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To elucidate the interplay between conformational dynamics and enzyme activity, we first focus on a very popular model system, adenylate kinase (AK) that carries outstanding features of having obvious conformational changes during catalysis. The X-ray structures of AK in substrate-bound and apo (ligand free) forms open and closed, respectively. Two domains are involved in the conformational change, the LID and NMP domains. The pressing questions of AK based on previous studies include what is the temporal order of conformational change, how do hinge dynamics affect conformational change, and does solvation play a role in conformational change. By designing in silico experiments using all-atom molecular dynamics (AK) simulations and different initial structures and substrate binding configurations, we characterize the pathways of AK conformational changes in explicit solvent without applying any bias potential. We observed a complete closed-to-open and a partial open-to-closed transition, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available X-ray structures and earlier works of coarse-grained modeling. The trajectories of all-atom molecular dynamics simulations reveal the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK do not show prominent variation during the transition between closed and open forms. Finally, we characterize the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identify a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevents the opening transition. This work is currently in press in the Biophysical Journal.

Secondly, we develop a new computational framework to model intra-protein communication. A key novelty is to bridge atomic and coarse-grain (CG) models by reaching thermodynamic consistency. In particular, configurations sampled in atomic molecular dynamics trajectories are used to compute bond lengths and force constants in an elastic network approximation of the distribution of protein structures. To go beyond the harmonic approximation, a procedure is devised that computes model parameters in consecutive time windows with a user-specified size to follow the time evolution of the mechanical coupling network of protein conformation. In analogy to spectrogram of sound waves, sequential elastic network models calculated from atomic trajectories are termed the fluctuogram of protein dynamics. By analyzing and comparing the fluctuograms of Ca2+-bound and apo subtilisin, we illustrate that intermittent conformational changes and mechanical coupling variation are important mechanisms of intra-protein communication. We also show that the fluctuogram can be used to predict residues with high tendency to co-evolve by comparing with the results of statistical coupling analysis of a multiple sequence alignment. In addition to the strength of mechanical coupling, we found that the fluctuation of inter-residue force constants is also an important descriptor for co-evolution. Together, the results of this work (a) reveal the intermittent nature of conformational changes and the mechanical coupling variation, (b) show that intra-protein communication can proceed without a drastic change of protein structure and the pathways of which can be identified by the fluctuogram, and (c) support the theory that mechanically coupled residues tend to co-evolve. This work has been submitted to Plos Computational Biology. Currently, we are applying the fluctuogram analysis to elucidate the effects of solvation in organic solvent on protein dynamics.