Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations

Berteotti, Anna; Cavalli, Andrea; Branduardi, Davide; Gervasio, Francesco Luigi; Recanatini, Maurizio; Parrinello, Michele

doi:10.1021/ja806846q

Cited by 131 publications

(166 citation statements)

References 71 publications

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“…In the ADA case, assuming that the initial and the final state correspond to ADA with the H3 α-helix in the closed and open conformation, respectively, a PCV is constructed with the cartesian coordinates of the alpha carbons of the residues that determine the α-helix movement. This type of CV has been successfully applied in recent studies on complex protein motion (29,30) and ligand/protein docking (20).…”

Section: Resultsmentioning

confidence: 99%

Sampling protein motion and solvent effect during ligand binding

Limongelli

Marinelli

Cosconati³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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106

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An exhaustive description of the molecular recognition mechanism between a ligand and its biological target is of great value because it provides the opportunity for an exogenous control of the related process. Very often this aim can be pursued using high resolution structures of the complex in combination with inexpensive computational protocols such as docking algorithms. Unfortunately, in many other cases a number of factors, like protein flexibility or solvent effects, increase the degree of complexity of ligand/protein interaction and these standard techniques are no longer sufficient to describe the binding event. We have experienced and tested these limits in the present study in which we have developed and revealed the mechanism of binding of a new series of potent inhibitors of Adenosine Deaminase. We have first performed a large number of docking calculations, which unfortunately failed to yield reliable results due to the dynamical character of the enzyme and the complex role of the solvent. Thus, we have stepped up the computational strategy using a protocol based on metadynamics. Our approach has allowed dealing with protein motion and solvation during ligand binding and finally identifying the lowest energy binding modes of the most potent compound of the series, 4-decyl-pyrazolo[1,5-a]pyrimidin-7-one.ADA | well-tempered metadynamics | ligand/protein docking | path collective variables | reweighting algorithm A denosine Deaminase (ADA) regulates the purine metabolism by catalyzing the irreversible hydrolysis of adenosine to inosine and 2′-deoxyadenosine to 2′-deoxyinosine. Thus, this enzyme plays a crucial role in many pathologies such as inflammation, some types of cancer, and others which are strictly connected to the physiological level of these nucleosides (1-5). Despite great efforts in developing ADA inhibitors, only Pentostatin is currently in clinical use (I in Fig. S1) (3). However, recent progress has been reported by Terasaka et al. and by some of us who have developed a new generation of nonnucleoside ADA inhibitors (II, III, and IV in Fig. S1) (6-11). Unfortunately, the understanding at molecular level of the ligand/ADA interaction is hampered by the pronounced ability of the active site to accommodate different inhibitors and by the crucial role played by water molecules during ligand binding. A rational drug design is further complicated by the fact that in response to different inhibitors, ADA can assume either an open or a closed conformation by changing the position of the H3 α-helix (Thr57-Ala73). The open conformation corresponds to the apo-form (PDB ID code 3iar) and is preferred when a nonnucleoside inhibitor is bound (12, 13). In this case, the active site presents a hydrophilic subsite S0 and three hydrophobic subsites F0, F1, and F2 (Fig. 1A) (13). The S0 subsite is defined by the structural gate formed by a β-strand (Leu182-Asp185) and two leucine side chains attached to the H3 α-helix while the F0 site is formed by the hydrophobic side chains of the H3 α-helix. In the op...

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Section: Resultsmentioning

confidence: 99%

Sampling protein motion and solvent effect during ligand binding

Limongelli

Marinelli

Cosconati³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

106

105

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“…[45] To reconstruct the freeenergy surface of the two copper dimers, we used well-tempered (WT) metadynamics, proved to be effective in previous studies, [46][47][48][49] within the framework of PLUMED. [50] Gaussians of 0.2 kcal mol À1 in height were deposited at one picosecond time interval, with a bias factor of 10.…”

Section: Metadynamics (Md)mentioning

confidence: 99%

Intramolecular Weak Interactions in the Thermodynamic Stereoselectivity of Copper(II) Complexes with Carnosine–Trehalose Conjugates

Grasso

Arena

Bellia

et al. 2011

Chemistry A European J

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The interactions of metal ions with chiral molecules are of particular interest for relevant biochemical processes, as many of them are made possible only with a selected chirality of the stereocenters. In this work we report a study of the stereoselectivity of copper(II) complexes with D-trehalose-L-carnosine and D-trehalose-D-carnosine as a prototypical case of natural chirality selection. The interest in L-carnosine dipeptide is compounded by its antioxidant and antitumor properties, which are further enhanced when combined with D-trehalose. Potentiometric, calorimetric, and UV/circular dichroism (CD) spectroscopic measurements show that the copper(II) dimer of D-trehalose-L-carnosine is more stable than the D-trehalose-D-carnosine diastereoisomeric copper(II) dimer (log β(L)(22-2) - log β(D)(22-2) = 3.6). Free-energy calculations highlight that the cause of this different behavior lies with different intramolecular weak interactions between the diastereoisomers. The different pattern of hydrogen bonds and the different CH-π interactions between the π-electron-rich imidazole and the α-glucose rings are more favorable by 5 kcal mol(-1) in the L dimer.

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“…This need is less stringent when enhanced sampling methods are combined with a multiple-replica approach, as in the case of the parallel-tempering metadynamics simulations approach (PTmetaD) (28,31). Indeed, it has been shown that PT-metaD is able to converge very complex conformational free-energy surfaces of kinases as a function of a few relevant variables (32,33).…”

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confidence: 99%

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase

Sutto

Gervasio

2013

Proc. Natl. Acad. Sci. U.S.A.

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Activating mutations in the epidermal growth factor receptor (EGFR) tyrosine kinase are frequently found in many cancers. It has been suggested that changes in the equilibrium between its active and inactive conformations are linked to its oncogenic potential. Here, we quantify the effects of some of the most common single (L858R and T790M) and double (T790M-L858R) oncogenic mutations on the conformational free-energy landscape of the EGFR kinase domain by using massive molecular dynamics simulations together with parallel tempering, metadynamics, and one of the best force-fields available. Whereas the wild-type EGFR catalytic domain monomer is mostly found in an inactive conformation, our results show a clear shift toward the active conformation for all of the mutants. The L858R mutation stabilizes the active conformation at the expense of the inactive conformation and rigidifies the αC-helix. The T790M gatekeeper mutant favors activation by stabilizing a hydrophobic cluster. Finally, T790M with L858R shows a significant positive epistasis effect. This combination not only stabilizes the active conformation, but in nontrivial ways changes the free-energy landscape lowering the transition barriers.conformational changes | resistance-causing mutations

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Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations

Cited by 131 publications

References 71 publications

Sampling protein motion and solvent effect during ligand binding

Sampling protein motion and solvent effect during ligand binding

Intramolecular Weak Interactions in the Thermodynamic Stereoselectivity of Copper(II) Complexes with Carnosine–Trehalose Conjugates

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase

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