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Li Q, Lenertz M, Armstrong Z, MacRae A, Feng L, Ugrinov A, Yang Z. A Protocol to Depict the Proteolytic Processes Using a Combination of Metal-Organic Materials (MOMs), Electron Paramagnetic Resonance (EPR), and Mass Spectrometry (MS). Bio Protoc 2024; 14:e4909. [PMID: 38213322 PMCID: PMC10777052 DOI: 10.21769/bioprotoc.4909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/13/2024] Open
Abstract
Proteolysis is a critical biochemical process yet a challenging field to study experimentally due to the self-degradation of a protease and the complex, dynamic degradation steps of a substrate. Mass spectrometry (MS) is the traditional way for proteolytic studies, yet it is challenging when time-resolved, step-by-step details of the degradation process are needed. We recently found a way to resolve the cleavage site, preference/selectivity of cleavage regions, and proteolytic kinetics by combining site-directed spin labeling (SDSL) of protein substrate, time-resolved two-dimensional (2D) electron paramagnetic resonance (EPR) spectroscopy, protease immobilization via metal-organic materials (MOMs), and MS. The method has been demonstrated on a model substrate and protease, yet there is a lack of details on the practical operations to carry out our strategy. Thus, this protocol summarizes the key steps and considerations when carrying out the EPR/MS study on proteolytic processes, which can be generalized to study other protein/polypeptide substrates in proteolysis. Details for the experimental operation and cautions of each step are reported with figures illustrating the concepts. This protocol provides an effective approach to understanding the proteolytic process with the advantages of offering time-resolved, residue-level resolution of structural basis underlying the process. Such information is important for revealing the cleavage site and proteolytic mechanisms of unknown proteases. The advantage of EPR, probing the target substrate regardless of the complexities caused by the proteases and their self-degradation, offers a practically effective, rapid, and easy-to-operate approach to studying proteolysis. Key features • Combining protease immobilization, EPR, spin labeling, and MS experimental methods allows for the analysis of proteolysis process in real time. • Reveals cleavage site, kinetics of product generation, and preference of cleavage regions via time-resolved SDSL-EPR. • MS confirms EPR findings and helps depict the sequences and populations of the cleaved segments in real time. • The demonstrated method can be generalized to other proteins or polypeptide substrates upon proteolysis by other proteases.
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Affiliation(s)
- Qiaobin Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Mary Lenertz
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Zoe Armstrong
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Austin MacRae
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Li Feng
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
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2
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Li Q, Armstrong Z, MacRae A, Ugrinov A, Feng L, Chen B, Huang Y, Li H, Pan Y, Yang Z. Metal-Organic Materials (MOMs) Enhance Proteolytic Selectivity, Efficiency, and Reusability of Trypsin: A Time-Resolved Study on Proteolysis. ACS APPLIED MATERIALS & INTERFACES 2023; 15:8927-8936. [PMID: 36757369 DOI: 10.1021/acsami.2c19873] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Proteases are involved in essential biological functions in nature and have become drug targets recently. In spite of the promising progress, two challenges, (i) the intrinsic instability and (ii) the difficulty in monitoring the catalytic process in real time, still hinder the further understanding and engineering of protease functionalities. These challenges are caused by the lack of proper materials/approaches to stabilize proteases and monitor proteolytic products (truncated polypeptides) in real time in a highly heterogeneous reaction mixture. This work combines metal-organic materials (MOMs), site-directed spin labeling-electron paramagnetic resonance (SDSL-EPR) spectroscopy, and mass spectrometry (MS) to overcome both barriers. A model protease, trypsin, which cleaves the peptide bonds at lysine or arginine residues, was immobilized on a Ca-MOM via aqueous-phase, one-pot cocrystallization, which allows for trypsin protection and ease of separation from its proteolytic products. Time-resolved EPR and MS were employed to monitor the populations, rotational motion, and sequences of the cleaved peptide truncations of a model protein substrate as the reaction proceeded. Our data suggest a significant (at least 5-10 times) enhancement in the catalytic efficiency (kcat/km) of trypsin@Ca-MOM and excellent reusability as compared to free trypsin in solution. Surprisingly, entrapping trypsin in Ca-MOMs results in cleavage site/region selectivity against the protein substrate, as compared to the near nonselective cleavage of all lysine and arginine residues of the substrate in solution. Remarkably, immobilizing trypsin allows for the separation and, thus, MS study on the sequences of truncated peptides in real time, leading to a time-resolved "movie" of trypsin proteolysis. This work demonstrates the use of MOMs and cocrystallization to enhance the selectivity, catalytic efficiency, and stability of trypsin, suggesting the possibility of tuning the catalytic performance of a general protease using MOMs.
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Affiliation(s)
- Qiaobin Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Zoe Armstrong
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Austin MacRae
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Li Feng
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Bingcan Chen
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Ying Huang
- Department of Civil, Construction, and Environmental Engineering, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Hui Li
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Yanxiong Pan
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Changchun 130022, China
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
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3
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Asadi M, Oanca G, Warshel A. Effect of Environmental Factors on the Catalytic Activity of Intramembrane Serine Protease. J Am Chem Soc 2022; 144:1251-1257. [PMID: 35023734 PMCID: PMC10349665 DOI: 10.1021/jacs.1c10494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The cleavage of protein inside cell membranes regulates pathological pathways and is a subject of major interest. Thus, the nature of the coupling between the physical environment and the function of such proteins has recently attracted significant experimental and theoretical efforts. However, it is difficult to determine the nature of this coupling uniquely by experimental and theoretical studies unless one can separate the chemical and the environmental factors. This work describes calculations of the activation barriers of the intramembrane rhomboid protease in neutral and charged lipid bilayers and in detergent micelle, trying to explore the environmental effect. The calculations of the chemical barrier are done using the empirical valence bond (EVB) method. Additionally, the renormalization method captures the energetics and dynamical effects of the conformational change. The simulations indicate that the physical environment around the rhomboid protease is not a major factor in changing the chemical catalysis and that the conformational and substrate dynamics do not exhibit long-time coupling. General issues about the action of membrane-embedded enzymes are also considered.
