Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly

Tyler M. Earnest1,2, Jonathan Lai3, Ke Chen3,4, Michael J. Hallock5, James R. Williamson6,7,8, Zaida Luthey-Schulten1,2,3,*

1Center for the Physics of Living Cells, 2Department of Physics, and 3Department of Chemistry, University of Illinois, Urbana, Illinois; 4Department of Bioengineering, University of California, San Diego, La Jolla, California; and 5School of Chemical Sciences, University of Illinois, Urbana, Illinois; 6Department of Integrative Structural and Computational Biology, 7Department of Chemistry, and 8Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, California, *Correspondence to zan@illinois.edu.

doi: 10.1016/j.bpj.2015.07.030

Lattice model of a slow-growing E. coli cell

Archive of all files

Readme file for models

SBML files describing the in vitro assembly model

Lattice Microbes 2.2.1 input file describing the in vivo biogenesis model

Lattice Microbes

Acknowledgements

This work is supported by National Science foundation grants PHY-1026550 and MCB-1244570 and the Department of Energy grant ORNL 4000134575 and it is part of the Blue Waters sustained-petascale computing project, which is supported byt he National Science Foundation (awards OCI-0725070 and ACI-1238993) and the state of Illinois. Blue Waters is a joint effort of the University of Illinois at Urbana-Chamapgin and its National Center for Supporting Applications. This work also used the Extreme Science and Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1053575.