1
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Phosphatidylglyerol Lipid Binding at the Active Site of an Intramembrane Protease. J Membr Biol 2020; 253:563-576. [PMID: 33210155 PMCID: PMC7688093 DOI: 10.1007/s00232-020-00152-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/04/2020] [Indexed: 10/25/2022]
Abstract
Transmembrane substrate cleavage by the small Escherichia coli rhomboid protease GlpG informs on mechanisms by which lipid interactions shape reaction coordinates of membrane-embedded enzymes. Here, I review and discuss new work on the molecular picture of protein-lipid interactions that might govern the formation of the substrate-enzyme complex in fluid lipid membranes. Negatively charged PG-type lipids are of particular interest, because they are a major component of bacterial membranes. Atomistic computer simulations indicate POPG and DOPG lipids bridge remote parts of GlpG and might pre-occupy the substrate-docking site. Inhibition of catalytic activity by PG lipids could arise from ligand-like lipid binding at the active site, which could delay or prevent substrate docking. Dynamic protein-lipid H-bond networks, water access to the active site, and fluctuations in the orientation of GlpG suggest that GlpG has lipid-coupled dynamics that could shape the energy landscape of transmembrane substrate docking.
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2
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Bondar AN. Mechanisms by Which Lipids Influence Conformational Dynamics of the GlpG Intramembrane Protease. J Phys Chem B 2019; 123:4159-4172. [PMID: 31059259 DOI: 10.1021/acs.jpcb.8b11291] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rhomboid intramembrane proteases are bound to lipid membranes, where they dock and cleave other transmembrane substrates. How the lipid membrane surrounding the protease impacts the conformational dynamics of the protease is essential to understand because it informs on the reaction coordinate of substrate binding. Atomistic molecular dynamics simulations allow us to probe protein motions and characterize the coupling between protein and lipids. Simulations performed here on GlpG, the rhomboid protease from Escherichia coli, indicate that the thickness of the lipid membrane close to GlpG depends on both the composition of the lipid membrane and the conformation of GlpG. Transient binding of a lipid headgroup at the active site of the protease, as observed in some of the simulations reported here, suggests that a lipid headgroup might compete with the substrate for access to the GlpG active site. Interactions identified between lipid headgroups and the protein influence the dynamics of lipid interactions close to the substrate-binding site. These observations suggest that the lipid membrane environment shapes the energy profile of the substrate-docking region of the enzyme reaction coordinate.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Freie Universität Berlin , Department of Physics, Theoretical Molecular Biophysics Group , Arnimallee 14 , D-14195 Berlin , Germany
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3
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Abstract
Membranes surrounding the biological cell and its internal compartments host proteins that catalyze chemical reactions essential for the functioning of the cell. Rather than being a passive structural matrix that holds membrane-embedded proteins in place, the membrane can largely shape the conformational energy landscape of membrane proteins and impact the energetics of their chemical reaction. Here, we highlight the challenges in understanding how lipids impact the conformational energy landscape of macromolecular membrane complexes whose functioning involves chemical reactions including proton transfer. We review here advances in our understanding of how chemical reactions occur at membrane interfaces gleaned with both theoretical and experimental advances using simple protein systems as guides. Our perspective is that of bridging experiments with theory to understand general physicochemical principles of membrane reactions, with a long term goal of furthering our understanding of the role of the lipids on the functioning of complex macromolecular assemblies at the membrane interface.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Freie Universität Berlin , Department of Physics, Theoretical Molecular Biophysics Group , Arnimallee 14 , D-14195 Berlin , Germany
| | - M Joanne Lemieux
- University of Alberta , Department of Biochemistry, Membrane Protein Disease Research Group , Edmonton , Alberta T6G 2H7 , Canada
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4
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Membrane properties that shape the evolution of membrane enzymes. Curr Opin Struct Biol 2018; 51:80-91. [PMID: 29597094 DOI: 10.1016/j.sbi.2018.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/14/2018] [Accepted: 03/15/2018] [Indexed: 02/07/2023]
Abstract
Spectacular recent progress in structural biology has led to determination of the structures of many integral membrane enzymes that catalyze reactions in which at least one substrate also is membrane bound. A pattern of results seems to be emerging in which the active site chemistry of these enzymes is usually found to be analogous to what is observed for water soluble enzymes catalyzing the same reaction types. However, in light of the chemical, structural, and physical complexity of cellular membranes plus the presence of transmembrane gradients and potentials, these enzymes may be subject to membrane-specific regulatory mechanisms that are only now beginning to be uncovered. We review the membrane-specific environmental traits that shape the evolution of membrane-embedded biocatalysts.