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Affiliation(s)
- Mojgan Asadi
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Gabriel Oanca
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
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4
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Brucella abortus Encodes an Active Rhomboid Protease: Proteome Response after Rhomboid Gene Deletion. Microorganisms 2022; 10:microorganisms10010114. [PMID: 35056563 PMCID: PMC8778405 DOI: 10.3390/microorganisms10010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 01/18/2023] Open
Abstract
Rhomboids are intramembrane serine proteases highly conserved in the three domains of life. Their key roles in eukaryotes are well understood but their contribution to bacterial physiology is still poorly characterized. Here we demonstrate that Brucella abortus, the etiological agent of the zoonosis called brucellosis, encodes an active rhomboid protease capable of cleaving model heterologous substrates like Drosophila melanogaster Gurken and Providencia stuartii TatA. To address the impact of rhomboid deletion on B. abortus physiology, the proteomes of mutant and parental strains were compared by shotgun proteomics. About 50% of the B. abortus predicted proteome was identified by quantitative proteomics under two experimental conditions and 108 differentially represented proteins were detected. Membrane associated proteins that showed variations in concentration in the mutant were considered as potential rhomboid targets. This class included nitric oxide reductase subunit C NorC (Q2YJT6) and periplasmic protein LptC involved in LPS transport to the outer membrane (Q2YP16). Differences in secretory proteins were also addressed. Differentially represented proteins included a putative lytic murein transglycosylase (Q2YIT4), nitrous-oxide reductase NosZ (Q2YJW2) and high oxygen affinity Cbb3-type cytochrome c oxidase subunit (Q2YM85). Deletion of rhomboid had no obvious effect in B. abortus virulence. However, rhomboid overexpression had a negative impact on growth under static conditions, suggesting an effect on denitrification enzymes and/or high oxygen affinity cytochrome c oxidase required for growth in low oxygen tension conditions.
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5
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Parsons WH, Rutland NT, Crainic JA, Cardozo JM, Chow AS, Andrews CL, Sheehan BK. Development of succinimide-based inhibitors for the mitochondrial rhomboid protease PARL. Bioorg Med Chem Lett 2021; 49:128290. [PMID: 34311087 DOI: 10.1016/j.bmcl.2021.128290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 01/26/2023]
Abstract
While the biochemistry of rhomboid proteases has been extensively studied since their discovery two decades ago, efforts to define the physiological roles of these enzymes are ongoing and would benefit from chemical probes that can be used to manipulate the functions of these proteins in their native settings. Here, we describe the use of activity-based protein profiling (ABPP) technology to conduct a targeted screen for small-molecule inhibitors of the mitochondrial rhomboid protease PARL, which plays a critical role in regulating mitophagy and cell death. We synthesized a series of succinimide-containing sulfonyl esters and sulfonamides and discovered that these compounds serve as inhibitors of PARL with the most potent sulfonamides having submicromolar affinity for the enzyme. A counterscreen against the bacterial rhomboid protease GlpG demonstrates that several of these compounds display selectivity for PARL over GlpG by as much as two orders of magnitude. Both the sulfonyl ester and sulfonamide scaffolds exhibit reversible binding and are able to engage PARL in mammalian cells. Collectively, our findings provide encouraging precedent for the development of PARL-selective inhibitors and establish N-[(arylsulfonyl)oxy]succinimides and N-arylsulfonylsuccinimides as new molecular scaffolds for inhibiting members of the rhomboid protease family.
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Affiliation(s)
- William H Parsons
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States.
| | - Nicholas T Rutland
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Jennifer A Crainic
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Joaquin M Cardozo
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Alyssa S Chow
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Charlotte L Andrews
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Brendan K Sheehan
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
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6
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Van Kersavond T, Konopatzki R, van der Plassche MAT, Yang J, Verhelst SHL. Rapid synthesis of internal peptidyl α-ketoamides by on resin oxidation for the construction of rhomboid protease inhibitors. RSC Adv 2021; 11:4196-4199. [PMID: 35424368 PMCID: PMC8694341 DOI: 10.1039/d0ra10614c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/01/2021] [Accepted: 01/08/2021] [Indexed: 11/21/2022] Open
Abstract
Rhomboid proteases are intramembrane serine proteases, which are involved in a wide variety of biological processes and have been implied in various human diseases. Recently, peptidyl α-ketoamides have been reported as rhomboid inhibitors with high potency and selectivity – owing to their interaction with both the primed and non-primed site of the target protease. However, their synthesis has been performed by solution phase chemistry. Here, we report a solid phase strategy towards ketoamides as rhomboid protease inhibitors, allowing rapid synthesis and optimization. We found that the primed site binding part of inhibitors is crucial for potency. Rhomboid intramembrane serine proteases are involved in various biological processes. A solid phase synthesis of internal α-ketoamides reported here shows that primed site elements are crucial for rhomboid protease inhibition.![]()
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Affiliation(s)
| | | | | | - Jian Yang
- KU Leuven
- Department of Cellular and Molecular Medicine
- Laboratory of Chemical Biology
- 3000 Leuven
- Belgium
| | - Steven H. L. Verhelst
- Leibniz Institute for Analytical Sciences ISAS
- 44227 Dortmund
- Germany
- KU Leuven
- Department of Cellular and Molecular Medicine
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7
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Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme. Proc Natl Acad Sci U S A 2020; 117:22146-22156. [PMID: 32848056 DOI: 10.1073/pnas.1917770117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Packing interaction is a critical driving force in the folding of helical membrane proteins. Despite the importance, packing defects (i.e., cavities including voids, pockets, and pores) are prevalent in membrane-integral enzymes, channels, transporters, and receptors, playing essential roles in function. Then, a question arises regarding how the two competing requirements, packing for stability vs. cavities for function, are reconciled in membrane protein structures. Here, using the intramembrane protease GlpG of Escherichia coli as a model and cavity-filling mutation as a probe, we tested the impacts of native cavities on the thermodynamic stability and function of a membrane protein. We find several stabilizing mutations which induce substantial activity reduction without distorting the active site. Notably, these mutations are all mapped onto the regions of conformational flexibility and functional importance, indicating that the cavities facilitate functional movement of GlpG while compromising the stability. Experiment and molecular dynamics simulation suggest that the stabilization is induced by the coupling between enhanced protein packing and weakly unfavorable lipid desolvation, or solely by favorable lipid solvation on the cavities. Our result suggests that, stabilized by the relatively weak interactions with lipids, cavities are accommodated in membrane proteins without severe energetic cost, which, in turn, serve as a platform to fine-tune the balance between stability and flexibility for optimal activity.
