1
|
Guan ZB, Deng XT, Zhang ZH, Xu GC, Cheng WL, Liao XR, Cai YJ. Engineering Glucosamine-6-Phosphate Synthase to Achieve Efficient One-Step Biosynthesis of Glucosamine. ACS Chem Biol 2024; 19:1237-1242. [PMID: 38723147 DOI: 10.1021/acschembio.4c00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
As an important functional monosaccharide, glucosamine (GlcN) is widely used in fields such as medicine, food nutrition, and health care. Here, we report a distinct GlcN biosynthesis method that utilizes engineered Bacillus subtilis glucosamine-6-phosphate synthase (BsGlmS) to convert D-fructose to directly generate GlcN. The best variant obtained by using a combinatorial active-site saturation test/iterative saturation mutagenesis (CAST/ISM) strategy was a quadruple mutant S596D/V597G/S347H/G299Q (BsGlmS-BK19), which has a catalytic activity 1736-fold that of the wild type toward D-fructose. Upon using mutant BK19 as a whole-cell catalyst, D-fructose was converted into GlcN with 65.32% conversion in 6 h, whereas the wild type only attained a conversion rate of 0.31% under the same conditions. Molecular docking and molecular dynamics simulations were implemented to provide insights into the mechanism underlying the enhanced activity of BK19. Importantly, the BsGlmS-BK19 variant specifically catalyzes D-fructose without the need for phosphorylated substrates, representing a significant advancement in GlcN biosynthesis.
Collapse
Affiliation(s)
- Zheng-Bing Guan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Xue-Ting Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zi-Hao Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Guo-Chao Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Wan-Li Cheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Xiang-Ru Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Yu-Jie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| |
Collapse
|
2
|
Quiroz RCN, Philot EA, General IJ, Perahia D, Scott AL. Effect of phosphorylation on the structural dynamics, thermal stability of human dopamine transporter: A simulation study using normal modes, molecular dynamics and Markov State Model. J Mol Graph Model 2023; 118:108359. [PMID: 36279761 DOI: 10.1016/j.jmgm.2022.108359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
The Human Dopamine Transporter (hDAT) plays an essential role in modulating the Influx/Efflux of dopamine, and it is involved in the mechanism of certain neurodegenerative diseases such as Parkinson's disease. Several studies have reported important states for Dopamine transport: outward-facing open state (OFo), the outward-facing closed state (OFc), the holo-occluded state closed (holo), and the inward-facing open state (IFo). Furthermore, experimental assays have shown that different phosphorylation conditions in hDAT can affect the rate of dopamine absorption. We present a protocol using hybrid simulation methods to study the conformational dynamics and stability of states of hDAT under different phosphorylation sites. With this protocol, we explored the conformational space of hDAT, identified the states, and evaluated the free energy differences and the transition probabilities between them in each of the phosphorylation cases. We also presented the conformational changes and correlated them with those described in the literature. There is a thesis/hypothesis that the phosphorylation condition corresponding to NP-333 system (where all sites Ser/Thr from residue 2 to 62 and 254 to 613 are phosphorylated, except residue 333) would decrease the rate of dopamine transport from the extracellular medium to the intracellular medium by hDAT as previously described in the literature by Lin et al., 2003. Our results corroborated this thesis/hypothesis and the data reported. It is probably due to the affectation/changes/alteration of the conformational dynamics of this system that makes the intermediate states more likely and makes it difficult to initial states associated with the uptake of dopamine in the extracellular medium, corroborating the experimental results. Furthermore, our results showed that just single phosphorylation/dephosphorylation could alter intrinsic protein motions affecting the sampling of one or more states necessary for dopamine transport. In this sense, the modification of phosphorylation influences protein movements and conformational preferences, affecting the stability of states and the transition between them and, therefore, the transport.
Collapse
Affiliation(s)
- R C N Quiroz
- Biossistemas, Universidade Federal do ABC, CCNH, Santo André, Brazil; Centro de Matemática, Computação e Cognição. Laboratório de Biofísica e Biologia Computacional. Universidade Federal do ABC, Santo André, São Paulo, Brazil
| | - E A Philot
- Centro de Matemática, Computação e Cognição. Laboratório de Biofísica e Biologia Computacional. Universidade Federal do ABC, Santo André, São Paulo, Brazil
| | - I J General
- School of Science and Technology, Universidad Nacional de San Martin, ICIFI and CONICET, 25 de Mayo y Francia, San Martín, 1650, Buenos Aires, Argentina
| | - D Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, UMR 8113, CNRS, 4 avenue des Sciences, 91190 Gif-sur-Yvette, France
| | - A L Scott
- UFABC - Universidade Federal Do ABC, Centro de Matemática, Computação e Cognição, Laboratório de Biofísica e Biologia Computacional, Brazil.
| |
Collapse
|
3
|
Ruegenberg S, Mayr FAMC, Atanassov I, Baumann U, Denzel MS. Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1. Nat Commun 2021; 12:2176. [PMID: 33846315 PMCID: PMC8041777 DOI: 10.1038/s41467-021-22320-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/10/2021] [Indexed: 02/01/2023] Open
Abstract
The hexosamine pathway (HP) is a key anabolic pathway whose product uridine 5'-diphospho-N-acetyl-D-glucosamine (UDP-GlcNAc) is an essential precursor for glycosylation processes in mammals. It modulates the ER stress response and HP activation extends lifespan in Caenorhabditis elegans. The highly conserved glutamine fructose-6-phosphate amidotransferase 1 (GFAT-1) is the rate-limiting HP enzyme. GFAT-1 activity is modulated by UDP-GlcNAc feedback inhibition and via phosphorylation by protein kinase A (PKA). Molecular consequences of GFAT-1 phosphorylation, however, remain poorly understood. Here, we identify the GFAT-1 R203H substitution that elevates UDP-GlcNAc levels in C. elegans. In human GFAT-1, the R203H substitution interferes with UDP-GlcNAc inhibition and with PKA-mediated Ser205 phosphorylation. Our data indicate that phosphorylation affects the interactions of the two GFAT-1 domains to control catalytic activity. Notably, Ser205 phosphorylation has two discernible effects: it lowers baseline GFAT-1 activity and abolishes UDP-GlcNAc feedback inhibition. PKA controls the HP by uncoupling the metabolic feedback loop of GFAT-1.
