1
|
Manor J, Arbely E, Beerlink A, Akkawi M, Arkin IT. Use of Isotope-Edited FTIR to Derive a Backbone Structure of a Transmembrane Protein. J Phys Chem Lett 2014; 5:2573-2579. [PMID: 26277945 DOI: 10.1021/jz501055d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Solving structures of membrane proteins has always been a formidable challenge, yet even upon success, the results are normally obtained in a mimetic environment that can be substantially different from a biological membrane. Herein, we use noninvasive isotope-edited FTIR spectroscopy to derive a structural model for the SARS coronavirus E protein transmembrane domain in lipid bilayers. Molecular-dynamics-based structural refinement, incorporating the IR-derived orientational restraints points to the formation of a helical hairpin structure. Disulfide cross-linking and X-ray reflectivity depth profiling provide independent support of the results. The unusually short helical hairpin structure of the protein might explain its ability to deform bilayers and is reminiscent of other peptides with membrane disrupting functionalities. Taken together, we show that isotope-edited FTIR is a powerful tool to analyze small membrane proteins in their native environment, enabling us to relate the unusual structure of the SARS E protein to its function.
Collapse
Affiliation(s)
- Joshua Manor
- †Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel
| | - Eyal Arbely
- †Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel
| | - Andrè Beerlink
- ‡Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, Göttingen 37077 Germany
| | - Mutaz Akkawi
- §Faculty of Science and Technology, Al-Quds University, Abu Dis, Palestinian National Authority
| | - Isaiah T Arkin
- †Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel
| |
Collapse
|
2
|
Naskar S, Deb SM, Kumar S, Niranjan SK, Sharma D, Sakaram D, Sharma A. Molecular characterisation of T cell receptor-zeta subunit (CD247) gene in buffalo (Bubalus bubalis). JOURNAL OF APPLIED ANIMAL RESEARCH 2013. [DOI: 10.1080/09712119.2013.822800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
3
|
Abstract
Despite the low affinity of the T-cell antigen receptor (TCR) for its peptide/major histocompatibility complex (pMHC) ligand, T cells are very sensitive to their antigens. This paradox can be resolved if we consider that the TCR may be organized into pre-existing oligomers or nanoclusters. Such structures could improve antigen recognition by increasing the functional affinity (avidity) of the TCR-pMHC interaction and by allowing cooperativity between individual TCRs. Up to approximately 20 TCRs become tightly apposed in these nanoclusters, often in a linear manner, and such structures could reflect a relatively generalized phenomenon: the non-random concentration of membrane receptors in specific areas of the plasma membrane known as protein islands. The association of TCRs into nanoclusters can explain the enhanced kinetics of the pMHC-TCR interaction in two dimensional versus three dimensional systems, but also their existence calls for a revision of the TCR triggering models based on pMHC-induced TCR clustering. Interestingly, the B-cell receptor and the FcεRI have also been shown to form nanoclusters, suggesting that the formation of pre-existing receptor oligomers could be widely used in the immune system.
Collapse
Affiliation(s)
- Wolfgang W A Schamel
- Department of Molecular Immunology, Institute of Biology III, Faculty of Biology, BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | | |
Collapse
|
4
|
Manor J, Arkin IT. Gaining insight into membrane protein structure using isotope-edited FTIR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012. [PMID: 23196348 DOI: 10.1016/j.bbamem.2012.11.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
FTIR spectroscopy has long been used as a tool used to gain average structural information on proteins. With the advent of stable isotope editing, FTIR can be used to derive accurate information on isolated amino acids. In particular, in an anisotropic sample such as membrane layers, it is possible to measure the orientation of the peptidic carbonyl groups. Herein, we review the theory that enables one to obtain accurate restraints from FTIR spectroscopy, alongside considerations for sample suitability and general applicability. We also propose approaches that may be used to generate structural models of simple membrane proteins based on FTIR orientational restraints. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.
