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Clark KM, Jenkins JL, Fedoriw N, Dumont ME. Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors. Protein Sci 2016; 26:242-257. [PMID: 27774687 DOI: 10.1002/pro.3074] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/17/2016] [Indexed: 12/24/2022]
Abstract
The function and localization of proteins and peptides containing C-terminal "CaaX" (Cys-aliphatic-aliphatic-anything) sequence motifs are modulated by post-translational attachment of isoprenyl groups to the cysteine sulfhydryl, followed by proteolytic cleavage of the aaX amino acids. The zinc metalloprotease ZMPSTE24 is one of two enzymes known to catalyze this cleavage. The only identified target of mammalian ZMPSTE24 is prelamin A, the precursor to the nuclear scaffold protein lamin A. ZMPSTE24 also cleaves prelamin A at a second site 15 residues upstream from the CaaX site. Mutations in ZMPSTE24 result in premature-aging diseases and inhibition of ZMPSTE24 activity has been reported to be an off-target effect of HIV protease inhibitors. We report here the expression (in yeast), purification, and crystallization of human ZMPSTE24 allowing determination of the structure to 2.0 Å resolution. Compared to previous lower resolution structures, the enhanced resolution provides: (1) a detailed view of the active site of ZMPSTE24, including water coordinating the catalytic zinc; (2) enhanced visualization of fenestrations providing access from the exterior to the interior cavity of the protein; (3) a view of the C-terminus extending away from the main body of the protein; (4) localization of ordered lipid and detergent molecules at internal and external surfaces and also projecting through fenestrations; (5) identification of water molecules associated with the surface of the internal cavity. We also used a fluorogenic assay of the activity of purified ZMPSTE24 to demonstrate that HIV protease inhibitors directly inhibit the human enzyme in a manner indicative of a competitive mechanism.
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Affiliation(s)
- Kathleen M Clark
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, 14642
| | - Jermaine L Jenkins
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, 14642
| | - Nadia Fedoriw
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, 14642
| | - Mark E Dumont
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, 14642.,Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, 14642
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Arshad Z, Smith J, Roberts M, Lee WH, Davies B, Bure K, Hollander GA, Dopson S, Bountra C, Brindley D. Open Access Could Transform Drug Discovery: A Case Study of JQ1. Expert Opin Drug Discov 2016; 11:321-32. [PMID: 26791045 DOI: 10.1517/17460441.2016.1144587] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The cost to develop a new drug from target discovery to market is a staggering $1.8 billion, largely due to the very high attrition rate of drug candidates and the lengthy transition times during development. Open access is an emerging model of open innovation that places no restriction on the use of information and has the potential to accelerate the development of new drugs. AREAS COVERED To date, no quantitative assessment has yet taken place to determine the effects and viability of open access on the process of drug translation. This need is addressed within this study. The literature and intellectual property landscapes of the drug candidate JQ1, which was made available on an open access basis when discovered, and conventionally developed equivalents that were not are compared using the Web of Science and Thomson Innovation software, respectively. EXPERT OPINION Results demonstrate that openly sharing the JQ1 molecule led to a greater uptake by a wider and more multi-disciplinary research community. A comparative analysis of the patent landscapes for each candidate also found that the broader scientific diaspora of the publically released JQ1 data enhanced innovation, evidenced by a greater number of downstream patents filed in relation to JQ1. The authors' findings counter the notion that open access drug discovery would leak commercial intellectual property. On the contrary, JQ1 serves as a test case to evidence that open access drug discovery can be an economic model that potentially improves efficiency and cost of drug discovery and its subsequent commercialization.
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Affiliation(s)
- Zeeshaan Arshad
- a Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , Oxford , UK.,b School of Medicine , University of St. Andrews , St. Andrews , UK
| | - James Smith
- c Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences , University of Oxford , Oxford , UK.,d The Oxford - UCL Centre for the Advancement of Sustainable Medical Innovation (CASMI) , The University of Oxford , Oxford , UK
| | - Mackenna Roberts
- d The Oxford - UCL Centre for the Advancement of Sustainable Medical Innovation (CASMI) , The University of Oxford , Oxford , UK
| | - Wen Hwa Lee
- a Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , Oxford , UK
| | - Ben Davies
- c Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences , University of Oxford , Oxford , UK.,d The Oxford - UCL Centre for the Advancement of Sustainable Medical Innovation (CASMI) , The University of Oxford , Oxford , UK
| | - Kim Bure
- e Sartorius Stedim , Göttingen , Germany
| | - Georg A Hollander
- f Department of Biomedicine , University of Basel, and Basel University Children's Hospital , Basel , Switzerland.,g Department of Pediatrics , University of Oxford , Oxford , United Kingdom
| | - Sue Dopson
- h Said Business School , University of Oxford , Oxford , UK
| | - Chas Bountra
- a Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , Oxford , UK
| | - David Brindley
- c Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences , University of Oxford , Oxford , UK.,d The Oxford - UCL Centre for the Advancement of Sustainable Medical Innovation (CASMI) , The University of Oxford , Oxford , UK.,h Said Business School , University of Oxford , Oxford , UK.,i Centre for Behavioral Medicine, UCL School of Pharmacy , University College London , London , UK.,j Harvard Stem Cell Institute , Cambridge , MA , USA.,k USCF-Stanford Center of Excellence in Regulatory Science and Innovation (CERSI) , San Fransisco , CA , USA
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53
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Matulevičienė A, Meškienė R, Morkūnienė A, Ambrozaitytė L, Meškauskas R, Garunkštienė R, Drazdienė N, Utkus A, Kučinskas V. Frame shift mutations of the ZMPSTE24 gene in two siblings with restrictive dermopathy. Clin Dysmorphol 2016; 25:7-11. [PMID: 26379196 DOI: 10.1097/mcd.0000000000000100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Restrictive dermopathy (RD) is a rare lethal autosomal recessive genodermatosis, characterized by abnormally rigid skin with prominent superficial vasculature, erosions and epidermal hyperkeratosis, dysplastic clavicles, joint contractures, mouth fixed in the 'O' position, small pinched nose, and neonatal death. Mutations of ZMPSTE24 and LMNA genes are reported as the causes of RD, with those of ZMPSTE24 being more prevalent. Here, we report on a familial c.50delA (p.Lys17Serfs*21) mutation of the ZMPSTE24 gene, causing RD in two siblings.
