Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase

Abstract

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. A comprehensive elucidation of the large-scale conformational motions that rule the functional mechanism of this enzyme is of great value to guide rationally the development of new medications. Here using a metadynamics-based computational protocol we elucidate the thermodynamics and structural properties underlying the AK functional transitions. The free energy estimation of the conformational motions of the enzyme allows characterizing the sequence of events that regulate its action. We reveal the atomistic details of the most relevant enzyme states, identifying residues such as Arg119 and Lys13, which play a key role during the conformational transitions and represent druggable spots to design enzyme inhibitors. Our study offers tools that open new areas of investigation on large-scale motion in proteins.

Substrate Binding Specifically Modulates Domain Arrangements in Adenylate Kinase

“…This is also supported by NMR studies on single substrate binding to ADK (42). Previous MD simulation studies that were either based on an implicit solvation model (26) or performed in explicit solvent also predicted a significant penalty for complete closing in the apo form (22,30). The simulations on holo ADK suggest that opening of the ATP-lid is the most likely first step in the release of the substrates (or products), as the free-energy landscape indicates a higher mobility of the ATP-lid compared to the AMP-lid in the holo form.…”

“…Alternatively, coarse-grained models allow more extensive sampling (20), but the accuracy of such models and the implicit treatment of the solvent may not be sufficient to analyze the influence of different substrates on the dynamics of ADK. More recently, progress has been made by employing advanced sampling methods in atomistic MD simulations on ADK (25)(26)(27)(28)(29)(30). Significant contributions have emerged from these studies, but as they focused on ADK in the apo state or bound to an inhibitor, the dynamics in the presence of natural substrates have not been covered.…”

Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate

“…The conformational spaces of different NMPKs like AMK, GMK, and UMK have been explored using several approaches like NMR, X-ray crystallography, and molecular dynamics simulations. These studies depicted the presence of considerable interdomain movements [9][10][11][12] during different steps of catalysis like substrate binding, phosphoryl transfer, product formation, and product release. An in-depth understanding of the catalytic steps at the molecular level is very useful in designing potent inhibitors for these enzymes.…”

The molecular mechanism behind resistance of the kinase FLT3 to the inhibitor quizartinib

“…Accordingly, several studies aimed at understanding resistance mutations in kinases, including ALK, Abl1, KIT, and EGFR . Many other studies applied MD simulations for a better understanding of the dynamics, diversity, and thermodynamics of kinases, their activation process, allostery, or in the process of drug design . A homology model of FLT3 was used to infer on the binding of certain drugs through computational docking …”