- 3:51 PM

Atomic Molecular Dynamics of Blood-Clotting Proteins

Coray M. Colina1, Robert E. Duke2, Lalith Perera2, Tom Darden2, and Lee Pedersen2. (1) Department of Materials Science and Engineering, Pennsylvania State University, 121 Steidle Building, University Park, PA 16802, (2) Laboratory of Quantitative and Computational Biology, National Institute of Environmental Health Science, Research Triangle Park, Raleigh, NC 27709

Enzymatic cascades are often employed in biochemistry systems to achieve a rapid response. In a cascade, an initial signal institutes a series of steps, each of which is catalyzed by an enzyme. At each step, the signal is amplified. Blood clots are formed by a cascade of zymogen activations: the activated form of one clotting factor catalyses the activation of the next. This series of events is known as the blood coagulation cascade.

Our group has been working on predicting structure and dynamics of several blood coagulation proteins for almost 10 years now. With our refine methodology and the computational power available, we are now able to study relatively long molecular dynamics simulations of systems of interest as potential targets for anti-coagulant inhibitors design.

We are currently pursuing molecular dynamics studies of blood-clotting proteins in order to learn more about the behavior of these proteins and hopefully discover more about how entropy influences their function. The simulations were performed for five different systems raging from 76,000 to 150,000 atoms. The time step used was one femtosecond due to the TIP3P water model and Amber forcefields were used, and our goal was to perform the finest simulations possible within the potentials selected. The 5 models were subjected to aqueous-phase molecular dynamics (MD) simulations, where unconstrained dynamics were performed using the Cornell et al. force-field (using AMBER8/PMEMD8 programs) and the ff99 parameter set. The Particle Mesh Ewald (PME) method was used in all aqueous simulations to account for long-range interactions during dynamics. NPT simulations at 300 K, SHAKE algorithm for bond constraints and a 1.0 fs time step were selected. The solute, ions/counter-ions and crystal water molecules, with a total up to 150,000 atoms, were immersed in rectilinear periodic boxes of minimum 15Å each side. Several steps of energy minimization and dynamics were carried out before beginning the “production run”. Finally, the post-equilibration NPT dynamics at 300 K, or production run, was completed normally for 20 ns, but in some cases up to 100 ns.

Even though some interesting changes in proteins, often occurs in the microsecond time scale and are outside the present computer power for the atomic detail selected to accomplish this project, we were able to study in several cases the dynamics of the blood coagulation proteins up to 100 ns. For the first time, changes in blood coagulation protein dynamics were observed within this time frame, which could help elucidate open questions in the literature. Specific examples for the dynamics of soluble tissue factor, factor VIIa and factor IXa as well as their binary and ternary complexes will be provided.

In each case, the simulations promoted the understanding of blood coagulation protein dynamics and in some cases helped guide in vivo experiments.