Coarse-Grained Molecular Dynamics Simulations of the Bacterial Cell Wall

  • Lam T. Nguyen
  • James C. Gumbart
  • Grant J. JensenEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1440)


Understanding mechanisms of bacterial sacculus growth is challenging due to the time and length scales involved. Enzymes three orders of magnitude smaller than the sacculus somehow coordinate and regulate their processes to double the length of the sacculus while preserving its shape and integrity, all over a period of tens of minutes to hours. Decades of effort using techniques ranging from biochemical analysis to microscopy have produced vast amounts of data on the structural and chemical properties of the cell wall, remodeling enzymes and regulatory proteins. The overall mechanism of cell wall synthesis, however, remains elusive. To approach this problem differently, we have developed a coarse-grained simulation method in which, for the first time to our knowledge, the activities of individual enzymes involved are modeled explicitly. We have already used this method to explore many potential molecular mechanisms governing cell wall synthesis, and anticipate applying the same method to other, related questions of bacterial morphogenesis. In this chapter, we present the details of our method, from coarse-graining the cell wall and modeling enzymatic activities to characterizing shape and visualizing sacculus growth.

Key words

Coarse-grained modeling Molecular dynamics simulations Cell wall synthesis Bacterial morphogenesis Rod shape maintenance 



The authors wish to thank Catherine Oikonomou for revising the manuscript for clarity.


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Lam T. Nguyen
    • 1
  • James C. Gumbart
    • 2
  • Grant J. Jensen
    • 1
    Email author
  1. 1.California Institute of Technology and Howard Hughes Medical InstitutePasadenaUSA
  2. 2.School of PhysicsGeorgia Institute of TechnologyAtlantaUSA

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