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Affiliation(s)
- Aušra Matulevičienė
- aDepartment of Human and Medical Genetics bCentre of Neonatology, Clinics of Children's Diseases, Faculty of Medicine, Vilnius University cNational Centre of Pathology dCentre of Neonatology, Children's Hospital, Affiliate of Vilnius University Hospital Santariškių Klinikos, Vilnius, Lithuania
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54
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Ast T, Michaelis S, Schuldiner M. The Protease Ste24 Clears Clogged Translocons. Cell 2016; 164:103-114. [PMID: 26771486 DOI: 10.1016/j.cell.2015.11.053] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 09/23/2015] [Accepted: 11/17/2015] [Indexed: 01/12/2023]
Abstract
Translocation into the endoplasmic reticulum (ER) is the first step in the biogenesis of thousands of eukaryotic endomembrane proteins. Although functional ER translocation has been avidly studied, little is known about the quality control mechanisms that resolve faulty translocational states. One such faulty state is translocon clogging, in which the substrate fails to properly translocate and obstructs the translocon pore. To shed light on the machinery required to resolve clogging, we carried out a systematic screen in Saccharomyces cerevisiae that highlighted a role for the ER metalloprotease Ste24. We could demonstrate that Ste24 approaches the translocon upon clogging, and it interacts with and generates cleavage fragments of the clogged protein. Importantly, these functions are conserved in the human homolog, ZMPSTE24, although disease-associated mutant forms of ZMPSTE24 fail to clear the translocon. These results shed light on a new and critical task of Ste24, which safeguards the essential process of translocation.
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Affiliation(s)
- Tslil Ast
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Susan Michaelis
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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55
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Hildebrandt ER, Arachea BT, Wiener MC, Schmidt WK. Ste24p Mediates Proteolysis of Both Isoprenylated and Non-prenylated Oligopeptides. J Biol Chem 2016; 291:14185-14198. [PMID: 27129777 DOI: 10.1074/jbc.m116.718197] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Indexed: 12/31/2022] Open
Abstract
Rce1p and Ste24p are integral membrane proteins involved in the proteolytic maturation of isoprenylated proteins. Extensive published evidence indicates that Rce1p requires the isoprenyl moiety as an important substrate determinant. By contrast, we report that Ste24p can cleave both isoprenylated and non-prenylated substrates in vitro, indicating that the isoprenyl moiety is not required for substrate recognition. Steady-state enzyme kinetics are significantly different for prenylated versus non-prenylated substrates, strongly suggestive of a role for substrate-membrane interaction in protease function. Mass spectroscopy analyses identify a cleavage preference at bonds where P1' is aliphatic in both isoprenylated and non-prenylated substrates, although this is not necessarily predictive. The identified cleavage sites are not at a fixed distance position relative to the C terminus. In this study, the substrates cleaved by Ste24p are based on known isoprenylated proteins (i.e. K-Ras4b and the yeast a-factor mating pheromone) and non-prenylated biological peptides (Aβ and insulin chains) that are known substrates of the M16A family of soluble zinc-dependent metalloproteases. These results establish that the substrate profile of Ste24p is broader than anticipated, being more similar to that of the M16A protease family than that of the Rce1p CAAX protease with which it has been functionally associated.
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Affiliation(s)
- Emily R Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Buenafe T Arachea
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Michael C Wiener
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Walter K Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602.
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56
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Pike ACW, Garman EF, Krojer T, von Delft F, Carpenter EP. An overview of heavy-atom derivatization of protein crystals. Acta Crystallogr D Struct Biol 2016; 72:303-18. [PMID: 26960118 PMCID: PMC4784662 DOI: 10.1107/s2059798316000401] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 01/08/2016] [Indexed: 11/11/2022] Open
Abstract
Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in low-resolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative.
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Affiliation(s)
- Ashley C. W. Pike
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
- Department of Biochemistry, University of Johannesburg, Aukland Park 2006, South Africa
| | - Elisabeth P. Carpenter
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
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57
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LMNA mutations resulting in lipodystrophy and HIV protease inhibitors trigger vascular smooth muscle cell senescence and calcification: Role of ZMPSTE24 downregulation. Atherosclerosis 2016; 245:200-11. [DOI: 10.1016/j.atherosclerosis.2015.12.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/21/2015] [Accepted: 12/07/2015] [Indexed: 11/23/2022]
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58
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Structural biology of intramembrane proteases: mechanistic insights from rhomboid and S2P to γ-secretase. Curr Opin Struct Biol 2016; 37:97-107. [PMID: 26811996 DOI: 10.1016/j.sbi.2015.12.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/14/2015] [Accepted: 12/28/2015] [Indexed: 12/21/2022]
Abstract
Intramembrane proteases catalyze hydrolysis of peptide bond within the lipid bilayer and play a key role in a variety of cellular processes. These membrane-embedded enzymes comprise four major classes: rhomboid serine proteases, site-2 metalloproteases, Rce1-type glutamyl proteases, and aspartyl proteases exemplified by signal peptide peptidase and γ-secretase. In the past several years, three-dimensional structures of representative members of these four classes of intramembrane protease have been reported at atomic resolutions, which reveal distinct protein folds and active site configurations. These structures, together with structure-guided biochemical analyses, shed light on the working mechanisms of water access and substrate entry. In this review, we discuss the shared as well as unique features of these intramembrane proteases, with a focus on presenilin-the catalytic component of γ-secretase.
