Paper Citing NAMD - Abstract
Martinez, Leandro; Laine, Elodie; Malliavin, Therese E.; Nilges, Michael; Blondel, Arnaud
ATP conformations and ion binding modes in the active site of anthrax edema factor: A computational analysis
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 77:971-983, DEC 2009
The Edema Factor (EF), one of the virulence factors of anthrax, is an adenylyl cyclase that promotes the overproduction of cyclic-AMP (cAMP) from ATP, and therefore perturbs cell signaling. Crystallographic structures of EF bound to ATP analogs and reaction products, cyclic-AMP, and Pyrophosphate (PPi), revealed different substrate conformations and catalytic-cation binding modes, one or two cations being observed in the active site. To shed light into the biological significance of these crystallographic structures, the energtics, geometry, and dynamics of the active site are analyzed using molecular dynamics simulations. The ATP conformation observed in the one-metal-ion structure allows stronger interactions with the catalytic ion, and ATP is more restrained than in the structure containing two Mg(2+) ions. Therefore, vie propose that the conformation observed in the one-ion crystal structure is a more probable starting point for the reaction. The simulations also suggest that a C3'-endo sugar pucker facilitates nucleophilic attack. Additionally, the two-cation binding mode restrains the mobility of the reaction products, and thus their tendency to dissociate. Proteins 209; 77:971-983. (C) 2009 Wiley-Liss, Inc.