Collapse
Affiliation(s)
- Joshua Manor
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem, 91904, Israel
| | | |
Collapse
|
5
|
Rossy J, Williamson DJ, Benzing C, Gaus K. The integration of signaling and the spatial organization of the T cell synapse. Front Immunol 2012. [PMID: 23189081 PMCID: PMC3504718 DOI: 10.3389/fimmu.2012.00352] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Engagement of the T cell antigen receptor (TCR) triggers signaling pathways that lead to T cell selection, differentiation and clonal expansion. Superimposed onto the biochemical network is a spatial organization that describes individual receptor molecules, dimers, oligomers and higher order structures. Here we discuss recent findings and new concepts that may regulate TCR organization in naïve and memory T cells. A key question that has emerged is how antigen-TCR interactions encode spatial information to direct T cell activation and differentiation. Single molecule super-resolution microscopy may become an important tool in decoding receptor organization at the molecular level.
Collapse
Affiliation(s)
- Jérémie Rossy
- Centre for Vascular Research and Australian Centre for Nanomedicine, University of New South Wales Sydney, NSW, Australia
| | | | | | | |
Collapse
|
6
|
Manor J, Feldblum ES, Zanni MT, Arkin IT. Environment Polarity in Proteins Mapped Noninvasively by FTIR Spectroscopy. J Phys Chem Lett 2012; 3:939-944. [PMID: 22563521 PMCID: PMC3341589 DOI: 10.1021/jz300150v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The polarity pattern of a macromolecule is of utmost importance to its structure and function. For example, one of the main driving forces for protein folding is the burial of hydrophobic residues. Yet polarity remains a difficult property to measure experimentally, due in part to its non-uniformity in the protein interior. Herein, we show that FTIR linewidth analysis of noninvasive 1-(13)C=(18)O labels can be used to obtain a reliable measure of the local polarity, even in a highly multi-phasic system, such as a membrane protein. We show that in the Influenza M2 H(+) channel, residues that line the pore are located in an environment that is as polar as fully solvated residues, while residues that face the lipid acyl chains are located in an apolar environment. Taken together, FTIR linewidth analysis is a powerful, yet chemically non-perturbing approach to examine one of the most important properties in proteins - polarity.
Collapse
Affiliation(s)
- Joshua Manor
- The Alexander Silberman Institute of Life Sciences. Department of Biological Chemistry. The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem, 91904, Israel
| | - Esther S. Feldblum
- The Alexander Silberman Institute of Life Sciences. Department of Biological Chemistry. The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem, 91904, Israel
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin, Madison, WI 53706-1396, USA
| | - Isaiah T. Arkin
- The Alexander Silberman Institute of Life Sciences. Department of Biological Chemistry. The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem, 91904, Israel
| |
Collapse
|
7
|
Abstract
The molecular basis of quicker and stronger responses by memory T cells is elusive. In this issue of Immunity, Kumar et al. (2011) demonstrate that more T cell receptor nanoclusters are present on memory cells than naive T cells before antigen stimulation, suggesting a basis for quick memory response.
Collapse
Affiliation(s)
- Takashi Saito
- Laboratory for Cell Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan.
| |
Collapse
|
8
|
Kumar R, Ferez M, Swamy M, Arechaga I, Rejas MT, Valpuesta JM, Schamel WWA, Alarcon B, van Santen HM. Increased sensitivity of antigen-experienced T cells through the enrichment of oligomeric T cell receptor complexes. Immunity 2011; 35:375-87. [PMID: 21903423 DOI: 10.1016/j.immuni.2011.08.010] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 05/11/2011] [Accepted: 08/23/2011] [Indexed: 12/25/2022]
Abstract
Although memory T cells respond more vigorously to stimulation and they are more sensitive to low doses of antigen than naive T cells, the molecular basis of this increased sensitivity remains unclear. We have previously shown that the T cell receptor (TCR) exists as different-sized oligomers on the surface of resting T cells and that large oligomers are preferentially activated in response to low antigen doses. Through biochemistry and electron microscopy, we now showed that previously stimulated and memory T cells have more and larger TCR oligomers at the cell surface than their naive counterparts. Reconstitution of cells and mice with a point mutant of the CD3ζ subunit, which impairs TCR oligomer formation, demonstrated that the increased size of TCR oligomers was directly responsible for the increased sensitivity of antigen-experienced T cells. Thus, we propose that an "avidity maturation" mechanism underlies T cell antigenic memory.