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59
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Sadaf A, Mortensen JS, Capaldi S, Tikhonova E, Hariharan P, de Castro Ribeiro O, Loland CJ, Guan L, Byrne B, Chae PS. A Class of Rigid Linker-bearing Glucosides for Membrane Protein Structural Study. Chem Sci 2015; 7:1933-1939. [PMID: 27110345 PMCID: PMC4836865 DOI: 10.1039/c5sc02900g] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Novel glycoside amphiphile (NDT-C11) displays favorable behavior in maintaining both protein stability and conformational flexibility compared to DDM and MNG-3.
Membrane proteins are amphipathic bio-macromolecules incompatible with the polar environments of aqueous media. Conventional detergents encapsulate the hydrophobic surfaces of membrane proteins allowing them to exist in aqueous solution. Membrane proteins stabilized by detergent micelles are used for structural and functional analysis. Despite the availability of a large number of detergents, only a few agents are sufficiently effective at maintaining the integrity of membrane proteins to allow successful crystallization. In the present study, we describe a novel class of synthetic amphiphiles with a branched tail group and a triglucoside head group. These head and tail groups were connected via an amide or ether linkage by using a tris(hydroxylmethyl)aminomethane (TRIS) or neopentyl glycol (NPG) linker to produce TRIS-derived triglucosides (TDTs) and NPG-derived triglucosides (NDTs), respectively. Members of this class conferred enhanced stability on target membrane proteins compared to conventional detergents. Because of straightforward synthesis of the novel agents and their favourable effects on a range of membrane proteins, these agents should be of wide applicability to membrane protein science.
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Affiliation(s)
- Aiman Sadaf
- Department of Bionanotechnology, Hanyang University, Ansan, 426-791 (Korea)
| | - Jonas S Mortensen
- Department of Neuroscience and Pharmacology, University of Copenhagen, DK-2200 Copenhagen (Denmark)
| | - Stefano Capaldi
- Department of Life Sciences, Imperial College London London, SW7 2AZ (UK) ; Department of Biotechnology, University of Verona, 37134 Verona (Italy)
| | - Elena Tikhonova
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences
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60
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8-Hydroxyquinoline-based inhibitors of the Rce1 protease disrupt Ras membrane localization in human cells. Bioorg Med Chem 2015; 24:160-78. [PMID: 26706114 DOI: 10.1016/j.bmc.2015.11.043] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/23/2015] [Accepted: 11/29/2015] [Indexed: 01/05/2023]
Abstract
Ras converting enzyme 1 (Rce1) is an endoprotease that catalyzes processing of the C-terminus of Ras protein by removing -aaX from the CaaX motif. The activity of Rce1 is crucial for proper localization of Ras to the plasma membrane where it functions. Ras is responsible for transmitting signals related to cell proliferation, cell cycle progression, and apoptosis. The disregulation of these pathways due to constitutively active oncogenic Ras can ultimately lead to cancer. Ras, its effectors and regulators, and the enzymes that are involved in its maturation process are all targets for anti-cancer therapeutics. Key enzymes required for Ras maturation and localization are the farnesyltransferase (FTase), Rce1, and isoprenylcysteine carboxyl methyltransferase (ICMT). Among these proteins, the physiological role of Rce1 in regulating Ras and other CaaX proteins has not been fully explored. Small-molecule inhibitors of Rce1 could be useful as chemical biology tools to understand further the downstream impact of Rce1 on Ras function and serve as potential leads for cancer therapeutics. Structure-activity relationship (SAR) analysis of a previously reported Rce1 inhibitor, NSC1011, has been performed to generate a new library of Rce1 inhibitors. The new inhibitors caused a reduction in Rce1 in vitro activity, exhibited low cell toxicity, and induced mislocalization of EGFP-Ras from the plasma membrane in human colon carcinoma cells giving rise to a phenotype similar to that observed with siRNA knockdowns of Rce1 expression. Several of the new inhibitors were more effective at mislocalizing K-Ras compared to a potent farnesyltransferase inhibitor (FTI), which is significant because of the preponderance of K-Ras mutations in cancer.
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61
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Abstract
The heterotrimeric SecY translocon complex is required for the cotranslational assembly of membrane proteins in bacteria and archaea. The insertion of transmembrane (TM) segments during nascent-chain passage through the translocon is generally viewed as a simple partitioning process between the water-filled translocon and membrane lipid bilayer, suggesting that partitioning is driven by the hydrophobic effect. Indeed, the apparent free energy of partitioning of unnatural aliphatic amino acids on TM segments is proportional to accessible surface area, which is a hallmark of the hydrophobic effect [Öjemalm K, et al. (2011) Proc Natl Acad Sci USA 108(31):E359-E364]. However, the apparent partitioning solvation parameter is less than one-half the value expected for simple bulk partitioning, suggesting that the water in the translocon departs from bulk behavior. To examine the state of water in a SecY translocon complex embedded in a lipid bilayer, we carried out all-atom molecular-dynamics simulations of the Pyrococcus furiosus SecYE, which was determined to be in a "primed" open state [Egea PF, Stroud RM (2010) Proc Natl Acad Sci USA 107(40):17182-17187]. Remarkably, SecYE remained in this state throughout our 450-ns simulation. Water molecules within SecY exhibited anomalous diffusion, had highly retarded rotational dynamics, and aligned their dipoles along the SecY transmembrane axis. The translocon is therefore not a simple water-filled pore, which raises the question of how anomalous water behavior affects the mechanism of translocon function and, more generally, the partitioning of hydrophobic molecules. Because large water-filled cavities are found in many membrane proteins, our findings may have broader implications.
