1
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Panina IS, Balandin SV, Tsarev AV, Chugunov AO, Tagaev AA, Finkina EI, Antoshina DV, Sheremeteva EV, Paramonov AS, Rickmeyer J, Bierbaum G, Efremov RG, Shenkarev ZO, Ovchinnikova TV. Specific Binding of the α-Component of the Lantibiotic Lichenicidin to the Peptidoglycan Precursor Lipid II Predetermines Its Antimicrobial Activity. Int J Mol Sci 2023; 24:ijms24021332. [PMID: 36674846 PMCID: PMC9863751 DOI: 10.3390/ijms24021332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/21/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
To date, a number of lantibiotics have been shown to use lipid II-a highly conserved peptidoglycan precursor in the cytoplasmic membrane of bacteria-as their molecular target. The α-component (Lchα) of the two-component lantibiotic lichenicidin, previously isolated from the Bacillus licheniformis VK21 strain, seems to contain two putative lipid II binding sites in its N-terminal and C-terminal domains. Using NMR spectroscopy in DPC micelles, we obtained convincing evidence that the C-terminal mersacidin-like site is involved in the interaction with lipid II. These data were confirmed by the MD simulations. The contact area of lipid II includes pyrophosphate and disaccharide residues along with the first isoprene units of bactoprenol. MD also showed the potential for the formation of a stable N-terminal nisin-like complex; however, the conditions necessary for its implementation in vitro remain unknown. Overall, our results clarify the picture of two component lantibiotics mechanism of antimicrobial action.
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Affiliation(s)
- Irina S. Panina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey V. Balandin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-495-335-0900
| | - Andrey V. Tsarev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Anton O. Chugunov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Andrey A. Tagaev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Ekaterina I. Finkina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Daria V. Antoshina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Elvira V. Sheremeteva
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alexander S. Paramonov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Jasmin Rickmeyer
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53117 Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53117 Bonn, Germany
| | - Roman G. Efremov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Applied Mathematics, National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Zakhar O. Shenkarev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Bioorganic Chemistry, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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2
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Alavizargar A, Elting A, Wedlich-Söldner R, Heuer A. Lipid-Mediated Association of the Slg1 Transmembrane Domains in Yeast Plasma Membranes. J Phys Chem B 2022; 126:3240-3256. [PMID: 35446028 DOI: 10.1021/acs.jpcb.2c00192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Clustering of transmembrane proteins underlies a multitude of fundamental biological processes at the plasma membrane (PM) such as receptor activation, lateral domain formation, and mechanotransduction. The self-association of the respective transmembrane domains (TMDs) has also been suggested to be responsible for the micron-scaled patterns seen for integral membrane proteins in the budding yeast PM. However, the underlying interplay between the local lipid composition and the TMD identity is still not mechanistically understood. In this work, we combined coarse-grained molecular dynamics simulations of simplified bilayer systems with high-resolution live-cell microscopy to analyze the distribution of a representative helical yeast TMD from the PM sensor Slg1 within different lipid environments. In our simulations, we specifically evaluated the effects of acyl chain saturation and anionic lipid head groups on the association of two TMDs. We found that weak lipid-protein interactions significantly affect the configuration of TMD dimers and the free energy of association. Increased amounts of unsaturated phospholipids (PLs) strongly reduced the helix-helix interaction, while the presence of anionic phosphatidylserine (PS) hardly affected the dimer formation. We could experimentally confirm this surprising lack of effect of PS using the network factor, a mesoscopic measure of PM pattern formation in yeast cells. Simulations also showed that the formation of TMD dimers in turn increased the order parameter of the surrounding lipids and induced long-range perturbations in lipid organization. In summary, our results shed new light on the mechanisms of lipid-mediated dimerization of TMDs in complex lipid mixtures.
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Affiliation(s)
- Azadeh Alavizargar
- Institute of Physical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Muenster, Germany
| | - Annegret Elting
- Institute of Cell Dynamics and Imaging, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany
| | - Roland Wedlich-Söldner
- Institute of Cell Dynamics and Imaging, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Muenster, Germany
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3
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Isothermal Titration Calorimetry of Membrane Proteins. Methods Mol Biol 2021. [PMID: 33877623 DOI: 10.1007/978-1-0716-1394-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The ability to quantify protein-protein interactions without adding labels to protein has made isothermal titration calorimetry (ITC) a preferred technique to study proteins in aqueous solution. Here, we describe the application of ITC to the study of protein-protein interactions in membrane mimics using the association of integrin αIIb and β3 transmembrane domains in phospholipid bicelles as an example. A higher conceptual and experimental effort compared to water-soluble proteins is required for membrane proteins and rewarded with rare thermodynamic insight into this central class of proteins.
