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Center for Nonlinear Studies |
Dynamic properties are functionally important in many proteins, including the enzyme adenylate kinase (AK), for which two small domains (LID and NMP) close over the larger CORE domain; the reverse (opening) motion limits the rate of catalytic turnover. Here, we compare our previously published coarse-grained (double-well Gō) simulation of mesophilic AK from E. coli (AKmeso) to simulations of thermophilic AK from Aquifex aeolicus (AKthermo) in terms of the critical rigid-body, backbone dihedral, and contact motions in open, closed, and transition state (TS) ensembles. Like AKmeso, AKthermo follows a LID-first closure pathway in the presence of ligand, but the amplitude of LID rigid-body motions in the O ensemble decreases significantly. Backbone unfolding in O and/or TS ensembles decreases significantly relative to AKmeso in most of the interdomain hinges and within LID. In contact space, the TS of AKthermo has a weaker CORE-LID interface but a stronger contact network surrounding the CORE-NMP interface than the TS of AKmeso. A “heated” simulation of AKthermo at 375K and the simulation of AKmeso at 300K show similar conformational ensembles, both in the amplitude of CORE-LID motions in O ensemble and in the flexibility of some hinge regions, which supports the corresponding states hypothesis. Furthermore, mutation of 7 prolines unique to AKthermo to the corresponding residues from AKmeso more fully shifts the dynamics toward the more flexible behavior of AKmeso in most of the key hinges and even in some regions distant from any mutation. However, some prolines in AKthermo appear to strengthen or even substitute for nearby contacts from AKmeso so that local flexibility increases excessively upon mutating the proline. Finally, this mutagenic framework can inform the rational design of functionally important dynamics and allostery in other proteins toward engineering novel biological control systems.
Host: Mike Wall, mewall@lanl.gov