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Markotić A, Omerović J, Marijan S, Režić-Mužinić N, Čikeš Čulić V. Biochemical Pathways Delivering Distinct Glycosphingolipid Patterns in MDA-MB-231 and MCF-7 Breast Cancer Cells. Curr Issues Mol Biol 2024; 46:10200-10217. [PMID: 39329960 PMCID: PMC11430773 DOI: 10.3390/cimb46090608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/30/2024] [Accepted: 09/06/2024] [Indexed: 09/28/2024] Open
Abstract
The complex structure of glycosphingolipids (GSLs) supports their important role in cell function as modulators of growth factor receptors and glutamine transporters in plasma membranes. The aberrant composition of clustered GSLs within signaling platforms, so-called lipid rafts, inevitably leads to tumorigenesis due to disturbed growth factor signal transduction and excessive uptake of glutamine and other molecules needed for increased energy and structural molecule cell supply. GSLs are also involved in plasma membrane processes such as cell adhesion, and their transition converts cells from epithelial to mesenchymal with features required for cell migration and metastasis. Glutamine activates the mechanistic target of rapamycin complex 1 (mTORC1), resulting in nucleotide synthesis and proliferation. In addition, glutamine contributes to the cancer stem cell GD2 ganglioside-positive phenotype in the triple-negative breast cancer cell line MDA-MB-231. Thieno[2,3-b]pyridine derivative possesses higher cytotoxicity against MDA-MB-231 than against MCF-7 cells and induces a shift to aerobic metabolism and a decrease in S(6)nLc4Cer GSL-positive cancer stem cells in the MDA-MB-231 cell line. In this review, we discuss findings in MDA-MB-231, MCF-7, and other breast cancer cell lines concerning their differences in growth factor receptors and recent knowledge of the main biochemical pathways delivering distinct glycosphingolipid patterns during tumorigenesis and therapy.
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Affiliation(s)
- Anita Markotić
- Department of Medical Chemistry and Biochemistry, University of Split School of Medicine, 21000 Split, Croatia
| | - Jasminka Omerović
- Department of Immunology, University of Split School of Medicine, 21000 Split, Croatia
| | - Sandra Marijan
- Department of Medical Chemistry and Biochemistry, University of Split School of Medicine, 21000 Split, Croatia
| | - Nikolina Režić-Mužinić
- Department of Medical Chemistry and Biochemistry, University of Split School of Medicine, 21000 Split, Croatia
| | - Vedrana Čikeš Čulić
- Department of Medical Chemistry and Biochemistry, University of Split School of Medicine, 21000 Split, Croatia
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2
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Medvedev KE, Schaeffer RD, Chen KS, Grishin NV. Pan-cancer structurome reveals overrepresentation of beta sandwiches and underrepresentation of alpha helical domains. Sci Rep 2023; 13:11988. [PMID: 37491511 PMCID: PMC10368619 DOI: 10.1038/s41598-023-39273-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/22/2023] [Indexed: 07/27/2023] Open
Abstract
The recent progress in the prediction of protein structures marked a historical milestone. AlphaFold predicted 200 million protein models with an accuracy comparable to experimental methods. Protein structures are widely used to understand evolution and to identify potential drug targets for the treatment of various diseases, including cancer. Thus, these recently predicted structures might convey previously unavailable information about cancer biology. Evolutionary classification of protein domains is challenging and different approaches exist. Recently our team presented a classification of domains from human protein models released by AlphaFold. Here we evaluated the pan-cancer structurome, domains from over and under expressed proteins in 21 cancer types, using the broadest levels of the ECOD classification: the architecture (A-groups) and possible homology (X-groups) levels. Our analysis reveals that AlphaFold has greatly increased the three-dimensional structural landscape for proteins that are differentially expressed in these 21 cancer types. We show that beta sandwich domains are significantly overrepresented and alpha helical domains are significantly underrepresented in the majority of cancer types. Our data suggest that the prevalence of the beta sandwiches is due to the high levels of immunoglobulins and immunoglobulin-like domains that arise during tumor development-related inflammation. On the other hand, proteins with exclusively alpha domains are important elements of homeostasis, apoptosis and transmembrane transport. Therefore cancer cells tend to reduce representation of these proteins to promote successful oncogeneses.