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8
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Liu G, Beaton SE, Grieve AG, Evans R, Rogers M, Strisovsky K, Armstrong FA, Freeman M, Exley RM, Tang CM. Bacterial rhomboid proteases mediate quality control of orphan membrane proteins. EMBO J 2020; 39:e102922. [PMID: 32337752 PMCID: PMC7232013 DOI: 10.15252/embj.2019102922] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023] Open
Abstract
Although multiprotein membrane complexes play crucial roles in bacterial physiology and virulence, the mechanisms governing their quality control remain incompletely understood. In particular, it is not known how unincorporated, orphan components of protein complexes are recognised and eliminated from membranes. Rhomboids, the most widespread and largest superfamily of intramembrane proteases, are known to play key roles in eukaryotes. In contrast, the function of prokaryotic rhomboids has remained enigmatic. Here, we show that the Shigella sonnei rhomboid proteases GlpG and the newly identified Rhom7 are involved in membrane protein quality control by specifically targeting components of respiratory complexes, with the metastable transmembrane domains (TMDs) of rhomboid substrates protected when they are incorporated into a functional complex. Initial cleavage by GlpG or Rhom7 allows subsequent degradation of the orphan substrate. Given the occurrence of this strategy in an evolutionary ancient organism and the presence of rhomboids in all domains of life, it is likely that this form of quality control also mediates critical events in eukaryotes and protects cells from the damaging effects of orphan proteins.
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Affiliation(s)
- Guangyu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Stephen E Beaton
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Adam G Grieve
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rhiannon Evans
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Miranda Rogers
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Praha 6, Czech Republic
| | | | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rachel M Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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9
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Cho S, Baker RP, Ji M, Urban S. Ten catalytic snapshots of rhomboid intramembrane proteolysis from gate opening to peptide release. Nat Struct Mol Biol 2019; 26:910-918. [PMID: 31570873 PMCID: PMC6858540 DOI: 10.1038/s41594-019-0296-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/09/2019] [Indexed: 12/04/2022]
Abstract
Protein cleavage inside the cell membrane triggers various patho-physiological signaling pathways, but the mechanism of catalysis is poorly understood. We solved ten structures of the Escherichia coli rhomboid protease in a bicelle membrane undergoing time-resolved steps that encompass the entire proteolytic reaction on a transmembrane substrate and an aldehyde inhibitor. Extensive gate opening accompanied substrate, but not inhibitor, binding, revealing that substrates and inhibitors take different paths to the active site. Catalysis unexpectedly commenced with, and was guided through subsequent catalytic steps by, motions of an extracellular loop, with local contributions from active site residues. We even captured the elusive tetrahedral intermediate that is uncleaved but covalently attached to the catalytic serine, around which the substrate was forced to bend dramatically. This unexpectedly stable intermediate indicates rhomboid catalysis uses an unprecedented reaction coordinate that may involve mechanically stressing the peptide bond, and could be selectively targeted by inhibitors.
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Affiliation(s)
- Sangwoo Cho
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rosanna P Baker
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ming Ji
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Siniša Urban
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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10
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Paschkowsky S, Hsiao JM, Young JC, Munter LM. The discovery of proteases and intramembrane proteolysis. Biochem Cell Biol 2019; 97:265-269. [DOI: 10.1139/bcb-2018-0186] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Sandra Paschkowsky
- Department of Pharmacology & Therapeutics, McGill University, Bellini Life Sciences Complex, 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
| | - Jacqueline Melissa Hsiao
- Department of Biochemistry, McGill University, McIntyre Building, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Jason C. Young
- Department of Biochemistry, McGill University, McIntyre Building, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Lisa Marie Munter
- Department of Pharmacology & Therapeutics, McGill University, Bellini Life Sciences Complex, 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
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11
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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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12
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Arutyunova E, Jiang Z, Yang J, Kulepa AN, Young HS, Verhelst S, O’Donoghue AJ, Lemieux MJ. An internally quenched peptide as a new model substrate for rhomboid intramembrane proteases. Biol Chem 2018; 399:1389-1397. [DOI: 10.1515/hsz-2018-0255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/09/2018] [Indexed: 12/31/2022]
Abstract
AbstractRhomboids are ubiquitous intramembrane serine proteases that cleave transmembrane substrates. Their functions include growth factor signaling, mitochondrial homeostasis, and parasite invasion. A recent study revealed that theEscherichia colirhomboid protease EcGlpG is essential for its extraintestinal pathogenic colonization within the gut. Crystal structures of EcGlpG and theHaemophilus influenzaerhomboid protease HiGlpG have deciphered an active site that is buried within the lipid bilayer but exposed to the aqueous environment via a cavity at the periplasmic face. A lack of physiological transmembrane substrates has hampered progression for understanding their catalytic mechanism and screening inhibitor libraries. To identify a soluble substrate for use in the study of rhomboid proteases, an array of internally quenched peptides were assayed with HiGlpG, EcGlpG and PsAarA fromProvidencia stuartti. One substrate was identified that was cleaved by all three rhomboid proteases, with HiGlpG having the highest cleavage efficiency. Mass spectrometry analysis determined that all enzymes hydrolyze this substrate between norvaline and tryptophan. Kinetic analysis in both detergent and bicellular systems demonstrated that this substrate can be cleaved in solution and in the lipid environment. The substrate was subsequently used to screen a panel of benzoxazin-4-one inhibitors to validate its use in inhibitor discovery.