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5
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Reading E, Hall Z, Martens C, Haghighi T, Findlay H, Ahdash Z, Politis A, Booth PJ. Interrogating Membrane Protein Conformational Dynamics within Native Lipid Compositions. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Eamonn Reading
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
| | - Zoe Hall
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
| | - Chloe Martens
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
| | - Tabasom Haghighi
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
| | - Heather Findlay
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
| | - Zainab Ahdash
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
| | - Argyris Politis
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
| | - Paula J. Booth
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
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6
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Reading E, Hall Z, Martens C, Haghighi T, Findlay H, Ahdash Z, Politis A, Booth PJ. Interrogating Membrane Protein Conformational Dynamics within Native Lipid Compositions. Angew Chem Int Ed Engl 2017; 56:15654-15657. [PMID: 29049865 DOI: 10.1002/anie.201709657] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/18/2017] [Indexed: 12/14/2022]
Abstract
The interplay between membrane proteins and the lipids of the membrane is important for cellular function, however, tools enabling the interrogation of protein dynamics within native lipid environments are scarce and often invasive. We show that the styrene-maleic acid lipid particle (SMALP) technology can be coupled with hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate membrane protein conformational dynamics within native lipid bilayers. We demonstrate changes in accessibility and dynamics of the rhomboid protease GlpG, captured within three different native lipid compositions, and identify protein regions sensitive to changes in the native lipid environment. Our results illuminate the value of this approach for distinguishing the putative role(s) of the native lipid composition in modulating membrane protein conformational dynamics.
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Affiliation(s)
- Eamonn Reading
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Zoe Hall
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Chloe Martens
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Tabasom Haghighi
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Heather Findlay
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Zainab Ahdash
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Paula J Booth
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
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7
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Li S, Zhang W, Han W. Initial Substrate Binding of γ-Secretase: The Role of Substrate Flexibility. ACS Chem Neurosci 2017; 8:1279-1290. [PMID: 28165225 DOI: 10.1021/acschemneuro.6b00425] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
γ-Secretase cleaves transmembrane domains (TMD) of amyloid precursor protein (APP), producing pathologically relevant amyloid-β proteins. Initial substrate binding represents a key step of the γ-secretase cleavage whose mechanism remains elusive. Through long time scale coarse-grained and atomic simulations, we have found that the APP TMD can bind to the catalytic subunit presenilin 1 (PS1) on an extended surface covering PS1's TMD2/6/9 and PAL motif that are all known to be essential for enzymatic activity. This initial substrate binding could lead to reduction in the vertical gap between APP's ε-cleavage sites and γ-secretase's active center, enhanced flexibility and hydration levels around the ε-sites, and the presentation of these sites to the enzyme. There are heterogeneous substrate binding poses in which the substrate is found to bind to either the N- or C-terminal parts of PS1, or both. Moreover, we also find that the stability of the binding poses can be modulated by the flexibility of substrate TMD. Especially, the APP substrate, when deprived of bending fluctuation, does not bind to TMD9 at PS1's C-terminus. Our simulations have revealed further that another substrate of γ-secretase, namely, notch receptors, though bearing a rigid TMD, can still bind to PS1 TMD9, but by a different mechanism, suggesting that the influence of substrate flexibility is context-dependent. Together, these findings shed light on the mechanism of initial substrate docking of γ-secretase and the role of substrate flexibility in this process.