Collapse
Affiliation(s)
- Rashmi Kumar
- Departamento de Biología Celular e Inmunología, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Ganoth A, Alhadeff R, Arkin IT. Computational study of the Na+/H + antiporter from Vibrio parahaemolyticus. J Mol Model 2010; 17:1877-90. [PMID: 21107625 DOI: 10.1007/s00894-010-0883-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 10/19/2010] [Indexed: 11/25/2022]
Abstract
Sodium proton antiporters are ubiquitous membrane proteins that catalyze the exchange of Na(+) for protons throughout the biological world. The Escherichia coli NhaA is the archetypal Na(+)/H(+) antiporter and is absolutely essential for survival in high salt concentrations under alkaline conditions. Its crystal structure, accompanied by extensive molecular dynamics simulations, have provided an atomically detailed model of its mechanism. In this study, we utilized a combination of computational methodologies in order to construct a structural model for the Na(+)/H(+) antiporter from the gram-negative bacterium Vibrio parahaemolyticus. We explored its overall architecture by computational means and validated its stability and robustness. This protein belongs to a novel group of NhaA proteins that transports not only Na(+) and Li(+) as substrate ions, but K(+) as well, and was also found to miss a β-hairpin segment prevalent in other homologs of the Bacteria domain. We propose, for the first time, a structure of a prototype model of a β-hairpin-less NhaA that is selective to K(+). Better understanding of the Vibrio parahaemolyticus NhaA structure-function may assist in studies on ion transport, pH regulation and designing selective blockers.
Collapse
Affiliation(s)
- Assaf Ganoth
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus Givat-Ram, Jerusalem 91904, Israel.
| | | | | |
Collapse
|
10
|
Bordag N, Keller S. α-Helical transmembrane peptides: A “Divide and Conquer” approach to membrane proteins. Chem Phys Lipids 2010; 163:1-26. [PMID: 19682979 DOI: 10.1016/j.chemphyslip.2009.07.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 07/21/2009] [Accepted: 07/21/2009] [Indexed: 11/26/2022]
|
11
|
Lin YS, Shorb JM, Mukherjee P, Zanni MT, Skinner JL. Empirical amide I vibrational frequency map: application to 2D-IR line shapes for isotope-edited membrane peptide bundles. J Phys Chem B 2009; 113:592-602. [PMID: 19053670 PMCID: PMC2633092 DOI: 10.1021/jp807528q] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The amide I vibrational mode, primarily associated with peptide-bond carbonyl stretches, has long been used to probe the structures and dynamics of peptides and proteins by infrared (IR) spectroscopy. A number of ab initio-based amide I vibrational frequency maps have been developed for calculating IR line shapes. In this paper, a new empirical amide I vibrational frequency map is developed. To evaluate its performance, we applied this map to a system of isotope-edited CD3-zeta membrane peptide bundles in aqueous solution. The calculated 2D-IR diagonal line widths vary from residue to residue and show an asymmetric pattern as a function of position in the membrane. The theoretical results are in fair agreement with experiments on the same system. Through analysis of the computed frequency time-correlation functions, it is found that the 2D-IR diagonal widths are dominated by contributions from the inhomogeneous frequency distributions, from which it follows that these widths are a good probe of the extent of local structural fluctuations. Thus, the asymmetric pattern of line widths follows from the asymmetric structure of the bundle in the membrane.