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13
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Gaffney KA, Hong H. The rhomboid protease GlpG has weak interaction energies in its active site hydrogen bond network. J Gen Physiol 2018; 151:282-291. [PMID: 30420443 PMCID: PMC6400518 DOI: 10.1085/jgp.201812047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/25/2018] [Indexed: 01/24/2023] Open
Abstract
Rhomboid proteases are membrane-integrated enzymes that hydrolyze peptide bonds in the transmembrane domains of protein substrates. Gaffney and Hong experimentally determine interaction energies between active site residues to reveal weak coupling, which may explain the slow proteolysis mediated by GlpG. Intramembrane rhomboid proteases are of particular interest because of their function to hydrolyze a peptide bond of a substrate buried in the membrane. Crystal structures of the bacterial rhomboid protease GlpG have revealed a catalytic dyad (Ser201-His254) and oxyanion hole (His150/Asn154/the backbone amide of Ser201) surrounded by the protein matrix and contacting a narrow water channel. Although multiple crystal structures have been solved, the catalytic mechanism of GlpG is not completely understood. Because it is a serine protease, hydrogen bonding interactions between the active site residues are thought to play a critical role in the catalytic cycle. Here, we dissect the interaction energies among the active site residues His254, Ser201, and Asn154 of Escherichia coli GlpG, which form a hydrogen bonding network. We combine double mutant cycle analysis with stability measurements using steric trapping. In mild detergent, the active site residues are weakly coupled with interaction energies (ΔΔGInter) of ‒1.4 kcal/mol between His254 and Ser201 and ‒0.2 kcal/mol between Ser201 and Asn154. Further, by analyzing the propagation of single mutations of the active site residues, we find that these residues are important not only for function but also for the folding cooperativity of GlpG. The weak interaction between Ser and His in the catalytic dyad may partly explain the unusually slow proteolysis by GlpG compared with other canonical serine proteases. Our result suggests that the weak hydrogen bonds in the active site are sufficient to carry out the proteolytic function of rhomboid proteases.
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Affiliation(s)
- Kristen A Gaffney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
| | - Heedeok Hong
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI .,Department of Chemistry, Michigan State University, East Lansing, MI
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14
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Yang J, Barniol-Xicota M, Nguyen MT, Ticha A, Strisovsky K, Verhelst SH. Benzoxazin-4-ones as novel, easily accessible inhibitors for rhomboid proteases. Bioorg Med Chem Lett 2018; 28:1423-1427. [DOI: 10.1016/j.bmcl.2017.12.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 12/13/2022]
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15
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Goel P, Jumpertz T, Tichá A, Ogorek I, Mikles DC, Hubalek M, Pietrzik CU, Strisovsky K, Schmidt B, Weggen S. Discovery and validation of 2-styryl substituted benzoxazin-4-ones as a novel scaffold for rhomboid protease inhibitors. Bioorg Med Chem Lett 2018; 28:1417-1422. [DOI: 10.1016/j.bmcl.2018.02.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/05/2018] [Accepted: 02/08/2018] [Indexed: 11/26/2022]
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16
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Goel P, Jumpertz T, Mikles DC, Tichá A, Nguyen MTN, Verhelst S, Hubalek M, Johnson DC, Bachovchin DA, Ogorek I, Pietrzik CU, Strisovsky K, Schmidt B, Weggen S. Discovery and Biological Evaluation of Potent and Selective N-Methylene Saccharin-Derived Inhibitors for Rhomboid Intramembrane Proteases. Biochemistry 2017; 56:6713-6725. [PMID: 29185711 DOI: 10.1021/acs.biochem.7b01066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rhomboids are intramembrane serine proteases and belong to the group of structurally and biochemically most comprehensively characterized membrane proteins. They are highly conserved and ubiquitously distributed in all kingdoms of life and function in a wide range of biological processes, including epidermal growth factor signaling, mitochondrial dynamics, and apoptosis. Importantly, rhomboids have been associated with multiple diseases, including Parkinson's disease, type 2 diabetes, and malaria. However, despite a thorough understanding of many structural and functional aspects of rhomboids, potent and selective inhibitors of these intramembrane proteases are still not available. In this study, we describe the computer-based rational design, chemical synthesis, and biological evaluation of novel N-methylene saccharin-based rhomboid protease inhibitors. Saccharin inhibitors displayed inhibitory potency in the submicromolar range, effectiveness against rhomboids both in vitro and in live Escherichia coli cells, and substantially improved selectivity against human serine hydrolases compared to those of previously known rhomboid inhibitors. Consequently, N-methylene saccharins are promising new templates for the development of rhomboid inhibitors, providing novel tools for probing rhomboid functions in physiology and disease.
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Affiliation(s)
- Parul Goel
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany.,Clemens Schoepf Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt , Alarich-Weiss-Strasse 4-8, 64287 Darmstadt, Germany
| | - Thorsten Jumpertz
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - David C Mikles
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Anežka Tichá
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Minh T N Nguyen
- Chemical Proteomics Group, Leibnitz Institute for Analytical Sciences (ISAS) e.V. , Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Steven Verhelst
- Chemical Proteomics Group, Leibnitz Institute for Analytical Sciences (ISAS) e.V. , Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, University of Leuven , Herestraat 49, Box 802, 3000 Leuven, Belgium
| | - Martin Hubalek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Darren C Johnson
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center , 1275 York Avenue, Box 428, New York, New York 10065, United States
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center , 1275 York Avenue, Box 428, New York, New York 10065, United States
| | - Isabella Ogorek
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - Claus U Pietrzik
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz , Duesbergweg 6, 55128 Mainz, Germany
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Boris Schmidt
- Clemens Schoepf Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt , Alarich-Weiss-Strasse 4-8, 64287 Darmstadt, Germany
| | - Sascha Weggen
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany
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17
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Verhelst SHL. Intramembrane proteases as drug targets. FEBS J 2017; 284:1489-1502. [PMID: 27889944 DOI: 10.1111/febs.13979] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/14/2016] [Accepted: 11/24/2016] [Indexed: 01/04/2023]
Abstract
Proteases are considered attractive drug targets. Various drugs targeting classical, soluble proteases have been approved for treatment of human disease. Intramembrane proteases (IMPs) are a more recently discovered group of proteolytic enzymes. They are embedded in lipid bilayers and their active sites are located in the plane of a membrane. All four mechanistic families of IMPs have been linked to disease, but currently, no drugs against IMPs have entered the market. In this review, I will outline the function of IMPs with a focus on the ones involved in human disease, which includes Alzheimer's disease, cancer, and infectious diseases by microorganisms. Inhibitors of IMPs are known for all mechanistic classes, but are not yet very potent or selective - aside from those targeting γ-secretase. I will here describe the different features of IMP inhibitors and discuss a list of issues that need attention in the near future in order to improve the drug development for IMPs.