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Affiliation(s)
- Kirill E Medvedev
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - R Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kenneth S Chen
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
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3
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Gopal SM, Pawar AB, Wassenaar TA, Sengupta D. Lipid-dependent conformational landscape of the ErbB2 growth factor receptor dimers. Chem Phys Lipids 2020; 230:104911. [PMID: 32353357 DOI: 10.1016/j.chemphyslip.2020.104911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/04/2020] [Accepted: 03/27/2020] [Indexed: 01/31/2023]
Abstract
Altered lipid metabolism has been linked to cancer development and progression. Several roles have been attributed to the increased saturation and length of lipid acyl tails observed in tumors, but its effect on signaling receptors is still emerging. In this work, we have analyzed the lipid dependence of the ErbB2 growth factor receptor dimerization that plays an important role in the pathogenesis of breast cancer. We have performed coarse-grain ensemble molecular dynamics simulations to comprehensively sample the ErbB2 monomer-dimer association. Our results indicate a dynamic dimer state with a complex conformational landscape that is modulated with increasing lipid tail length. We resolve the native N-terminal "active" and C-terminal "inactive" conformations in all membrane compositions. However, the relative population of the N-terminal and C-terminal conformers is dependent on length of the saturated lipid tails. In short-tail membranes, additional non-specific dimers are observed which are reduced or absent in long-tailed bilayers. Our results indicate that the relative population as well as the structure of the dimer state is modulated by membrane composition. We have correlated these differences to local perturbations of the membrane around the receptor. Our work is an important step in characterizing ErbB dimers in healthy and diseased states and emphasize the importance of sampling lipid dynamics in understanding receptor association.
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Affiliation(s)
- Srinivasa M Gopal
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India; Lehrstuhl fur Theoretische Chemie, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Aiswarya B Pawar
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India; AcSIR, Mathura Road, New Delhi, 110 025, India
| | - Tsjerk A Wassenaar
- Molecular Dynamics, University of Groningen, Nijenborgh 7, 9747AG Groningen, the Netherlands
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India; AcSIR, Mathura Road, New Delhi, 110 025, India.
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4
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Krainer G, Keller S, Schlierf M. Structural dynamics of membrane-protein folding from single-molecule FRET. Curr Opin Struct Biol 2019; 58:124-137. [DOI: 10.1016/j.sbi.2019.05.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
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5
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Frotscher E, Krainer G, Hartmann A, Schlierf M, Keller S. Conformational Dynamics Govern the Free-Energy Landscape of a Membrane-Interacting Protein. ACS OMEGA 2018; 3:12026-12032. [PMID: 31459283 PMCID: PMC6690567 DOI: 10.1021/acsomega.8b01609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/11/2018] [Indexed: 05/08/2023]
Abstract
The equilibrium stabilities and the folding rates of membrane-bound proteins are determined by hydrophobic and polar intermolecular contacts with their environment as well as by intramolecular packing and conformational dynamics. The contributions of these factors, however, remain elusive and might vary considerably among proteins. Mistic from Bacillus subtilis is a particularly intriguing example of an α-helical protein that associates with membranes in spite of its unusual hydrophilicity. In micelles, Mistic is stabilized by hydrophobic and polar interactions with detergents, but it is unclear whether and how these intermolecular contacts are coupled to structural and dynamic adaptations of the protein itself. Here, we investigated the packing and the conformational dynamics of Mistic as functions of detergent headgroup chemistry and chain length, employing single-molecule Förster resonance energy transfer spectroscopy and time-resolved intrinsic tryptophan fluorescence spectroscopy. Surprisingly, in nonionic detergents, more effective hydrophobic burial and, thus, greater protein stability with increasing hydrophobic micellar thickness were accompanied by a gradual loosening of the helical bundle. By contrast, Mistic was found to assume a stable, compact fold in zwitterionic detergents that allowed faster dynamics on the nanosecond timescale. Thus, intramolecular packing per se is insufficient for conferring high protein stability; instead, enhanced nanosecond dynamics and, consequently, greater conformational entropy in the compact folded state account for Mistic's high equilibrium stability and fast folding rates in zwitterionic micelles even at the expense of less effective hydrophobic burial.
