1
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Sahoo AR, Souza PCT, Meng Z, Buck M. Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer. Structure 2023; 31:735-745.e2. [PMID: 37075749 PMCID: PMC10833135 DOI: 10.1016/j.str.2023.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/07/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Structures and dynamics of transmembrane (TM) receptor regions are key to understanding their signaling mechanism across membranes. Here we examine configurations of TM region dimers, assembled using the recent Martini 3 force field for coarse-grain (CG) molecular dynamics simulations. At first glance, our results show only a reasonable agreement with ab initio predictions using PREDDIMER and AlphaFold2 Multimer and with nuclear magnetic resonance (NMR)-derived structures. 5 of 11 CG TM structures are similar to the NMR structures (within <3.5 Å root-mean-square deviation [RMSD]) compared with 10 and 9 using PREDDIMER and AlphaFold2, respectively (with 8 structures of the later within 1.5 Å). Surprisingly, AlphaFold2 predictions are closer to NMR structures when the 2001 instead of 2020 database is used for training. The CG simulations reveal that alternative configurations of TM dimers readily interconvert with a predominant population. The implications for transmembrane signaling are discussed, including for the development of peptide-based pharmaceuticals.
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Affiliation(s)
- Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Zhiyuan Meng
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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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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Mero HR, Lyantagaye SL, Bongcam-Rudloff E. Cassava Brown Streak Viruses express second 6-kilodalton (6K2) protein with varied polarity and three dimensional (3D) structures: Basis for trait discrepancy between the virus species. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105219. [PMID: 35066168 DOI: 10.1016/j.meegid.2022.105219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 12/15/2021] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
Abstract
Cassava Brown Streak Virus (CBSV) and Ugandan Cassava Brown Streak Virus (UCBSV) are the two among six virus species speculated to cause the most catastrophic Brown Streak Disease of Cassava (CBSD) in Africa and Asia. Cassava Brown Streak Virus (CBSV) is hard to breed resistance for compared to Ugandan Cassava Brown Streak Virus (UCBSV) species. This is exemplified by incidences of CBSV species rather than UCBSV species in elite breeding line, KBH 2006/0026 at Bagamoyo, Tanzania. It is not yet understood as to why CBSV species could breakdown CBSD-resistance in the KBH 2006/0026 unlike the UCBSV species. This marks the first in silico study conducted to understand molecular basis for the trait discrepancy between CBSV and UCBSV species from structural biology view point. Following ab initio modelling and analysis of physical-chemical properties of second 6-kilodalton (6K2) protein encoded by CBSV and UCBSV species, using ROBETTA server and Protein Parameters tool, respectively we report that; three dimensional (3D) structures and polarity of the protein differs significantly between the two virus species. (95% and 5%) and (85% and 15%) strains of 20 CBSV and 20 UCBSV species respectively, expressed the protein in homo-trimeric and homo-tetrameric forms, correspondingly. 95% and 85% of studied strain population of the two virus species expressed hydrophilic and hydrophobic 6K2, respectively. Based on findings of the curent study, we hypothesize that; (i) The hydrophilic 6K2 expressed by the CBSV species, favour its faster systemic movement via vascular tissues of cassava host and hence result into higher tissue titres than the UCBSV species encoding hydrophobic form of the protein. t and (ii) The hydrophilic 6K2 expressed byCBSV species have additional interaction advantage with Nuclear Inclusion b protease domain (NIb) and Viral genome-linked protein (VPg), components of Virus Replication Complex (VRC) and hence contributing to faster replication of viral genome than the hydrophobic 6K2 expressed by the UCBSV species. Experimental studies are needed to resolve the 3D structures of the 6K2, VPg and NIb and comprehend complex molecular interactions between them. We suggest that, the 6K2 gene should be targeted for improvement of RNA interference (RNAi)-directed transgenesis of virus-resistant cassava as a more effective way to control the CBSD besides breeding.
