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Costa MGS, Batista PR, Gomes A, Bastos LS, Louet M, Floquet N, Bisch PM, Perahia D. MDexciteR: Enhanced Sampling Molecular Dynamics by Excited Normal Modes or Principal Components Obtained from Experiments. J Chem Theory Comput 2023; 19:412-425. [PMID: 36622950 DOI: 10.1021/acs.jctc.2c00599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular dynamics with excited normal modes (MDeNM) is an enhanced sampling method for exploring conformational changes in proteins with minimal biases. The excitation corresponds to injecting kinetic energy along normal modes describing intrinsic collective motions. Herein, we developed a new automated open-source implementation, MDexciteR (https://github.com/mcosta27/MDexciteR), enabling the integration of MDeNM with two commonly used simulation programs with GPU support. Second, we generalized the method to include the excitation of principal components calculated from experimental ensembles. Finally, we evaluated whether the use of coarse-grained normal modes calculated with elastic network representations preserved the performance and accuracy of the method. The advantages and limitations of these new approaches are discussed based on results obtained for three different protein test cases: two globular and a protein/membrane system.
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Affiliation(s)
- Mauricio G S Costa
- Programa de Computação Científica, Vice-Presidência de Educação Informação e Comunicação, Fundação Oswaldo Cruz, Av. Brasil 4365, Residência Oficial, Manguinhos, 21040-900Rio de Janeiro, Brasil
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113, CNRS, École Normale Supérieure Paris-Saclay, 4 Avenue des Sciences, 91190Gif-sur-Yvette, France
| | - Paulo R Batista
- Programa de Computação Científica, Vice-Presidência de Educação Informação e Comunicação, Fundação Oswaldo Cruz, Av. Brasil 4365, Residência Oficial, Manguinhos, 21040-900Rio de Janeiro, Brasil
| | - Antoniel Gomes
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brasil
| | - Leonardo S Bastos
- Programa de Computação Científica, Vice-Presidência de Educação Informação e Comunicação, Fundação Oswaldo Cruz, Av. Brasil 4365, Residência Oficial, Manguinhos, 21040-900Rio de Janeiro, Brasil
| | - Maxime Louet
- Institut des Biomolecules Max Mousseron, UMR5247, CNRS, Université De Montpellier, ENSCM, 1919 Route de Mende, Montpellier, Cedex 0534095, France
| | - Nicolas Floquet
- Institut des Biomolecules Max Mousseron, UMR5247, CNRS, Université De Montpellier, ENSCM, 1919 Route de Mende, Montpellier, Cedex 0534095, France
| | - Paulo M Bisch
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brasil
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113, CNRS, École Normale Supérieure Paris-Saclay, 4 Avenue des Sciences, 91190Gif-sur-Yvette, France
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Renault P, Giraldo J. Dynamical Correlations Reveal Allosteric Sites in G Protein-Coupled Receptors. Int J Mol Sci 2020; 22:ijms22010187. [PMID: 33375427 PMCID: PMC7795036 DOI: 10.3390/ijms22010187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled Receptors (GPCRs) play a central role in many physiological processes and, consequently, constitute important drug targets. In particular, the search for allosteric drugs has recently drawn attention, since they could be more selective and lead to fewer side effects. Accordingly, computational tools have been used to estimate the druggability of allosteric sites in these receptors. In spite of many successful results, the problem is still challenging, particularly the prediction of hydrophobic sites in the interface between the protein and the membrane. In this work, we propose a complementary approach, based on dynamical correlations. Our basic hypothesis was that allosteric sites are strongly coupled to regions of the receptor that undergo important conformational changes upon activation. Therefore, using ensembles of experimental structures, normal mode analysis and molecular dynamics simulations we calculated correlations between internal fluctuations of different sites and a collective variable describing the activation state of the receptor. Then, we ranked the sites based on the strength of their coupling to the collective dynamics. In the β2 adrenergic (β2AR), glucagon (GCGR) and M2 muscarinic receptors, this procedure allowed us to correctly identify known allosteric sites, suggesting it has predictive value. Our results indicate that this dynamics-based approach can be a complementary tool to the existing toolbox to characterize allosteric sites in GPCRs.
