Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain

Abstract

The catalytic domain of the adenyl cyclase (AC) toxin from Bordetella pertussis is activated by interaction with calmodulin (CaM), resulting in cAMP overproduction in the infected cell. In the X-ray crystallographic structure of the complex between AC and the C terminal lobe of CaM, the toxin displays a markedly elongated shape. As for the structure of the isolated protein, experimental results support the hypothesis that more globular conformations are sampled, but information at atomic resolution is still lacking. Here, we use temperature-accelerated molecular dynamics (TAMD) simulations to generate putative all-atom models of globular conformations sampled by CaM-free AC. As collective variables, we use centers of mass coordinates of groups of residues selected from the analysis of standard molecular dynamics (MD) simulations. Results show that TAMD allows extended conformational sampling and generates AC conformations that are more globular than in the complexed state. These structures are then refined via energy minimization and further unrestrained MD simulations to optimize inter-domain packing interactions, thus resulting in the identification of a set of hydrogen bonds present in the globular conformations.

Molecular Modeling of the Catalytic Domain of CyaA Deepened the Knowledge of Its Functional Dynamics

“…The residues involved being located in the C-loop (Q302, E301 and N304) and in the C-terminal extremity (R338, D360 and N347), the hydrogen bonds connecting them and C-CaM, draw a network from C-CaM to the AC catalytic site and are thus directly related to the AC function. The importance of these residues was confirmed by mutagenesis studies [ 32 ], which shows that mutating these residues in Alanines induces a decrease of the affinity of AC for CaM. As the simultaneous mutations of the three residues is required to significantly reduce this affinity, it seems that the residues act cooperatively, which agrees with a model of the network transmitting the conformational transition from CaM to the AC catalytic site.…”

“…This barrier may also arise from an inappropriate choice of the collective variables, which pushes the system toward a free energy barrier. The detection of a water molecule bridging residues from the domains SA and CA made possible obtaining one less elongated conformation, which is relatively stable along several tenths of ns of MD trajectories [ 32 ].…”

Computational methods in drug discovery

“…Enhanced sampling methods introduce a bias on the system being simulated. Several methods of enhanced sampling are introduced in literature, including: accelerated molecular dynamics [196–197], metadynamics [198–199], umbrella sampling [200] and temperature-accelerated molecular dynamics [201–202]. …”

Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information

“…The previously recorded 39 MD and TAMD trajectories sample similar R g values in the range 24.5−26.5 Å, whereas the current sr-TAMD samples a distinct range of R g values: 22.5− 24 Å (Figure 2). Furthermore, the continuing MD trajectories (Table S1, Supporting Information) starting from sr-TAMD conformations sample the same gyration values as the sr-TAMD trajectories, which supports the stability of globular conformations extracted from sr-TAMD.…”

“…49 In conclusion, using the soft-ratcheting criterion together with TAMD permitted a broader exploration of the AC conformational space with respect to the previous TAMD calculation. 39 Furthermore, the sr-TAMD allowed us to obtain globular, metastable conformations as demonstrated by subsequent standard MD trajectories.…”