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Affiliation(s)
- Herieth Rhodes Mero
- University of Dar es Salaam, Mkwawa University College of Education (MUCE), P. O. Box 2513, Iringa, Tanzania; Swedish University of Agricultural Sciences (SLU), SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, P. 0. BOX 7054, 750 07 Uppsala, Sweden.
| | | | - Erik Bongcam-Rudloff
- Swedish University of Agricultural Sciences (SLU), SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, P. 0. BOX 7054, 750 07 Uppsala, Sweden
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4
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Resolving the conformational dynamics of ErbB growth factor receptor dimers. J Struct Biol 2019; 207:225-233. [PMID: 31163211 DOI: 10.1016/j.jsb.2019.05.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/20/2019] [Accepted: 05/31/2019] [Indexed: 12/30/2022]
Abstract
The combinatorial dimerization of the ErbB growth factor receptors (ErbB1- ErbB4) are critical for their function. Here, we have characterized the conformational dynamics of ErbB transmembrane homo-dimers and hetero-dimers by using a coarse-grain simulation framework. All dimers, except ErbB4-4 and ErbB1-4, exhibit at least two conformations. The reported NMR structures correspond to one of these conformations, representing the N-terminal active state in ErbB1-1 (RH2), ErbB2-2 (RH1) and ErbB4-4 (RH) homo-dimers and the LH dimer in ErbB3-3 homo-dimer, validating the computational approach. Further, we predict a right-handed ErbB3-3 dimer conformer that warrants experimental testing. The five hetero-dimers that have not yet been experimentally resolved display prominent right-handed dimers associating by the SmXXXSm motif. Our results provide insights into the constitutive signaling of ErbB4 after cleavage of the extracellular region. The presence of the inactive-like dimer conformers leading to symmetric kinase domains gives clues on the autoinhibition of the receptor dimers. The dimer states characterized here represent an important step towards understanding the combinatorial cross associations in the ErbB family.
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5
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Pawar AB, Sengupta D. Effect of Membrane Composition on Receptor Association: Implications of Cancer Lipidomics on ErbB Receptors. J Membr Biol 2018; 251:359-368. [DOI: 10.1007/s00232-018-0015-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
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6
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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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7
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Cao H, Ng MCK, Jusoh SA, Tai HK, Siu SWI. TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers. J Comput Aided Mol Des 2017; 31:855-865. [DOI: 10.1007/s10822-017-0047-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/17/2017] [Indexed: 12/01/2022]
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8
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Localisation Microscopy of Breast Epithelial ErbB-2 Receptors and Gap Junctions: Trafficking after γ-Irradiation, Neuregulin-1β, and Trastuzumab Application. Int J Mol Sci 2017; 18:ijms18020362. [PMID: 28208769 PMCID: PMC5343897 DOI: 10.3390/ijms18020362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 12/28/2022] Open
Abstract
In cancer, vulnerable breast epithelium malignance tendency correlates with number and activation of ErbB receptor tyrosine kinases. In the presented work, we observe ErbB receptors activated by irradiation-induced DNA injury or neuregulin-1β application, or alternatively, attenuated by a therapeutic antibody using high resolution fluorescence localization microscopy. The gap junction turnover coinciding with ErbB receptor activation and co-transport is simultaneously recorded. DNA injury caused by 4 Gray of 6 MeV photon γ-irradiation or alternatively neuregulin-1β application mobilized ErbB receptors in a nucleograde fashion—a process attenuated by trastuzumab antibody application. This was accompanied by increased receptor density, indicating packing into transport units. Factors mobilizing ErbB receptors also mobilized plasma membrane resident gap junction channels. The time course of ErbB receptor activation and gap junction mobilization recapitulates the time course of non-homologous end-joining DNA repair. We explain our findings under terms of DNA injury-induced membrane receptor tyrosine kinase activation and retrograde trafficking. In addition, we interpret the phenomenon of retrograde co-trafficking of gap junction connexons stimulated by ErbB receptor activation.
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9
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Steindorf D, Schneider D. In vivo selection of heterotypically interacting transmembrane helices: Complementary helix surfaces, rather than conserved interaction motifs, drive formation of transmembrane hetero-dimers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:245-256. [DOI: 10.1016/j.bbamem.2016.11.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/23/2016] [Accepted: 11/29/2016] [Indexed: 11/16/2022]
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10
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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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11
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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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12
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Trenker R, Call MJ, Call ME. Progress and prospects for structural studies of transmembrane interactions in single-spanning receptors. Curr Opin Struct Biol 2016; 39:115-123. [DOI: 10.1016/j.sbi.2016.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/20/2016] [Accepted: 07/01/2016] [Indexed: 11/28/2022]
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13
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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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14
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Peng B, Ding XY, Sun C, Liu W, Zhang JZH, Zhao X. The effect of POPC acyl chains packing by aromatic amino acid methyl esters investigated by ATR-FTIR combined with QM calculations. RSC Adv 2016. [DOI: 10.1039/c6ra05903a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The packing of POPC acyl chains can be influenced by aromatic amino acid methyl esters significantly, thus the HCCH motif is packed closed to the other one of an adjacent acyl chain with enhancement by dispersion interactions.