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4
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Kaplan AR, Olson R, Alexandrescu AT. Protein yoga: Conformational versatility of the Hemolysin II C-terminal domain detailed by NMR structures for multiple states. Protein Sci 2021; 30:990-1005. [PMID: 33733504 DOI: 10.1002/pro.4066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/10/2021] [Accepted: 03/13/2021] [Indexed: 11/05/2022]
Abstract
The C-terminal domain of Bacillus cereus hemolysin II (HlyIIC), stabilizes the trans-membrane-pore formed by the HlyII toxin and may aid in target cell recognition. Initial efforts to determine the NMR structure of HlyIIC were hampered by cis/trans isomerization about the single proline at position 405 that leads to doubling of NMR resonances. We used the mutant P405M-HlyIIC that eliminates the cis proline to determine the NMR structure of the domain, which revealed a novel fold. Here, we extend earlier studies to the NMR structure determination of the cis and trans states of WT-HlyIIC that exist simultaneously in solution. The primary structural differences between the cis and trans states are in the loop that contains P405, and structurally adjacent loops. Thermodynamic linkage analysis shows that at 25 C the cis proline, which already has a large fraction of 20% in the unfolded protein, increases to 50% in the folded state due to coupling with the global stability of the domain. The P405M or P405A substitutions eliminate heterogeneity due to proline isomerization but lead to the formation of a new dimeric species. The NMR structure of the dimer shows that it is formed through domain-swapping of strand β5, the last segment of secondary structure following P405. The presence of P405 in WT-HlyIIC strongly disfavors the dimer compared to the P405M-HlyIIC or P405A-HlyIIC mutants. The WT proline may thus act as a "gatekeeper," warding off aggregative misfolding.
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Affiliation(s)
- Anne R Kaplan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Rich Olson
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut, USA
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
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5
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Oligomerization analysis as a tool to elucidate the mechanism of EBV latent membrane protein 1 inhibition by pentamidine. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183380. [DOI: 10.1016/j.bbamem.2020.183380] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 01/06/2023]
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6
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Franco ML, Nadezhdin KD, Goncharuk SA, Mineev KS, Arseniev AS, Vilar M. Structural basis of the transmembrane domain dimerization and rotation in the activation mechanism of the TRKA receptor by nerve growth factor. J Biol Chem 2020; 295:275-286. [PMID: 31801826 PMCID: PMC6952603 DOI: 10.1074/jbc.ra119.011312] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/26/2019] [Indexed: 01/03/2023] Open
Abstract
Tropomyosin-receptor kinases (TRKs) are essential for the development of the nervous system. The molecular mechanism of TRKA activation by its ligand nerve growth factor (NGF) is still unsolved. Recent results indicate that at endogenous levels most of TRKA is in a monomer-dimer equilibrium and that the binding of NGF induces an increase of the dimeric and oligomeric forms of this receptor. An unsolved issue is the role of the TRKA transmembrane domain (TMD) in the dimerization of TRKA and the structural details of the TMD in the active dimer receptor. Here, we found that the TRKA-TMD can form dimers, identified the structural determinants of the dimer interface in the active receptor, and validated this interface through site-directed mutagenesis together with functional and cell differentiation studies. Using in vivo cross-linking, we found that the extracellular juxtamembrane region is reordered after ligand binding. Replacement of some residues in the juxtamembrane region with cysteine resulted in ligand-independent active dimers and revealed the preferred dimer interface. Moreover, insertion of leucine residues into the TMD helix induced a ligand-independent TRKA activation, suggesting that a rotation of the TMD dimers underlies NGF-induced TRKA activation. Altogether, our findings indicate that the transmembrane and juxtamembrane regions of TRKA play key roles in its dimerization and activation by NGF.
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Affiliation(s)
- María L Franco
- Molecular Basis of Neurodegeneration Unit, Institute of Biomedicine of València, Consejo Superior de Investigaciones Científicas, 46010 València, Spain
| | - Kirill D Nadezhdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Sergey A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Alexander S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow Region 141700, Russian Federation.
| | - Marçal Vilar
- Molecular Basis of Neurodegeneration Unit, Institute of Biomedicine of València, Consejo Superior de Investigaciones Científicas, 46010 València, Spain.
