Compartmentation of proteins in cells is important to proper cell function. Interactions of F-actin and glycolytic enzymes is one mechanism by which glycolytic enzymes can compartment. Brownian dynamics (BD) simulations of the binding of the muscle form of the glycolytic enzyme fructose-1,6-bisphosphate aldolase (aldolase) to F- or G-actin provide first-encounter snapshots of these interactions. Using x-ray structures of aldolase, G-actin, and three-dimensional models of F-actin, the electrostatic potential about each protein was predicted by solving the linearized Poisson-Boltzmann equation for use in BD simulations. The BD simulations provided solution complexes of aldolase with F- or G-actin. All complexes demonstrate the close contacts between oppositely charged regions of the protein surfaces. Positively charged surface regions of aldolase (residues Lys 13, 27, 288, 293, and 341 and Arg 257) are attracted to the negatively charged amino terminus (Asp 1 and Glu 2 and 4) and other patches (Asp 24, 25, and 363 and Glu 361, 364, 99, and 100) of actin subunits. According to BD results, the most important factor for aldolase binding to actin is the quaternary structure of aldolase and actin. Two pairs of adjacent aldolase subunits greatly add to the positive electrostatic potential of each other creating a region of attraction for the negatively charged subdomain 1 of the actin subunit that is exposed to solvent in the quaternary F-actin structure.
The Brownian dynamics (BD) simulation method has been
employed to study the energetics of nonspecific
binding of λ Cro repressor protein (Cro) to model B-DNA. BD
simulates the diffusional dynamics as the
protein encounters the DNA surface and describes (i) the steric effects
of encounter between the irregular
surfaces of the protein and DNA molecules based on crystallograhpic
coordinates and (ii) the electrostatic
effects of encounter based on finite difference numerical solutions of
the Poisson−Boltzmann (PB) equation.
Using BD as a means of generating a statistical ensemble of docked
complexes in a Boltzmann distribution,
a direct calculation of the free energy and entropy of the encounter is
performed as a function of the radial
distance from the DNA helix axis to the protein center. During the
simulation electrostatic energies of protein
interaction with DNA are taken from prior solutions of the PB equation
stored on a cubic lattice. The PB
equation is solved in three different forms: (i) the linearized form
(LPB), (ii) the full nonlinear form (FPB),
and (iii) the full form with periodic boundary conditions implemented
(FPBBC). All three methods give
qualitatively similar free energy curves, but different depths for the
minima. For example, with FPBBC
electrostatics a free energy well-depth of −5.2 ± 0.5 kcal/mol was
obtained. The LPB method yielded a
well-depth of −6.1 ± 0.5 kcal/mol. Using the free energy
profile of nonspecific docking predicted with
FPBBC electrostatics and assuming free one-dimensional lateral
diffusion (sliding) of docked pairs, we estimated
the lifetime of a nonspecifically docked state to be 5 μs. The
protein should be able to slide laterally
approximately 50 base pairs before becoming detached.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.