Collapse
Affiliation(s)
- Sabine Ruegenberg
- grid.419502.b0000 0004 0373 6590Max Planck Institute for Biology of Ageing, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Felix A. M. C. Mayr
- grid.419502.b0000 0004 0373 6590Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Ilian Atanassov
- grid.419502.b0000 0004 0373 6590Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Ulrich Baumann
- grid.6190.e0000 0000 8580 3777Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Martin S. Denzel
- grid.419502.b0000 0004 0373 6590Max Planck Institute for Biology of Ageing, Cologne, Germany ,grid.6190.e0000 0000 8580 3777CECAD - Cluster of Excellence, University of Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| |
Collapse
|
4
|
Oliveira IA, Allonso D, Fernandes TVA, Lucena DMS, Ventura GT, Dias WB, Mohana-Borges RS, Pascutti PG, Todeschini AR. Enzymatic and structural properties of human glutamine:fructose-6-phosphate amidotransferase 2 (hGFAT2). J Biol Chem 2020; 296:100180. [PMID: 33303629 PMCID: PMC7948480 DOI: 10.1074/jbc.ra120.015189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 11/24/2022] Open
Abstract
Glycoconjugates play a central role in several cellular processes, and alteration in their composition is associated with numerous human pathologies. Substrates for cellular glycosylation are synthesized in the hexosamine biosynthetic pathway, which is controlled by the glutamine:fructose-6-phosphate amidotransfera-se (GFAT). Human isoform 2 GFAT (hGFAT2) has been implicated in diabetes and cancer; however, there is no information about structural and enzymatic properties of this enzyme. Here, we report a successful expression and purification of a catalytically active recombinant hGFAT2 (rhGFAT2) in Escherichia coli cells fused or not to a HisTag at the C-terminal end. Our enzyme kinetics data suggest that hGFAT2 does not follow the expected ordered bi–bi mechanism, and performs the glucosamine-6-phosphate synthesis much more slowly than previously reported for other GFATs. In addition, hGFAT2 is able to isomerize fructose-6-phosphate into glucose-6-phosphate even in the presence of equimolar amounts of glutamine, which results in unproductive glutamine hydrolysis. Structural analysis of a three-dimensional model of rhGFAT2, corroborated by circular dichroism data, indicated the presence of a partially structured loop in the glutaminase domain, whose sequence is present in eukaryotic enzymes but absent in the E. coli homolog. Molecular dynamics simulations suggest that this loop is the most flexible portion of the protein and plays a key role on conformational states of hGFAT2. Thus, our study provides the first comprehensive set of data on the structure, kinetics, and mechanics of hGFAT2, which will certainly contribute to further studies on the (patho)physiology of hGFAT2.
Collapse
Affiliation(s)
- Isadora A Oliveira
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
| | - Diego Allonso
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, UFRJ, Rio de Janeiro, RJ, Brazil
| | - Tácio V A Fernandes
- Laboratório de Modelagem e Dinâmica Molecular, IBCCF, UFRJ, Rio de Janeiro, RJ, Brazil; Laboratório de Macromoléculas, Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Duque de Caxias, RJ, Brazil
| | - Daniela M S Lucena
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Gustavo T Ventura
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Wagner Barbosa Dias
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Pedro G Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, IBCCF, UFRJ, Rio de Janeiro, RJ, Brazil
| | - Adriane R Todeschini
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
| |
Collapse
|
5
|
Krieger JM, Doruker P, Scott AL, Perahia D, Bahar I. Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods. Curr Opin Struct Biol 2020; 64:34-41. [PMID: 32622329 DOI: 10.1016/j.sbi.2020.05.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 11/28/2022]
Abstract
With the explosion of normal mode analyses (NMAs) based on elastic network models (ENMs) in the last decade, and the proven precision of MD simulations for visualizing interactions at atomic scale, many hybrid methods have been proposed in recent years. These aim at exploiting the best of both worlds: the atomic precision of MD that often fall short of exploring time and length scales of biological interest, and the capability of ENM-NMA to predict the cooperative and often functional rearrangements of large structures and assemblies, albeit at low resolution. We present an overview of recent progress in the field with examples of successful applications highlighting the utility of such hybrid methods and pointing to emerging future directions guided by advances in experimental characterization of biomolecular systems structure and dynamics.
Collapse
Affiliation(s)
- James M Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - Ana Ligia Scott
- Laboratory of Bioinformatics and Computational Biology, Federal University of ABC, Santo André, SP, Brazil
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Superieure Paris-Saclay, UMR 8113, CNRS, 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA.
| |
Collapse
|
6
|
Unveiling functional motions based on point mutations in biased signaling systems: A normal mode study on nerve growth factor bound to TrkA. PLoS One 2020; 15:e0231542. [PMID: 32497034 PMCID: PMC7272051 DOI: 10.1371/journal.pone.0231542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/26/2020] [Indexed: 11/19/2022] Open
Abstract
Many receptors elicit signal transduction by activating multiple intracellular pathways. This transduction can be triggered by a non-specific ligand, which simultaneously activates all the signaling pathways of the receptors. However, the binding of one biased ligand preferentially trigger one pathway over another, in a process called biased signaling. The identification the functional motions related to each of these distinct pathways has a direct impact on the development of new effective and specific drugs. We show here how to detect specific functional motions by considering the case of the NGF/TrkA-Ig2 complex. NGF-mediated TrkA receptor activation is dependent on specific structural motions that trigger the neuronal growth, development, and survival of neurons in nervous system. The R221W mutation in the ngf gene impairs nociceptive signaling. We discuss how the large-scale structural effects of this mutation lead to the suppression of collective motions necessary to induce TrkA activation of nociceptive signaling. Our results suggest that subtle changes in the NGF interaction network due to the point mutation are sufficient to inhibit the motions of TrkA receptors putatively linked to nociception. The methodological approach presented in this article, based jointly on the normal mode analysis and the experimentally observed functional alterations due to point mutations provides an essential tool to reveal the structural changes and motions linked to the disease, which in turn could be necessary for a drug design study.