Collapse
Affiliation(s)
- Y-S Lin
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | | | | | | | | |
Collapse
|
12
|
Affiliation(s)
- Minhaeng Cho
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea.
| |
Collapse
|
13
|
Lin X, Tan SM, Law SKA, Torres J. Unambiguous prediction of human integrin transmembrane heterodimer interactions using only homologous sequences. Proteins 2006; 65:274-9. [PMID: 16909419 DOI: 10.1002/prot.21072] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Part of the interaction between the alpha- and beta-subunits of integrins is known to take place at the transmembrane (TM) domain, where both heteromeric and homomeric aggregates have been reported in vivo and in vitro. In a recent computational study, totally independent from biochemical or biophysical data, we explored the plausibility of various TM homo-oligomers using evolutionary conservation data as a filter for non-native interactions. We showed that several homodimeric and homotrimeric interactions for alpha- and beta-chains are evolutionarily conserved. We report herein the results of the application of the same exhaustive approach to the integrin heterodimer. We have studied all known human TM integrin alphabeta pairs, and we show unambiguously that two models of interaction are evolutionarily conserved. These two models are consistent with those proposed previously based on mutagenesis and crosslinking. Comparison with previous experimental data strongly supports that a glycophorin A-like model is an intermediate form of interaction between the resting state and the active form, where chain separation occurs. Surprisingly, these two models are also conserved when considering most of the possible alphabeta pair combinations, suggesting that specific pairing of integrins is not determined by the TM domain, which has remained unchanged in spite of the variety of known integrin functions. This fact highlights a common ancestral mechanism for signal transduction that has remained through evolution. In a broader context, our results show that it is possible to obtain correct and detailed interactions of alpha-helical heterodimers with total independence of experimental data.
Collapse
Affiliation(s)
- Xin Lin
- School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, 637551 Singapore
| | | | | | | |
Collapse
|
14
|
Mukherjee P, Kass I, Arkin IT, Zanni MT. Structural disorder of the CD3zeta transmembrane domain studied with 2D IR spectroscopy and molecular dynamics simulations. J Phys Chem B 2006; 110:24740-9. [PMID: 17134238 PMCID: PMC2722928 DOI: 10.1021/jp0640530] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In a recently reported study [Mukherjee, et al. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 3528] we used 2D IR spectroscopy and 1-(13)C=(18)O isotope labeling to measure the vibrational dynamics of 11 amide I modes in the CD3zeta transmembrane domain. We found that the homogeneous line widths and population relaxation times were all nearly identical, but that the amount of inhomogeneous broadening correlated with the position of the amide group inside the membrane. In this study, we use molecular dynamics simulations to investigate the structural and dynamical origins of these experimental observations. We use two models to convert the simulations to frequency trajectories from which the mean frequencies, standard deviations, frequency correlation functions, and 2D IR spectra are calculated. Model 1 correlates the hydrogen-bond length to the amide I frequency, whereas model 2 uses an ab initio-based electrostatic model. We find that the structural distributions of the peptidic groups and their environment are reflected in the vibrational dynamics of the amide I modes. Environmental forces from the water and lipid headgroups partially denature the helices, shifting the infrared frequencies and creating larger inhomogeneous distributions for residues near the ends. The least inhomogeneously broadened residues are those located in the middle of the membrane where environmental electrostatic forces are weakest and the helices are most ordered. Comparison of the simulations to experiment confirms that the amide I modes near the C-terminal are larger than at the N-terminal because of the asymmetric structure of the peptide bundle in the membrane. The comparison also reveals that residues at a kink in the alpha-helices have broader line widths than more helical parts of the peptide because the peptide backbone at the kink exhibits a larger amount of structural disorder. Taken together, the simulations and experiments reveal that infrared line shapes are sensitive probes of membrane protein structural and environmental heterogeneity.
Collapse
Affiliation(s)
- Prabuddha Mukherjee
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Itamar Kass
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University, Givat-Ram, Jerusalem 91904, Israel
| | - Isaiah T. Arkin
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University, Givat-Ram, Jerusalem 91904, Israel
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| |
Collapse
|
15
|
Arkin IT. Isotope-edited IR spectroscopy for the study of membrane proteins. Curr Opin Chem Biol 2006; 10:394-401. [PMID: 16935550 PMCID: PMC7185810 DOI: 10.1016/j.cbpa.2006.08.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 08/15/2006] [Indexed: 11/25/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy has long been a powerful tool for structural analysis of membrane proteins. However, because of difficulties in resolving contributions from individual residues, most of the derived measurements tend to yield average properties for the system under study. Isotope editing, through its ability to resolve individual vibrations, establishes FTIR as a method that is capable of yielding accurate structural data on individual sites in a protein.
