Paper Citing NAMD - Abstract
Ramirez, E.; Santana, A.; Cruz, A.; Plasencia, I.; Lopez, G.E.
Molecular dynamics of surfactant protein C: From single molecule to heptameric aggregates
BIOPHYSICAL JOURNAL, 90:2698-2705, APR 2006
Surfactant protein C (SP-C) is a membrane-associated protein essential for normal respiration. It has been found that the alpha-helix form of SP-C can undergo, under certain conditions, a transformation from an alpha-helix to a beta-strand conformation that closely resembles amyloid fibrils, which are possible contributors to the pathogenesis of pulmonary alveolar proteinosis. Molecular dynamics simulations using the NAMD2 package were performed for systems containing from one to seven SP-C molecules to study their behavior in water. The results of our simulations show that unfolding of the protein occurs at the amino terminal, and despite this unfolding, no transition from alpha-helix to beta-strand was observed.