Collapse
|
7
|
Figueiredo CR, Azevedo RA, Mousdell S, Resende-Lara PT, Ireland L, Santos A, Girola N, Cunha RLOR, Schmid MC, Polonelli L, Travassos LR, Mielgo A. Blockade of MIF-CD74 Signalling on Macrophages and Dendritic Cells Restores the Antitumour Immune Response Against Metastatic Melanoma. Front Immunol 2018; 9:1132. [PMID: 29875777 PMCID: PMC5974174 DOI: 10.3389/fimmu.2018.01132] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/04/2018] [Indexed: 12/15/2022] Open
Abstract
Mounting an effective immune response against cancer requires the activation of innate and adaptive immune cells. Metastatic melanoma is the most aggressive form of skin cancer. While immunotherapies have shown a remarkable success in melanoma treatment, patients develop resistance by mechanisms that include the establishment of an immune suppressive tumor microenvironment. Thus, understanding how metastatic melanoma cells suppress the immune system is vital to develop effective immunotherapies against this disease. In this study, we find that macrophages (MOs) and dendritic cells (DCs) are suppressed in metastatic melanoma and that the Ig-CDR-based peptide C36L1 is able to restore MOs and DCs' antitumorigenic and immunogenic functions and to inhibit metastatic growth in lungs. Specifically, C36L1 treatment is able to repolarize M2-like immunosuppressive MOs into M1-like antitumorigenic MOs, and increase the number of immunogenic DCs, and activated cytotoxic T cells, while reducing the number of regulatory T cells and monocytic myeloid-derived suppressor cells in metastatic lungs. Mechanistically, we find that C36L1 directly binds to the MIF receptor CD74 which is expressed on MOs and DCs, disturbing CD74 structural dynamics and inhibiting MIF signaling on these cells. Interfering with MIF-CD74 signaling on MOs and DCs leads to a decrease in the expression of immunosuppressive factors from MOs and an increase in the capacity of DCs to activate cytotoxic T cells. Our findings suggest that interfering with MIF-CD74 immunosuppressive signaling in MOs and DCs, using peptide-based immunotherapy can restore the antitumor immune response in metastatic melanoma. Our study provides the rationale for further development of peptide-based therapies to restore the antitumor immune response in metastatic melanoma.
Collapse
Affiliation(s)
- Carlos R. Figueiredo
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
- Experimental Oncology Unit (UNONEX), Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Ricardo A. Azevedo
- Experimental Oncology Unit (UNONEX), Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Sasha Mousdell
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Pedro T. Resende-Lara
- Laboratory of Computational Biology and Bioinformatics, Federal University of ABC, Santo André, Brazil
- Laboratoire de Biologie et Pharmacologie Appliquées (LBPA), UMR 8113, Ecole Normale Supérieure, Cachan, France
| | - Lucy Ireland
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Almudena Santos
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Natalia Girola
- Experimental Oncology Unit (UNONEX), Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Rodrigo L. O. R. Cunha
- Chemical Biology Laboratory, Natural and Human Sciences Center, Federal University of ABC, Santo André, Brazil
| | - Michael C. Schmid
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Luciano Polonelli
- Unit of Biomedical, Biotechnological and Translational Sciences, Department of Medicine and Surgery, Universitá degli Studi di Parma, Parma, Italy
| | - Luiz R. Travassos
- Experimental Oncology Unit (UNONEX), Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Ainhoa Mielgo
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
8
|
Horvath D, Baskin I, Marcou G, Varnek A. Generative Topographic Mapping of Conformational Space. Mol Inform 2017; 36. [PMID: 28421706 DOI: 10.1002/minf.201700036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/31/2017] [Indexed: 12/17/2022]
Abstract
Herein, Generative Topographic Mapping (GTM) was challenged to produce planar projections of the high-dimensional conformational space of complex molecules (the 1LE1 peptide). GTM is a probability-based mapping strategy, and its capacity to support property prediction models serves to objectively assess map quality (in terms of regression statistics). The properties to predict were total, non-bonded and contact energies, surface area and fingerprint darkness. Map building and selection was controlled by a previously introduced evolutionary strategy allowed to choose the best-suited conformational descriptors, options including classical terms and novel atom-centric autocorrellograms. The latter condensate interatomic distance patterns into descriptors of rather low dimensionality, yet precise enough to differentiate between close favorable contacts and atom clashes. A subset of 20 K conformers of the 1LE1 peptide, randomly selected from a pool of 2 M geometries (generated by the S4MPLE tool) was employed for map building and cross-validation of property regression models. The GTM build-up challenge reached robust three-fold cross-validated determination coefficients of Q2 =0.7…0.8, for all modeled properties. Mapping of the full 2 M conformer set produced intuitive and information-rich property landscapes. Functional and folding subspaces appear as well-separated zones, even though RMSD with respect to the PDB structure was never used as a selection criterion of the maps.
Collapse
Affiliation(s)
- Dragos Horvath
- Laboratoire de Chémoinformatique, UMR 7140 CNRS-Univ. Strasbourg, 1 rue Blaise Pascal, Strasbourg, 67000, France
| | | | - Gilles Marcou
- Laboratoire de Chémoinformatique, UMR 7140 CNRS-Univ. Strasbourg, 1 rue Blaise Pascal, Strasbourg, 67000, France
| | - Alexandre Varnek
- Laboratoire de Chémoinformatique, UMR 7140 CNRS-Univ. Strasbourg, 1 rue Blaise Pascal, Strasbourg, 67000, France
| |
Collapse
|
9
|
Structure and functional dynamics characterization of the ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domain by combining molecular dynamics with excited normal modes. J Mol Model 2016; 22:286. [PMID: 27817112 DOI: 10.1007/s00894-016-3150-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 10/13/2016] [Indexed: 01/02/2023]
Abstract
The human respiratory syncytial virus (hRSV) is the major cause of lower respiratory tract infection in children and elderly people worldwide. Its genome encodes 11 proteins including SH protein, whose functions are not well known. Studies show that SH protein increases RSV virulence degree and permeability to small compounds, suggesting it is involved in the formation of ion channels. The knowledge of SH structure and function is fundamental for a better understanding of its infection mechanism. The aim of this study was to model, characterize, and analyze the structural behavior of SH protein in the phospholipids bilayer environment. Molecular modeling of SH pentameric structure was performed, followed by traditional molecular dynamics (MD) simulations of the protein immersed in the lipid bilayer. Molecular dynamics with excited normal modes (MDeNM) was applied in the resulting system in order to investigate long time scale pore dynamics. MD simulations support that SH protein is stable in its pentameric form. Simulations also showed the presence of water molecules within the bilayer by density distribution, thus confirming that SH protein is a viroporin. This water transport was also observed in MDeNM studies with histidine residues of five chains (His22 and His51), playing a key role in pore permeability. The combination of traditional MD and MDeNM was a very efficient protocol to investigate functional conformational changes of transmembrane proteins that act as molecular channels. This protocol can support future investigations of drug candidates by acting on SH protein to inhibit viral infection. Graphical Abstract The ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domainᅟ.
