Paper Citing NAMD - Abstract
Cortes-Ciriano, Isidro; Bouvier, Guillaume; Nilges, Michael; Maragliano, Luca; Malliavin, Therese E.
Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3446-3454, JUL 2015
Many proteins exhibit an equilibrium between multiple Conformations, some of them being characterized only by low-resolution information. Visiting all conformations is a demanding task for computational techniques performing enhanced but unfocused exploration of collective variable (CV) space. Otherwise, pulling a structure toward a target condition biases the exploration in a way difficult to assess. To address this problem; we introduce here the soft-ratcheting temperature-accelerated molecular dynamics (sr-TAMD), Where the exploration of CV space by TAMD is coupled to a soft-ratcheting algorithm that filters the evolving CV values according to a predefined criterion. Any low resolution or even qualitative information can be used to orient the exploration. We validate this technique by exploring the conformational space of the inactive state of the catalytic domain of the adenyl cyclase AC from Bordetella pertussis. The domain AC gets activated by association with calmodulin (CaM), and the available crystal structure shows that in the complex the protein has an elongated shape. High-resolution data are not available for the inactive, CaM-free protein state, but hydrodynamic measurements have shown that the inactive AC displays a more globular conformation. Here, using as CVs several geometric centers, we use sr-TAMD to enhance CV space sampling while filtering for CV values that correspond to centers moving close to each other) and we thus rapidly visit regions of conformational space that correspond to globular structures. The set of conformations sampled using sr-TAMD provides the most extensive description of the inactive state of AC up to now, consistent with available experimental information.