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Affiliation(s)
- Pedro Renault
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
- Correspondence:
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Renault P, Louet M, Marie J, Labesse G, Floquet N. Molecular Dynamics Simulations of the Allosteric Modulation of the Adenosine A2A Receptor by a Mini-G Protein. Sci Rep 2019; 9:5495. [PMID: 30940903 PMCID: PMC6445292 DOI: 10.1038/s41598-019-41980-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 03/19/2019] [Indexed: 01/14/2023] Open
Abstract
Through their coupling to G proteins, G Protein-Coupled Receptors (GPCRs) trigger cellular responses to various signals. Some recent experiments have interestingly demonstrated that the G protein can also act on the receptor by favoring a closed conformation of its orthosteric site, even in the absence of a bound agonist. In this work, we explored such an allosteric modulation by performing extensive molecular dynamics simulations on the adenosine A2 receptor (A2aR) coupled to the Mini-Gs protein. In the presence of the Mini-Gs, we confirmed a restriction of the receptor’s agonist binding site that can be explained by a modulation of the intrinsic network of contacts of the receptor. Of interest, we observed similar effects with the C-terminal helix of the Mini-Gs, showing that the observed effect on the binding pocket results from direct local contacts with the bound protein partner that cause a rewiring of the whole receptor’s interaction network.
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Affiliation(s)
- Pedro Renault
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université de Montpellier, ENSCM, 34090, Montpellier, France.,Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090, Montpellier, France
| | - Maxime Louet
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université de Montpellier, ENSCM, 34090, Montpellier, France
| | - Jacky Marie
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université de Montpellier, ENSCM, 34090, Montpellier, France
| | - Gilles Labesse
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090, Montpellier, France
| | - Nicolas Floquet
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université de Montpellier, ENSCM, 34090, Montpellier, France.
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Duc NM, Kim HR, Chung KY. Recent Progress in Understanding the Conformational Mechanism of Heterotrimeric G Protein Activation. Biomol Ther (Seoul) 2017; 25:4-11. [PMID: 28035078 PMCID: PMC5207459 DOI: 10.4062/biomolther.2016.169] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/26/2016] [Accepted: 09/01/2016] [Indexed: 12/05/2022] Open
Abstract
Heterotrimeric G proteins are key intracellular coordinators that receive signals from cells through activation of cognate G protein-coupled receptors (GPCRs). The details of their atomic interactions and structural mechanisms have been described by many biochemical and biophysical studies. Specifically, a framework for understanding conformational changes in the receptor upon ligand binding and associated G protein activation was provided by description of the crystal structure of the β2-adrenoceptor-Gs complex in 2011. This review focused on recent findings in the conformational dynamics of G proteins and GPCRs during activation processes.
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Affiliation(s)
- Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
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Meissner GO, de Resende Lara PT, Scott LPB, Braz ASK, Chaves-Moreira D, Matsubara FH, Soares EM, Trevisan-Silva D, Gremski LH, Veiga SS, Chaim OM. Molecular cloning and in silico characterization of knottin peptide, U2-SCRTX-Lit2, from brown spider (Loxosceles intermedia) venom glands. J Mol Model 2016; 22:196. [PMID: 27488102 DOI: 10.1007/s00894-016-3067-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 07/10/2016] [Indexed: 01/16/2023]
Abstract
Inhibitor cystine knots (ICKs) are a family of structural peptides with a large number of cysteine residues that form intramolecular disulfide bonds, resulting in a knot. These peptides are involved in a variety of biological functions including predation and defense, and are found in various species, such as spiders, scorpions, sea anemones, and plants. The Loxosceles intermedia venom gland transcriptome identified five groups of ICK peptides that represent more than 50 % of toxin-coding transcripts. Here, we describe the molecular cloning of U2-Sicaritoxin-Lit2 (U2-SCRTX-Lit2), bioinformatic characterization, structure prediction, and molecular dynamic analysis. The sequence of U2-SCRTX-Lit2 obtained from the transcriptome is similar to that of μ-Hexatoxin-Mg2, a peptide that inhibits the insect Nav channel. Bioinformatic analysis of sequences classified as ICK family members also showed a conservation of cysteine residues among ICKs from different spiders, with the three dimensional molecular model of U2-SCRTX-Lit2 similar in structure to the hexatoxin from μ-hexatoxin-Mg2a. Molecular docking experiments showed the interaction of U2-SCRTX-Lit2 to its predictable target-the Spodoptera litura voltage-gated sodium channel (SlNaVSC). After 200 ns of molecular dynamic simulation, the final structure of the complex showed stability in agreement with the experimental data. The above analysis corroborates the existence of a peptide toxin with insecticidal activity from a novel ICK family in L. intermedia venom and demonstrates that this peptide targets Nav channels.