Collapse
Affiliation(s)
- Isaiah T Arkin
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University of Jerusalem, Edmund J Safra Campus, Givat-Ram, Jerusalem, Israel.
| |
Collapse
|
16
|
Adamian L, Liang J. Prediction of transmembrane helix orientation in polytopic membrane proteins. BMC STRUCTURAL BIOLOGY 2006; 6:13. [PMID: 16792816 PMCID: PMC1540425 DOI: 10.1186/1472-6807-6-13] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Accepted: 06/22/2006] [Indexed: 11/28/2022]
Abstract
Background Membrane proteins compose up to 30% of coding sequences within genomes. However, their structure determination is lagging behind compared with soluble proteins due to the experimental difficulties. Therefore, it is important to develop reliable computational methods to predict structures of membrane proteins. Results We present a method for prediction of the TM helix orientation, which is an essential step in ab initio modeling of membrane proteins. Our method is based on a canonical model of the heptad repeat originally developed for coiled coils. We identify the helical surface patches that interface with lipid molecules at an accuracy of about 88% from the sequence information alone, using an empirical scoring function LIPS (LIPid-facing Surface), which combines lipophilicity and conservation of residues in the helix. We test and discuss results of prediction of helix-lipid interfaces on 162 transmembrane helices from 18 polytopic membrane proteins and present predicted orientations of TM helices in TRPV1 channel. We also apply our method to two structures of homologous cytochrome b6f complexes and find discrepancy in the assignment of TM helices from subunits PetG, PetN and PetL. The results of LIPS calculations and analysis of packing and H-bonding interactions support the helix assignment found in the cytochrome b6f structure from green alga but not the assignment of TM helices in the cyanobacterium b6f structure. Conclusion LIPS calculations can be used for the prediction of helix orientation in ab initio modeling of polytopic membrane proteins. We also show with the example of two cytochrome b6f structures that our method can identify questionable helix assignments in membrane proteins. The LIPS server is available online at .
Collapse
Affiliation(s)
- Larisa Adamian
- Department of Bioengineering, University of Illinois at Chicago, M/C 563, 835 S. Wolcott St, Chicago, IL 60612-7340, USA
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, M/C 563, 835 S. Wolcott St, Chicago, IL 60612-7340, USA
| |
Collapse
|
17
|
Torres J, Parthasarathy K, Lin X, Saravanan R, Kukol A, Liu DX. Model of a putative pore: the pentameric alpha-helical bundle of SARS coronavirus E protein in lipid bilayers. Biophys J 2006; 91:938-47. [PMID: 16698774 PMCID: PMC1563757 DOI: 10.1529/biophysj.105.080119] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The coronavirus responsible for the severe acute respiratory syndrome contains a small envelope protein, E, with putative involvement in host apoptosis and virus morphogenesis. To perform these functions, it has been suggested that protein E can form a membrane destabilizing transmembrane (TM) hairpin, or homooligomerize to form a TM pore. Indeed, in a recent study we reported that the α-helical putative transmembrane domain of E protein (ETM) forms several SDS-resistant TM interactions: a dimer, a trimer, and two pentameric forms. Further, these interactions were found to be evolutionarily conserved. Herein, we have studied multiple isotopically labeled ETM peptides reconstituted in model lipid bilayers, using the orientational parameters derived from infrared dichroic data. We show that the topology of ETM is consistent with a regular TM α-helix. Further, the orientational parameters obtained unequivocally correspond to a homopentameric model, by comparison with previous predictions. We have independently confirmed that the full polypeptide of E protein can also aggregate as pentamers after expression in Escherichia coli. This interaction must be stabilized, at least partially, at the TM domain. The model we report for this pentameric α-helical bundle may explain some of the permabilizing properties of protein E, and should be the basis of mutagenesis efforts in future functional studies.