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Affiliation(s)
- Steven H L Verhelst
- Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Belgium.,AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, Dortmund, Germany
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18
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Cordier B, Lemberg M. Probing the Activity of Eukaryotic Rhomboid Proteases In Vitro. Methods Enzymol 2017; 584:99-126. [DOI: 10.1016/bs.mie.2016.09.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Abstract
Rhomboids are ubiquitous intramembrane serine proteases that are involved in various signaling pathways. This fascinating class of proteases harbors an active site buried within the lipid milieu. High-resolution structures of the Escherichia coli rhomboid GlpG with various inhibitors revealed the catalytic mechanism for rhomboid-mediated proteolysis; however, a quantitative characterization was lacking. Assessing an enzyme's catalytic parameters is important for understanding the details of its proteolytic reaction and regulatory mechanisms. To assay rhomboid protease activity, many challenges exist such as the lipid environment and lack of known substrates. Here, we summarize various enzymatic assays developed over the last decade to study rhomboid protease activity. We present detailed protocols for gel-shift and FRET-based assays, and calculation of KM and Vmax to measure catalytic parameters, using detergent solubilized rhomboids with TatA, the only known substrate for bacterial rhomboids, and the model substrate fluorescently labeled casein.
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20
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Abstract
Intramembrane serine proteases of the rhomboid family are widespread, and their gradually uncovered functions in different organisms already suggest medical relevance for infectious diseases and cancer. However, selective inhibitors that could serve as research tools for rhomboids, for validation of their disease relevance, or as templates for drug development are lacking. Here I summarize the current knowledge about rhomboid protease mechanism and specificity, overview the currently used inhibitors, and conclude by proposing avenues for future development of rhomboid protease inhibitors.
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Affiliation(s)
- K Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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21
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Abstract
Intramembrane proteases catalyze peptide bond hydrolysis in the lipid bilayer and play a key role in numerous cellular processes. These integral membrane enzymes consist of four classes: site-2 protease (S2P), rhomboid serine protease, Rce1-type glutamyl protease, and aspartyl protease exemplified by presenilin and signal peptide peptidase (SPP). Structural elucidation of these enzymes is important for mechanistic understanding of their functions, particularly their roles in cell signaling and debilitating diseases such as Parkinson's disease and Alzheimer's disease. In the past decade, rigorous effort has led to determination of the crystal structures of S2P from archaebacterium, rhomboid serine protease from E. coli (GlpG), and presenilin/SPP from archaebacterium (PSH). A novel method has been developed to express well-behaved human γ-secretase, which facilitated its structure determination by cryoelectron microscopy (cryo-EM). In this chapter, we will discuss the expression and purification of intramembrane proteases including human γ-secretase and describe the enzymatic activity assays for these intramembrane proteases.
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22
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Arutyunova E, Smithers CC, Corradi V, Espiritu AC, Young HS, Tieleman DP, Lemieux MJ. Probing catalytic rate enhancement during intramembrane proteolysis. Biol Chem 2016; 397:907-19. [DOI: 10.1515/hsz-2016-0124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/06/2016] [Indexed: 11/15/2022]
Abstract
Abstract
Rhomboids are ubiquitous intramembrane serine proteases involved in various signaling pathways. While the high-resolution structures of the Escherichia coli rhomboid GlpG with various inhibitors revealed an active site comprised of a serine-histidine dyad and an extensive oxyanion hole, the molecular details of rhomboid catalysis were unclear because substrates are unknown for most of the family members. Here we used the only known physiological pair of AarA rhomboid with its psTatA substrate to decipher the contribution of catalytically important residues to the reaction rate enhancement. An MD-refined homology model of AarA was used to identify residues important for catalysis. We demonstrated that the AarA active site geometry is strict and intolerant to alterations. We probed the roles of H83 and N87 oxyanion hole residues and determined that substitution of H83 either abolished AarA activity or reduced the transition state stabilization energy (ΔΔG‡) by 3.1 kcal/mol; substitution of N87 decreased ΔΔG‡ by 1.6–3.9 kcal/mol. Substitution M154, a residue conserved in most rhomboids that stabilizes the catalytic general base, to tyrosine, provided insight into the mechanism of nucleophile generation for the catalytic dyad. This study provides a quantitative evaluation of the role of several residues important for hydrolytic efficiency and oxyanion stabilization during intramembrane proteolysis.
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23
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Paschkowsky S, Hamzé M, Oestereich F, Munter LM. Alternative Processing of the Amyloid Precursor Protein Family by Rhomboid Protease RHBDL4. J Biol Chem 2016; 291:21903-21912. [PMID: 27563067 DOI: 10.1074/jbc.m116.753582] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 12/13/2022] Open
Abstract
The amyloid precursor protein (APP) is an ubiquitously expressed cell surface protein and a key molecule in the etiology of Alzheimer disease. Amyloidogenic processing of APP through secretases leads to the generation of toxic amyloid β (Aβ) peptides, which are regarded as the molecular cause of the disease. We report here an alternative processing pathway of APP through the mammalian intramembrane rhomboid protease RHBDL4. RHBDL4 efficiently cleaves APP inside the cell, thus bypassing APP from amyloidogenic processing, leading to reduced Aβ levels. RHBDL4 cleaves APP multiple times in the ectodomain, resulting in several N- and C-terminal fragments that are not further degraded by classical APP secretases. Knockdown of endogenous RHBDL4 results in decreased levels of C-terminal fragments derived from endogenous APP. Similarly, we found the APP family members APLP1 and APLP2 to be substrates of RHBDL4. We conclude that RHBDL4-mediated APP processing provides insight into APP and rhomboid physiology and qualifies for further investigations to elaborate its impact on Alzheimer disease pathology.