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Affiliation(s)
- Gabriel Otto Meissner
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil
| | - Pedro Túlio de Resende Lara
- Laboratory of Computational Biology and Bioinformatics, Federal University of ABC, Santo André, São Paulo, Brazil
| | - Luis Paulo Barbour Scott
- Laboratory of Computational Biology and Bioinformatics, Federal University of ABC, Santo André, São Paulo, Brazil
| | - Antônio Sérgio Kimus Braz
- Laboratory of Computational Biology and Bioinformatics, Federal University of ABC, Santo André, São Paulo, Brazil
| | - Daniele Chaves-Moreira
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil
| | - Fernando Hitomi Matsubara
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil
| | - Eduardo Mendonça Soares
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil
| | - Dilza Trevisan-Silva
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil
| | - Luiza Helena Gremski
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil.,Laboratory of Molecular Immunopathology, Department of Clinical Pathology, Clinical Hospital of Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Silvio Sanches Veiga
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil
| | - Olga Meiri Chaim
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil.
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Louet M, Seifert C, Hensen U, Gräter F. Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces. PLoS Comput Biol 2015; 11:e1004358. [PMID: 26244893 PMCID: PMC4526232 DOI: 10.1371/journal.pcbi.1004358] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 05/28/2015] [Indexed: 11/23/2022] Open
Abstract
The Catabolite Activator Protein (CAP) is a showcase example for entropic allostery. For full activation and DNA binding, the homodimeric protein requires the binding of two cyclic AMP (cAMP) molecules in an anti-cooperative manner, the source of which appears to be largely of entropic nature according to previous experimental studies. We here study at atomic detail the allosteric regulation of CAP with Molecular dynamics (MD) simulations. We recover the experimentally observed entropic penalty for the second cAMP binding event with our recently developed force covariance entropy estimator and reveal allosteric communication pathways with Force Distribution Analyses (FDA). Our observations show that CAP binding results in characteristic changes in the interaction pathways connecting the two cAMP allosteric binding sites with each other, as well as with the DNA binding domains. We identified crucial relays in the mostly symmetric allosteric activation network, and suggest point mutants to test this mechanism. Our study suggests inter-residue forces, as opposed to coordinates, as a highly sensitive measure for structural adaptations that, even though minute, can very effectively propagate allosteric signals. The Catabolite Activator Protein (CAP) is a well-studied example for how cellular catabolite levels are integrated into the gene regulation. Its affinity for a specific stretch of DNA can be switched on by the binding of two nucleotide molecules termed cAMP to its two protomers. Even though the nucleotides occupy structurally identical binding pockets, the second cAMP binding occurs at an affinity orders of magnitude lower than the first cAMP binding. The question arises how, in the absence of structural changes, the first binding can affect the second. An answer from experiments has been that the communication is largely of entropic nature, i.e. the second cAMP binding would lead to a pronounced reduction in atomic fluctuations of the protein without affecting the atomic mean positions. We here revisited this question by performing Molecular Dynamics simulations. By measuring correlations of forces, a newly derived method outperforming the more common coordinate-based approach, we could recover the previously determined entropic penalty. In addition, however, we observed unobtrusive structural changes of side-chain interactions leading to the occlusion of the second binding pocket that add a critical ‘enthalpic’ component hitherto overlooked. Our study provides a mechanistic view onto the intriguing anti-cooperativity of CAP.
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Affiliation(s)
- Maxime Louet
- Heidelberg Institutes for Theoretical Studies gGmbH, Heidelberg, Germany
| | - Christian Seifert
- Heidelberg Institutes for Theoretical Studies gGmbH, Heidelberg, Germany
| | - Ulf Hensen
- Eidgenössische Technische Hochschule Zürich, Department of Biosystem Science and Engineering, Basel, Switzerland
| | - Frauke Gräter
- Heidelberg Institutes for Theoretical Studies gGmbH, Heidelberg, Germany; CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China
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Pachov DV, van den Bedem H. Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs. PLoS Comput Biol 2015; 11:e1004361. [PMID: 26218073 PMCID: PMC4517867 DOI: 10.1371/journal.pcbi.1004361] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 05/22/2015] [Indexed: 11/19/2022] Open
Abstract
Proteins perform their function or interact with partners by exchanging between conformational substates on a wide range of spatiotemporal scales. Structurally characterizing these exchanges is challenging, both experimentally and computationally. Large, diffusional motions are often on timescales that are difficult to access with molecular dynamics simulations, especially for large proteins and their complexes. The low frequency modes of normal mode analysis (NMA) report on molecular fluctuations associated with biological activity. However, NMA is limited to a second order expansion about a minimum of the potential energy function, which limits opportunities to observe diffusional motions. By contrast, kino-geometric conformational sampling (KGS) permits large perturbations while maintaining the exact geometry of explicit conformational constraints, such as hydrogen bonds. Here, we extend KGS and show that a conformational ensemble of the α subunit Gαs of heterotrimeric stimulatory protein Gs exhibits structural features implicated in its activation pathway. Activation of protein Gs by G protein-coupled receptors (GPCRs) is associated with GDP release and large conformational changes of its α-helical domain. Our method reveals a coupled α-helical domain opening motion while, simultaneously, Gαs helix α5 samples an activated conformation. These motions are moderated in the activated state. The motion centers on a dynamic hub near the nucleotide-binding site of Gαs, and radiates to helix α4. We find that comparative NMA-based ensembles underestimate the amplitudes of the motion. Additionally, the ensembles fall short in predicting the accepted direction of the full activation pathway. Taken together, our findings suggest that nullspace sampling with explicit, holonomic constraints yields ensembles that illuminate molecular mechanisms involved in GDP release and protein Gs activation, and further establish conformational coupling between key structural elements of Gαs.