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Affiliation(s)
- Bo Peng
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
| | - Xiao-Yan Ding
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
| | - Chao Sun
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
| | - Wei Liu
- State Key Laboratory of Precision Spectroscopy
- Department of Physics
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
| | - John Z. H. Zhang
- State Key Laboratory of Precision Spectroscopy
- Department of Physics
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
| | - Xin Zhao
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
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15
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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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16
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Berglund NA, Kargas V, Ortiz-Suarez ML, Bond PJ. The role of protein–protein interactions in Toll-like receptor function. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:72-83. [DOI: 10.1016/j.pbiomolbio.2015.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 12/12/2022]
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17
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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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18
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Wang Y, Barth P. Evolutionary-guided de novo structure prediction of self-associated transmembrane helical proteins with near-atomic accuracy. Nat Commun 2015; 6:7196. [PMID: 25995083 DOI: 10.1038/ncomms8196] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 04/15/2015] [Indexed: 11/09/2022] Open
Abstract
How specific protein associations regulate the function of membrane receptors remains poorly understood. Conformational flexibility currently hinders the structure determination of several classes of membrane receptors and associated oligomers. Here we develop EFDOCK-TM, a general method to predict self-associated transmembrane protein helical (TMH) structures from sequence guided by co-evolutionary information. We show that accurate intermolecular contacts can be identified using a combination of protein sequence covariation and TMH binding surfaces predicted from sequence. When applied to diverse TMH oligomers, including receptors characterized in multiple conformational and functional states, the method reaches unprecedented near-atomic accuracy for most targets. Blind predictions of structurally uncharacterized receptor tyrosine kinase TMH oligomers provide a plausible hypothesis on the molecular mechanisms of disease-associated point mutations and binding surfaces for the rational design of selective inhibitors. The method sets the stage for uncovering novel determinants of molecular recognition and signalling in single-spanning eukaryotic membrane receptors.
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Affiliation(s)
- Y Wang
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - P Barth
- 1] Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA [2] Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA [3] Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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19
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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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20
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Reddy T, Manrique S, Buyan A, Hall BA, Chetwynd A, Sansom MSP. Primary and secondary dimer interfaces of the fibroblast growth factor receptor 3 transmembrane domain: characterization via multiscale molecular dynamics simulations. Biochemistry 2014; 53:323-32. [PMID: 24397339 DOI: 10.1021/bi401576k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Receptor tyrosine kinases are single-pass membrane proteins that form dimers within the membrane. The interactions of their transmembrane domains (TMDs) play a key role in dimerization and signaling. Fibroblast growth factor receptor 3 (FGFR3) is of interest as a G380R mutation in its TMD is the underlying cause of ~99% of the cases of achondroplasia, the most common form of human dwarfism. The structural consequences of this mutation remain uncertain: the mutation shifts the position of the TMD relative to the lipid bilayer but does not alter the association free energy. We have combined coarse-grained and all-atom molecular dynamics simulations to study the dimerization of wild-type, heterodimer, and mutant FGFR3 TMDs. The simulations reveal that the helices pack together in the dimer to form a flexible interface. The primary packing mode is mediated by a Gx3G motif. There is also a secondary dimer interface that is more highly populated in heterodimer and mutant configurations that may feature in the molecular mechanism of pathology. Both coarse-grained and atomistic simulations reveal a significant shift of the G380R mutant dimer TMD relative to the bilayer to allow interactions of the arginine side chain with lipid headgroup phosphates.