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7
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Wäschenbach L, Gertzen CGW, Keitel V, Gohlke H. Dimerization energetics of the G-protein coupled bile acid receptor TGR5 from all-atom simulations. J Comput Chem 2019; 41:874-884. [PMID: 31880348 DOI: 10.1002/jcc.26135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 12/20/2022]
Abstract
We describe the first extensive energetic evaluation of GPCR dimerization on the atomistic level by means of potential of mean force (PMF) computations and implicit solvent/implicit membrane end-point free energy calculations (MM-PBSA approach). Free energies of association computed from the PMFs show that the formation of both the 1/8 and 4/5 interface is energetically favorable for TGR5, the first GPCR known to be activated by hydrophobic bile acids and neurosteroids. Furthermore, formation of the 1/8 interface is favored over that of the 4/5 interface. Both results are in line with our previous FRET experiments in live cells. Differences in lipid-protein interactions are identified to contribute to the observed differences in free energies of association. A per-residue decomposition of the MM-PBSA effective binding energy reveals hot spot residues specific for both interfaces that form clusters. This knowledge may be used to guide the design of dimerization inhibitors or perform mutational studies to explore physiological consequences of distorted TGR5 association. Finally, we characterized the role of Y111, located in the conserved (D/E)RY motif, as a facilitator of TGR5 interactions. The types of computations performed here should be transferable to other transmembrane proteins that form dimers or higher oligomers as long as good structural models of the dimeric or oligomeric states are available. Such computations may help to overcome current restrictions due to an imperfect energetic representation of protein association at the coarse-grained level. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Lucas Wäschenbach
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.,Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Verena Keitel
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
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8
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Bragin PE, Kuznetsov AS, Bocharova OV, Volynsky PE, Arseniev AS, Efremov RG, Mineev KS. Probing the effect of membrane contents on transmembrane protein-protein interaction using solution NMR and computer simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2486-2498. [PMID: 30279150 DOI: 10.1016/j.bbamem.2018.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/03/2018] [Accepted: 09/17/2018] [Indexed: 12/18/2022]
Abstract
The interaction between the secondary structure elements is the key process, determining the spatial structure and activity of a membrane protein. Transmembrane (TM) helix-helix interaction is known to be especially important for the function of so-called type I or bitopic membrane proteins. In the present work, we present the approach to study the helix-helix interaction in the TM domains of membrane proteins in various lipid environment using solution NMR spectroscopy and phospholipid bicelles. The technique is based on the ability of bicelles to form particles with the size, depending on the lipid/detergent ratio. To implement the approach, we report the experimental parameters of "ideal bicelle" models for four kinds of zwitterionic phospholipids, which can be also used in other structural studies. We show that size of bicelles and type of the rim-forming detergent do not affect substantially the spatial structure and stability of the model TM dimer. On the other hand, the effect of bilayer thickness on the free energy of the dimer is dramatic, while the structure of the protein is unchanged in various lipids with fatty chains having a length from 12 to 18 carbon atoms. The obtained data is analyzed using the computer simulations to find the physical origin of the observed effects.
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Affiliation(s)
- P E Bragin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Lomonosov Moscow State University, Leninskiye Gory, 1, Moscow 119991, Russian Federation
| | - A S Kuznetsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudnyi, Russian Federation; National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia
| | - O V Bocharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudnyi, Russian Federation
| | - P E Volynsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - A S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudnyi, Russian Federation
| | - R G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudnyi, Russian Federation; National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia
| | - K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudnyi, Russian Federation.
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9
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Bocharov EV, Lesovoy DM, Bocharova OV, Urban AS, Pavlov KV, Volynsky PE, Efremov RG, Arseniev AS. Structural basis of the signal transduction via transmembrane domain of the human growth hormone receptor. Biochim Biophys Acta Gen Subj 2018; 1862:1410-1420. [DOI: 10.1016/j.bbagen.2018.03.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 12/18/2022]
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10
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Lesovoy DM, Mineev KS, Bragin PE, Bocharova OV, Bocharov EV, Arseniev AS. NMR relaxation parameters of methyl groups as a tool to map the interfaces of helix-helix interactions in membrane proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 69:165-179. [PMID: 29063258 DOI: 10.1007/s10858-017-0146-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/14/2017] [Indexed: 06/07/2023]
Abstract
In the case of soluble proteins, chemical shift mapping is used to identify the intermolecular interfaces when the NOE-based calculations of spatial structure of the molecular assembly are impossible or impracticable. However, the reliability of the membrane protein interface mapping based on chemical shifts or other relevant parameters was never assessed. In the present work, we investigate the predictive power of various NMR parameters that can be used for mapping of helix-helix interfaces in dimeric TM domains. These parameters are studied on a dataset containing three structures of helical dimers obtained for two different proteins in various membrane mimetics. We conclude that the amide chemical shifts have very little predictive value, while the methyl chemical shifts could be used to predict interfaces, though with great care. We suggest an approach based on conversion of the carbon NMR relaxation parameters of methyl groups into parameters of motion, and one of such values, the characteristic time of methyl rotation, appears to be a reliable sensor of interhelix contacts in transmembrane domains. The carbon NMR relaxation parameters of methyl groups can be measured accurately and with high sensitivity and resolution, making the proposed parameter a useful tool for investigation of protein-protein interfaces even in large membrane proteins. An approach to build the models of transmembrane dimers based on perturbations of methyl parameters and TMDOCK software is suggested.
