Molecular Dynamics Study of an Actin Septamer: Testing the Holmes Model and the Hydrophobic Plug Loop Hypothesis
EMSL Project ID
19600
Abstract
This proposal is in response to the Science Theme Call. We are requesting standard access with non-proprietary status.Actin is a cellular protein which polymerizes into helical filaments. These filaments are involved in cell structure, muscle contraction, and cell motility. Various atomic models of the filament have been proposed, the most popular of which is the "Holmes model" (1). A controversial aspect of the Holmes model is the hydrophobic plug loop hypothesis, which suggests that residues 264-273 move away from their position on the monomer to insert into a pocket formed by the N+1 and N-1 protomers of the genetic helix.
Previous molecular dynamics studies of actin that we are aware of examined only one monomer (2), and hence provided little information about the behavior of actin when monomers contact one another. In our study we will perform energy minimization and molecular dynamics on an actin septamer. Preliminary simulations suggest that we should restrain the protomer at each end to minimize the effects of solvent exposure, and a given actin protomer interacts closely with the N+2 and N-2 protomers but not the N+3 and N-3 protomers. Thus, if we simulate a septamer, the central protomer will be in close contact only with other protomers that are unrestrained.
Our simulated structure will be the septamer according to the Holmes model. Dr. Holmes has provided us with two structures: one includes the hydrophobic plug loop rebuilt into its hypothesized position, while the other represents the Holmes model minus the rebuilt plug loop. We will perform simulations on both, with explicit solvent.
After minimization, simulated annealing will be performed, followed by a simulation at 300 K. Locally enhanced sampling will be used in the hydrophobic plug loop region.
By observing the stability of the two structures and the behavior of the hydrophobic plug loop, we will test the validity of the Holmes model. Understanding the structure of filamentous actin will not only clarify actin-actin interactions, but may also contribute to our knowledge of actin's interactions with a wide range of actin-binding proteins, with its bound divalent cation, and with the ATP/ADP of its enzymatic site. Understanding the actin filament will shed light on many issues relevant to national health, such as the actin-myosin interaction and the metastasis of cancer.
1) Holmes KC, Popp D, Gebhard W, and Kabsch W, Atomic model of the actin filament, Nature, 1990, 347: 44-49.
2) Wriggers W and Schulten K, Stability and dynamics of G-actin: Back-door water diffusion and behavior of a subdomain ¾ loop, Biophysical Journal, 1997, 73: 624-639; and Suda H and Saito M, Molecular dynamics simulations for actin monomers in solution, Journal of Theoretical Biology, 1994, 171: 347-349; and Wriggers W, Tang JX, Azuma T, Marks PW, Jamney PA, Cofilin and gelsolin segment-1: Molecular dynamics simulation and biochemical analysis predict a similar actin binding mode, Journal of Molecular Biology, 1998, 282: 921-932; and Wriggers W and Schulten K, Investigating a back door mechanism of actin phosphate release by steered molecular dynamics, Proteins: Structure, Function, and Genetics, 1999, 35: 262-273.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2006-07-21
End Date
2008-12-04
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members