Title: ChemCell : a particle-based model of protein chemistry and diffusion in microbial cells.

Abstract

Prokaryotic single-cell microbes are the simplest of all self-sufficient living organisms. Yet microbes create and use much of the molecular machinery present in more complex organisms, and the macro-molecules in microbial cells interact in regulatory, metabolic, and signaling pathways that are prototypical of the reaction networks present in all cells. We have developed a simple simulation model of a prokaryotic cell that treats proteins, protein complexes, and other organic molecules as particles which diffuse via Brownian motion and react with nearby particles in accord with chemical rate equations. The code models protein motion and chemistry within an idealized cellular geometry. It has been used to simulate several simple reaction networks and compared to more idealized models which do not include spatial effects. In this report we describe an initial version of the simulation code that was developed with FY03 funding. We discuss the motivation for the model, highlight its underlying equations, and describe simulations of a 3-stage kinase cascade and a portion of the carbon fixation pathway in the Synechococcus microbe.

Authors:

Plimpton, Steven James; Slepoy, Alexander

Publication Date:

Mon Dec 01 00:00:00 EST 2003

Research Org.:

Sandia National Laboratories

Sponsoring Org.:

USDOE

OSTI Identifier:

918231

Report Number(s):

SAND2003-4509
TRN: US200818%%319

DOE Contract Number:

AC04-94AL85000

Resource Type:

Technical Report

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; CARBON; CHEMISTRY; DIFFUSION; GEOMETRY; MACHINERY; PROTEINS; SIMULATION; Molecular biology.; Molecules-Models-Computer simulation.; Microbial biotechnology; Protein Structure; Molecular dynamics-Simulation methods.; Molecular dynamics.