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Affiliation(s)
- Tyler Reddy
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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21
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Mineev KS, Lesovoy DM, Usmanova DR, Goncharuk SA, Shulepko MA, Lyukmanova EN, Kirpichnikov MP, Bocharov EV, Arseniev AS. NMR-based approach to measure the free energy of transmembrane helix–helix interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:164-72. [DOI: 10.1016/j.bbamem.2013.08.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 08/27/2013] [Accepted: 08/30/2013] [Indexed: 11/30/2022]
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22
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Zoonens M, Comer J, Masscheleyn S, Pebay-Peyroula E, Chipot C, Miroux B, Dehez F. Dangerous liaisons between detergents and membrane proteins. The case of mitochondrial uncoupling protein 2. J Am Chem Soc 2013; 135:15174-82. [PMID: 24021091 DOI: 10.1021/ja407424v] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The extraction of membrane proteins from their native environment by detergents is central to their biophysical characterization. Recent studies have emphasized that detergents may perturb the structure locally and modify the dynamics of membrane proteins. However, it remains challenging to determine whether these perturbations are negligible or could be responsible for misfolded conformations, altering the protein's function. In this work, we propose an original strategy combining functional studies and molecular simulations to address the physiological relevance of membrane protein structures obtained in the presence of detergents. We apply our strategy to a structure of isoform 2 of an uncoupling protein (UCP2) binding an inhibitor recently obtained in dodecylphosphocholine detergent micelles. Although this structure shares common traits with the ADP/ATP carrier, a member of the same protein family, its functional and biological significance remains to be addressed. In the present investigation, we demonstrate how dodecylphosphocholine severely alters the structure as well as the function of UCPs. The proposed original strategy opens new vistas for probing the physiological relevance of three-dimensional structures of membrane proteins obtained in non-native environments.
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Affiliation(s)
- Manuela Zoonens
- CNRS UMR 7099, Institut de Biologie Physico Chimique (IBPC), 75005 Paris, France
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23
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Mineev KS, Lyukmanova EN, Krabben L, Serebryakova MV, Shulepko MA, Arseniev AS, Kordyukova LV, Veit M. Structural investigation of influenza virus hemagglutinin membrane-anchoring peptide. Protein Eng Des Sel 2013; 26:547-52. [PMID: 23873663 DOI: 10.1093/protein/gzt034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hemagglutinin (HA), the trimeric spike of influenza virus, catalyzes fusion of viral and cellular membranes. We have synthesized the anchoring peptide including the linker, transmembrane region and cytoplasmic tail (HA-TMR-CT) in a cell-free system. Furthermore, to mimic the palmitoylation of three conserved cysteines within the CT, we chemically alkylated HA-TMR-CT using hexadecyl-methanethiosulfonate. While the nuclear magnetic resonance spectroscopy showed pure and refolded peptides, the formation of multiple oligomers of higher order impeded further structural analysis. Circular dichroism spectroscopy of both alkylated and non-alkylated HA-TMR-CT revealed an α-helical secondary structure. No major impact of the fatty acids on the secondary structure was detected.
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Affiliation(s)
- Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, 117997 Moscow, Russia
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24
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Sharma P, Kaywan-Lutfi M, Krshnan L, Byrne EFX, Call MJ, Call ME. Production of disulfide-stabilized transmembrane peptide complexes for structural studies. J Vis Exp 2013:e50141. [PMID: 23486227 DOI: 10.3791/50141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Physical interactions among the lipid-embedded alpha-helical domains of membrane proteins play a crucial role in folding and assembly of membrane protein complexes and in dynamic processes such as transmembrane (TM) signaling and regulation of cell-surface protein levels. Understanding the structural features driving the association of particular sequences requires sophisticated biophysical and biochemical analyses of TM peptide complexes. However, the extreme hydrophobicity of TM domains makes them very difficult to manipulate using standard peptide chemistry techniques, and production of suitable study material often proves prohibitively challenging. Identifying conditions under which peptides can adopt stable helical conformations and form complexes spontaneously adds a further level of difficulty. Here we present a procedure for the production of homo- or hetero-dimeric TM peptide complexes from materials that are expressed in E. coli, thus allowing incorporation of stable isotope labels for nuclear magnetic resonance (NMR) or non-natural amino acids for other applications relatively inexpensively. The key innovation in this method is that TM complexes are produced and purified as covalently associated (disulfide-crosslinked) assemblies that can form stable, stoichiometric and homogeneous structures when reconstituted into detergent, lipid or other membrane-mimetic materials. We also present carefully optimized procedures for expression and purification that are equally applicable whether producing single TM domains or crosslinked complexes and provide advice for adapting these methods to new TM sequences.