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Affiliation(s)
- Shu Li
- Key Laboratory of Chemical Genomics, School
of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wan Zhang
- Key Laboratory of Chemical Genomics, School
of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wei Han
- Key Laboratory of Chemical Genomics, School
of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
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8
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Bondar AN. Biophysical mechanism of rhomboid proteolysis: Setting a foundation for therapeutics. Semin Cell Dev Biol 2016; 60:46-51. [DOI: 10.1016/j.semcdb.2016.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 08/12/2016] [Accepted: 09/12/2016] [Indexed: 11/16/2022]
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9
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10
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Reddy T, Sansom MSP. The Role of the Membrane in the Structure and Biophysical Robustness of the Dengue Virion Envelope. Structure 2016; 24:375-82. [PMID: 26833387 PMCID: PMC4780862 DOI: 10.1016/j.str.2015.12.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/15/2015] [Accepted: 12/22/2015] [Indexed: 01/11/2023]
Abstract
The dengue virion is surrounded by an envelope of membrane proteins surrounding a lipid bilayer. We have combined the cryoelectron microscopy structures of the membrane proteins (PDB: 3J27) with a lipid bilayer whose composition is based on lipidomics data for insect cell membranes, to obtain a near-atomic resolution computational model of the envelope of the dengue virion. A coarse-grained molecular dynamics simulation on the microsecond timescale enables analysis of key biophysical properties of the dengue outer envelope. Properties analyzed include area per lipid values (for a spherical virion with a mixed lipid composition), bilayer thickness, and lipid diffusion coefficients. Despite the absence of cholesterol from the lipid bilayer, the virion exhibits biophysical robustness (slow lipid diffusion alongside stable bilayer thickness, virion diameter, and shape) that matches the cholesterol-rich membrane of influenza A, with similarly anomalous diffusion of lipids. Biophysical robustness of the envelope may confer resilience to environmental perturbations. The dengue virus envelope is a lipid bilayer plus an outer layer of membrane proteins The structures of the proteins plus lipidomics data were used to model the envelope Microsecond MD simulations revealed the dynamic behavior of the lipid bilayer Protein interactions confer “raft-like” robustness on a cholesterol-free membrane
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Affiliation(s)
- Tyler Reddy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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11
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Nishizawa M, Nishizawa K. Free energy of helical transmembrane peptide dimerization in OPLS-AA/Berger force field simulations: inaccuracy and implications for partner-specific Lennard-Jones parameters between peptides and lipids. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1112006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Langosch D, Scharnagl C, Steiner H, Lemberg MK. Understanding intramembrane proteolysis: from protein dynamics to reaction kinetics. Trends Biochem Sci 2015; 40:318-27. [PMID: 25941170 DOI: 10.1016/j.tibs.2015.04.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 12/12/2022]
Abstract
Intramembrane proteolysis - cleavage of proteins within the plane of a membrane - is a widespread phenomenon that can contribute to the functional activation of substrates and is involved in several diseases. Although different families of intramembrane proteases have been discovered and characterized, we currently do not know how these enzymes discriminate between substrates and non-substrates, how site-specific cleavage is achieved, or which factors determine the rate of proteolysis. Focusing on γ-secretase and rhomboid proteases, we argue that answers to these questions may emerge from connecting experimental readouts, such as reaction kinetics and the determination of cleavage sites, to the structures and the conformational dynamics of substrates and enzymes.
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Affiliation(s)
- D Langosch
- Technische Universität München, Lehrstuhl Chemie der Biopolymere, Weihenstephaner Berg 3, 85354 Freising, and Munich Center for Integrated Protein Science (CIMPS(M)), Germany.
| | - C Scharnagl
- Fakultät für Physik E14, Technische Universität München, Maximus-von-Imhof-Forum 4, 85354 Freising, Germany
| | - H Steiner
- Ludwig-Maximilians-University Munich, Metabolic Biochemistry and DZNE (German Center for Neurodegenerative Diseases), Munich, Germany
| | - M K Lemberg
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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13
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Foo ACY, Harvey BGR, Metz JJ, Goto NK. Influence of hydrophobic mismatch on the catalytic activity of Escherichia coli GlpG rhomboid protease. Protein Sci 2014; 24:464-73. [PMID: 25307614 DOI: 10.1002/pro.2585] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 10/09/2014] [Indexed: 12/21/2022]
Abstract
Rhomboids comprise a broad family of intramembrane serine proteases that are found in a wide range of organisms and participate in a diverse array of biological processes. High-resolution structures of the catalytic transmembrane domain of the Escherichia coli GlpG rhomboid have provided numerous insights that help explain how hydrolytic cleavage can be achieved below the membrane surface. Key to this are observations that GlpG hydrophobic domain dimensions may not be sufficient to completely span the native lipid bilayer. This formed the basis for a model where hydrophobic mismatch Induces thinning of the local membrane environment to promote access to transmembrane substrates. However, hydrophobic mismatch also has the potential to alter the functional properties of the rhomboid, a possibility we explore in the current work. For this purpose, we purified the catalytic transmembrane domain of GlpG into phosphocholine or maltoside detergent micelles of varying alkyl chain lengths, and assessed proteolytic function with a model water-soluble substrate. Catalytic turnover numbers were found to depend on detergent alkyl chain length, with saturated chains containing 10-12 carbon atoms supporting maximal activity. Similar results were obtained in phospholipid bicelles, with no proteolytic activity being detected in longer-chain lipids. Although differences in thermal stability and GlpG oligomerization could not explain these activity differences, circular dichroism spectra suggest that mismatch gives rise to a small change in structure. Overall, these results demonstrate that hydrophobic mismatch can exert an inhibitory effect on rhomboid activity, with the potential for changes in local membrane environment to regulate activity in vivo.
