A Concerted Mechanism for Opening the GDP Binding Pocket and Release of the Nucleotide in Hetero-Trimeric G-Proteins

Louet, Maxime; Pérahia, David; Martinez, Jean; Floquet, Nicolas

doi:10.1016/j.jmb.2011.05.034

Cited by 30 publications

(51 citation statements)

References 55 publications

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“…Interestingly, our calculations supported a much easier extraction of the GDP on the phosphate side. Moreover, the forced extraction of GDP on this side promoted large amplitude motions of the protein that were in close agreement with those we described previously as putatively involved in GDP release [13].…”

Section: Introductionsupporting

confidence: 90%

“…The PDB:1GP2 structure was anchored to the membrane as described previously [13] and was subjected to a first all-atoms 40 ns unconstrained Molecular Dynamics (MD) trajectory. At the end of this simulation, we concluded to a significant increase of the GDP total Solvent Accessible Surface Area from 4% to 10% (∼50 Å 2 ).…”

Section: Resultsmentioning

confidence: 99%

“…Using normal modes calculations in vacuo performed on the whole heterotrimeric protein, we previously proposed that the unbinding of GDP might require (or promote) large, collective motions of the protein [13]. The involved mode (mode 17) described an inter-domain motion intrinsic to the G α subunit, leading to the partial opening of the GDP binding pocket.…”

Section: Resultsmentioning

confidence: 99%

“…For each extraction pathway, about 25 intermediate positions of the GDP were further selected and used as starting points for 0.5 ns constrained MD, allowing the reconstruction of free energy profiles using the WHAM algorithm [12]. The sampling of the system was good as proven by a quasi-harmonic analysis of all concatenated data which reproduced the intrinsic, large collective motions we described previously for the same complex [13]. Interestingly, our calculations supported a much easier extraction of the GDP on the phosphate side.…”

Section: Introductionmentioning

confidence: 95%

See 3 more Smart Citations

GDP Release Preferentially Occurs on the Phosphate Side in Heterotrimeric G-proteins

Louet¹,

Martinez²,

Floquet

2012

PLoS Comput Biol

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After extra-cellular stimulation of G-Protein Coupled Receptors (GPCRs), GDP/GTP exchange appears as the key, rate limiting step of the intracellular activation cycle of heterotrimeric G-proteins. Despite the availability of a large number of X-ray structures, the mechanism of GDP release out of heterotrimeric G-proteins still remains unknown at the molecular level. Starting from the available X-ray structure, extensive unconstrained/constrained molecular dynamics simulations were performed on the complete membrane-anchored Gi heterotrimer complexed to GDP, for a total simulation time overcoming 500 ns. By combining Targeted Molecular Dynamics (TMD) and free energy profiles reconstruction by umbrella sampling, our data suggest that the release of GDP was much more favored on its phosphate side. Interestingly, upon the forced extraction of GDP on this side, the whole protein encountered large, collective motions in perfect agreement with those we described previously including a domain to domain motion between the two ras-like and helical sub-domains of Gα.

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Section: Introductionsupporting

confidence: 90%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 95%

See 2 more Smart Citations

GDP Release Preferentially Occurs on the Phosphate Side in Heterotrimeric G-proteins

Louet¹,

Martinez²,

Floquet

2012

PLoS Comput Biol

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“…From NMA, the eigenvectors corresponding to the lowest frequencies are associated to the most collective motions of the protein, and are generally involved in its function (23). We have previously shown that although normal modes (NMs) are calculated in vacuum, these directions can successfully describe conformational transitions in proteins, showing remarkable agreement with structural observations (24)(25)(26). However, the major drawback of NMA resides in the fact that it neglects the structural and energetical effects of the surrounding water molecules, thus impairing proper estimation of the amplitude of the modes.…”

Section: Introductionmentioning

confidence: 85%

Conformational Equilibrium of CDK/Cyclin Complexes by Molecular Dynamics with Excited Normal Modes

Floquet

Costa

Batista

et al. 2015

Biophysical Journal

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Cyclin-dependent kinases (CDKs) and their associated regulatory cyclins are central for timely regulation of cell-cycle progression. They constitute attractive pharmacological targets for development of anticancer therapeutics, since they are frequently deregulated in human cancers and contribute to sustained, uncontrolled tumor proliferation. Characterization of their structural/dynamic features is essential to gain in-depth insight into structure-activity relationships. In addition, the identification of druggable pockets or key intermediate conformations yields potential targets for the development of novel classes of inhibitors. Structural studies of CDK2/cyclin A have provided a wealth of information concerning monomeric/heterodimeric forms of this kinase. There is, however, much less structural information for other CDK/cyclin complexes, including CDK4/cyclin D1, which displays an alternative (open) position of the cyclin partner relative to CDK, contrasting with the closed CDK2/cyclin A conformation. In this study, we carried out normal-mode analysis and enhanced sampling simulations with our recently developed method, molecular dynamics with excited normal modes, to understand the conformational equilibrium on these complexes. Interestingly, the lowest-frequency normal mode computed for each complex described the transition between the open and closed conformations. Exploration of these motions with an explicit-solvent representation using molecular dynamics with excited normal modes confirmed that the closed conformation is the most stable for the CDK2/cyclin A complex, in agreement with their experimentally available structures. On the other hand, we clearly show that an open↔closed equilibrium may exist in CDK4/cyclin D1, with closed conformations resembling that captured for CDK2/cyclin A. Such conformational preferences may result from the distinct distributions of frustrated contacts in each complex. Using the same approach, the putative roles of the Thr(160) phosphoryl group and the T-loop conformation were investigated. These results provide a dynamic view of CDKs revealing intermediate conformations not yet characterized for CDK members other than CDK2, which will be useful for the design of inhibitors targeting critical conformational transitions.

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Computational structure‐based drug design: Predicting target flexibility

Iglesias¹,

Saen‐oon²,

Soliva³

et al. 2018

WIREs Comput Mol Sci

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The role of molecular modeling in drug design has experienced a significant revamp in the last decade. The increase in computational resources and molecular models, along with software developments, is finally introducing a competitive advantage in early phases of drug discovery. Medium and small companies with strong focus on computational chemistry are being created, some of them having introduced important leads in drug design pipelines. An important source for this success is the extraordinary development of faster and more efficient techniques for describing flexibility in three‐dimensional structural molecular modeling. At different levels, from docking techniques to atomistic molecular dynamics, conformational sampling between receptor and drug results in improved predictions, such as screening enrichment, discovery of transient cavities, etc. In this review article we perform an extensive analysis of these modeling techniques, dividing them into high and low throughput, and emphasizing in their application to drug design studies. We finalize the review with a section describing our Monte Carlo method, PELE, recently highlighted as an outstanding advance in an international blind competition and industrial benchmarks. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Software > Molecular Modeling

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A Concerted Mechanism for Opening the GDP Binding Pocket and Release of the Nucleotide in Hetero-Trimeric G-Proteins

Cited by 30 publications

References 55 publications

GDP Release Preferentially Occurs on the Phosphate Side in Heterotrimeric G-proteins

GDP Release Preferentially Occurs on the Phosphate Side in Heterotrimeric G-proteins

Conformational Equilibrium of CDK/Cyclin Complexes by Molecular Dynamics with Excited Normal Modes

Computational structure‐based drug design: Predicting target flexibility

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