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Affiliation(s)
| | - Mehdi Hamzé
- From the Department of Pharmacology and Therapeutics and
| | - Felix Oestereich
- From the Department of Pharmacology and Therapeutics and Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3G 0B1, Canada
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24
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Strisovsky K. Rhomboid protease inhibitors: Emerging tools and future therapeutics. Semin Cell Dev Biol 2016; 60:52-62. [PMID: 27567709 DOI: 10.1016/j.semcdb.2016.08.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/16/2016] [Accepted: 08/24/2016] [Indexed: 02/01/2023]
Abstract
Rhomboid-family intramembrane serine proteases are evolutionarily widespread. Their functions in different organisms are gradually being uncovered and already suggest medical relevance for infectious diseases and cancer. In contrast to these advances, selective inhibitors that could serve as efficient tools for investigation of physiological functions of rhomboids, validation of their disease relevance or as templates for drug development are lacking. In this review I extract what is known about rhomboid protease mechanism and specificity, examine the currently used inhibitors, their mechanism of action and limitations, and conclude by proposing routes for future development of rhomboid protease inhibitors.
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Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic.
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25
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26
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Cho S, Dickey SW, Urban S. Crystal Structures and Inhibition Kinetics Reveal a Two-Stage Catalytic Mechanism with Drug Design Implications for Rhomboid Proteolysis. Mol Cell 2016; 61:329-340. [PMID: 26805573 DOI: 10.1016/j.molcel.2015.12.022] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 11/20/2015] [Accepted: 12/15/2015] [Indexed: 12/28/2022]
Abstract
Intramembrane proteases signal by releasing proteins from the membrane, but despite their importance, their enzymatic mechanisms remain obscure. We probed rhomboid proteases with reversible, mechanism-based inhibitors that allow precise kinetic analysis and faithfully mimic the transition state structurally. Unexpectedly, inhibition by peptide aldehydes is non-competitive, revealing that in the Michaelis complex, substrate does not contact the catalytic center. Structural analysis in a membrane revealed that all extracellular loops of rhomboid make stabilizing interactions with substrate, but mainly through backbone interactions, explaining rhomboid's broad sequence selectivity. At the catalytic site, the tetrahedral intermediate lies covalently attached to the catalytic serine alone, with the oxyanion stabilized by unusual tripartite interactions with the side chains of H150, N154, and the backbone of S201. We also visualized unexpected substrate-enzyme interactions at the non-essential P2/P3 residues. These "extra" interactions foster potent rhomboid inhibition in living cells, thereby opening avenues for rational design of selective rhomboid inhibitors.
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Affiliation(s)
- Sangwoo Cho
- Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, Maryland, USA, 21205
| | - Seth W Dickey
- Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, Maryland, USA, 21205
| | - Siniša Urban
- Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, Maryland, USA, 21205
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27
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Nguyen MTN, Kersavond TV, Verhelst SHL. Chemical Tools for the Study of Intramembrane Proteases. ACS Chem Biol 2015; 10:2423-34. [PMID: 26473325 DOI: 10.1021/acschembio.5b00693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intramembrane proteases (IMPs) reside inside lipid bilayers and perform peptide hydrolysis in transmembrane or juxtamembrane regions of their substrates. Many IMPs are involved in crucial regulatory pathways and human diseases, including Alzheimer's disease, Parkinson's disease, and diabetes. In the past, chemical tools have been instrumental in the study of soluble proteases, enabling biochemical and biomedical research in complex environments such as tissue lysates or living cells. However, IMPs place special challenges on probe design and applications, and progress has been much slower than for soluble proteases. In this review, we will give an overview of the available chemical tools for IMPs, including activity-based probes, affinity-based probes, and synthetic substrates. We will discuss how these have been used to increase our structural and functional understanding of this fascinating group of enzymes, and how they might be applied to address future questions and challenges.
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Affiliation(s)
- Minh T. N. Nguyen
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Tim Van Kersavond
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Steven H. L. Verhelst
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
- KU Leuven − University of Leuven, Department
of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49 Box 802, 3000 Leuven, Belgium
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28
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Wolf EV, Zeissler A, Verhelst SHL. Inhibitor Fingerprinting of Rhomboid Proteases by Activity-Based Protein Profiling Reveals Inhibitor Selectivity and Rhomboid Autoprocessing. ACS Chem Biol 2015. [PMID: 26218717 DOI: 10.1021/acschembio.5b00514] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rhomboid proteases were discovered almost 15 years ago and are structurally the best characterized intramembrane proteases. Apart from the general serine protease inhibitor 3,4-dichloro-isocoumarin (DCI) and a few crystal structures of the Escherichia coli rhomboid GlpG with other inhibitors, there is surprisingly little information about inhibitors of rhomboids from other species, probably because of a lack of general methods to measure inhibition against different rhomboid species. We here present activity-based protein profiling (ABPP) as a general method to screen rhomboids for their activity and inhibition. Using ABPP, we compare the inhibitory capacity of 50 small molecules against 13 different rhomboids. We find one new pan rhomboid inhibitor and several inhibitors that display selectivity. We also demonstrate that inhibition profile and sequence similarity of rhomboids are not related, which suggests that related rhomboids may be selectively inhibited. Finally, by making use of the here discovered inhibitors, we were able to show that two bacterial rhomboids autoprocess themselves in their N-terminal part.
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Affiliation(s)
- Eliane V. Wolf
- Chair
for Chemistry of Biopolymers, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Annett Zeissler
- Chair
for Chemistry of Biopolymers, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Steven H. L. Verhelst
- Chair
for Chemistry of Biopolymers, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
- Laboratory
of Chemical Biology, Department of Cellular and Molecular Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
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29
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Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, Bondar AN. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. J Membr Biol 2015; 248:611-40. [PMID: 26063070 PMCID: PMC4515176 DOI: 10.1007/s00232-015-9802-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/26/2015] [Indexed: 01/05/2023]
Abstract
Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.