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Affiliation(s)
- D M Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
| | - K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700
| | - P E Bragin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Lomonosov Moscow State University, Leninskiye Gory, 1, Moscow, Russian Federation, 119991
| | - O V Bocharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700
| | - E V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997.
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700.
- National Research Centre "Kurchatov Institute", Kurchatov Complex of NBICS-technologies, Akad. Kurchatova Sqr., 1, Moscow, Russian Federation, 123182.
| | - A S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700
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11
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He L, Steinocher H, Shelar A, Cohen EB, Heim EN, Kragelund BB, Grigoryan G, DiMaio D. Single methyl groups can act as toggle switches to specify transmembrane Protein-protein interactions. eLife 2017; 6:27701. [PMID: 28869036 PMCID: PMC5597333 DOI: 10.7554/elife.27701] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 09/01/2017] [Indexed: 01/13/2023] Open
Abstract
Transmembrane domains (TMDs) engage in protein-protein interactions that regulate many cellular processes, but the rules governing the specificity of these interactions are poorly understood. To discover these principles, we analyzed 26-residue model transmembrane proteins consisting exclusively of leucine and isoleucine (called LIL traptamers) that specifically activate the erythropoietin receptor (EPOR) in mouse cells to confer growth factor independence. We discovered that the placement of a single side chain methyl group at specific positions in a traptamer determined whether it associated productively with the TMD of the human EPOR, the mouse EPOR, or both receptors. Association of the traptamers with the EPOR induced EPOR oligomerization in an orientation that stimulated receptor activity. These results highlight the high intrinsic specificity of TMD interactions, demonstrate that a single methyl group can dictate specificity, and define the minimal chemical difference that can modulate the specificity of TMD interactions and the activity of transmembrane proteins.
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Affiliation(s)
- Li He
- Department of Genetics, Yale School of Medicine, New Haven, United States
| | - Helena Steinocher
- Department of Biology, Structural and NMR Laboratory, University of Copenhagen, Copenhagen, Denmark
| | - Ashish Shelar
- Department of Genetics, Yale School of Medicine, New Haven, United States
| | - Emily B Cohen
- Department of Genetics, Yale School of Medicine, New Haven, United States
| | - Erin N Heim
- Department of Genetics, Yale School of Medicine, New Haven, United States
| | - Birthe B Kragelund
- Department of Biology, Structural and NMR Laboratory, University of Copenhagen, Copenhagen, Denmark
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, United States
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, United States.,Department of Therapeutic Radiology, Yale School of Medicine, New Haven, United States.,Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, United States.,Yale Cancer Center, New Haven, United States
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12
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Death Receptor 5 Activation Is Energetically Coupled to Opening of the Transmembrane Domain Dimer. Biophys J 2017; 113:381-392. [PMID: 28746849 DOI: 10.1016/j.bpj.2017.05.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/17/2017] [Accepted: 05/22/2017] [Indexed: 01/01/2023] Open
Abstract
The precise mechanism by which binding of tumor necrosis factor ligands to the extracellular domain of their corresponding receptors transmits signals across the plasma membrane has remained elusive. Recent studies have proposed that activation of several tumor necrosis factor receptors, including Death Receptor 5, involves a scissorlike opening of the disulfide-linked transmembrane (TM) dimer. Using time-resolved fluorescence resonance energy transfer, we provide, to our knowledge, the first direct biophysical evidence that Death Receptor 5 TM-dimers open in response to ligand binding. Then, to probe the importance of the closed-to-open TM domain transition in the overall energetics of receptor activation, we designed point-mutants (alanine to phenylalanine) in the predicted, tightly packed TM domain dimer interface. We hypothesized that the bulky residues should destabilize the closed conformation and eliminate the ∼3 kcal/mol energy barrier to TM domain opening and the ∼2 kcal/mol energy difference between the closed and open states, thus oversensitizing the receptor. To test this, we used all-atom molecular dynamics simulations of the isolated TM domain in explicit lipid bilayers coupled to thermodynamic potential of mean force calculations. We showed that single point mutants at the interface altered the energy landscape as predicted, but were not enough to completely eliminate the barrier to opening. However, the computational model did predict that a double mutation at i, i+4 positions at the center of the TM domain dimer eliminates the barrier and stabilizes the open conformation relative to the closed. We tested these mutants in cells with time-resolved fluorescence resonance energy transfer and death assays, and show remarkable agreement with the calculations. The single mutants had a small effect on TM domain separation and cell death, whereas the double mutant significantly increased the TM domain separation and more than doubled the sensitivity of cells to ligand stimulation.
