Dynamic equilibrium between fast and slow forms of thrombin: A structural investigation of thrombin paradox

COMP 225

Divi Venkateswarlu, divi@ncat.edu, Department of Chemistry, North Carolina A & T State University, 338, Science Building, Greensboro, NC 27411 and Lee G. Pedersen, pedersen@email.unc.edu, Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.
Thrombin continues to dominate the blood coagulation cascade as a unique enzyme with functional modulation by sodium-ion binding that renders the enzyme to play a dual role as a pro-coagulant and anticoagulant. By performing extensive molecular dynamics (MD) simulations on thrombin structure for over 40 nanoseconds of simulation time in explicit water solvent in which sodium-ion binding was modeled to mimic both fast (Na+-bound) and slow (Na+-free) forms, we provide a structural rationale for the functional switch triggered by ion-binding. The simulations unambiguously demonstrate that the sodium-ion binding results in three major conformational changes that are dynamically linked: 1) A major restructuring of the water-channel that extends the sodium-binding site to the S2-specificity pocket 2) A 120 conformational switch in the side-chain of 192Glu522, that follows water restructuring, results in a dramatic break down of the dynamic linkage between the 60s loop and 192Glu522 and drifts away the 60s loop by ~3Ǻ and 3) the loss of the oxy-anion hole following a kink in the conformation of 193Gly523. We propose that the thrombin specificity is perhaps governed by a combination of these changes. The reduced interactions between the S2' specificity pocket residues and the incoming P2' substrate residues may play a key role in switching the thrombin function. These simulations provide a detailed look at the dynamic changes in the thrombin structure for the first time in true sodium-ion bound and free forms devoid of any active-site or exosite-inhibitors and corroborate with some of the recently reported experimental and structural findings to explain the thrombin paradox.

Poster Session -- Sponsored by Novartis Institutes for BioMedical Research
6:00 PM-8:00 PM, Tuesday, 30 August 2005 Washington DC Convention Center -- Hall A, Poster

8:00 PM-10:00 PM, Monday, 29 August 2005 Washington DC Convention Center -- Hall A, Sci-Mix

Division of Computers in Chemistry

The 230th ACS National Meeting, in Washington, DC, Aug 28-Sept 1, 2005