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Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Toby W. Allen
- School of Applied Sciences & Health Innovations Research Institute, RMIT University, GPO Box 2476, Melbourne, Vic, 3001, Australia; and Department of Chemistry, University of California, Davis. Davis, CA 95616, USA
| | - Ioan Andricioaei
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Bruno Antonny
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Daniel Baum
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Grace Brannigan
- Center for Computational and Integrative Biology and Department of Physics, Rutgers University-Camden, Camden, NJ, USA
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Lucie Delemotte
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Coral del Val
- Department of Artificial Intelligence, University of Granada, E-18071 Granada, Spain
| | - Ran Friedman
- Linnæus University, Department of Chemistry and Biomedical Sciences & Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
| | - Paraskevi Gkeka
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Hans-Christian Hege
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, IBPC and CNRS, Paris, France
| | - Marina A. Kasimova
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Antonios Kolocouris
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Michael L. Klein
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Syma Khalid
- Department of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - M. Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, and Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
| | - Norbert Lindow
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Mahua Roy
- Department of Chemistry, University of California, Irvine
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Mounir Tarek
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- CNRS, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
| | - Florentina Tofoleanu
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stefano Vanni
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Sinisa Urban
- Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, 725 N. Wolfe Street, 507 Preclinical Teaching Building, Baltimore, MD 21205, USA
| | - David J. Wales
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jeremy C. Smith
- Oak Ridge National Laboratory, PO BOX 2008 MS6309, Oak Ridge, TN 37831-6309, USA
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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30
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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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31
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Freeman M. The Rhomboid-Like Superfamily: Molecular Mechanisms and Biological Roles. Annu Rev Cell Dev Biol 2014; 30:235-54. [DOI: 10.1146/annurev-cellbio-100913-012944] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew Freeman
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom;
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32
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Zoll S, Stanchev S, Began J, Skerle J, Lepšík M, Peclinovská L, Majer P, Strisovsky K. Substrate binding and specificity of rhomboid intramembrane protease revealed by substrate-peptide complex structures. EMBO J 2014; 33:2408-21. [PMID: 25216680 PMCID: PMC4253528 DOI: 10.15252/embj.201489367] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The mechanisms of intramembrane proteases are incompletely understood due to the lack of structural data on substrate complexes. To gain insight into substrate binding by rhomboid proteases, we have synthesised a series of novel peptidyl-chloromethylketone (CMK) inhibitors and analysed their interactions with Escherichia coli rhomboid GlpG enzymologically and structurally. We show that peptidyl-CMKs derived from the natural rhomboid substrate TatA from bacterium Providencia stuartii bind GlpG in a substrate-like manner, and their co-crystal structures with GlpG reveal the S1 to S4 subsites of the protease. The S1 subsite is prominent and merges into the 'water retention site', suggesting intimate interplay between substrate binding, specificity and catalysis. Unexpectedly, the S4 subsite is plastically formed by residues of the L1 loop, an important but hitherto enigmatic feature of the rhomboid fold. We propose that the homologous region of members of the wider rhomboid-like protein superfamily may have similar substrate or client-protein binding function. Finally, using molecular dynamics, we generate a model of the Michaelis complex of the substrate bound in the active site of GlpG.
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Affiliation(s)
- Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Stancho Stanchev
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jakub Began
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic Department of Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Skerle
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lucie Peclinovská
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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33
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Arutyunova E, Panwar P, Skiba PM, Gale N, Mak MW, Lemieux MJ. Allosteric regulation of rhomboid intramembrane proteolysis. EMBO J 2014; 33:1869-81. [PMID: 25009246 DOI: 10.15252/embj.201488149] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Proteolysis within the lipid bilayer is poorly understood, in particular the regulation of substrate cleavage. Rhomboids are a family of ubiquitous intramembrane serine proteases that harbour a buried active site and are known to cleave transmembrane substrates with broad specificity. In vitro gel and Förster resonance energy transfer (FRET)-based kinetic assays were developed to analyse cleavage of the transmembrane substrate psTatA (TatA from Providencia stuartii). We demonstrate significant differences in catalytic efficiency (kcat/K0.5) values for transmembrane substrate psTatA (TatA from Providencia stuartii) cleavage for three rhomboids: AarA from P. stuartii, ecGlpG from Escherichia coli and hiGlpG from Haemophilus influenzae demonstrating that rhomboids specifically recognize this substrate. Furthermore, binding of psTatA occurs with positive cooperativity. Competitive binding studies reveal an exosite-mediated mode of substrate binding, indicating allostery plays a role in substrate catalysis. We reveal that exosite formation is dependent on the oligomeric state of rhomboids, and when dimers are dissociated, allosteric substrate activation is not observed. We present a novel mechanism for specific substrate cleavage involving several dynamic processes including positive cooperativity and homotropic allostery for this interesting class of intramembrane proteases.
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Affiliation(s)
- Elena Arutyunova
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Pauline M Skiba
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Nicola Gale
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Michelle W Mak
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
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34
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Dickey SW, Baker RP, Cho S, Urban S. Proteolysis inside the membrane is a rate-governed reaction not driven by substrate affinity. Cell 2014; 155:1270-81. [PMID: 24315097 DOI: 10.1016/j.cell.2013.10.053] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 08/04/2013] [Accepted: 10/28/2013] [Indexed: 10/25/2022]
Abstract
Enzymatic cleavage of transmembrane anchors to release proteins from the membrane controls diverse signaling pathways and is implicated in more than a dozen diseases. How catalysis works within the viscous, water-excluding, two-dimensional membrane is unknown. We developed an inducible reconstitution system to interrogate rhomboid proteolysis quantitatively within the membrane in real time. Remarkably, rhomboid proteases displayed no physiological affinity for substrates (K(d) ~190 μM/0.1 mol%). Instead, ~10,000-fold differences in proteolytic efficiency with substrate mutants and diverse rhomboid proteases were reflected in k(cat) values alone. Analysis of gate-open mutant and solvent isotope effects revealed that substrate gating, not hydrolysis, is rate limiting. Ultimately, a single proteolytic event within the membrane normally takes minutes. Rhomboid intramembrane proteolysis is thus a slow, kinetically controlled reaction not driven by transmembrane protein-protein affinity. These properties are unlike those of other studied proteases or membrane proteins but are strikingly reminiscent of one subset of DNA-repair enzymes, raising important mechanistic and drug-design implications.
