Paper Citing NAMD - Abstract
Averett, Rodney D.; Menn, Bryant; Lee, Eric H.; Helms, Christine C.; Barker, Thomas; Guthold, Martin
A Modular Fibrinogen Model that Captures the Stress-Strain Behavior of Fibrin Fibers
BIOPHYSICAL JOURNAL, 103:1537-1544, OCT 3 2012
We tested what to our knowledge is a new computational model for fibrin fiber mechanical behavior. The model is composed of three distinct elements: the folded fibrinogen core as seen in the crystal structure, the unstructured alpha-C connector, and the partially folded alpha-C domain. Previous studies have highlighted the importance of all three regions and how they may contribute to fibrin fiber stress-strain behavior. Yet no molecular model has been computationally tested that takes into account the individual contributions of all these regions. Constant velocity, steered molecular dynamics studies at 0.025 angstrom/ps were conducted on the folded fibrinogen core and the alpha-C domain to determine their force-displacement behavior. A wormlike chain model with a persistence length of 0.8 nm (Kuhn length = 1.6 nm) was used to model the mechanical behavior of the unfolded alpha-C connector. The three components were combined to calculate the total stress-strain response, which was then compared to experimental data. The results show that the three-component model successfully captures the experimentally determined stress-strain behavior of fibrin fibers. The model evinces the key contribution of the alpha-C domains to fibrin fiber stress-strain behavior. However, conversion of the alpha-helical coiled coils to beta-strands, and partial unfolding of the protein, may also contribute.
