Energetics and structural characterization of the large-scale functional motion of adenylate kinase.

Elena Formoso,Michele Parrinello,Vittorio Limongelli

doi:10.1038/srep08425

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.

Highlights

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations
During the metadynamics simulations the major conformational changes occur at the LID and the NMP domains, as expected
While the LID motion is barrier free, the NMP domain has a relatively high free-energy barrier between the open and closed states, 4 kBT (Figure 3a and 3b). These findings indicate that the rate-delimiting step for the functional conformational changes of AK is the motion of the NMP domain

Summary

Introduction

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. C ellular homeostasis is preserved through finely regulated molecular mechanisms, some of them involving macromolecules called metabolic monitors These systems control the cellular energy state by generating signaling molecules that counteract energy unbalancing through the stimulation of specific molecular targets. Once the two ADP molecules are formed, the enzyme opens the LID and NMP domains releasing the products Despite all this information, an exhaustive elucidation of the molecular mechanism of the motion between the different AK states is missing. We identified residues such as Arg[88], Arg[119] and Lys[13] that are involved in the enzyme conformational changes as potential druggable spots This detailed description of the events complements the picture coming from previous studies, revealing new structural information on the AK functional mechanism of great value to guide drug discovery strategies

Methods

Results

Conclusion