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62
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Stansfeld PJ, Goose JE, Caffrey M, Carpenter EP, Parker JL, Newstead S, Sansom MSP. MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes. Structure 2015; 23:1350-61. [PMID: 26073602 PMCID: PMC4509712 DOI: 10.1016/j.str.2015.05.006] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/24/2015] [Accepted: 05/02/2015] [Indexed: 01/26/2023]
Abstract
There has been exponential growth in the number of membrane protein structures determined. Nevertheless, these structures are usually resolved in the absence of their lipid environment. Coarse-grained molecular dynamics (CGMD) simulations enable insertion of membrane proteins into explicit models of lipid bilayers. We have automated the CGMD methodology, enabling membrane protein structures to be identified upon their release into the PDB and embedded into a membrane. The simulations are analyzed for protein-lipid interactions, identifying lipid binding sites, and revealing local bilayer deformations plus molecular access pathways within the membrane. The coarse-grained models of membrane protein/bilayer complexes are transformed to atomistic resolution for further analysis and simulation. Using this automated simulation pipeline, we have analyzed a number of recently determined membrane protein structures to predict their locations within a membrane, their lipid/protein interactions, and the functional implications of an enhanced understanding of the local membrane environment of each protein. A simulation pipeline for predicting the location of a membrane protein in a bilayer A protocol for identifying novel membrane protein structures in the PDB Analysis of lipid binding sites and local bilayer deformation by membrane proteins Functional implications from enhanced understanding of local membrane environments
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Affiliation(s)
- Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joseph E Goose
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Caffrey
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Joanne L Parker
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Simon Newstead
- 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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63
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Cho KH, Du Y, Scull NJ, Hariharan P, Gotfryd K, Loland CJ, Guan L, Byrne B, Kobilka BK, Chae PS. Novel Xylene-Linked Maltoside Amphiphiles (XMAs) for Membrane Protein Stabilisation. Chemistry 2015; 21:10008-13. [PMID: 26013293 DOI: 10.1002/chem.201501083] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Indexed: 01/14/2023]
Abstract
Membrane proteins are key functional players in biological systems. These biomacromolecules contain both hydrophilic and hydrophobic regions and thus amphipathic molecules are necessary to extract membrane proteins from their native lipid environments and stabilise them in aqueous solutions. Conventional detergents are commonly used for membrane protein manipulation, but membrane proteins surrounded by these agents often undergo denaturation and aggregation. In this study, a novel class of maltoside-bearing amphiphiles, with a xylene linker in the central region, designated xylene-linked maltoside amphiphiles (XMAs) was developed. When these novel agents were evaluated with a number of membrane proteins, it was found that XMA-4 and XMA-5 have particularly favourable efficacy with respect to membrane protein stabilisation, indicating that these agents hold significant potential for membrane protein structural study.
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Affiliation(s)
- Kyung Ho Cho
- Department of Bionanotechnology, Hanyang University, Ansan, 426-791 (Republic of Korea)
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305 (USA)
| | - Nicola J Scull
- Department of Life Sciences, Imperial College London, London, SW7 2AZ (UK)
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430 (USA)
| | - Kamil Gotfryd
- Department of Neuroscience and Pharmacology, University of Copenhagen, 2200 Copenhagen (Denmark).,Present address: Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen (Denmark)
| | - Claus J Loland
- Department of Neuroscience and Pharmacology, University of Copenhagen, 2200 Copenhagen (Denmark)
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430 (USA)
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ (UK)
| | - Brian K Kobilka
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305 (USA)
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan, 426-791 (Republic of Korea).
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64
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Maxson T, Deane CD, Molloy EM, Cox CL, Markley AL, Lee SW, Mitchell DA. HIV protease inhibitors block streptolysin S production. ACS Chem Biol 2015; 10:1217-26. [PMID: 25668590 DOI: 10.1021/cb500843r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Streptolysin S (SLS) is a post-translationally modified peptide cytolysin that is produced by the human pathogen Streptococcus pyogenes. SLS belongs to a large family of azole-containing natural products that are biosynthesized via an evolutionarily conserved pathway. SLS is an important virulence factor during S. pyogenes infections, but despite an extensive history of study, further investigations are needed to clarify several steps of its biosynthesis. To this end, chemical inhibitors of SLS biosynthesis would be valuable tools to interrogate the various maturation steps of both SLS and biosynthetically related natural products. Such chemical inhibitors could also potentially serve as antivirulence therapeutics, which in theory may alleviate the spread of antibiotic resistance. In this work, we demonstrate that FDA-approved HIV protease inhibitors, especially nelfinavir, block a key proteolytic processing step during SLS production. This inhibition was demonstrated in live S. pyogenes cells and through in vitro protease inhibition assays. A panel of 57 nelfinavir analogs was synthesized, leading to a series of compounds with improved anti-SLS activity while illuminating structure-activity relationships. Nelfinavir was also found to inhibit the maturation of other azole-containing natural products, namely those involved in listeriolysin S, clostridiolysin S, and plantazolicin production. The use of nelfinavir analogs as inhibitors of SLS production has allowed us to begin examining the proteolysis event in SLS maturation and will aid in further investigations of the biosynthesis of SLS and related natural products.
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Affiliation(s)
- Tucker Maxson
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| | - Caitlin D. Deane
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| | - Evelyn M. Molloy
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| | - Courtney L. Cox
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
- Department
of Microbiology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| | - Andrew L. Markley
- Department
of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States
| | - Shaun W. Lee
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
- Department
of Microbiology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
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65
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Hu NJ, Rada H, Rahman N, Nettleship JE, Bird L, Iwata S, Drew D, Cameron AD, Owens RJ. GFP-based expression screening of membrane proteins in insect cells using the baculovirus system. Methods Mol Biol 2015; 1261:197-209. [PMID: 25502201 DOI: 10.1007/978-1-4939-2230-7_11] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A key step in the production of recombinant membrane proteins for structural studies is the optimization of protein yield and quality. One commonly used approach is to fuse the protein to green fluorescent protein (GFP), enabling expression to be tracked without the need to purify the protein. Combining fusion to green fluorescent protein with the baculovirus expression system provides a useful platform for both screening and production of eukaryotic membrane proteins. In this chapter we describe our protocol for the expression screening of membrane proteins in insect cells using fusion to GFP as a reporter. We use both SDS-PAGE with in-gel fluorescence imaging and fluorescence-detection size-exclusion chromatography (FSEC) to screen for expression.