Collapse
|
10
|
Moran ET. Gastric digestion of protein through pancreozyme action optimizes intestinal forms for absorption, mucin formation and villus integrity. Anim Feed Sci Technol 2016. [DOI: 10.1016/j.anifeedsci.2016.05.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
11
|
Substitution of a non-active-site residue located on the T3 loop increased the catalytic efficiency of endo -polygalacturonases. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
Costa MGS, Batista PR, Bisch PM, Perahia D. Exploring free energy landscapes of large conformational changes: molecular dynamics with excited normal modes. J Chem Theory Comput 2016; 11:2755-67. [PMID: 26575568 DOI: 10.1021/acs.jctc.5b00003] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Proteins are found in solution as ensembles of conformations in dynamic equilibrium. Exploration of functional motions occurring on micro- to millisecond time scales by molecular dynamics (MD) simulations still remains computationally challenging. Alternatively, normal mode (NM) analysis is a well-suited method to characterize intrinsic slow collective motions, often associated with protein function, but the absence of anharmonic effects preclude a proper characterization of conformational distributions in a multidimensional NM space. Using both methods jointly appears to be an attractive approach that allows an extended sampling of the conformational space. In line with this view, the MDeNM (molecular dynamics with excited normal modes) method presented here consists of multiple-replica short MD simulations in which motions described by a given subset of low-frequency NMs are kinetically excited. This is achieved by adding additional atomic velocities along several randomly determined linear combinations of NM vectors, thus allowing an efficient coupling between slow and fast motions. The relatively high-energy conformations generated with MDeNM are further relaxed with standard MD simulations, enabling free energy landscapes to be determined. Two widely studied proteins were selected as examples: hen egg lysozyme and HIV-1 protease. In both cases, MDeNM provides a larger extent of sampling in a few nanoseconds, outperforming long standard MD simulations. A high degree of correlation with motions inferred from experimental sources (X-ray, EPR, and NMR) and with free energy estimations obtained by metadynamics was observed. Finally, the large sets of conformations obtained with MDeNM can be used to better characterize relevant dynamical populations, allowing for a better interpretation of experimental data such as SAXS curves and NMR spectra.
Collapse
Affiliation(s)
- Mauricio G S Costa
- Programa de Computação Científica, Fundação Oswaldo Cruz , 21040-360, Rio de Janeiro, Brazil.,Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21949-901 Rio de Janeiro, Brazil.,Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique , 61, F-94235 Cachan, France
| | - Paulo R Batista
- Programa de Computação Científica, Fundação Oswaldo Cruz , 21040-360, Rio de Janeiro, Brazil
| | - Paulo M Bisch
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21949-901 Rio de Janeiro, Brazil
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique , 61, F-94235 Cachan, France
| |
Collapse
|
14
|
Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis. Future Med Chem 2015; 7:2317-31. [DOI: 10.4155/fmc.15.150] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aim: Molecular dynamics simulations and normal mode analysis are well-established approaches to generate receptor conformational ensembles (RCEs) for ligand docking and virtual screening. Here, we report new fast molecular dynamics-based and normal mode analysis-based protocols combined with conformational pocket classifications to efficiently generate RCEs. Materials & Methods: We assessed our protocols on two well-characterized protein targets showing local active site flexibility, dihydrofolate reductase and large collective movements, CDK2. The performance of the RCEs was validated by distinguishing known ligands of dihydrofolate reductase and CDK2 among a dataset of diverse chemical decoys. Results & discussion: Our results show that different simulation protocols can be efficient for generation of RCEs depending on different kind of protein flexibility.[Formula: see text]
Collapse
|
15
|
Floquet N, Costa MGS, Batista PR, Renault P, Bisch PM, Raussin F, Martinez J, Morris MC, Perahia D. Conformational Equilibrium of CDK/Cyclin Complexes by Molecular Dynamics with Excited Normal Modes. Biophys J 2015; 109:1179-89. [PMID: 26255588 PMCID: PMC4576171 DOI: 10.1016/j.bpj.2015.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/16/2015] [Accepted: 07/01/2015] [Indexed: 01/21/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Nicolas Floquet
- Institut des Biomolécules Max Mousseron (IBMM), Centre National de la Recherche Scientifique UMR 5247, Université de Montpellier, Ecole Normale Supérieure de Chimie de Montpellier, Faculté de Pharmacie, Montpellier, France.
| | - Mauricio G S Costa
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Paulo R Batista
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Pedro Renault
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo M Bisch
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Florent Raussin
- Institut des Biomolécules Max Mousseron (IBMM), Centre National de la Recherche Scientifique UMR 5247, Université de Montpellier, Ecole Normale Supérieure de Chimie de Montpellier, Faculté de Pharmacie, Montpellier, France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM), Centre National de la Recherche Scientifique UMR 5247, Université de Montpellier, Ecole Normale Supérieure de Chimie de Montpellier, Faculté de Pharmacie, Montpellier, France
| | - May C Morris
- Institut des Biomolécules Max Mousseron (IBMM), Centre National de la Recherche Scientifique UMR 5247, Université de Montpellier, Ecole Normale Supérieure de Chimie de Montpellier, Faculté de Pharmacie, Montpellier, France
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique, Cachan, France.
| |
Collapse
|
16
|
De Conto V, Braz ASK, Perahia D, Scott LPB. Recovery of the wild type atomic flexibility in the HIV-1 protease double mutants. J Mol Graph Model 2015; 59:107-16. [PMID: 25948548 DOI: 10.1016/j.jmgm.2015.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 04/09/2015] [Accepted: 04/17/2015] [Indexed: 02/04/2023]
Abstract
The emergence of drug resistant mutations due to the selective pressure exerted by antiretrovirals, including protease inhibitors (PIs), remains a major problem in the treatment of AIDS. During PIs therapy, the occurrence of primary mutations in the wild type HIV-1 protease reduces both the affinity for the inhibitors and the viral replicative capacity compared to the wild type (WT) protein, but additional mutations compensate for this reduced viral fitness. To investigate this phenomenon from the structural point of view, we combined Molecular Dynamics and Normal Mode Analysis to analyze and compare the variations of the flexibility of C-alpha atoms and the differences in hydrogen bond (h-bond) network between the WT and double mutants. In most cases, the flexibility profile of the double mutants was more often similar to that of the WT than to that of the related single base mutants. All single mutants showed a significant alteration in h-bond formation compared to WT. Most of the significant changes occur in the border between the flap and cantilever regions. We found that all the considered double mutants have their h-bond pattern significantly altered in comparison to the respective single base mutants affecting their flexibility profile that becomes more similar to that of WT. This WT flexibility restoration in the double mutants appears as an important factor for the HIV-1 fitness recovery observed in patients.