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13
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Spatial structure of TLR4 transmembrane domain in bicelles provides the insight into the receptor activation mechanism. Sci Rep 2017; 7:6864. [PMID: 28761155 PMCID: PMC5537299 DOI: 10.1038/s41598-017-07250-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/26/2017] [Indexed: 01/16/2023] Open
Abstract
Toll-like receptors (TLRs) play a key role in the innate and adaptive immune systems. While a lot of structural data is available for the extracellular and cytoplasmic domains of TLRs, and a model of the dimeric full-length TLR3 receptor in the active state was build, the conformation of the transmembrane (TM) domain and juxtamembrane regions in TLR dimers is still unclear. In the present work, we study the transmembrane and juxtamembrane parts of human TLR4 receptor using solution NMR spectroscopy in a variety of membrane mimetics, including phospholipid bicelles. We show that the juxtamembrane hydrophobic region of TLR4 includes a part of long TM α-helix. We report the dimerization interface of the TM domain and claim that long TM domains with transmembrane charged aminoacids is a common feature of human toll-like receptors. This fact is analyzed from the viewpoint of protein activation mechanism, and a model of full-length TLR4 receptor in the dimeric state has been proposed.
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14
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Sarabipour S. Parallels and Distinctions in FGFR, VEGFR, and EGFR Mechanisms of Transmembrane Signaling. Biochemistry 2017. [DOI: 10.1021/acs.biochem.7b00399] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sarvenaz Sarabipour
- Institute for Computational
Medicine and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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15
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Abstract
Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
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16
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Bocharov EV, Bragin PE, Pavlov KV, Bocharova OV, Mineev KS, Polyansky AA, Volynsky PE, Efremov RG, Arseniev AS. The Conformation of the Epidermal Growth Factor Receptor Transmembrane Domain Dimer Dynamically Adapts to the Local Membrane Environment. Biochemistry 2017; 56:1697-1705. [DOI: 10.1021/acs.biochem.6b01085] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eduard V. Bocharov
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Pavel E. Bragin
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Konstantin V. Pavlov
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Olga V. Bocharova
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Konstantin S. Mineev
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Anton A. Polyansky
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
- Department of Structural and Computational
Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna
Biocenter 5, Vienna AT-1030, Austria
| | - Pavel E. Volynsky
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Roman G. Efremov
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
- Higher School of Economics, Myasnitskaya ul. 20, Moscow 101000, Russian Federation
| | - Alexander S. Arseniev
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
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17
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Bocharov EV, Mineev KS, Pavlov KV, Akimov SA, Kuznetsov AS, Efremov RG, Arseniev AS. Helix-helix interactions in membrane domains of bitopic proteins: Specificity and role of lipid environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:561-576. [PMID: 27884807 DOI: 10.1016/j.bbamem.2016.10.024] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/18/2016] [Accepted: 10/20/2016] [Indexed: 12/23/2022]
Abstract
Interaction between transmembrane helices often determines biological activity of membrane proteins. Bitopic proteins, a broad subclass of membrane proteins, form dimers containing two membrane-spanning helices. Some aspects of their structure-function relationship cannot be fully understood without considering the protein-lipid interaction, which can determine the protein conformational ensemble. Experimental and computer modeling data concerning transmembrane parts of bitopic proteins are reviewed in the present paper. They highlight the importance of lipid-protein interactions and resolve certain paradoxes in the behavior of such proteins. Besides, some properties of membrane organization provided a clue to understanding of allosteric interactions between distant parts of proteins. Interactions of these kinds appear to underlie a signaling mechanism, which could be widely employed in the functioning of many membrane proteins. Treatment of membrane proteins as parts of integrated fine-tuned proteolipid system promises new insights into biological function mechanisms and approaches to drug design. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation; National Research Centre "Kurchatov Institute", Akad. Kurchatova pl. 1, Moscow, 123182, Russian Federation.