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Affiliation(s)
- Erik Frotscher
- Molecular
Biophysics, Technische Universität
Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Georg Krainer
- Molecular
Biophysics, Technische Universität
Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Andreas Hartmann
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Michael Schlierf
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
- E-mail: (M.S.)
| | - Sandro Keller
- Molecular
Biophysics, Technische Universität
Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- E-mail: (S.K.)
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6
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Krainer G, Hartmann A, Anandamurugan A, Gracia P, Keller S, Schlierf M. Ultrafast Protein Folding in Membrane-Mimetic Environments. J Mol Biol 2018; 430:554-564. [DOI: 10.1016/j.jmb.2017.10.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/12/2017] [Accepted: 10/27/2017] [Indexed: 01/06/2023]
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7
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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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8
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Abstract
In vitro, computational, and theoretical studies of protein folding have converged to paint a rich and complex energy landscape. This landscape is sensitively modulated by environmental conditions and subject to evolutionary pressure on protein function. Of these environments, none is more complex than the cell itself, where proteins function in the cytosol, in membranes, and in different compartments. A wide variety of kinetic and thermodynamics experiments, ranging from single-molecule studies to jump kinetics and from nuclear magnetic resonance to imaging on the microscope, have elucidated how protein energy landscapes facilitate folding and how they are subject to evolutionary constraints and environmental perturbation. Here we review some recent developments in the field and refer the reader to some original work and additional reviews that cover this broad topic in protein science.
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Affiliation(s)
- Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801; , .,Department of Chemistry, University of Illinois, Urbana, Illinois 61801; .,Department of Physics, University of Illinois, Urbana, Illinois 61801
| | - Kapil Dave
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801; ,
| | - Shahar Sukenik
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801;
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9
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Deshpande SA, Pawar AB, Dighe A, Athale CA, Sengupta D. Role of spatial inhomogenity in GPCR dimerisation predicted by receptor association–diffusion models. Phys Biol 2017; 14:036002. [DOI: 10.1088/1478-3975/aa6b68] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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10
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Scanlon DP, Bah A, Krzeminski M, Zhang W, Leduc-Pessah HL, Dong YN, Forman-Kay JD, Salter MW. An evolutionary switch in ND2 enables Src kinase regulation of NMDA receptors. Nat Commun 2017; 8:15220. [PMID: 28508887 PMCID: PMC5440837 DOI: 10.1038/ncomms15220] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/10/2017] [Indexed: 12/22/2022] Open
Abstract
The non-receptor tyrosine kinase Src is a key signalling hub for upregulating the function of N-methyl D-aspartate receptors (NMDARs). Src is anchored within the NMDAR complex via NADH dehydrogenase subunit 2 (ND2), a mitochondrially encoded adaptor protein. The interacting regions between Src and ND2 have been broadly identified, but the interaction between ND2 and the NMDAR has remained elusive. Here we generate a homology model of ND2 and dock it onto the NMDAR via the transmembrane domain of GluN1. This interaction is enabled by the evolutionary loss of three helices in bilaterian ND2 proteins compared to their ancestral homologues. We experimentally validate our model and demonstrate that blocking this interaction with an ND2 fragment identified in our experimental studies prevents Src-mediated upregulation of NMDAR currents in neurons. Our findings establish the mode of interaction between an NMDAR accessory protein with one of the core subunits of the receptor. N-methyl D-aspartate receptor (NMDAR) activity is modulated by Src tyrosine kinase via the mitochondrial protein NADH dehydrogenase subunit 2 (ND2). Here the authors show that ND2 interacts with the transmembrane region of NMDAR GluN1 subunit, a process that is crucial for Src regulation of NMDAR activity.
