stochastic aspects of cellular signal transduction Journal of Chemical Physics. ,vol. 125, pp. 124106- 124106 ,(2006) , 10.1063/1.2353835
J. D. Rabinowitz, C. Beeson, D. S. Lyons, M. M. Davis, H. M. McConnell, Kinetic discrimination in T-cell activation Proceedings of the National Academy of Sciences of the United States of America. ,vol. 93, pp. 1401- 1405 ,(1996) , 10.1073/PNAS.93.4.1401
Z.-J. Liu, H. Haleem-Smith, H. Chen, H. Metzger, Unexpected signals in a system subject to kinetic proofreading. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 98, pp. 7289- 7294 ,(2001) , 10.1073/PNAS.121171998