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation
| | - Konstantin V Pavlov
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninskiy prospect 31/5, Moscow, 119071, Russian Federation
| | - Sergey A Akimov
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninskiy prospect 31/5, Moscow, 119071, Russian Federation; National University of Science and Technology "MISiS", Leninskiy prospect 4, Moscow, 119049, Russian Federation
| | - Andrey S Kuznetsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation; Higher School of Economics, Myasnitskaya ul. 20, Moscow, 101000, Russian Federation
| | - Alexander S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation.
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18
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Qureshi T, Goto NK. Impact of Differential Detergent Interactions on Transmembrane Helix Dimerization Affinities. ACS OMEGA 2016; 1:277-285. [PMID: 31457129 PMCID: PMC6640775 DOI: 10.1021/acsomega.6b00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 08/18/2016] [Indexed: 06/10/2023]
Abstract
Interactions between transmembrane (TM) helices play a critical role in the fundamental processes required for cells to communicate and exchange materials with their surroundings. Our understanding of the factors that promote TM helix interactions has greatly benefited from our ability to study these interactions in the solution phase through the use of membrane-mimetic micelles. However, less is known about the potential influence of juxtamembrane regions flanking the interacting TM helices that may modulate dimerization affinities, even when the interacting surface itself is not altered. To investigate this question, we used solution NMR to quantitate the dimerization affinity of the major coat protein from the M13 bacteriophage in sodium dodecyl sulfate (SDS), a well-characterized model of a single-spanning self-associating TM protein. Here, we showed that a shorter construct lacking the N-terminal amphipathic helix has a higher dimerization affinity relative to that of the full-length protein, with no change in the helical structure between the monomeric and dimeric states in both cases. Although this translated into a 0.6 kcal/mol difference in free energy when the SDS solvent was approximated as a continuous phase, there were deviations from this model at high protein to detergent ratios. Instead, the equilibria were better fit to a model that treats the empty micelle as an active participant in the reaction, giving rise to standard free energies of association that were the same for both full-length and TM-segment constructs. According to this model, the higher apparent affinity of the shorter peptide could be completely explained by the enhanced detergent binding by the monomer relative to that bound by the dimer. Therefore, differential detergent binding between the monomeric and dimeric states provides a mechanism by which TM helix interactions can be modulated by noninteracting juxtamembrane regions.
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19
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Bugge K, Lindorff-Larsen K, Kragelund BB. Understanding single-pass transmembrane receptor signaling from a structural viewpoint-what are we missing? FEBS J 2016; 283:4424-4451. [PMID: 27350538 DOI: 10.1111/febs.13793] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/10/2016] [Accepted: 06/27/2016] [Indexed: 11/30/2022]
Abstract
Single-pass transmembrane receptors are involved in essential processes of both physiological and pathological nature and represent more than 1300 proteins in the human genome. Despite the high biological relevance of these receptors, the mechanisms of the signal transductions they facilitate are incompletely understood. One major obstacle is the lack of structures of the transmembrane domains that connect the extracellular ligand-binding domains to the intracellular signaling platforms. Over a period of almost 20 years since the first structure was reported, only 21 of these receptors have become represented by a transmembrane domain structure. This scarceness stands in strong contrast to the significance of these transmembrane α-helices for receptor functionality. In this review, we explore the properties and qualities of the current set of structures, as well as the methodological difficulties associated with their characterization and the challenges left to be overcome. Without an increased and focused effort to bring this class of proteins on par with the remaining membrane protein field, a serious lag in their biological understanding looms. Design of pharmaceutical agents, prediction of mutational affects in relation to disease, and deciphering of functional mechanisms require high-resolution structural information, especially when dealing with a domain carrying so much functionality in so few residues.
