Lattice Models of Bacterial Nucleoids

David S. Goodsell, Ludovic Autin, Arthur J. Olson

Research output: Contribution to journalArticle

9 Scopus citations

Abstract

Mesoscale molecular modeling is providing a new window into the inner workings of living cells. Modeling of genomes, however, remains a technical challenge, due to their large size and complexity. We describe a lattice method for rapid generation of bacterial nucleoid models that integrates experimental data from a variety of biophysical techniques and provides a starting point for simulation and hypothesis generation. The current method builds models of a circular bacterial genome with supercoiled plectonemes, packed within the small space of the bacterial cell. Lattice models are generated for Mycoplasma genitalium and Escherichia coli nucleoids, and used to simulate interaction data. The method is rapid enough to allow generation of multiple models when analyzing structure/function relationships, and we demonstrate use of the lattice models in creation of an all-atom representation of an entire cell.

Original languageEnglish (US)
Pages (from-to)5441-5447
Number of pages7
JournalJournal of Physical Chemistry B
Volume122
Issue number21
DOIs
StatePublished - May 31 2018

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All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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