Collapse
Affiliation(s)
- Jaume Torres
- School of Biological Sciences, Nanyang Technological University, Singapore.
| | | | | | | | | | | |
Collapse
|
18
|
Mukherjee P, Kass I, Arkin IT, Zanni MT. Picosecond dynamics of a membrane protein revealed by 2D IR. Proc Natl Acad Sci U S A 2006; 103:3528-33. [PMID: 16505377 PMCID: PMC1383493 DOI: 10.1073/pnas.0508833103] [Citation(s) in RCA: 174] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fast protein dynamics can be missed with techniques that have relatively slow observation times. Using 2D IR spectroscopy and isotope labeling, we have probed the rapid, picosecond dynamics of a membrane protein in its native environment. By measuring the homogeneous and inhomogeneous IR linewidths of 11 amide I modes (backbone carbonyl stretch), we have captured the structural distributions and dynamics of the CD3zeta protein along its transmembrane segment that are lost with slower time-scale techniques. We find that the homogeneous lifetimes and population relaxation times are the same for almost all of the residues. In contrast, the inhomogeneous linewidths vary significantly with the largest inhomogeneous distribution occurring for residues near the N terminus and the narrowest near the center. This behavior is highly consistent with a recently reported experimental model of the protein and water accessibility as observed by molecular dynamics simulations. The data support the proposed CD3zeta peptide structure, and the simulations point to the structural disorder of water and lipid head-groups as the main source of inhomogeneous broadening. Taken together, this rigorous analysis of the vibrational dynamics of a membrane peptide provides experimental insight into a time regime of motions that has so far been largely unexplored.
Collapse
Affiliation(s)
- Prabuddha Mukherjee
- Department of Chemistry, University of Wisconsin, Madison, WI 53706-1396; and
| | - Itamar Kass
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, Hebrew University of Jerusalem, Edmund Safra Campus, Givat-Ram, Jerusalem 91904, Israel
| | - Isaiah T. Arkin
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, Hebrew University of Jerusalem, Edmund Safra Campus, Givat-Ram, Jerusalem 91904, Israel
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin, Madison, WI 53706-1396; and
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
19
|
Sigalov AB. Multichain immune recognition receptor signaling: different players, same game? Trends Immunol 2005; 25:583-9. [PMID: 15489186 DOI: 10.1016/j.it.2004.08.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Alexander B Sigalov
- Department of Pathology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
| |
Collapse
|
20
|
Abstract
We have tested the hypothesis that severe acute respiratory syndrome (SARS) coronavirus protein E (SCoVE) and its homologs in other coronaviruses associate through their putative transmembrane domain to form homooligomeric α-helical bundles in vivo. For this purpose, we have analyzed the results of molecular dynamics simulations where all possible conformational and aggregational space was systematically explored. Two main assumptions were considered; the first is that protein E contains one transmembrane α-helical domain, with its N- and C-termini located in opposite faces of the lipid bilayer. The second is that protein E forms the same type of transmembrane oligomer and with identical backbone structure in different coronaviruses. The models arising from the molecular dynamics simulations were tested for evolutionary conservation using 13 coronavirus protein E homologous sequences. It is extremely unlikely that if any of our assumptions were not correct we would find a persistent structure for all the sequences tested. We show that a low energy dimeric, trimeric and two pentameric models appear to be conserved through evolution, and are therefore likely to be present in vivo. In support of this, we have observed only dimeric, trimeric, and pentameric aggregates for the synthetic transmembrane domain of SARS protein E in SDS. The models obtained point to residues essential for protein E oligomerization in the life cycle of the SARS virus, specifically N15. In addition, these results strongly support a general model where transmembrane domains transiently adopt many aggregation states necessary for function.