Collapse
Affiliation(s)
- Valderes De Conto
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Antônio S K Braz
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), Ecole Normale Supérieure de Cachan, Cachan, France
| | - Luis P B Scott
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil; Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), Ecole Normale Supérieure de Cachan, Cachan, France.
| |
Collapse
|
17
|
Dance I. A molecular pathway for the egress of ammonia produced by nitrogenase. Sci Rep 2013; 3:3237. [PMID: 24241241 PMCID: PMC3831235 DOI: 10.1038/srep03237] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/01/2013] [Indexed: 01/19/2023] Open
Abstract
Nitrogenase converts N2 to NH3, at one face of an Fe-Mo-S cluster (FeMo-co) buried in the protein. Through exploration of cavities in the structures of nitrogenase proteins, a pathway for the egress of ammonia from its generation site to the external medium is proposed. This pathway is conserved in the three species Azotobacter vinelandii, Klebsiella pneumoniae and Clostridium pasteurianum. A molecular mechanism for the translocation of NH3 by skipping through a sequence of hydrogen bonds involving eleven water molecules and surrounding aminoacids has been developed. The putative mechanism requires movement aside of some water molecules by up to ~ 1Å. Consistent with this, the surrounding protein is comprised of different chains and has little secondary structure: protein fluctuations are part of the mechanism. This NH3 pathway is well separated from the water chain and embedded proton wire that have been proposed for serial supply of protons to FeMo-co. Verification procedures are suggested.
Collapse
Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
| |
Collapse
|
18
|
Zotti MJ, De Geyter E, Swevers L, Braz ASK, Scott LPB, Rougé P, Coll J, Grutzmacher AD, Lenardão EJ, Smagghe G. A cell-based reporter assay for screening for EcR agonist/antagonist activity of natural ecdysteroids in Lepidoptera (Bm5) and Diptera (S2) cell cultures, followed by modeling of ecdysteroid-EcR interactions and normal mode analysis. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2013; 107:309-320. [PMID: 24267692 DOI: 10.1016/j.pestbp.2013.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 09/16/2013] [Accepted: 09/17/2013] [Indexed: 06/02/2023]
Abstract
Ecdysteroid signal transduction is a key process in insect development and therefore an important target for insecticide development. We employed an in vitro cell-based reporter bioassay for the screening of potential ecdysone receptor (EcR) agonistic and antagonistic compounds. Natural ecdysteroids were assayed with ecdysteroid-responsive cell line cultures that were transiently transfected with the reporter plasmid ERE-b.act.luc. We used the dipteran Schneider S2 cells of Drosophila melanogaster and the lepidopteran Bm5 cells of Bombyx mori, representing important pest insects in medicine and agriculture. Measurements showed an EcR agonistic activity only for cyasterone both in S2 (EC50=3.3μM) and Bm5 cells (EC50=5.3μM), which was low compared to that of the commercial dibenzoylhydrazine-based insecticide tebufenozide (EC50=0.71μM and 0.00089μM, respectively). Interestingly, a strong antagonistic activity was found for castasterone in S2 cells with an IC50 of 0.039μM; in Bm5 cells this effect only became visible at much higher concentrations (IC50=18μM). To gain more insight in the EcR interaction, three-dimensional modeling of dipteran and lepidopteran EcR-LBD was performed. In conclusion, we showed that the EcR cell-based reporter bioassay tested here is a useful and practical tool for the screening of candidate EcR agonists and antagonists. The docking experiments as well as the normal mode analysis provided evidence that the antagonist activity of castasterone may be through direct binding with the receptor with specific changes in protein flexibility. The search for new ecdysteroid-like compounds may be particularly relevant for dipterans because the activity of dibenzoylhydrazines appears to be correlated with an extension of the EcR-LBD binding pocket that is prominent in lepidopteran receptors but less so in the modeled dipteran structure.
Collapse
Affiliation(s)
- Moisés J Zotti
- Department of Crop Protection, Ghent University, Coupure links 653, 9000 Ghent, Belgium; Department of Phytosanitary, FAEM, Federal University of Pelotas, P.O. Box 354, CEP, 96010-900 Pelotas, RS, Brazil; Department of Crop Protection, Federal University of Santa Maria, Santa Maria, Brazil.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Philot EA, Perahia D, Braz ASK, Costa MGDS, Scott LPB. Binding sites and hydrophobic pockets in Human Thioredoxin 1 determined by normal mode analysis. J Struct Biol 2013; 184:293-300. [DOI: 10.1016/j.jsb.2013.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 08/28/2013] [Accepted: 09/03/2013] [Indexed: 11/26/2022]
|
20
|
Louet M, Karakas E, Perret A, Perahia D, Martinez J, Floquet N. Conformational restriction of G-proteins Coupled Receptors (GPCRs) upon complexation to G-proteins: a putative activation mode of GPCRs? FEBS Lett 2013; 587:2656-61. [PMID: 23851072 DOI: 10.1016/j.febslet.2013.06.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 06/13/2013] [Accepted: 06/29/2013] [Indexed: 10/26/2022]
Abstract
GPCRs undergo large conformational changes during their activation. Starting from existing X-ray structures, we used Normal Modes Analyses to study the collective motions of the agonist-bound β2-adrenergic receptor both in its isolated "uncoupled" and G-protein "coupled" conformations. We interestingly observed that the receptor was able to adopt only one major motion in the protein:protein complex. This motion corresponded to an anti-symmetric rotation of both its extra- and intra-cellular parts, with a key role of previously identified highly conserved proline residues. Because this motion was also retrieved when performing NMA on 7 other GPCRs which structures were available, it is strongly suspected to possess a significant biological role, possibly being the "activation mode" of a GPCR when coupled to G-proteins.