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Affiliation(s)
- Nien-Jen Hu
- Institute of Biochemistry, National Chung Hsing University, Taichung, 40227, Taiwan,
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66
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Cerdà-Costa N, Gomis-Rüth FX. Architecture and function of metallopeptidase catalytic domains. Protein Sci 2014; 23:123-44. [PMID: 24596965 DOI: 10.1002/pro.2400] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The cleavage of peptide bonds by metallopeptidases (MPs) is essential for life. These ubiquitous enzymes participate in all major physiological processes, and so their deregulation leads to diseases ranging from cancer and metastasis, inflammation, and microbial infection to neurological insults and cardiovascular disorders. MPs cleave their substrates without a covalent intermediate in a single-step reaction involving a solvent molecule, a general base/acid, and a mono- or dinuclear catalytic metal site. Most monometallic MPs comprise a short metal-binding motif (HEXXH), which includes two metal-binding histidines and a general base/acid glutamate, and they are grouped into the zincin tribe of MPs. The latter divides mainly into the gluzincin and metzincin clans. Metzincins consist of globular ∼ 130-270-residue catalytic domains, which are usually preceded by N-terminal pro-segments, typically required for folding and latency maintenance. The catalytic domains are often followed by C-terminal domains for substrate recognition and other protein-protein interactions, anchoring to membranes, oligomerization, and compartmentalization. Metzincin catalytic domains consist of a structurally conserved N-terminal subdomain spanning a five-stranded β-sheet, a backing helix, and an active-site helix. The latter contains most of the metal-binding motif, which is here characteristically extended to HEXXHXXGXX(H,D). Downstream C-terminal subdomains are generally shorter, differ more among metzincins, and mainly share a conserved loop--the Met-turn--and a C-terminal helix. The accumulated structural data from more than 300 deposited structures of the 12 currently characterized metzincin families reviewed here provide detailed knowledge of the molecular features of their catalytic domains, help in our understanding of their working mechanisms, and form the basis for the design of novel drugs.
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67
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He Y, Wang K, Yan N. The recombinant expression systems for structure determination of eukaryotic membrane proteins. Protein Cell 2014; 5:658-72. [PMID: 25119489 PMCID: PMC4145085 DOI: 10.1007/s13238-014-0086-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/16/2014] [Indexed: 01/17/2023] Open
Abstract
Eukaryotic membrane proteins, many of which are key players in various biological processes, constitute more than half of the drug targets and represent important candidates for structural studies. In contrast to their physiological significance, only very limited number of eukaryotic membrane protein structures have been obtained due to the technical challenges in the generation of recombinant proteins. In this review, we examine the major recombinant expression systems for eukaryotic membrane proteins and compare their relative advantages and disadvantages. We also attempted to summarize the recent technical strategies in the advancement of eukaryotic membrane protein purification and crystallization.
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Affiliation(s)
- Yuan He
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua university, Beijing, 100084, China
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68
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Navarro CL, Esteves-Vieira V, Courrier S, Boyer A, Duong Nguyen T, Huong LTT, Meinke P, Schröder W, Cormier-Daire V, Sznajer Y, Amor DJ, Lagerstedt K, Biervliet M, van den Akker PC, Cau P, Roll P, Lévy N, Badens C, Wehnert M, De Sandre-Giovannoli A. New ZMPSTE24 (FACE1) mutations in patients affected with restrictive dermopathy or related progeroid syndromes and mutation update. Eur J Hum Genet 2014; 22:1002-11. [PMID: 24169522 PMCID: PMC4350588 DOI: 10.1038/ejhg.2013.258] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/20/2013] [Accepted: 09/27/2013] [Indexed: 01/24/2023] Open
Abstract
Restrictive dermopathy (RD) is a rare and extremely severe congenital genodermatosis, characterized by a tight rigid skin with erosions at flexure sites, multiple joint contractures, low bone density and pulmonary insufficiency generally leading to death in the perinatal period. RD is caused in most patients by compound heterozygous or homozygous ZMPSTE24 null mutations. This gene encodes a metalloprotease specifically involved in lamin A post-translational processing. Here, we report a total of 16 families for whom diagnosis and molecular defects were clearly established. Among them, we report seven new ZMPSTE24 mutations, identified in classical RD or Mandibulo-acral dysplasia (MAD) affected patients. We also report nine families with one or two affected children carrying the common, homozygous thymine insertion in exon 9 and demonstrate the lack of a founder effect. In addition, we describe several new ZMPSTE24 variants identified in unaffected controls or in patients affected with non-classical progeroid syndromes. In addition, this mutation update includes a comprehensive search of the literature on previously described ZMPSTE24 mutations and associated phenotypes. Our comprehensive analysis of the molecular pathology supported the general rule: complete loss-of-function of ZMPSTE24 leads to RD, whereas other less severe phenotypes are associated with at least one haploinsufficient allele.
