150 CATALYZING INQUIRY
5.4.2.4.2 The Movement of Listeria Bacteria Alberts and Odell have developed a computational model
of Listera monocytogenes based on an explicit simulation of a large number of monomer-scale biochemi-
cal and mechanical interactions,^63 representing all protein-protein binding interactions with on-rate and
off-rate kinetic equations. These equations characterize individual actin filaments: the bulk properties of
the actin “gel” arise from the contributions of the many individual filaments of the actin network; and
the growth of any particular filament depends on that filament’s precise location, orientation, and
biochemical state, all of which change through time. Mechanical interactions, which resolve collisions
and accommodate the stretching of protein-protein linkages, follow Newton’s laws.
The model is based on a large set of differential equations that determine how the relevant state
variables change with time. These equations are solved numerically, taking into account the fact that
discontinuities in time occur frequently as objects suddenly collide and as objects suddenly spring into
existence or disappear (due to new filament nucleation and depolymerization). The model accommo-
FIGURE 5.8 The binding free energy between two protofilaments as a function of the subunit rise between adja-
cent dimmers. Sept et al. used electrostatic calculations to determine the binding energy between two protofila-
ments as a function of the subunit rise between adjacent dimers. Viewed from the growing (+) end of the tubule,
the graph demonstrates the most favorable configuration at various points during assembly. SOURCE: Reprinted
by permission from D. Sept, N.A. Baker, and J.A. McCammon, “The Physical Basis of Microtubule Structure and
Stability,” Protein Science 12:2257-2261, 2003. Copyright 2003 by the Protein Society.
(^63) J.B. Alberts and G.M. Odell, “In Silico Reconstitution of Listeria Propulsion Exhibits Nano-Saltation,” PLoS Biology 2(12):e412,
2004, available at http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=532387.