Large conformational changes in the LID and NMP domains of adenylate kinase (AKE) are known to be key to ligand binding and catalysis, yet the order of binding events and domain motion is not well understood. Combining the multiple available structures for AKE with the energy landscape theory for protein folding, a theoretical model was developed for allostery, order of binding events, and efficient catalysis. Coarse-grained models and nonlinear normal mode analysis were used to infer that

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... nsic structural fluctuations dominate LID motion, whereas ligand-protein interactions and cracking (local unfolding) are more important during NMP motion. In addition, LID-NMP domain interactions are indispensable for efficient catalysis. LID domain motion precedes NMP domain motion, during both opening and closing. These findings provide a mechanistic explanation for the observed 1:1:1 correspondence between LID domain closure, NMP domain closure, and substrate turnover. This catalytic cycle has likely evolved to reduce misligation, and thus inhibition, of AKE. The separation of allosteric motion into intrinsic structural fluctuations and ligand-induced contributions can be generalized to further our understanding of allosteric transitions in other proteins. Downloaded from FIGURE 4. Proposed mechanism for AKE catalysis. All results presented suggest the following catalytic mechanism for AKE. a, open, unligated AKE. b, ATP binds while the LID domain closes. c.1, closure is followed by AMP binding/NMP domain closure. c.2, phosphoryl transfer occurs, resulting in two bound ADPs. d, thermal fluctuations open LID domain and one ADP is released. a, the loss of LID-CORE interactions induces opening of NMP domain, loss of the second ADP, and a return to the open conformation. States c.1 and c.2 are modeled by the deletion of one phosphoryl group from Ap5A in PDB code 1AKE.