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Affiliation(s)
- David P Scanlon
- Program in Neurosciences &Mental Health, The Hospital for Sick Children, 686 Bay St, Toronto, Ontario, Canada M5G 0A4.,Department of Physiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Alaji Bah
- Program in Molecular Medicine, The Hospital for Sick Children, 686 Bay St, Toronto, Ontario, Canada M5G 0A4.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Mickaël Krzeminski
- Program in Molecular Medicine, The Hospital for Sick Children, 686 Bay St, Toronto, Ontario, Canada M5G 0A4.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Wenbo Zhang
- Program in Neurosciences &Mental Health, The Hospital for Sick Children, 686 Bay St, Toronto, Ontario, Canada M5G 0A4.,Department of Physiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Heather L Leduc-Pessah
- Program in Neurosciences &Mental Health, The Hospital for Sick Children, 686 Bay St, Toronto, Ontario, Canada M5G 0A4.,Department of Physiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Yi Na Dong
- Program in Neurosciences &Mental Health, The Hospital for Sick Children, 686 Bay St, Toronto, Ontario, Canada M5G 0A4.,Department of Physiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, 686 Bay St, Toronto, Ontario, Canada M5G 0A4.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Michael W Salter
- Program in Neurosciences &Mental Health, The Hospital for Sick Children, 686 Bay St, Toronto, Ontario, Canada M5G 0A4.,Department of Physiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
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11
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Dubey V, Prasanna X, Sengupta D. Estimating the Lipophobic Contributions in Model Membranes. J Phys Chem B 2017; 121:2111-2120. [DOI: 10.1021/acs.jpcb.6b09863] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Vikas Dubey
- Physical Chemistry Division, National Chemical Laboratory, Pune 411008, India
| | - Xavier Prasanna
- Physical Chemistry Division, National Chemical Laboratory, Pune 411008, India
| | - Durba Sengupta
- Physical Chemistry Division, National Chemical Laboratory, Pune 411008, India
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12
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Gordon SM, Pourmousa M, Sampson M, Sviridov D, Islam R, Perrin BS, Kemeh G, Pastor RW, Remaley AT. Identification of a novel lipid binding motif in apolipoprotein B by the analysis of hydrophobic cluster domains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:135-145. [PMID: 27814978 DOI: 10.1016/j.bbamem.2016.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/11/2016] [Accepted: 10/27/2016] [Indexed: 02/05/2023]
Abstract
Apolipoprotein B (apoB) is a large amphipathic protein that is the structural scaffold for the formation of several classes of lipoproteins involved in lipid transport throughout the body. The goal of the present study was to identify specific domains in the apoB sequence that contribute to its lipid binding properties. A sequence analysis algorithm was developed to identify stretches of hydrophobic amino acids devoid of charged amino acids, which are referred to as hydrophobic cluster domains (HCDs). This analysis identified 78 HCDs in apoB with hydrophobic stretches ranging from 6 to 26 residues. Each HCD was analyzed in silico for secondary structure and lipid binding properties, and a subset was synthesized for experimental evaluation. One HCD peptide, B38, showed high affinity binding to both isolated HDL and LDL, and could exchange between lipoproteins. All-atom molecular dynamics simulations indicate that B38 inserts 3.7Å below the phosphate plane of the bilayer. B38 forms an unusual α-helix with a broad hydrophobic face and polar serine and threonine residues on the opposite face. Based on this structure, we hypothesized that B38 could efflux cholesterol from cells. B38 showed a 12-fold greater activity than the 5A peptide, a bihelical Class A amphipathic helix (EC50 of 0.2658 vs. 3.188μM; p<0.0001), in promoting cholesterol efflux from ABCA1 expressing BHK-1 cells. In conclusion, we have identified novel domains within apoB that contribute to its lipid biding properties. Additionally, we have discovered a unique amphipathic helix design for efficient ABCA1-specific cholesterol efflux.