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Affiliation(s)
- Alexander C Y Foo
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
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14
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Ghasriani H, Kwok JKC, Sherratt AR, Foo ACY, Qureshi T, Goto NK. Micelle-Catalyzed Domain Swapping in the GlpG Rhomboid Protease Cytoplasmic Domain. Biochemistry 2014; 53:5907-15. [DOI: 10.1021/bi500919v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Houman Ghasriani
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Jason K. C. Kwok
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Allison R. Sherratt
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Alexander C. Y. Foo
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Tabussom Qureshi
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Natalie K. Goto
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
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15
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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 PMCID: PMC4871223 DOI: 10.1021/bi401576k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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16
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Untangling structure-function relationships in the rhomboid family of intramembrane proteases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2862-72. [PMID: 24099005 DOI: 10.1016/j.bbamem.2013.05.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/04/2013] [Accepted: 05/04/2013] [Indexed: 12/30/2022]
Abstract
Rhomboid proteases are a family of integral membrane proteins that have been implicated in critical regulatory roles in a wide array of cellular processes and signaling events. The determination of crystal structures of the prokaryotic rhomboid GlpG from Escherichia coli and Haemophilus influenzae has ushered in an era of unprecedented understanding into molecular aspects of intramembrane proteolysis by this fascinating class of protein. A combination of structural studies by X-ray crystallography, and biophysical and spectroscopic analyses, combined with traditional enzymatic and functional analysis has revealed fundamental aspects of rhomboid structure, substrate recognition and the catalytic mechanism. This review summarizes these remarkable advances by examining evidence for the proposed catalytic mechanism derived from inhibitor co-crystal structures, conflicting models of rhomboid-substrate interaction, and recent work on the structure and function of rhomboid cytosolic domains. In addition to exploring progress on aspects of rhomboid structure, areas for future research and unaddressed questions are emphasized and highlighted. This article is part of a Special Issue entitled: Intramembrane Proteases.
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17
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Intramembrane proteolysis by rhomboids: catalytic mechanisms and regulatory principles. Curr Opin Struct Biol 2013; 23:851-8. [DOI: 10.1016/j.sbi.2013.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/06/2013] [Accepted: 07/19/2013] [Indexed: 12/20/2022]
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18
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Strisovsky K. Structural and mechanistic principles of intramembrane proteolysis--lessons from rhomboids. FEBS J 2013; 280:1579-603. [PMID: 23432912 DOI: 10.1111/febs.12199] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 02/11/2013] [Accepted: 02/18/2013] [Indexed: 02/03/2023]
Abstract
Intramembrane proteases cleave membrane proteins in their transmembrane helices to regulate a wide range of biological processes. They catalyse hydrolytic reactions within the hydrophobic environment of lipid membranes where water is normally excluded. How? Do the different classes of intramembrane proteases share any mechanistic principles? In this review these questions will be discussed in view of the crystal structures of prokaryotic members of the three known catalytic types of intramembrane proteases published over the past 7 years. Rhomboids, the intramembrane serine proteases that are the best understood family, will be the initial area of focus, and the principles that have arisen from a number of structural and biochemical studies will be considered. The site-2 metalloprotease and GXGD-type aspartyl protease structures will then be discussed, with parallels drawn and differences highlighted between these enzymes and the rhomboids. Despite the significant advances achieved so far, to obtain a detailed understanding of the mechanism of any intramembrane protease, high-resolution structural information on the substrate-enzyme complex is required. This remains a major challenge for the field.