Collapse
Affiliation(s)
- Maxime Louet
- Institut des Biomolécules Max Mousseron (IBMM, CNRS UMR5247), Faculté de Pharmacie, 15 avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 05, France
| | | | | | | | | | | |
Collapse
|
21
|
Braz ASK, Tufanetto P, Perahia D, Scott LPB. Relation between flexibility and positively selected HIV-1 protease mutants against inhibitors. Proteins 2012; 80:2680-91. [DOI: 10.1002/prot.24151] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 05/31/2012] [Accepted: 07/11/2012] [Indexed: 11/09/2022]
|
22
|
Mouilleron S, Badet-Denisot MA, Pecqueur L, Madiona K, Assrir N, Badet B, Golinelli-Pimpaneau B. Structural basis for morpheein-type allosteric regulation of Escherichia coli glucosamine-6-phosphate synthase: equilibrium between inactive hexamer and active dimer. J Biol Chem 2012; 287:34533-46. [PMID: 22851174 DOI: 10.1074/jbc.m112.380378] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The amino-terminal cysteine of glucosamine-6-phosphate synthase (GlmS) acts as a nucleophile to release and transfer ammonia from glutamine to fructose 6-phosphate through a channel. The crystal structure of the C1A mutant of Escherichia coli GlmS, solved at 2.5 Å resolution, is organized as a hexamer, where the glutaminase domains adopt an inactive conformation. Although the wild-type enzyme is active as a dimer, size exclusion chromatography, dynamic and quasi-elastic light scattering, native polyacrylamide gel electrophoresis, and ultracentrifugation data show that the dimer is in equilibrium with a hexameric state, in vitro and in cellulo. The previously determined structures of the wild-type enzyme, alone or in complex with glucosamine 6-phosphate, are also consistent with a hexameric assembly that is catalytically inactive because the ammonia channel is not formed. The shift of the equilibrium toward the hexameric form in the presence of cyclic glucosamine 6-phosphate, together with the decrease of the specific activity with increasing enzyme concentration, strongly supports product inhibition through hexamer stabilization. Altogether, our data allow us to propose a morpheein model, in which the active dimer can rearrange into a transiently stable form, which has the propensity to form an inactive hexamer. This would account for a physiologically relevant allosteric regulation of E. coli GlmS. Finally, in addition to cyclic glucose 6-phosphate bound at the active site, the hexameric organization of E. coli GlmS enables the binding of another linear sugar molecule. Targeting this sugar-binding site to stabilize the inactive hexameric state is therefore suggested for the development of specific antibacterial inhibitors.
Collapse
Affiliation(s)
- Stéphane Mouilleron
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | | | | | | | | | | | | |
Collapse
|
23
|
Louet M, Martinez J, Floquet N. GDP release preferentially occurs on the phosphate side in heterotrimeric G-proteins. PLoS Comput Biol 2012; 8:e1002595. [PMID: 22829757 PMCID: PMC3400569 DOI: 10.1371/journal.pcbi.1002595] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 05/21/2012] [Indexed: 11/18/2022] Open
Abstract
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. Despite the availability of many structural and biochemical data, the activation of G-proteins remains to be understood at the molecular level. We used a computation tool to decipher the first limiting step of this activation: GDP release. Combining different methods of analysis, we propose that the GDP exit occurs on its phosphate side. This study helped to rationalize some experimental observations from the literature and opens many perspectives concerning the study of G-proteins activation and their putative inhibition.
Collapse
Affiliation(s)
| | | | - Nicolas Floquet
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université Montpellier 1, Université Montpellier 2, Faculté de Pharmacie, Montpellier, France
- * E-mail:
| |
Collapse
|
24
|
Foley BL, Tessier MB, Woods RJ. Carbohydrate force fields. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2012; 2:652-697. [PMID: 25530813 PMCID: PMC4270206 DOI: 10.1002/wcms.89] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.
Collapse
Affiliation(s)
- B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Matthew B. Tessier
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- School of Chemistry, National University of Ireland, Galway, Ireland
| |
Collapse
|
25
|
Ho BK, Perahia D, Buckle AM. Hybrid approaches to molecular simulation. Curr Opin Struct Biol 2012; 22:386-93. [PMID: 22633678 DOI: 10.1016/j.sbi.2012.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 05/07/2012] [Accepted: 05/08/2012] [Indexed: 10/28/2022]
Abstract
Molecular dynamics (MD) simulation is an established method for studying the conformational changes that are important for protein function. Recent advances in hardware and software have allowed MD simulations over the same timescales as experiment, improving the agreement between theory and experiment to a large extent. However, running such simulations are costly, in terms of resources, storage, and trajectory analysis. There is still a place for techniques that involve short MD simulations. In order to overcome the sampling paucity of short time-scales, hybrid methods that include some form of MD simulation can exploit certain features of the system of interest, often combining experimental information in surprising ways. Here, we review some recent hybrid approaches to the simulation of proteins.
Collapse
Affiliation(s)
- Bosco K Ho
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | | | | |
Collapse
|
26
|
Bhat JY, Venkatachala R, Balaram H. Substrate-induced conformational changes in Plasmodium falciparum guanosine monophosphate synthetase. FEBS J 2011; 278:3756-68. [PMID: 21827625 DOI: 10.1111/j.1742-4658.2011.08296.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
GMP synthetase is a glutamine amidotransferase that incorporates ammonia derived from glutamine into the nucleotide xanthosine 5'-monophosphate (XMP) to form guanosine 5'-monophosphate (GMP). Functional coordination of domains in glutamine amidotransferases leads to upregulation of glutamine hydrolysis in the presence of acceptor substrates and is a common feature in this class of enzymes. We have shown earlier that binding of substrates to the acceptor domain of Plasmodium falciparum GMP synthetase (PfGMPS) leads to enhancement in both glutaminase activity and rate of glutaminase inactivation, by the irreversible inhibitors acivicin and diazo-oxonorleucine [Bhat JY et al. (2008) Biochem J409, 263-273], a process that must be driven by conformational alterations. In this paper, through the combined use of biochemical assays, optical spectroscopy and mass spectrometry, we demonstrate that PfGMPS undergoes conformational transitions upon binding of substrates to the acceptor domain. Limited proteolysis and hydrogen-deuterium exchange in conjunction with mass spectrometry unveil region-specific conformational changes in the ATP + XMP bound state of PfGMPS. Decreased accessibility of R294 and K428 residues to trypsin in the ATP pyrophosphatase domain and reduced deuterium incorporation in the 143-155 region, pertaining to the glutaminase domain, suggest that in PfGMPS ligand-induced conformational changes are not only local but also transmitted over a long range across the domains. Overall, these results provide a detailed understanding of the substrate-induced changes in PfGMPS that could be essential for the overall catalytic process.
