Paper Citing NAMD - Abstract
Garrido-Arandia, Maria; Gomez-Casado, Cristina; Diaz-Perales, Araceli; Pacios, Luis F.
Molecular Dynamics of Major Allergens from Alternaria, Birch Pollen and Peach
MOLECULAR INFORMATICS, 33:682-694, OCT 2014
In the search for factors that make a protein allergenic (an issue that remains so far elusive) some common features of allergens such as small size, high stability and lipid binding are recognized in spite of their structural diversity. Other relevant but still poorly understood feature is their capability to form homodimers. We investigated by means of Molecular Dynamics (MD) calculations the stability in solution of several dimers of three major allergens from Alternaria mold, birch pollen, and peach fruit known to play essential roles in allergic disease. By running 20 ns MD simulations we found essential properties on solution that provide information of interest on their dimerization, stability of their epitopes and dynamical features of ligand binding cavities. Our results show that three essential allergen proteins display a distinct behavior on their trends to form homodimers in solution.
