The dynamics of enzymatic switch cascades

We examine the dynamics of the mitogen-activated protein kinase (MAPK) multi-step enzymatic switching cascade, a highly conserved architecture utilised in cellular signal transduction. In treating the equations of motion, we replace the usual deterministic differential equation formalism with stochastic equations to accurately model the 'effective collisions' picture of the biochemical reactions that constitute the network. Furthermore we measure the fidelity of the signaling process through the mutual information content between the output of a given switch and the original environmental input to the system. We find that the enzymatic switches act as low-pass filters, with each switch in the cascade able to average over high frequency stochastic fluctuations in the network and throughput cleaner signals to downstream switches. We find optimal regions of mutual information transfer with respect to reaction velocity and species number parameters, and observe the dynamical memory-gain and memory-loss as well as decay in mutual information in quadruple-linked switch systems.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Physics.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2004

Author dc:creator

• Mukherji, Shankar, 1982-

Advisor dc:contributor.advisor

• Leonid A. Mirny.

• Physics.
• Mathematics.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/32747

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/32747