Collapse
Affiliation(s)
- Jaume Torres
- School of Biological Sciences, Nanyang Technological University, Singapore.
| | | | | | | |
Collapse
|
21
|
Ash WL, Zlomislic MR, Oloo EO, Tieleman DP. Computer simulations of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1666:158-89. [PMID: 15519314 DOI: 10.1016/j.bbamem.2004.04.012] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 04/29/2004] [Indexed: 11/30/2022]
Abstract
Computer simulations are rapidly becoming a standard tool to study the structure and dynamics of lipids and membrane proteins. Increasing computer capacity allows unbiased simulations of lipid and membrane-active peptides. With the increasing number of high-resolution structures of membrane proteins, which also enables homology modelling of more structures, a wide range of membrane proteins can now be simulated over time spans that capture essential biological processes. Longer time scales are accessible by special computational methods. We review recent progress in simulations of membrane proteins.
Collapse
Affiliation(s)
- Walter L Ash
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary AB, Canada T2N 1N4
| | | | | | | |
Collapse
|
22
|
Kochva U, Leonov H, Arkin IT. Modeling the structure of the respiratory syncytial virus small hydrophobic protein by silent-mutation analysis of global searching molecular dynamics. Protein Sci 2004; 12:2668-74. [PMID: 14627728 PMCID: PMC2366976 DOI: 10.1110/ps.03151103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Human respiratory syncytial virus (RSV) encodes a small hydrophobic (SH) protein, whose function in the life cycle of the virus is unknown. Recent channel activity measurements of the protein suggest that like other viroporins, SH may assemble into a homo-oligomeric ion channel. To further our understanding of this potentially important protein, a new strategy was implemented in order to model the transmembrane oligomeric bundle of the protein. Global searching molecular dynamic simulations of SH proteins from eight different viral strains, each at different oligomeric states, as well as different lengths of the putative transmembrane domain, were undertaken. Taken together, a total of 45 different global molecular dynamic simulations pointed to a single pentameric structure for the protein that was found in all of the different variants. The model of the structure obtained is a channel-like homopentamer whose minimal transmembrane pore diameter is 1.46 A.
Collapse
Affiliation(s)
- Uzi Kochva
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | | | | |
Collapse
|
23
|
Abstract
Infrared spectroscopy has long been used to examine the average secondary structure and orientation of membrane proteins. With the recent utilization of site-specific isotope labeling (e.g., peptidic 1-(13)C = (18)O) it is now possible to examine localized properties, rather than global averages. The technique of site-specific infrared dichroism (SSID) capitalized on this fact, and derives site-specific orientational restraints for the labeled amino acids. These restraints can then be used to solve the backbone structure of simple alpha-helical bundles, emphasizing the capabilities of this approach. So far SSID has been carried out in attenuated total internal reflection optical mode, with all of the respective caveats of attenuated total internal reflection. In this report we extend SSID through the use of transmission infrared spectroscopy tilt series. We develop the corresponding theory and demonstrate that accurate site-specific orientational restraints can be derived from a simple transmission experiment.
Collapse
Affiliation(s)
- Eyal Arbely
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University, Givat-Ram, Jerusalem, Israel
| | | | | |
Collapse
|
24
|
Kochva U, Leonov H, Arkin IT, Adams PD. Modeling Membrane Proteins Utilizing Information from Silent Amino Acid Substitutions. ACTA ACUST UNITED AC 2004; Chapter 5:Unit5.3. [DOI: 10.1002/0471250953.bi0503s04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
25
|
Overton MC, Chinault SL, Blumer KJ. Oligomerization, Biogenesis, and Signaling Is Promoted by a Glycophorin A-like Dimerization Motif in Transmembrane Domain 1 of a Yeast G Protein-coupled Receptor. J Biol Chem 2003; 278:49369-77. [PMID: 14506226 DOI: 10.1074/jbc.m308654200] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
G protein-coupled receptors (GPCRs) can form dimeric or oligomeric complexes in vivo. However, the functions and mechanisms of oligomerization remain poorly understood for most GPCRs, including the alpha-factor receptor (STE2 gene product) of the yeast Saccharomyces cerevisiae. Here we provide evidence indicating that alpha-factor receptor oligomerization involves a GXXXG motif in the first transmembrane domain (TM1), similar to the transmembrane dimerization domain of glycophorin A. Results of fluorescence resonance energy transfer, fluorescence microscopy, endocytosis assays of receptor oligomerization in living cells, and agonist binding assays indicated that amino acid substitutions affecting the glycine residues of the GXXXG motif impaired alpha-factor receptor oligomerization and biogenesis in vivo but did not significantly impair agonist binding affinity. Mutant receptors exhibited signaling defects that were not due to impaired cell surface expression, indicating that oligomerization promotes alpha-factor receptor signal transduction. Structure-function studies suggested that the GXXXG motif in TM1 of the alpha-factor receptor promotes oligomerization by a mechanism similar to that used by the GXXXG dimerization motif of glycophorin A. In many mammalian GPCRs, motifs related to the GXXXG sequence are present in TM1 or other TM domains, suggesting that similar mechanisms are used by many GPCRs to form dimers or oligomeric arrays.
