Paper Citing NAMD - Abstract
Diaz, Natalia; Suarez, Dimas
Extensive Simulations of the Full-Length Matrix Metalloproteinase-2 Enzyme in a Prereactive Complex with a Collagen Triple-Helical Peptide
BIOCHEMISTRY, 54:1243-1258, FEB 10 2015
Collagen hydrolysis catalyzed by matrix metalloproteinases is an important and complex process involved in a variety of physiological and pathological conditions. To contribute to its characterization at the molecular level, herein we analyze three different models for the complex formed between the full-length matrix metalloproteinase-2 (MMP-2) enzyme and a synthetic triple-helical peptide (fTHP-5). The considered MMP-2/fTHP-5 complexes mainly differ in the location of the C-terminal hemopexin-like domain, but in all of them, the middle a-chain of the substrate (B-chain) is placed within the active site groove. We performed extended molecular dynamics (MD) simulations to determine the most likely rearrangements of the MMP-2 domains in response to the presence of the triple helix. The relative stability of the MD models is assessed in terms of molecular mechanics Poisson-Boltzmann calculations and approximate estimations of configurational entropy. In addition, the most significant MMP-2 ... fTHP-5 interactions at the catalytic and noncatalytic domains are also analyzed to gather some clues about the role of the different domains during collagenolysis.