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Affiliation(s)
- Scott M Gordon
- Lipoprotein Metabolism Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Mohsen Pourmousa
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | - Maureen Sampson
- Lipoprotein Metabolism Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Denis Sviridov
- Lipoprotein Metabolism Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rafique Islam
- Lipoprotein Metabolism Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA; School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - B Scott Perrin
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | - Georgina Kemeh
- Lipoprotein Metabolism Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | - Alan T Remaley
- Lipoprotein Metabolism Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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13
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Oh KI, Smith-Dupont KB, Markiewicz BN, Gai F. Kinetics of peptide folding in lipid membranes. Biopolymers 2016; 104:281-90. [PMID: 25808575 DOI: 10.1002/bip.22640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/12/2015] [Accepted: 02/14/2015] [Indexed: 12/31/2022]
Abstract
Despite our extensive understanding of water-soluble protein folding kinetics, much less is known about the folding dynamics and mechanisms of membrane proteins. However, recent studies have shown that for relatively simple systems, such as peptides that form a transmembrane α-helix, helical dimer, or helix-turn-helix, it is possible to assess the kinetics of several important steps, including peptide binding to the membrane from aqueous solution, peptide folding on the membrane surface, helix insertion into the membrane, and helix-helix association inside the membrane. Herein, we provide a brief review of these studies and also suggest new initiation and probing methods that could lead to improved temporal and structural resolution in future experiments.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Kathryn B Smith-Dupont
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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14
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Khadria AS, Senes A. Fluorophores, environments, and quantification techniques in the analysis of transmembrane helix interaction using FRET. Biopolymers 2016; 104:247-64. [PMID: 25968159 DOI: 10.1002/bip.22667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/15/2015] [Accepted: 05/04/2015] [Indexed: 12/31/2022]
Abstract
Förster resonance energy transfer (FRET) has been widely used as a spectroscopic tool in vitro to study the interactions between transmembrane (TM) helices in detergent and lipid environments. This technique has been instrumental to many studies that have greatly contributed to quantitative understanding of the physical principles that govern helix-helix interactions in the membrane. These studies have also improved our understanding of the biological role of oligomerization in membrane proteins. In this review, we focus on the combinations of fluorophores used, the membrane mimetic environments, and measurement techniques that have been applied to study model systems as well as biological oligomeric complexes in vitro. We highlight the different formalisms used to calculate FRET efficiency and the challenges associated with accurate quantification. The goal is to provide the reader with a comparative summary of the relevant literature for planning and designing FRET experiments aimed at measuring TM helix-helix associations.
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Affiliation(s)
- Ambalika S Khadria
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Alessandro Senes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706
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15
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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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16
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Nadeau VG, Gao A, Deber CM. Design and characterization of a membrane protein unfolding platform in lipid bilayers. PLoS One 2015; 10:e0120253. [PMID: 25799099 PMCID: PMC4370600 DOI: 10.1371/journal.pone.0120253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/20/2015] [Indexed: 11/29/2022] Open
Abstract
Accurate measurement of membrane protein stability—and particularly how it may vary as a result of disease-phenotypic mutations—ideally requires a denaturant that can unfold a membrane-embedded structure while leaving the solubilizing environment unaffected. The steric trap method fulfills this requirement by using monovalent streptavidin (mSA) molecules to unfold membrane proteins engineered with two spatially close biotin tags. Here we adapted this method to an 87-residue helix-loop-helix (hairpin) construct derived from helices 3 and 4 in the transmembrane domain of the human cystic fibrosis transmembrane conductance regulator (CFTR), wherein helix-helix tertiary interactions are anticipated to confer a portion of construct stability. The wild type CFTR TM3/4 hairpin construct was modified with two accessible biotin tags for mSA-induced unfolding, along with two helix-terminal pyrene labels to monitor loss of inter-helical contacts by pyrene excimer fluorescence. A series of eight constructs with biotin tags at varying distances from the helix-terminal pyrene labels were expressed, purified and labeled appropriately; all constructs exhibited largely helical circular dichroism spectra. We found that addition of mSA to an optimized construct in lipid vesicles led to a complete and reversible loss in pyrene excimer fluorescence and mSA binding, and hence hairpin unfolding—results further supported by SDS-PAGE visualization of mSA bound and unbound species. While some dimeric/oligomeric populations persist that may affect quantitation of the unfolding step, our characterization of the design yields a promising prototype of a future platform for the systematic study of membrane protein folding in a lipid bilayer environment.
