Insights into MAPK DFG flip mechanism by accelerated molecular dynamics
Graphical abstract
Introduction
The p38 proteins belong to the mitogen-activated protein kinases (MAPKs), a super-family of enzymes that is involved in many critical cellular processes such as proliferation, apoptosis and differentiation.1 Their activation mechanism is based on a dual phosphorylation reaction taking place on specific threonine and tyrosine residues belonging to the flexible activation loop responsible for the opening and the closing of the binding cavity,2, 3 where one ATP molecule binds during the activation process (see Fig. 1a).
The activation loop carries a DFG (Asp-Phe-Gly) motif, largely conserved among most of the proteins belonging to the kinase protein super-family.4 The conformations assumed by this flexible loop (or DFG-loop) are mainly characterized by the shift of the F side-chain ( in the protein) from its usual buried conformation (DFG-in) (see Fig. 1b) to a conformation that sterically interferes with ATP binding (DFG-out) (see Fig. 1c and d).
To date, a large number of completely resolved DFG-in three-dimensional structures, both in their apo and ligand-complexed forms, are collected in the RSCB Protein Data Bank,5 thus simplifying the development of new drugs designed to compete with ATP binding (type-I inhibitors6, 7, 8) (Fig. 1b). On the contrary, the number of published DFG-out three-dimensional structures with the activation loop completely resolved is not as significant. Moreover, until now, this latter conformation of the loop has been experimentally observed only in the presence of particular inhibitors based on a modified urea or amide scaffold capable to bind meanwhile to the ATP site and to a nearby allosteric hydrophobic pocket which becomes accessible by the flip of the DFG-loop (type-II inhibitors9) or exclusively within the allosteric pocket (type-III inhibitors10) (Fig. 1c and d). The urea/amide moiety of the allosteric inhibitors is considered to be fundamental for the DFG flip11 triggered by the establishment of two specific H-bonds with residues (belonging to the activation loop) and residue (belonging to Helix-C).12, 13
Whereas the hypothesis of a DFG-out conformation induced by allosteric inhibitors is generally supported by the results of X-ray experiments and by their slow binding kinetics experimentally observed,14, 12 the existence of a dynamic equilibrium between the DFG-in and DFG-out conformations of in its apo and complexed form has been first advanced on the basis of the results of NMR studies.15 The authors hypothesize that the DFG-out state is sampled less frequently than the DFG-in conformation; type-II inhibitors bind to the DFG-out form, freezing the protein in this conformation and suppressing the conformational exchange, while the binding of traditional inhibitors (ATP-site binders) affects the DFG equilibrium to a lesser extent. Besides NMR, Molecular Dynamics (MD) simulations are also being used extensively to sample the accessible protein conformations and build adequate pharmacophoric models. In particular, the dynamic behaviour of the DFG-loop was taken into account in a recent paper by Fremberg-Kesner and Elcock,16 who applied a high temperature (HT) molecular dynamics simulation to fasten the DFG-in to DFG-out transition and back, combined with a docking protocol to analyze the ligand binding properties of the different conformations. They described the presence of two transitional conformations defined as pseudo-DFG-in and pseudo-DFG-out, due to their respective similarity to the DFG-in and DFG-out states, and demonstrated that type-II inhibitors are able to bind not only to the DFG-out state but also to its DFG-in state. Thus, this observation supports the hypothesis that the pre-existence of the DFG-out conformation is not a prerequisite for inhibitor binding to , rather the DFG-out conformation might be triggered by the initial binding of type-II-inhibitor into the DFG-in conformation.
Recently, a detailed interpretation of the DFG flip in the Abl kinase has been given in the paper by Shana et al.17 Here, a combined experimental and theoretical approach, was applied to demonstrate that the DFG flip is regulated by the protonation of the DFG-loop aspartate residue; this allows the formation of a H-bond between the aspartate side-chain and the backbone carbonyl of a nearby valine, which promotes the DFG-loop conformational switch. Also in this work, evidence is provided for the existence of a stable intermediate conformation, which allows binding of a specific DFG-out binder inhibitor.
This thesis finds support in other computational and experimental studies recently performed. In particular, Kufareva and Abagyan,9 by applying a structure-based approach to design and evaluate type-II kinase inhibitors, demonstrated that the determinants for allosteric binding are preserved in most DFG-in structures. In 2007, an experimental analysis of the DFG conformational transition in has been attempted by Bukhtiyarova et al.18 They classified five DFG-motif mutants (F169G, F169R, F169Y, F169A and D166G) according to their local DFG conformation and, beside pointing out the determinant role played by residue in the structural dynamics of the activation loop, they suggested the existence in the free protein of a peculiar spatial organization, called -DFG-out, which could be intended as an intermediate between the DFG-in and the DFG-out conformations and which could provide a transient root of entry for type-II inhibitors. Similar intermediate conformations, also named DFG-‘in between’, were found depending on the structure of the ligands co-crystallized with the proteins manipulated in positions different from the DFG-motive and under different crystallization conditions.19, 20, 21, 10 In summary, two mechanisms have been up to now envisaged in the literature for allosteric inhibitors: (1) exclusively binding to proteins in the DFG-out conformation, which, although sampled less frequently, exists in equilibrium with the DFG-in conformation; (2) initial binding to proteins in the DFG-in conformation with subsequent promotion of the DFG-in to -out transition. Besides the recent evidences brought to support this second thesis, no description of the mechanism at the atomic level has yet produced.
In this work, a computational procedure, based on an Accelerated Molecular Dynamics (AMD) technique, will be applied to the human protein, in order to highlight the main interactions which take part in the DFG-in to DFG-out conformational change triggered by the binding of allosteric inhibitors. A viable transition mechanism will be proposed and implications to drug design will be discussed.
Section snippets
Materials and methods
The accelerated molecular dynamics technique, as implemented in GROMACS 3.3.3,22, 23, 24 has been applied to neglect non-energetically convenient pathways by driving the system to a pre-defined direction.
The X-ray structure of from mouse (PDB ID: 1P38) was chosen as the starting conformation since the whole structure is resolved. First, this structure was changed to the human sequence by computationally mutating and into and , respectively, with the software QUANTA
Results and discussion
The results of the AMD simulations performed in this work are analyzed to obtain a picture of the interaction network and the structural intermediates which lead the protein to change its active site conformation. The study is based on the assumption of fan-shaped motion of during the DFG transition between the initial DFG-in and final DFG-out states determined by X-ray crystallography.
The inter-residue interactions involved in the DFG flip
The analysis of the interaction energies (IE) between residues in the binding site region, together with detailed visual inspections of the protein structure conformations along the whole simulations, allow the determination of the main interactions responsible for the DFG-in/out transition.
The initial DFG-in conformation is characterized by the presence of two H-bonds between two residues of the DFG loop and ) and one residue belonging to the C-terminal domain. By analyzing
Conclusion
This work is based on the assumption that the conformational change of the activation loop is induced by the presence of allosteric inhibitors in the binding cavity in agreement with recently published findings which support the idea that it is more probable for allosteric inhibitors to bind first a DFG-in protein and then turn it into a DFG-out state than to encounter a free protein in the DFG-out conformation and directly bind to it.
The DFG-in to DFG-out mechanism proposed here describes at
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