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Affiliation(s)
- Pooja Sharma
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Australia
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25
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Zhang L, Sodt AJ, Venable RM, Pastor RW, Buck M. Prediction, refinement, and persistency of transmembrane helix dimers in lipid bilayers using implicit and explicit solvent/lipid representations: microsecond molecular dynamics simulations of ErbB1/B2 and EphA1. Proteins 2012; 81:365-76. [PMID: 23042146 DOI: 10.1002/prot.24192] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/12/2012] [Accepted: 09/21/2012] [Indexed: 12/26/2022]
Abstract
All-atom simulations are carried out on ErbB1/B2 and EphA1 transmembrane helix dimers in lipid bilayers starting from their solution/DMPC bicelle NMR structures. Over the course of microsecond trajectories, the structures remain in close proximity to the initial configuration and satisfy the majority of experimental tertiary contact restraints. These results further validate CHARMM protein/lipid force fields and simulation protocols on Anton. Separately, dimer conformations are generated using replica exchange in conjunction with an implicit solvent and lipid representation. The implicit model requires further improvement, and this study investigates whether lengthy all-atom molecular dynamics simulations can alleviate the shortcomings of the initial conditions. The simulations correct many of the deficiencies. For example, excessive helix twisting is eliminated over a period of hundreds of nanoseconds. The helix tilt, crossing angles, and dimer contacts approximate those of the NMR-derived structure, although the detailed contact surface remains off-set for one of two helices in both systems. Hence, even microsecond simulations are not long enough for extensive helix rotations. The alternate structures can be rationalized with reference to interaction motifs and may represent still sought after receptor states that are important in ErbB1/B2 and EphA1 signaling.
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Affiliation(s)
- Liqun Zhang
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106, USA
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26
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Bocharov EV, Mineev KS, Goncharuk MV, Arseniev AS. Structural and thermodynamic insight into the process of “weak” dimerization of the ErbB4 transmembrane domain by solution NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2158-70. [DOI: 10.1016/j.bbamem.2012.05.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 04/20/2012] [Accepted: 05/01/2012] [Indexed: 10/28/2022]
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27
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Polyansky AA, Volynsky PE, Efremov RG. Multistate Organization of Transmembrane Helical Protein Dimers Governed by the Host Membrane. J Am Chem Soc 2012; 134:14390-400. [DOI: 10.1021/ja303483k] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Anton A. Polyansky
- Department of Structural and
Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna, AT-1030,
Austria
- M.M. Shemyakin
and Yu.A. Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Pavel E. Volynsky
- M.M. Shemyakin
and Yu.A. Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Roman G. Efremov
- M.M. Shemyakin
and Yu.A. Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny,
Moscow Region, 141700, Russia
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28
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Abstract
Of great interest to the academic and pharmaceutical research communities, helical transmembrane proteins are characterized by their ability to dissolve and fold in lipid bilayers—properties conferred by polypeptide spans termed transmembrane domains (TMDs). The apolar nature of TMDs necessitates the use of membrane-mimetic solvents for many structure and folding studies. This review examines the relationship between TMD structure and solvent environment, focusing on principles elucidated largely in membrane-mimetic environments with single-TMD protein and peptide models. Following a brief description of TMD sequence and conformational characteristics gleaned from the structural database, we present an overview of the conceptual models used to study folding in vitro. The impact of sequence and solvent context on the incorporation of TMDs into membranes, and its role in measurements of TMD self-assembly strengths, is then described. We conclude with a discussion of the nonspecific effects of membrane components on TMD stability.
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Affiliation(s)
- Arianna Rath
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 1X8 Canada
| | - Charles M. Deber
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 1X8 Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
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29
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Muhle-Goll C, Hoffmann S, Afonin S, Grage SL, Polyansky AA, Windisch D, Zeitler M, Bürck J, Ulrich AS. Hydrophobic matching controls the tilt and stability of the dimeric platelet-derived growth factor receptor (PDGFR) β transmembrane segment. J Biol Chem 2012; 287:26178-86. [PMID: 22619173 DOI: 10.1074/jbc.m111.325555] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The platelet-derived growth factor receptor β is a member of the cell surface receptor tyrosine kinase family and dimerizes upon activation. We determined the structure of the transmembrane segment in dodecylphosphocholine micelles by liquid-state NMR and found that it forms a stable left-handed helical dimer. Solid-state NMR and oriented circular dichroism were used to measure the tilt angle of the helical segments in macroscopically aligned model membranes with different acyl chain lengths. Both methods showed that decreasing bilayer thickness (DEPC-POPC-DMPC) led to an increase in the helix tilt angle from 10° to 30° with respect to the bilayer normal. At the same time, reconstitution of the comparatively long hydrophobic segment became less effective, eventually resulting in complete protein aggregation in the short-chain lipid DLPC. Unrestrained molecular dynamics simulations of the dimer were carried out in explicit lipid bilayers (DEPC, POPC, DMPC, sphingomyelin), confirming the observed dependence of the helix tilt angle on bilayer thickness. Notably, molecular dynamics revealed that the left-handed dimer gets tilted en bloc, whereas conformational transitions to alternative (e.g. right-handed dimeric) states were not supported. The experimental data along with the simulation results demonstrate a pronounced interplay between the platelet-directed growth factor receptor β transmembrane segment and the bilayer thickness. The effect of hydrophobic mismatch might play a key role in the redistribution and activation of the receptor within different lipid microdomains of the plasma membrane in vivo.