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Affiliation(s)
- Dimitar V. Pachov
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Henry van den Bedem
- Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, Stanford University, Stanford, California, United States of America
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Ghrelin receptor conformational dynamics regulate the transition from a preassembled to an active receptor:Gq complex. Proc Natl Acad Sci U S A 2015; 112:1601-6. [PMID: 25605885 DOI: 10.1073/pnas.1414618112] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
How G protein-coupled receptor conformational dynamics control G protein coupling to trigger signaling is a key but still open question. We addressed this question with a model system composed of the purified ghrelin receptor assembled into lipid discs. Combining receptor labeling through genetic incorporation of unnatural amino acids, lanthanide resonance energy transfer, and normal mode analyses, we directly demonstrate the occurrence of two distinct receptor:Gq assemblies with different geometries whose relative populations parallel the activation state of the receptor. The first of these assemblies is a preassembled complex with the receptor in its basal conformation. This complex is specific of Gq and is not observed with Gi. The second one is an active assembly in which the receptor in its active conformation triggers G protein activation. The active complex is present even in the absence of agonist, in a direct relationship with the high constitutive activity of the ghrelin receptor. These data provide direct evidence of a mechanism for ghrelin receptor-mediated Gq signaling in which transition of the receptor from an inactive to an active conformation is accompanied by a rearrangement of a preassembled receptor:G protein complex, ultimately leading to G protein activation and signaling.
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Sun X, Ågren H, Tu Y. Microsecond Molecular Dynamics Simulations Provide Insight into the Allosteric Mechanism of the Gs Protein Uncoupling from the β2 Adrenergic Receptor. J Phys Chem B 2014; 118:14737-44. [PMID: 25453446 DOI: 10.1021/jp506579a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Experiments have revealed that in the β(2) adrenergic receptor (β(2)AR)-Gs protein complex the α subunit (Gαs) of the Gs protein can adopt either an "open" conformation or a "closed" conformation. In the "open" conformation the Gs protein prefers to bind to the β(2)AR, while in the "closed" conformation an uncoupling of the Gs protein from the β(2)AR occurs. However, the mechanism that leads to such different behaviors of the Gs protein remains unclear. Here, we report results from microsecond molecular dynamics simulations and community network analysis of the β(2)AR-Gs complex with Gαs in the "open" and "closed" conformations. We observed that the complex is stabilized differently in the "open" and "closed" conformations. The community network analysis reveals that in the "closed" conformation there exists strong allosteric communication between the β(2)AR and Gβγ, mediated by Gαs. We suggest that such high information flows are necessary for the Gs protein uncoupling from the β(2)AR.
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Affiliation(s)
- Xianqiang Sun
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology , S-106 91 Stockholm, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology , S-106 91 Stockholm, Sweden
| | - Yaoquan Tu
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology , S-106 91 Stockholm, Sweden
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Good DB, Wang S, Ward ME, Struppe J, Brown LS, Lewandowski JR, Ladizhansky V. Conformational Dynamics of a Seven Transmembrane Helical Protein Anabaena Sensory Rhodopsin Probed by Solid-State NMR. J Am Chem Soc 2014; 136:2833-42. [DOI: 10.1021/ja411633w] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | | | | | - Jochem Struppe
- Bruker Biospin Ltd., Billerica, Massachusetts 01821, United States
| | | | - Józef R. Lewandowski
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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