Enhanced Sampling of the Catalytic Domain of the Adenyl Cyclase CyaA from Bordetella Pertussis

Abstract

The catalytic domain (AC) of the CyaA adenyl cyclase toxin of Bordetella pertussis undergoes a conformational transition from the inactive (calmodulin-free) to the active (calmodulin-bound) conformation upon binding to calmodulin. In the structure of the complex between AC and the C terminal lobe of calmodulin (C-CaM) elucidated by X-ray crystallography (Guo et al, EMBO J, 24:3190, 2005), AC displays an elongated shape. On the contrary, the calmodulin-free inactive conformation has been only qualitatively characterized as more globular by hydrodynamics measurements (Karts et al, Biochemistry, 49:318, 2010).To better understand at the molecular level the conformational transition of AC from the active to the inactive conformation, we introduce here a variant of the Temperature Accelerated Molecular Dynamics (TAMD, Maragliano and Vanden-Eijnden, Chem Phys Lett, 426:168, 2006), the soft-ratcheting TAMD (sr-TAMD). TAMD is a an enhanced sampling method designed to explore the free energy surface associated to a set of variables describing the process under study. In sr-TAMD, a soft-ratcheting criterion (Perilla et al, J Comput Chem, 32:196, 2011) IS introduced to accept values of collective variables proposed at each step of TAMD. Hence, the sr-TAMD allows us to drive the sampling of the AC conformational space to those regions where the protein displays a more globular shape.The resulting conformations were further clustered using Self-organizing Maps (Bouvier et al, Bioinformatics, 26:53,2010), allowing us to identify intra-protein hydrogen bonds specific of the appearance of the compact conformations.