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Affiliation(s)
- Claire Laure Navarro
- Inserm, UMR_S 910, Marseille, France
- Aix Marseille Université, GMGF, Marseille, France
| | - Vera Esteves-Vieira
- Laboratory of Molecular Genetics, Medical Genetics Department, La Timone Children's Hospital, Marseille, France
| | - Sébastien Courrier
- Inserm, UMR_S 910, Marseille, France
- Aix Marseille Université, GMGF, Marseille, France
| | - Amandine Boyer
- Laboratory of Molecular Genetics, Medical Genetics Department, La Timone Children's Hospital, Marseille, France
| | - Thuy Duong Nguyen
- Institute of Human Genetics and Interfaculty Institute of Genetics and Functional Genomics, Department of University Medicine, Ernst-Moritz-Arndt University, Greifswald, Germany
- Institute of Genome Research (IGR), Vietnam Academy of Science and Technology (VAST), Hà Nô̇i, Vietnam
| | - Le Thi Thanh Huong
- Institute of Human Genetics and Interfaculty Institute of Genetics and Functional Genomics, Department of University Medicine, Ernst-Moritz-Arndt University, Greifswald, Germany
- National Institute of Hygiene and Epidemiology, Hà Nô̇i, Vietnam
| | - Peter Meinke
- Institute of Human Genetics and Interfaculty Institute of Genetics and Functional Genomics, Department of University Medicine, Ernst-Moritz-Arndt University, Greifswald, Germany
| | - Winnie Schröder
- Institute of Human Genetics and Interfaculty Institute of Genetics and Functional Genomics, Department of University Medicine, Ernst-Moritz-Arndt University, Greifswald, Germany
| | | | - Yves Sznajer
- Center for Human Genetics, Cliniques Universitaires St-Luc, U.C.L, Bruxelles, Belgique
| | - David J Amor
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Kristina Lagerstedt
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Martine Biervliet
- Department of Medical Genetics, University Hospital Antwerp, Antwerp, Belgium
| | - Peter C van den Akker
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pierre Cau
- Inserm, UMR_S 910, Marseille, France
- Aix Marseille Université, GMGF, Marseille, France
- Laboratory of Cellular Biology, Medical Genetics Department, La Timone Children's Hospital, Marseille, France
| | - Patrice Roll
- Inserm, UMR_S 910, Marseille, France
- Aix Marseille Université, GMGF, Marseille, France
- Laboratory of Cellular Biology, Medical Genetics Department, La Timone Children's Hospital, Marseille, France
| | - Nicolas Lévy
- Inserm, UMR_S 910, Marseille, France
- Aix Marseille Université, GMGF, Marseille, France
- Laboratory of Molecular Genetics, Medical Genetics Department, La Timone Children's Hospital, Marseille, France
| | - Catherine Badens
- Inserm, UMR_S 910, Marseille, France
- Aix Marseille Université, GMGF, Marseille, France
- Laboratory of Molecular Genetics, Medical Genetics Department, La Timone Children's Hospital, Marseille, France
| | - Manfred Wehnert
- Institute of Human Genetics and Interfaculty Institute of Genetics and Functional Genomics, Department of University Medicine, Ernst-Moritz-Arndt University, Greifswald, Germany
| | - Annachiara De Sandre-Giovannoli
- Inserm, UMR_S 910, Marseille, France
- Aix Marseille Université, GMGF, Marseille, France
- Laboratory of Molecular Genetics, Medical Genetics Department, La Timone Children's Hospital, Marseille, France
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69
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Chang Y, Bruni R, Kloss B, Assur Z, Kloppmann E, Rost B, Hendrickson WA, Liu Q. Structural basis for a pH-sensitive calcium leak across membranes. Science 2014; 344:1131-5. [PMID: 24904158 DOI: 10.1126/science.1252043] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Calcium homeostasis balances passive calcium leak and active calcium uptake. Human Bax inhibitor-1 (hBI-1) is an antiapoptotic protein that mediates a calcium leak and is representative of a highly conserved and widely distributed family, the transmembrane Bax inhibitor motif (TMBIM) proteins. Here, we present crystal structures of a bacterial homolog and characterize its calcium leak activity. The structure has a seven-transmembrane-helix fold that features two triple-helix sandwiches wrapped around a central C-terminal helix. Structures obtained in closed and open conformations are reversibly interconvertible by change of pH. A hydrogen-bonded, pKa (where Ka is the acid dissociation constant)-perturbed pair of conserved aspartate residues explains the pH dependence of this transition, and biochemical studies show that pH regulates calcium influx in proteoliposomes. Homology models for hBI-1 provide insights into TMBIM-mediated calcium leak and cytoprotective activity.
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Affiliation(s)
- Yanqi Chang
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA
| | - Renato Bruni
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA
| | - Brian Kloss
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA
| | - Zahra Assur
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Edda Kloppmann
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA. Department of Bioinformatics and Computational Biology, Fakultät für Informatik, Technische Universität München, Garching, Germany
| | - Burkhard Rost
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA. Department of Bioinformatics and Computational Biology, Fakultät für Informatik, Technische Universität München, Garching, Germany
| | - Wayne A Hendrickson
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA. Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA. New York Structural Biology Center, National Synchrotron Light Source (NSLS) X4, Brookhaven National Laboratory, Upton, NY 11973, USA. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Qun Liu
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA. New York Structural Biology Center, National Synchrotron Light Source (NSLS) X4, Brookhaven National Laboratory, Upton, NY 11973, USA.
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70
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Arolas JL, García-Castellanos R, Goulas T, Akiyama Y, Gomis-Rüth FX. Expression and purification of integral membrane metallopeptidase HtpX. Protein Expr Purif 2014; 99:113-8. [PMID: 24769134 DOI: 10.1016/j.pep.2014.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/24/2014] [Accepted: 04/16/2014] [Indexed: 11/29/2022]
Abstract
Little is known about the catalytic mechanism of integral membrane (IM) peptidases. HtpX is an IM metallopeptidase that plays a central role in protein quality control by preventing the accumulation of misfolded proteins in the membrane. Here we report the recombinant overexpression and purification of a catalytically ablated form of HtpX from Escherichia coli. Several E. coli strains, expression vectors, detergents, and purification strategies were tested to achieve maximum yields of pure and well-folded protein. HtpX was successfully overexpressed in E. coli BL21(DE3) cells using a pET-derived vector attaching a C-terminal His8-tag, extracted from the membranes using octyl-β-d-glucoside, and purified to homogeneity in the presence of this detergent in three consecutive steps: cobalt-affinity, anion-exchange, and size-exclusion chromatography. The production of HtpX in milligram amounts paves the way for structural studies, which will be essential to understand the catalytic mechanism of this IM peptidase and related family members.