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Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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19
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Rather P. Role of rhomboid proteases in bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2849-54. [PMID: 23518036 DOI: 10.1016/j.bbamem.2013.03.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/28/2013] [Accepted: 03/07/2013] [Indexed: 11/20/2022]
Abstract
The first member of the rhomboid family of intramembrane serine proteases in bacteria was discovered almost 20years ago. It is now known that rhomboid proteins are widely distributed in bacteria, with some bacteria containing multiple rhomboids. At the present time, only a single rhomboid-dependent function in bacteria has been identified, which is the cleavage of TatA in Providencia stuartii. Mutational analysis has shown that loss of the GlpG rhomboid in Escherichia coli alters cefotaxime resistance, loss of the YqgP (GluP) rhomboid in Bacillus subtilis alters cell division and glucose uptake, and loss of the MSMEG_5036 and MSMEG_4904 genes in Mycobacterium smegmatis results in altered colony morphology, biofilm formation and antibiotic susceptibilities. However, the cellular substrates for these proteins have not been identified. In addition, analysis of the rhombosortases, together with their possible Gly-Gly CTERM substrates, may shed new light on the role of these proteases in bacteria. This article is part of a Special Issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Philip Rather
- Department of Microbiology and Immunology, 3001 Rollins Research Bldg, Emory University School of Medicine, Atlanta, GA 30322, USA; Atlanta VA Medical Center, Decatur, GA, USA.
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20
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Lemberg MK. Sampling the membrane: function of rhomboid-family proteins. Trends Cell Biol 2013; 23:210-7. [PMID: 23369641 DOI: 10.1016/j.tcb.2013.01.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 12/19/2012] [Accepted: 01/03/2013] [Indexed: 12/29/2022]
Abstract
Rhomboids constitute a conserved protein superfamily that specifically binds membrane proteins and directs them into various different cellular pathways ranging from regulated secretion to endoplasmic reticulum (ER)-associated degradation (ERAD). Rhomboid proteases are known to release protein domains from membranes by a cut in their membrane anchor, whereas an emerging new class of rhomboid-family proteins lacks key catalytic residues and is not proteolytically active. Recent work has shown that these rhomboid pseudoproteases, including iRhoms and derlins, bind membrane proteins to regulate their fate, but the underlying molecular mechanism is not known. This review summarizes recent advances in the molecular understanding of rhomboid-family proteins and discusses common principles in how they recognize and bind proteins in the plane of the membrane.
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Affiliation(s)
- Marius K Lemberg
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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21
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Lazareno-Saez C, Arutyunova E, Coquelle N, Lemieux MJ. Domain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease. J Mol Biol 2013; 425:1127-42. [PMID: 23353827 DOI: 10.1016/j.jmb.2013.01.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/14/2013] [Accepted: 01/16/2013] [Indexed: 01/01/2023]
Abstract
Rhomboids are membrane-embedded serine proteases that cleave membrane protein substrates. Escherichia coli rhomboid GlpG (ecGlpG) consists of an N-terminal cytoplasmic domain and a membrane domain containing the active site. We determined the crystal structure of the soluble cytoplasmic domain of ecGlpG at 1.35Å resolution and examined whether this domain affected the catalytic activity of the enzyme. The structure revealed that the ecGlpG cytoplasmic domain exists as a dimer with extensive domain swapping between the two monomers. Domain-swapped dimers can be isolated from the full-length protein, suggesting that this is a physiologically relevant structure. An extensive steady-state kinetic analysis of the full-length ecGlpG and its membrane domain using soluble and transmembrane model protein substrates resulted in an unexpected conclusion: removal of the cytoplasmic domain does not alter the catalytic parameters for detergent-solubilized rhomboid for both substrates.
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Affiliation(s)
- Christelle Lazareno-Saez
- Membrane Protein Disease Research Group, Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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22
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Uritsky N, Shokhen M, Albeck A. The Catalytic Machinery of Rhomboid Proteases: Combined MD and QM Simulations. J Chem Theory Comput 2012; 8:4663-71. [DOI: 10.1021/ct3003767] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Neta Uritsky
- The Julius
Spokojny Bioorganic Chemistry Laboratory,
Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Michael Shokhen
- The Julius
Spokojny Bioorganic Chemistry Laboratory,
Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Amnon Albeck
- The Julius
Spokojny Bioorganic Chemistry Laboratory,
Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
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