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Affiliation(s)
- Vincent G. Nadeau
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Anqi Gao
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Charles M. Deber
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- * E-mail:
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Pawar AB, Deshpande SA, Gopal SM, Wassenaar TA, Athale CA, Sengupta D. Thermodynamic and kinetic characterization of transmembrane helix association. Phys Chem Chem Phys 2015; 17:1390-8. [DOI: 10.1039/c4cp03732d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The transient dimerization of transmembrane proteins is an important event in several cellular processes and here we use coarse-grain and meso-scale modeling methods to quantify their underlying dynamics.
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Affiliation(s)
| | | | | | - Tsjerk A. Wassenaar
- Department of Biology
- Computational Biology
- University of Erlangen-Nürnberg
- 91058 Erlangen
- Germany
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18
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Effect of Lipid Bilayer Composition on Membrane Protein Association. ADVANCES IN PLANAR LIPID BILAYERS AND LIPOSOMES 2015. [DOI: 10.1016/bs.adplan.2015.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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19
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Veit M, Matczuk AK, Sinhadri BC, Krause E, Thaa B. Membrane proteins of arterivirus particles: structure, topology, processing and function. Virus Res 2014; 194:16-36. [PMID: 25278143 PMCID: PMC7172906 DOI: 10.1016/j.virusres.2014.09.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/20/2014] [Accepted: 09/23/2014] [Indexed: 01/01/2023]
Abstract
Arteriviruses are important pathogens in veterinary medicine. We review the structure and processing of their membrane proteins. Some features are unique from a cell biological point of view. New data on this topic are also presented. We speculate on the role of the membrane proteins during virus entry and budding.
Arteriviruses, such as equine arteritis virus (EAV) and porcine reproductive and respiratory syndrome virus (PRRSV), are important pathogens in veterinary medicine. Despite their limited genome size, arterivirus particles contain a multitude of membrane proteins, the Gp5/M and the Gp2/3/4 complex, the small and hydrophobic E protein and the ORF5a protein. Their function during virus entry and budding is understood only incompletely. We summarize current knowledge of their primary structure, membrane topology, (co-translational) processing and intracellular targeting to membranes of the exocytic pathway, which are the budding site. We profoundly describe experimental data that led to widely believed conceptions about the function of these proteins and also report new results about processing steps for each glycoprotein. Further, we depict the location and characteristics of epitopes in the membrane proteins since the late appearance of neutralizing antibodies may lead to persistence, a characteristic hallmark of arterivirus infection. Some molecular features of the arteriviral proteins are rare or even unique from a cell biological point of view, particularly the prevention of signal peptide cleavage by co-translational glycosylation, discovered in EAV-Gp3, and the efficient use of overlapping sequons for glycosylation. This article reviews the molecular mechanisms of these cellular processes. Based on this, we present hypotheses on the structure and variability of arteriviral membrane proteins and their role during virus entry and budding.
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Affiliation(s)
- Michael Veit
- Institut für Virologie, Veterinärmedizin, Freie Universität Berlin, Germany.