Collapse
Affiliation(s)
- Mark C Overton
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | | | | |
Collapse
|
26
|
Abstract
Historically, the task of determining the structure of membrane proteins has been hindered by experimental difficulties associated with their lipid-embedded domains. Here, we provide an overview of recently developed experimental and predictive tools that are changing our view of this largely unexplored territory - the 'Wild West' of structural biology. Crystallography, single-particle methods and atomic force microscopy are being used to study huge membrane proteins with increasing detail. Solid-state nuclear magnetic resonance strategies provide orientational constraints for structure determination of transmembrane (TM) alpha-helices and accurate measurements of intramolecular distances, even in very complex systems. Longer distance constraints are determined by site-directed spin-labelling electron paramagnetic resonance, but current labelling strategies still constitute some limitation. Other methods, such as site-specific infrared dichroism, enable orientational analysis of TM alpha-helices in aligned bilayers and, combined with novel computational and predictive tools that use evolutionary conservation data, are being used to analyze TM alpha-helical bundles.
Collapse
Affiliation(s)
- Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 637616, Singapore.
| | | | | |
Collapse
|
27
|
Arkin IT. Structural aspects of oligomerization taking place between the transmembrane alpha-helices of bitopic membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1565:347-63. [PMID: 12409206 DOI: 10.1016/s0005-2736(02)00580-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recent advances in biophysical methods have been able to shed more light on the structures of helical bundles formed by the transmembrane segments of bitopic membrane proteins. In this manuscript, I attempt to review the biological importance and diversity of these interactions, the energetics of bundle formation, motifs capable of inducing oligomerization and methods capable of detecting, solving and predicting the structures of these oligomeric bundles. Finally, the structures of the best characterized instances of transmembrane alpha-helical bundles formed by bitopic membrane proteins are described in detail.
Collapse
Affiliation(s)
- Isaiah T Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel.
| |
Collapse
|
28
|
Torres J, Briggs JAG, Arkin IT. Multiple site-specific infrared dichroism of CD3-zeta, a transmembrane helix bundle. J Mol Biol 2002; 316:365-74. [PMID: 11851344 DOI: 10.1006/jmbi.2001.5267] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of the transmembrane domain of CD3-zeta a component of the T-cell receptor involved in signal transduction, has been studied in its native state (a lipid bilayer) by multiple site-specific infrared dichroism. For the first time, the transmembrane domain has been labelled at multiple positions along the sequence, representing a total of 11 samples, each labelled at a different residue with an isotopically modified carbonyl group, (13)C [double bond] (18)O. A strategy is outlined that, based on the above data, can yield the rotational orientation and the local helix tilt for each labelled residue, giving a detailed description of helix geometry. The results obtained indicate that the transmembrane segment is in an alpha-helical conformation throughout, with an average helix tilt of 12 degrees. The N-terminal side of the helix is more tilted than the C-terminal. In an accompanying paper we describe the implementation of the infrared data in a model-building study of the CD3-zeta transmembrane complex. The model obtained is entirely consistent with results based on evolutionary conservation data. Taken together, this study represents the first step towards elucidation of the backbone structure of a transmembrane alpha-helical bundle by infrared spectroscopy.
Collapse
Affiliation(s)
- Jaume Torres
- Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | | | | |
Collapse
|