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Affiliation(s)
- Claudia Muhle-Goll
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021 Karlsruhe, Germany
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30
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Nadezhdin KD, Bocharova OV, Bocharov EV, Arseniev AS. Dimeric structure of transmembrane domain of amyloid precursor protein in micellar environment. FEBS Lett 2012; 586:1687-92. [PMID: 22584060 DOI: 10.1016/j.febslet.2012.04.062] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 04/12/2012] [Accepted: 04/30/2012] [Indexed: 01/27/2023]
Abstract
Some pathogenic mutations associated with Alzheimer's disease are thought to affect structural-dynamic properties and the lateral dimerization of amyloid precursor protein (APP) in neuron membrane. Dimeric structure of APP transmembrane fragment Gln(686)-Lys(726) was determined in membrane-mimicking dodecylphosphocholine micelles using high-resolution NMR spectroscopy. The APP membrane-spanning α-helix Lys(699)-Lys(724) self-associates in a left-handed parallel dimer through extended heptad repeat motif I(702)X(3)M(706)X(2)G(709)X(3)A(713)X(2)I(716)X(3)I(720)X(2)I(723), whereas the juxtamembrane region Gln(686)-Val(695) constitutes the nascent helix, also sensing the dimerization. The dimerization mechanism of APP transmembrane domain has been described at atomic resolution for the first time and is important for understanding molecular events of APP sequential proteolytical cleavage resulting in amyloid-β peptide.
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Affiliation(s)
- Kirill D Nadezhdin
- Division of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
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31
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Lyukmanova EN, Shenkarev ZO, Khabibullina NF, Kopeina GS, Shulepko MA, Paramonov AS, Mineev KS, Tikhonov RV, Shingarova LN, Petrovskaya LE, Dolgikh DA, Arseniev AS, Kirpichnikov MP. Lipid-protein nanodiscs for cell-free production of integral membrane proteins in a soluble and folded state: comparison with detergent micelles, bicelles and liposomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:349-58. [PMID: 22056981 DOI: 10.1016/j.bbamem.2011.10.020] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 10/03/2011] [Accepted: 10/18/2011] [Indexed: 11/26/2022]
Abstract
Production of integral membrane proteins (IMPs) in a folded state is a key prerequisite for their functional and structural studies. In cell-free (CF) expression systems membrane mimicking components could be added to the reaction mixture that promotes IMP production in a soluble form. Here lipid-protein nanodiscs (LPNs) of different lipid compositions (DMPC, DMPG, POPC, POPC/DOPG) have been compared with classical membrane mimicking media such as detergent micelles, lipid/detergent bicelles and liposomes by their ability to support CF synthesis of IMPs in a folded and soluble state. Three model membrane proteins of different topology were used: homodimeric transmembrane (TM) domain of human receptor tyrosine kinase ErbB3 (TM-ErbB3, 1TM); voltage-sensing domain of K(+) channel KvAP (VSD, 4TM); and bacteriorhodopsin from Exiguobacterium sibiricum (ESR, 7TM). Structural and/or functional properties of the synthesized proteins were analyzed. LPNs significantly enhanced synthesis of the IMPs in a soluble form regardless of the lipid composition. A partial disintegration of LPNs composed of unsaturated lipids was observed upon co-translational IMP incorporation. Contrary to detergents the nanodiscs resulted in the synthesis of ~80% active ESR and promoted correct folding of the TM-ErbB3. None of the tested membrane mimetics supported CF synthesis of correctly folded VSD, and the protocol of the domain refolding was developed. The use of LPNs appears to be the most promising approach to CF production of IMPs in a folded state. NMR analysis of (15)N-Ile-TM-ErbB3 co-translationally incorporated into LPNs shows the great prospects of this membrane mimetics for structural studies of IMPs produced by CF systems.