| | | | | | - Eberhard Krause
- Leibniz Institute of Molecular Pharmacology (FMP), Berlin, Germany
| | - Bastian Thaa
- Institut für Virologie, Veterinärmedizin, Freie Universität Berlin, Germany
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20
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Khadria AS, Mueller BK, Stefely JA, Tan CH, Pagliarini DJ, Senes A. A Gly-zipper motif mediates homodimerization of the transmembrane domain of the mitochondrial kinase ADCK3. J Am Chem Soc 2014; 136:14068-77. [PMID: 25216398 PMCID: PMC4195374 DOI: 10.1021/ja505017f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Interactions between α-helices within the hydrophobic environment of lipid bilayers are integral to the folding and function of transmembrane proteins; however, the major forces that mediate these interactions remain debated, and our ability to predict these interactions is still largely untested. We recently demonstrated that the frequent transmembrane association motif GASright, the GxxxG-containing fold of the glycophorin A dimer, is optimal for the formation of extended networks of Cα-H hydrogen bonds, supporting the hypothesis that these bonds are major contributors to association. We also found that optimization of Cα-H hydrogen bonding and interhelical packing is sufficient to computationally predict the structure of known GASright dimers at near atomic level. Here, we demonstrate that this computational method can be used to characterize the structure of a protein not previously known to dimerize, by predicting and validating the transmembrane dimer of ADCK3, a mitochondrial kinase. ADCK3 is involved in the biosynthesis of the redox active lipid, ubiquinone, and human ADCK3 mutations cause a cerebellar ataxia associated with ubiquinone deficiency, but the biochemical functions of ADCK3 remain largely undefined. Our experimental analyses show that the transmembrane helix of ADCK3 oligomerizes, with an interface based on an extended Gly-zipper motif, as predicted by our models. The data provide strong evidence for the hypothesis that optimization of Cα-H hydrogen bonding is an important factor in the association of transmembrane helices. This work also provides a structural foundation for investigating the role of transmembrane association in regulating the biological activity of ADCK3.
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Affiliation(s)
- Ambalika S Khadria
- Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States
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21
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Pogozheva ID, Mosberg HI, Lomize AL. Life at the border: adaptation of proteins to anisotropic membrane environment. Protein Sci 2014; 23:1165-96. [PMID: 24947665 DOI: 10.1002/pro.2508] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 12/25/2022]
Abstract
This review discusses main features of transmembrane (TM) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen-bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region-between double bonds and carbonyl groups of lipids. These "midpolar" regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side-chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein-lipid binding.
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Affiliation(s)
- Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, 48109-1065
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22
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Nadeau VG, Deber CM. Loop Sequence Dictates the Secondary Structure of a Human Membrane Protein Hairpin. Biochemistry 2013; 52:2419-26. [DOI: 10.1021/bi400187w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Vincent G. Nadeau
- Program in Molecular Structure and Function,
Research Institute, Hospital for Sick Children, Toronto M5G 1X8, Ontario,
Canada, and Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Charles M. Deber
- Program in Molecular Structure and Function,
Research Institute, Hospital for Sick Children, Toronto M5G 1X8, Ontario,
Canada, and Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Ontario, Canada
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23
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Nordholm J, da Silva DV, Damjanovic J, Dou D, Daniels R. Polar residues and their positional context dictate the transmembrane domain interactions of influenza A neuraminidases. J Biol Chem 2013; 288:10652-60. [PMID: 23447533 DOI: 10.1074/jbc.m112.440230] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Interactions that facilitate transmembrane domain (TMD) dimerization have been identified mainly using synthetic TMDs. Here, we investigated how inherent properties within natural TMDs modulate their interaction strength by exploiting the sequence variation in the nine neuraminidase subtypes (N1-N9) and the prior knowledge that a N1 TMD oligomerizes. Initially, consensus TMDs were created from the influenza A virus database, and their interaction strengths were measured in a biological membrane system. The TMD interactions increased with respect to decreasing hydrophobicity across the subtypes (N1-N9) and within the human N1 subtype where the N1 TMDs from the pandemic H1N1 strain of swine origin were found to be significantly less hydrophobic. The hydrophobicity correlation was attributed to the conserved amphipathicity within the TMDs as the interactions were abolished by mutating residues on the polar faces that are unfavorably positioned in the membrane. Similarly, local changes enhanced the interactions only when a larger polar residue existed on the appropriate face in an unfavorable membrane position. Together, the analysis of this unique natural TMD data set demonstrates how polar-mediated TMD interactions from bitopic proteins depend on which polar residues are involved and their positioning with respect to the helix and the membrane bilayer.
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Affiliation(s)
- Johan Nordholm
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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24
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Prasanna X, Praveen PJ, Sengupta D. Sequence dependent lipid-mediated effects modulate the dimerization of ErbB2 and its associative mutants. Phys Chem Chem Phys 2013; 15:19031-41. [DOI: 10.1039/c3cp52447g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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