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Affiliation(s)
- Katrine Bugge
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
| | - Birthe B Kragelund
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
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20
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Nadezhdin KD, García-Carpio I, Goncharuk SA, Mineev KS, Arseniev AS, Vilar M. Structural Basis of p75 Transmembrane Domain Dimerization. J Biol Chem 2016; 291:12346-57. [PMID: 27056327 DOI: 10.1074/jbc.m116.723585] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 12/14/2022] Open
Abstract
Dimerization of single span transmembrane receptors underlies their mechanism of activation. p75 neurotrophin receptor plays an important role in the nervous system, but the understanding of p75 activation mechanism is still incomplete. The transmembrane (TM) domain of p75 stabilizes the receptor dimers through a disulfide bond, essential for the NGF signaling. Here we solved by NMR the three-dimensional structure of the p75-TM-WT and the functionally inactive p75-TM-C257A dimers. Upon reconstitution in lipid micelles, p75-TM-WT forms the disulfide-linked dimers spontaneously. Under reducing conditions, p75-TM-WT is in a monomer-dimer equilibrium with the Cys(257) residue located on the dimer interface. In contrast, p75-TM-C257A forms dimers through the AXXXG motif on the opposite face of the α-helix. Biochemical and cross-linking experiments indicate that AXXXG motif is not on the dimer interface of p75-TM-WT, suggesting that the conformation of p75-TM-C257A may be not functionally relevant. However, rather than mediating p75 homodimerization, mutagenesis of the AXXXG motif reveals its functional role in the regulated intramembrane proteolysis of p75 catalyzed by the γ-secretase complex. Our structural data provide an insight into the key role of the Cys(257) in stabilization of the weak transmembrane dimer in a conformation required for the NGF signaling.
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Affiliation(s)
- Kirill D Nadezhdin
- From the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation and
| | - Irmina García-Carpio
- Neurodegeneration Unit, Unidad Funcional de Investigación de Enfermedades Crónicas-Instituto de Salud Carlos III, Crta Majadahonda a Pozuelo km.2 Majadahonda, Madrid 28220, Spain
| | - Sergey A Goncharuk
- From the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation and
| | - Konstantin S Mineev
- From the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation and
| | - Alexander S Arseniev
- From the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation and
| | - Marçal Vilar
- Neurodegeneration Unit, Unidad Funcional de Investigación de Enfermedades Crónicas-Instituto de Salud Carlos III, Crta Majadahonda a Pozuelo km.2 Majadahonda, Madrid 28220, Spain
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21
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Bocharov EV, Lesovoy DM, Pavlov KV, Pustovalova YE, Bocharova OV, Arseniev AS. Alternative packing of EGFR transmembrane domain suggests that protein-lipid interactions underlie signal conduction across membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1254-61. [PMID: 26903218 DOI: 10.1016/j.bbamem.2016.02.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 10/22/2022]
Abstract
The human epidermal growth factor receptor (EGFR) of HER/ErbB receptor tyrosine kinase family mediates a broad spectrum of cellular responses transducing biochemical signals via lateral dimerization in plasma membrane, while inactive receptors can exist in both monomeric and dimeric forms. Recently, the dimeric conformation of the helical single-span transmembrane domains of HER/ErbB employing the relatively polar N-terminal motifs in a fashion permitting proper kinase activation was experimentally determined. Here we describe the EGFR transmembrane domain dimerization via an alternative weakly polar C-terminal motif A(661)xxxG(665) presumably corresponding to the inactive receptor state. During association, the EGFR transmembrane helices undergo a structural adjustment with adaptation of inter-molecular polar and hydrophobic interactions depending upon the surrounding membrane properties that directly affect the transmembrane helix packing. This might imply that signal transduction through membrane and allosteric regulation are inclusively mediated by coupled protein-protein and protein-lipid interactions, elucidating paradoxically loose linkage between ligand binding and kinase activation.
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Affiliation(s)
- Eduard V Bocharov
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation.
| | - Dmitry M Lesovoy
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Konstantin V Pavlov
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Yulia E Pustovalova
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Olga V Bocharova
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Alexander S Arseniev
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
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22
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Mineev KS, Panova SV, Bocharova OV, Bocharov EV, Arseniev AS. The Membrane Mimetic Affects the Spatial Structure and Mobility of EGFR Transmembrane and Juxtamembrane Domains. Biochemistry 2015; 54:6295-8. [DOI: 10.1021/acs.biochem.5b00851] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute
of Bioorganic Chemistry, Russian Academy of Sciences RAS, str.
Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
| | - Stanislava V. Panova
- Shemyakin-Ovchinnikov Institute
of Bioorganic Chemistry, Russian Academy of Sciences RAS, str.
Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
| | - Olga V. Bocharova
- Shemyakin-Ovchinnikov Institute
of Bioorganic Chemistry, Russian Academy of Sciences RAS, str.
Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
| | - Eduard V. Bocharov
- Shemyakin-Ovchinnikov Institute
of Bioorganic Chemistry, Russian Academy of Sciences RAS, str.
Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
| | - Alexander S. Arseniev
- Shemyakin-Ovchinnikov Institute
of Bioorganic Chemistry, Russian Academy of Sciences RAS, str.
Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
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23
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Kuznetsov AS, Polyansky AA, Fleck M, Volynsky PE, Efremov RG. Adaptable Lipid Matrix Promotes Protein–Protein Association in Membranes. J Chem Theory Comput 2015; 11:4415-26. [DOI: 10.1021/acs.jctc.5b00206] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Andrey S. Kuznetsov
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
| | - Anton A. Polyansky
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
- Department
of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
| | - Markus Fleck
- Department
of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
| | - Pavel E. Volynsky
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
| | - Roman G. Efremov
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
- Higher School of Economics, Myasnitskaya Str., 20, Moscow 101000, Russia
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24
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Carlier L, Joanne P, Khemtémourian L, Lacombe C, Nicolas P, El Amri C, Lequin O. Investigating the role of GXXXG motifs in helical folding and self-association of plasticins, Gly/Leu-rich antimicrobial peptides. Biophys Chem 2015; 196:40-52. [DOI: 10.1016/j.bpc.2014.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/16/2014] [Accepted: 09/19/2014] [Indexed: 12/24/2022]
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25
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Mineev KS, Goncharuk SA, Arseniev AS. Toll-like receptor 3 transmembrane domain is able to perform various homotypic interactions: An NMR structural study. FEBS Lett 2014; 588:3802-7. [DOI: 10.1016/j.febslet.2014.08.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/27/2014] [Accepted: 08/27/2014] [Indexed: 11/26/2022]
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26
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Walther TH, Ulrich AS. Transmembrane helix assembly and the role of salt bridges. Curr Opin Struct Biol 2014; 27:63-8. [DOI: 10.1016/j.sbi.2014.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 10/25/2022]
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27
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Manni S, Mineev KS, Usmanova D, Lyukmanova EN, Shulepko MA, Kirpichnikov MP, Winter J, Matkovic M, Deupi X, Arseniev AS, Ballmer-Hofer K. Structural and functional characterization of alternative transmembrane domain conformations in VEGF receptor 2 activation. Structure 2014; 22:1077-1089. [PMID: 24980797 DOI: 10.1016/j.str.2014.05.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 05/16/2014] [Accepted: 05/17/2014] [Indexed: 10/25/2022]
Abstract
Transmembrane signaling by receptor tyrosine kinases (RTKs) entails ligand-mediated dimerization and structural rearrangement of the extracellular domains. RTK activation also depends on the specific orientation of the transmembrane domain (TMD) helices, as suggested by pathogenic, constitutively active RTK mutants. Such mutant TMDs carry polar amino acids promoting stable transmembrane helix dimerization, which is essential for kinase activation. We investigated the effect of polar amino acids introduced into the TMD of vascular endothelial growth factor receptor 2, regulating blood vessel homeostasis. Two mutants showed constitutive kinase activity, suggesting that precise TMD orientation is mandatory for kinase activation. Nuclear magnetic resonance spectroscopy revealed that TMD helices in activated constructs were rotated by 180° relative to the interface of the wild-type conformation, confirming that ligand-mediated receptor activation indeed results from transmembrane helix rearrangement. A molecular dynamics simulation confirmed the transmembrane helix arrangement of wild-type and mutant TMDs revealed by nuclear magnetic resonance spectroscopy.
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Affiliation(s)
- Sandro Manni
- Paul Scherrer Institute, Biomolecular Research, 5232 Villigen PSI, Switzerland
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Dinara Usmanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Ekaterina N Lyukmanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Mikhail A Shulepko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation; Lomonosov Moscow State University, Leninskie Gori 1, Moscow 119234, Russian Federation
| | - Mikhail P Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation; Lomonosov Moscow State University, Leninskie Gori 1, Moscow 119234, Russian Federation
| | - Jonas Winter
- Paul Scherrer Institute, Biomolecular Research, 5232 Villigen PSI, Switzerland
| | - Milos Matkovic
- Paul Scherrer Institute, Biomolecular Research, 5232 Villigen PSI, Switzerland
| | - Xavier Deupi
- Paul Scherrer Institute, Biomolecular Research, 5232 Villigen PSI, Switzerland; Paul Scherrer Institute, Condensed Matter Theory Group, 5232 Villigen PSI, Switzerland
| | - Alexander S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Kurt Ballmer-Hofer
- Paul Scherrer Institute, Biomolecular Research, 5232 Villigen PSI, Switzerland.
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