Collapse
Affiliation(s)
- Javaid Y Bhat
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | | | | |
Collapse
|
27
|
Batista PR, Pandey G, Pascutti PG, Bisch PM, Perahia D, Robert CH. Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening. J Chem Theory Comput 2011; 7:2348-52. [PMID: 26606609 DOI: 10.1021/ct200237u] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Describing biological macromolecular energetics from computer simulations can pose major challenges, and often necessitates enhanced conformational sampling. We describe the calculation of conformational free-energy profiles along carefully chosen collective coordinates: "consensus" normal modes, developed recently as robust alternatives to conventional normal modes. In an application to the HIV-1 protease, we obtain efficient sampling of significant flap opening movements governing inhibitor binding from relatively short simulations, in close correspondence with experimental results.
Collapse
Affiliation(s)
- Paulo R Batista
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21941-902, Brasil.,CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.,CNRS BIMoDyM -Laboratoire de Biologie et Pharmacologie Appliquées - École Normale Supérieure de Cachan , 94235 Cachan, France
| | - Gaurav Pandey
- Indian Institute of Technology , Roorkee, 247667, India.,CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France
| | - Pedro G Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21941-902, Brasil
| | - Paulo M Bisch
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21941-902, Brasil
| | - David Perahia
- CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.,CNRS BIMoDyM -Laboratoire de Biologie et Pharmacologie Appliquées - École Normale Supérieure de Cachan , 94235 Cachan, France
| | - Charles H Robert
- CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.,CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico Chimique, Université Paris Diderot, Sorbonne Paris Cité , 75005 Paris, France
| |
Collapse
|
28
|
Laine E, Chauvot de Beauchêne I, Perahia D, Auclair C, Tchertanov L. Mutation D816V alters the internal structure and dynamics of c-KIT receptor cytoplasmic region: implications for dimerization and activation mechanisms. PLoS Comput Biol 2011; 7:e1002068. [PMID: 21698178 PMCID: PMC3116893 DOI: 10.1371/journal.pcbi.1002068] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 04/11/2011] [Indexed: 12/02/2022] Open
Abstract
The type III receptor tyrosine kinase (RTK) KIT plays a crucial role in the transmission of cellular signals through phosphorylation events that are associated with a switching of the protein conformation between inactive and active states. D816V KIT mutation is associated with various pathologies including mastocytosis and cancers. D816V-mutated KIT is constitutively active, and resistant to treatment with the anti-cancer drug Imatinib. To elucidate the activating molecular mechanism of this mutation, we applied a multi-approach procedure combining molecular dynamics (MD) simulations, normal modes analysis (NMA) and binding site prediction. Multiple 50-ns MD simulations of wild-type KIT and its mutant D816V were recorded using the inactive auto-inhibited structure of the protein, characteristic of type III RTKs. Computed free energy differences enabled us to quantify the impact of D816V on protein stability in the inactive state. We evidenced a local structural alteration of the activation loop (A-loop) upon mutation, and a long-range structural re-organization of the juxta-membrane region (JMR) followed by a weakening of the interaction network with the kinase domain. A thorough normal mode analysis of several MD conformations led to a plausible molecular rationale to propose that JMR is able to depart its auto-inhibitory position more easily in the mutant than in wild-type KIT and is thus able to promote kinase mutant dimerization without the need for extra-cellular ligand binding. Pocket detection at the surface of NMA-displaced conformations finally revealed that detachment of JMR from the kinase domain in the mutant was sufficient to open an access to the catalytic and substrate binding sites. Protein kinases are involved in a huge amount of cellular processes through phosphorylation, a crucial mechanism in cell signaling, and their misregulation often results in disease. The deactivation of protein tyrosine kinases (PTKs) or their oncogenic activation arises from mutations which affect the protein primary structure and the configuration of the enzymatic site apparently by stabilizing the activation loop (A-loop) extended conformation. Particularly, mutation D816V of receptor tyrosine kinase (RTK) KIT, found in patients with pediatric mastocytosis, acute leukemia or germ cell tumors, can be considered as the archetype of mutation inducing a displacement of the population equilibrium toward the active conformation. We present a comprehensive computational study of the activating mechanism(s) of this mutation. Our multi-approach in silico procedure evidenced a local alteration of the A-loop structure, and a long-range structural re-organization of the juxta-membrane region (JMR) followed by a weakening of the interaction network with the kinase domain. Our results provided a plausible conception of how the observed departure of JMR from kinase domain in the mutant promotes kinase mutant dimerization without requiring extra-cellular ligand binding. The pocket profiles we obtained suggested putative allosteric binding sites that could be targeted by ligands/modulators that trap the mutated enzyme.
Collapse
Affiliation(s)
- Elodie Laine
- LBPA, CNRS - ENS de Cachan, Cachan, France
- * E-mail: (EL); (LT)
| | | | | | | | - Luba Tchertanov
- LBPA, CNRS - ENS de Cachan, Cachan, France
- * E-mail: (EL); (LT)
| |
Collapse
|
29
|
Louet M, Perahia D, Martinez J, Floquet N. A concerted mechanism for opening the GDP binding pocket and release of the nucleotide in hetero-trimeric G-proteins. J Mol Biol 2011; 411:298-312. [PMID: 21663745 DOI: 10.1016/j.jmb.2011.05.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 05/14/2011] [Accepted: 05/20/2011] [Indexed: 11/26/2022]
Abstract
G-protein hetero-trimers play a fundamental role in cell function. Their dynamic behavior at the atomic level remains to be understood. We have studied the Gi hetero-trimer through a combination of molecular dynamics simulations and normal mode analyses. We showed that these big proteins could undergo large-amplitude conformational changes, without any energy penalty and with an intrinsic dynamics centered on their GDP binding pocket. Among the computed collective motions, one of the modes (mode 17) was particularly able to significantly open both the base and the phosphate sides of the GDP binding pocket. This mode describing mainly a motion between the Ras-like and the helical domains of G(α) was in close agreement with some available X-ray data and with many other biochemical/biophysical observations including the kink of helix α5. The use of a new protocol, which allows extraction of the GDP ligand along the computed normal modes, supported that the exit of GDP was largely coupled to an opening motion along mode 17. We propose for the first time a "concerted mechanism" model in which the opening of the GDP pocket and the kink of the α5 helix occur concomitantly and favor GDP release from G(αβγ) complexes. This model is discussed in the context of the G-protein-coupled receptor/G-protein interaction close to the cell membrane.