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Affiliation(s)
- Joan L Arolas
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, E-08028 Barcelona, Spain.
| | - Raquel García-Castellanos
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, E-08028 Barcelona, Spain
| | - Theodoros Goulas
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, E-08028 Barcelona, Spain
| | - Yoshinori Akiyama
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - F Xavier Gomis-Rüth
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, E-08028 Barcelona, Spain.
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71
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Manolaridis I, Kulkarni K, Dodd RB, Ogasawara S, Zhang Z, Bineva G, Reilly NO, Hanrahan SJ, Thompson AJ, Cronin N, Iwata S, Barford D. Mechanism of farnesylated CAAX protein processing by the intramembrane protease Rce1. Nature 2013; 504:301-5. [PMID: 24291792 PMCID: PMC3864837 DOI: 10.1038/nature12754] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 10/11/2013] [Indexed: 12/31/2022]
Abstract
CAAX proteins have essential roles in multiple signalling pathways, controlling processes such as proliferation, differentiation and carcinogenesis. The ∼120 mammalian CAAX proteins function at cellular membranes and include the Ras superfamily of small GTPases, nuclear lamins, the γ-subunit of heterotrimeric GTPases, and several protein kinases and phosphatases. The proper localization of CAAX proteins to cell membranes is orchestrated by a series of post-translational modifications of the carboxy-terminal CAAX motifs (where C is cysteine, A is an aliphatic amino acid and X is any amino acid). These reactions involve prenylation of the cysteine residue, cleavage at the AAX tripeptide and methylation of the carboxyl-prenylated cysteine residue. The major CAAX protease activity is mediated by Rce1 (Ras and a-factor converting enzyme 1), an intramembrane protease (IMP) of the endoplasmic reticulum. Information on the architecture and proteolytic mechanism of Rce1 has been lacking. Here we report the crystal structure of a Methanococcus maripaludis homologue of Rce1, whose endopeptidase specificity for farnesylated peptides mimics that of eukaryotic Rce1. Its structure, comprising eight transmembrane α-helices, and catalytic site are distinct from those of other IMPs. The catalytic residues are located ∼10 Å into the membrane and are exposed to the cytoplasm and membrane through a conical cavity that accommodates the prenylated CAAX substrate. We propose that the farnesyl lipid binds to a site at the opening of two transmembrane α-helices, which results in the scissile bond being positioned adjacent to a glutamate-activated nucleophilic water molecule. This study suggests that Rce1 is the founding member of a novel IMP family, the glutamate IMPs.
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Affiliation(s)
| | - Kiran Kulkarni
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Roger B Dodd
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Satoshi Ogasawara
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- JST, Research Acceleration Program, Membrane Protein, Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Ziguo Zhang
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Ganka Bineva
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London, WC2A 3LY, UK
| | - Nicola O' Reilly
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London, WC2A 3LY, UK
| | - Sarah J Hanrahan
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | | | - Nora Cronin
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- JST, Research Acceleration Program, Membrane Protein, Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Division of Molecular Biosciences, Imperial College, London, SW7 2AZ, UK
| | - David Barford
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
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72
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Yeagle PL. Non-covalent binding of membrane lipids to membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1548-59. [PMID: 24269542 DOI: 10.1016/j.bbamem.2013.11.009] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/01/2013] [Accepted: 11/09/2013] [Indexed: 01/30/2023]
Abstract
Polar lipids and membrane proteins are major components of biological membranes, both cell membranes and membranes of enveloped viruses. How these two classes of membrane components interact with each other to influence the function of biological membranes is a fundamental question that has attracted intense interest since the origins of the field of membrane studies. One of the most powerful ideas that driven the field is the likelihood that lipids bind to membrane proteins at specific sites, modulating protein structure and function. However only relatively recently has high resolution structure determination of membrane proteins progressed to the point of providing atomic level structure of lipid binding sites on membrane proteins. Analysis of X-ray diffraction, electron crystallography and NMR data over 100 specific lipid binding sites on membrane proteins. These data demonstrate tight lipid binding of both phospholipids and cholesterol to membrane proteins. Membrane lipids bind to membrane proteins by their headgroups, or by their acyl chains, or binding is mediated by the entire lipid molecule. When headgroups bind, binding is stabilized by polar interactions between lipid headgroups and the protein. When acyl chains bind, van der Waals effects dominate as the acyl chains adopt conformations that complement particular sites on the rough protein surface. No generally applicable motifs for binding have yet emerged. Previously published biochemical and biophysical data link this binding with function. This Article is Part of a Special Issue Entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy.
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Affiliation(s)
- Philip L Yeagle
- Rutgers University Newark, 325 Hill Hall, 360 MLK Blvd, Newark, NJ 07102-1801, USA.