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Affiliation(s)
- E N Lyukmanova
- Russian Academy of Sciences, Moscow, Russian Federation.
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32
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Li E, Wimley WC, Hristova K. Transmembrane helix dimerization: beyond the search for sequence motifs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:183-93. [PMID: 21910966 DOI: 10.1016/j.bbamem.2011.08.031] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/25/2011] [Accepted: 08/26/2011] [Indexed: 01/07/2023]
Abstract
Studies of the dimerization of transmembrane (TM) helices have been ongoing for many years now, and have provided clues to the fundamental principles behind membrane protein (MP) folding. Our understanding of TM helix dimerization has been dominated by the idea that sequence motifs, simple recognizable amino acid sequences that drive lateral interaction, can be used to explain and predict the lateral interactions between TM helices in membrane proteins. But as more and more unique interacting helices are characterized, it is becoming clear that the sequence motif paradigm is incomplete. Experimental evidence suggests that the search for sequence motifs, as mediators of TM helix dimerization, cannot solve the membrane protein folding problem alone. Here we review the current understanding in the field, as it has evolved from the paradigm of sequence motifs into a view in which the interactions between TM helices are much more complex. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Edwin Li
- Department of Biology, Saint Joseph's University, Philadelphia, PA 19131, USA
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33
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He L, Hristova K. Physical-chemical principles underlying RTK activation, and their implications for human disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:995-1005. [PMID: 21840295 DOI: 10.1016/j.bbamem.2011.07.044] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 07/27/2011] [Accepted: 07/29/2011] [Indexed: 12/15/2022]
Abstract
RTKs, the second largest family of membrane receptors, exert control over cell proliferation, differentiation and migration. In recent years, our understanding of RTK structure and activation in health and disease has skyrocketed. Here we describe experimental approaches used to interrogate RTKs, and we review the quantitative biophysical frameworks and structural considerations that shape our understanding of RTK function. We discuss current knowledge about RTK interactions, focusing on the role of different domains in RTK homodimerization, and on the importance and challenges in RTK heterodimerization studies. We also review our understanding of pathogenic RTK mutations, and the underlying physical-chemical causes for the pathologies. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Affiliation(s)
- Lijuan He
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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34
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Cymer F, Veerappan A, Schneider D. Transmembrane helix-helix interactions are modulated by the sequence context and by lipid bilayer properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:963-73. [PMID: 21827736 DOI: 10.1016/j.bbamem.2011.07.035] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 07/19/2011] [Accepted: 07/24/2011] [Indexed: 12/22/2022]
Abstract
Folding of polytopic transmembrane proteins involves interactions of individual transmembrane helices, and multiple TM helix-helix interactions need to be controlled and aligned to result in the final TM protein structure. While defined interaction motifs, such as the GxxxG motif, might be critically involved in transmembrane helix-helix interactions, the sequence context as well as lipid bilayer properties significantly modulate the strength of a sequence specific transmembrane helix-helix interaction. Structures of 11 transmembrane helix dimers have been described today, and the influence of the sequence context as well as of the detergent and lipid environment on a sequence specific dimerization is discussed in light of the available structural information. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Affiliation(s)
- Florian Cymer
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Johann-Becher-Weg 30, 55128 Mainz, Germany
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Qureshi T, Goto NK. Contemporary methods in structure determination of membrane proteins by solution NMR. Top Curr Chem (Cham) 2011; 326:123-85. [PMID: 22160391 DOI: 10.1007/128_2011_306] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Integral membrane proteins are vital to life, being responsible for information and material exchange between a cell and its environment. Although high-resolution structural information is needed to understand how these functions are achieved, membrane proteins remain an under-represented subset of the protein structure databank. Solution NMR is increasingly demonstrating its ability to help address this knowledge shortfall, with the development of a diverse array of techniques to counter the challenges presented by membrane proteins. Here we document the advances that are helping to define solution NMR as an effective tool for membrane protein structure determination. Developments introduced over the last decade in the production of isotope-labeled samples, reconstitution of these samples into the growing selection of NMR-compatible membrane-mimetic systems, and the approaches used for the acquisition and application of structural restraints from these complexes are reviewed.
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Affiliation(s)
- Tabussom Qureshi
- Department of Chemistry, University of Ottawa, Ottawa, ON, Canada
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