Collapse
Affiliation(s)
- Maxime Louet
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université Montpellier 1-Université Montpellier 2, Faculté de Pharmacie, 15 Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 05, France
| | | | | | | |
Collapse
|
30
|
Meyer ME, Gutierrez JA, Raushel FM, Richards NGJ. A conserved glutamate controls the commitment to acyl-adenylate formation in asparagine synthetase. Biochemistry 2010; 49:9391-401. [PMID: 20853825 PMCID: PMC2975022 DOI: 10.1021/bi1010688] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Inhibitor docking studies have implicated a conserved glutamate residue (Glu-348) as a general base in the synthetase active site of the enzyme asparagine synthetase B from Escherichia coli (AS-B). We now report steady-state kinetic, isotope transfer, and positional isotope exchange experiments for a series of site-directed AS-B mutants in which Glu-348 is substituted by conservative amino acid replacements. We find that formation of the β-aspartyl-AMP intermediate, and therefore the eventual production of asparagine, is dependent on the presence of a carboxylate side chain at this position in the synthetase active site. In addition, Glu-348 may also play a role in mediating the conformational changes needed to (i) coordinate, albeit weakly, the glutaminase and synthetase activities of the enzyme and (ii) establish the structural integrity of the intramolecular tunnel along which ammonia is translocated. The importance of Glu-348 in mediating acyl-adenylate formation contrasts with the functional role of the cognate residues in β-lactam synthetase (BLS) and carbapenem synthetase (CPS) (Tyr-348 and Tyr-345, respectively), which both likely evolved from asparagine synthetase. Given the similarity of the chemistry catalyzed by AS-B, BLS, and CPS, our work highlights the difficulty of predicting the functional outcome of single site mutations on enzymes that catalyze almost identical chemical transformations.
Collapse
Affiliation(s)
- Megan E. Meyer
- Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, FL 32611
| | - Jemy A. Gutierrez
- Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, FL 32611
| | - Frank M. Raushel
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, TX 77843
| | - Nigel G. J. Richards
- Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, FL 32611
| |
Collapse
|
31
|
Mouilleron S, Badet-Denisot MA, Badet B, Golinelli-Pimpaneau B. Dynamics of glucosamine-6-phosphate synthase catalysis. Arch Biochem Biophys 2010; 505:1-12. [PMID: 20709015 DOI: 10.1016/j.abb.2010.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 08/06/2010] [Accepted: 08/08/2010] [Indexed: 11/19/2022]
Abstract
Glucosamine-6P synthase, which catalyzes glucosamine-6P synthesis from fructose-6P and glutamine, channels ammonia over 18Å between its glutaminase and synthase active sites. The crystal structures of the full-length Escherichia coli enzyme have been determined alone, in complex with the first bound substrate, fructose-6P, in the presence of fructose-6P and a glutamine analog, and in the presence of the glucosamine-6P product. These structures represent snapshots of reaction intermediates, and their comparison sheds light on the dynamics of catalysis. Upon fructose-6P binding, the C-terminal loop and the glutaminase domains get ordered, leading to the closure of the synthase site, the opening of the sugar ring and the formation of a "closed" ammonia channel. Then, glutamine binding leads to the closure of the Q-loop to protect the glutaminase site, the activation of the catalytic residues involved in glutamine hydrolysis, the swing of the side chain of Trp74, which allows the communication between the two active sites through an "open" channel, and the rotation of the glutaminase domains relative to the synthase domains dimer. Therefore, binding of the substrates at the appropriate reaction time is responsible for the formation and opening of the ammonia channel and for the activation of the enzyme glutaminase function.
Collapse
Affiliation(s)
- Stéphane Mouilleron
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
| | | | | | | |
Collapse
|
32
|
Bahar I, Lezon TR, Bakan A, Shrivastava IH. Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev 2010; 110:1463-97. [PMID: 19785456 PMCID: PMC2836427 DOI: 10.1021/cr900095e] [Citation(s) in RCA: 377] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Ivet Bahar
- Department of Computational Biology, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA.
| | | | | | | |
Collapse
|
33
|
Batista PR, Robert CH, Maréchal JD, Hamida-Rebaï MB, Pascutti PG, Bisch PM, Perahia D. Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease. Phys Chem Chem Phys 2010; 12:2850-9. [DOI: 10.1039/b919148h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
34
|
Floquet N, M'Kadmi C, Perahia D, Gagne D, Bergé G, Marie J, Banères JL, Galleyrand JC, Fehrentz JA, Martinez J. Activation of the ghrelin receptor is described by a privileged collective motion: a model for constitutive and agonist-induced activation of a sub-class A G-protein coupled receptor (GPCR). J Mol Biol 2009; 395:769-84. [PMID: 19782690 DOI: 10.1016/j.jmb.2009.09.051] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 09/18/2009] [Accepted: 09/20/2009] [Indexed: 10/20/2022]
Abstract
Three homology models of the human ghrelin receptor (GHS-R1a) have been generated from the available X-ray structures of rhodopsin (RHO model), opsin (OPS model) and beta-2 adrenergic receptor (B2 model). The latter was used as a starting point for combined molecular dynamics simulation (MDS) and full atom normal modes analysis (NMA). A low-frequency normal mode (mode 16) perfectly reproduced the intracellular motions observed between B2 and RHO models; in the opposite direction along the same mode, the generated structures are closer to the OPS model, suggesting a direct link with GHS-R1a activation. This was in agreement with motions of the seven transmembranous segments, increase of the solvent accessibility of the 140-ERY-142 sequence, and flip of the Trp276 (C WLP) residue, some features related to GPCRs activation. According to our model, His280 was proposed to stabilize Trp276 in the active state; this was verified by site-directed mutagenesis and biochemical characterization of the resulting H280A and H280S mutants, which were fully functional but sharing an important decrease of their basal activities. Docking performed with short ghrelin derivatives Gly-Ser-Ser ([octa])-Phe-NH (2) and Gly-Ser-Ser ([octa])-Phe-Leu-NH (2) allowed the identification of a robust position of these peptides in the active site of the receptor. This model was refined by MDS and validated by docking experiments performed on a set of 55 ghrelin receptor ligands based on the 1,2,4- triazole scaffold. Finally, NMA performed on the obtained peptide-receptor complex suggested stabilization of the Trp276 residue and of the whole receptor in the active state, preventing the motion observed along mode 16 computed for the unbound receptor. Our results show that NMA offers a powerful approach to study the conformational diversity and the activation mechanism of GPCRs.
Collapse
Affiliation(s)
- Nicolas Floquet
- Institut des Biomolécules Max Mousseron (I.B.M.M.), CNRS UMR5247 - Université Montpellier 1 - Université Montpellier 2, Faculté de Pharmacie, 15 avenue Charles Flahault, B.P. 14 491, 34093 Montpellier Cedex 5, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|