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73
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Hildebrandt ER, Davis DM, Deaton J, Krishnankutty RK, Lilla E, Schmidt WK. Topology of the yeast Ras converting enzyme as inferred from cysteine accessibility studies. Biochemistry 2013; 52:6601-14. [PMID: 23972033 DOI: 10.1021/bi400647c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The Ras converting enzyme (Rce1p) is an endoprotease that is involved in the post-translational processing of the Ras GTPases and other isoprenylated proteins. Its role in Ras biosynthesis marks Rce1p as an anticancer target. By assessing the chemical accessibility of cysteine residues substituted throughout the Saccharomyces cerevisiae Rce1p sequence, we have determined that yeast Rce1p has eight segments that are protected from chemical modification. Notably, the three residues that are essential for yeast Rce1p function (E156, H194, and H248) are all chemically inaccessible and associated with separate protected segments. By specifically assessing the chemical reactivity and glycosylation potential of the NH2 and COOH termini of Rce1p, we further demonstrate that Rce1p has an odd number of transmembrane spans. Substantial evidence that the most NH2-terminal segment functions as a transmembrane segment with the extreme NH2 terminus projecting into the endoplasmic reticulum (ER) lumen is presented. Because each of the remaining seven segments is too short to contain two spans and is flanked by chemically reactive positions, we infer that these segments are not transmembrane segments but rather represent compact structural features and/or hydrophobic loops that penetrate but do not fully span the bilayer (i.e., re-entrant helices). We thus propose a topological model in which yeast Rce1p contains a single transmembrane helix localized at its extreme NH2 terminus and one or more re-entrant helices and/or compact structural domains that populate the cytosolic face of the ER membrane. Lastly, we demonstrate that the natural cysteine residues of Rce1p are chemically inaccessible and fully dispensable for in vivo enzyme activity, formally eliminating the possibility of a cysteine-based enzymatic mechanism for this protease.
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Affiliation(s)
- Emily R Hildebrandt
- Department of Biochemistry and Molecular Biology, The University of Georgia , Athens, Georgia 30602, United States
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74
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López-Pelegrín M, Cerdà-Costa N, Martínez-Jiménez F, Cintas-Pedrola A, Canals A, Peinado JR, Marti-Renom MA, López-Otín C, Arolas JL, Gomis-Rüth FX. A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral membrane metallopeptidases. J Biol Chem 2013; 288:21279-21294. [PMID: 23733187 PMCID: PMC3774397 DOI: 10.1074/jbc.m113.476580] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/13/2013] [Indexed: 11/06/2022] Open
Abstract
In the search for structural models of integral-membrane metallopeptidases (MPs), we discovered three related proteins from thermophilic prokaryotes, which we grouped into a novel family called "minigluzincins." We determined the crystal structures of the zymogens of two of these (Pyrococcus abyssi proabylysin and Methanocaldococcus jannaschii projannalysin), which are soluble and, with ∼100 residues, constitute the shortest structurally characterized MPs to date. Despite relevant sequence and structural similarity, the structures revealed two unique mechanisms of latency maintenance through the C-terminal segments previously unseen in MPs as follows: intramolecular, through an extended tail, in proabylysin, and crosswise intermolecular, through a helix swap, in projannalysin. In addition, structural and sequence comparisons revealed large similarity with MPs of the gluzincin tribe such as thermolysin, leukotriene A4 hydrolase relatives, and cowrins. Noteworthy, gluzincins mostly contain a glutamate as third characteristic zinc ligand, whereas minigluzincins have a histidine. Sequence and structural similarity further allowed us to ascertain that minigluzincins are very similar to the catalytic domains of integral membrane MPs of the MEROPS database families M48 and M56, such as FACE1, HtpX, Oma1, and BlaR1/MecR1, which are provided with trans-membrane helices flanking or inserted into a minigluzincin-like catalytic domain. In a time where structural biochemistry of integral-membrane proteins in general still faces formidable challenges, the minigluzincin soluble minimal scaffold may contribute to our understanding of the working mechanisms of these membrane MPs and to the design of novel inhibitors through structure-aided rational drug design approaches.
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Affiliation(s)
- Mar López-Pelegrín
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona
| | - Núria Cerdà-Costa
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona
| | - Francisco Martínez-Jiménez
- the Genome Biology Group, Centre Nacional d'Anàlisi Genòmic, c/Baldiri Reixac, 4, 08028 Barcelona,; the Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation, c/Dr. Aiguader, 88, 08003 Barcelona
| | - Anna Cintas-Pedrola
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona
| | - Albert Canals
- the Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas and Institute for Research in Biomedicine, c/Baldiri Reixac, 10-12, 08028 Barcelona, and
| | - Juan R Peinado
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona
| | - Marc A Marti-Renom
- the Genome Biology Group, Centre Nacional d'Anàlisi Genòmic, c/Baldiri Reixac, 4, 08028 Barcelona,; the Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation, c/Dr. Aiguader, 88, 08003 Barcelona
| | - Carlos López-Otín
- the Departamento de Bioquímica y Biología Molecular and Instituto Universitario de Oncología, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Joan L Arolas
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona,.
| | - F Xavier Gomis-Rüth
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona,.
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75
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Pryor EE, Horanyi PS, Clark KM, Fedoriw N, Connelly SM, Koszelak-Rosenblum M, Zhu G, Malkowski MG, Wiener MC, Dumont ME. Structure of the integral membrane protein CAAX protease Ste24p. Science 2013; 339:1600-4. [PMID: 23539602 DOI: 10.1126/science.1232048] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Posttranslational lipidation provides critical modulation of the functions of some proteins. Isoprenoids (i.e., farnesyl or geranylgeranyl groups) are attached to cysteine residues in proteins containing C-terminal CAAX sequence motifs (where A is an aliphatic residue and X is any residue). Isoprenylation is followed by cleavage of the AAX amino acid residues and, in some cases, by additional proteolytic cuts. We determined the crystal structure of the CAAX protease Ste24p, a zinc metalloprotease catalyzing two proteolytic steps in the maturation of yeast mating pheromone a-factor. The Ste24p core structure is a ring of seven transmembrane helices enclosing a voluminous cavity containing the active site and substrate-binding groove. The cavity is accessible to the external milieu by means of gaps between splayed transmembrane helices. We hypothesize that cleavage proceeds by means of a processive mechanism of substrate insertion, translocation, and ejection.
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Affiliation(s)
- Susan Michaelis
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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