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Affiliation(s)
- Seth W Dickey
- Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA
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35
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Kroos L, Akiyama Y. Biochemical and structural insights into intramembrane metalloprotease mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2873-85. [PMID: 24099006 DOI: 10.1016/j.bbamem.2013.03.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 03/07/2013] [Accepted: 03/27/2013] [Indexed: 01/11/2023]
Abstract
Intramembrane metalloproteases are nearly ubiquitous in living organisms and they function in diverse processes ranging from cholesterol homeostasis and the unfolded protein response in humans to sporulation, stress responses, and virulence of bacteria. Understanding how these enzymes function in membranes is a challenge of fundamental interest with potential applications if modulators can be devised. Progress is described toward a mechanistic understanding, based primarily on molecular genetic and biochemical studies of human S2P and bacterial SpoIVFB and RseP, and on the structure of the membrane domain of an archaeal enzyme. Conserved features of the enzymes appear to include transmembrane helices and loops around the active site zinc ion, which may be near the membrane surface. Extramembrane domains such as PDZ (PSD-95, DLG, ZO-1) or CBS (cystathionine-β-synthase) domains govern substrate access to the active site, but several different mechanisms of access and cleavage site selection can be envisioned, which might differ depending on the substrate and the enzyme. More work is needed to distinguish between these mechanisms, both for enzymes that have been relatively well-studied, and for enzymes lacking PDZ and CBS domains, which have not been studied. This article is part of a Special Issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Lee Kroos
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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36
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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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37
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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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38
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Residues in conserved loops of intramembrane metalloprotease SpoIVFB interact with residues near the cleavage site in pro-σK. J Bacteriol 2013; 195:4936-46. [PMID: 23995631 DOI: 10.1128/jb.00807-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Intramembrane metalloproteases (IMMPs) control critical biological processes by cleaving membrane-associated proteins within a transmembrane segment or at a site near the membrane surface. Phylogenetic analysis divides IMMPs into four groups. SpoIVFB is a group III IMMP that regulates Bacillus subtilis endospore formation by cleaving Pro-σ(K) and releasing the active sigma factor from a membrane. To elucidate the enzyme-substrate interaction, single-cysteine versions of catalytically inactive SpoIVFB and C-terminally truncated Pro-σ(K)(1-126) (which can be cleaved by active SpoIVFB) were coexpressed in Escherichia coli, and proximity was tested by disulfide cross-linking in vivo. As expected, the results provided evidence that catalytic residue Glu-44 of SpoIVFB is near the cleavage site in the substrate. Also near the cleavage site were two residues of SpoIVFB in predicted conserved loops; Pro-135 in a short loop and Val-70 in a longer loop. Pro-135 corresponds to Pro-399 of RseP, a group I IMMP, and Pro-399 was reported previously to interact with substrate near the cleavage site, suggesting a conserved interaction across IMMP subfamilies. Val-70 follows a newly recognized conserved motif, PXGG (X is a large hydrophobic residue), which is in a hydrophobic region predicted to be a membrane reentrant loop. Following the hydrophobic region is a negatively charged region that is conserved in IMMPs of groups I and III. At least two residues with a negatively charged side chain are required in this region for activity of SpoIVFB. The region exhibits other features in IMMPs of groups II and IV. Its possible roles, as well as that of the short loop, are discussed. New insights into IMMP-substrate interaction build toward understanding how IMMPs function and may facilitate manipulation of their activity.
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39
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A new class of rhomboid protease inhibitors discovered by activity-based fluorescence polarization. PLoS One 2013; 8:e72307. [PMID: 23991088 PMCID: PMC3750051 DOI: 10.1371/journal.pone.0072307] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 07/10/2013] [Indexed: 01/01/2023] Open
Abstract
Rhomboids are intramembrane serine proteases that play diverse biological roles, including some that are of potential therapeutical relevance. Up to date, rhomboid inhibitor assays are based on protein substrate cleavage. Although rhomboids have an overlapping substrate specificity, substrates cannot be used universally. To overcome the need for substrates, we developed a screening assay using fluorescence polarization activity-based protein profiling (FluoPol ABPP) that is compatible with membrane proteases. With FluoPol ABPP, we identified new inhibitors for the E. coli rhomboid GlpG. Among these was a structural class that has not yet been reported as rhomboid inhibitors: β-lactones. They form covalent and irreversible complexes with the active site serine of GlpG. The presence of alkyne handles on the β-lactones also allowed activity-based labeling. Overall, these molecules represent a new scaffold for future inhibitor and activity-based probe development, whereas the assay will allow inhibitor screening of ill-characterized membrane proteases.
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40
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Vinothkumar K, Pierrat O, Large J, Freeman M. Structure of rhomboid protease in complex with β-lactam inhibitors defines the S2' cavity. Structure 2013; 21:1051-8. [PMID: 23665170 PMCID: PMC3690538 DOI: 10.1016/j.str.2013.03.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 03/17/2013] [Accepted: 03/30/2013] [Indexed: 10/31/2022]
Abstract
Rhomboids are evolutionarily conserved serine proteases that cleave transmembrane proteins within the membrane. The increasing number of known rhomboid functions in prokaryotes and eukaryotes makes them attractive drug targets. Here, we describe structures of the Escherichia coli rhomboid GlpG in complex with β-lactam inhibitors. The inhibitors form a single bond to the catalytic serine and the carbonyl oxygen of the inhibitor faces away from the oxyanion hole. The hydrophobic N-substituent of β-lactam inhibitors points into a cavity within the enzyme, providing a structural explanation for the specificity of β-lactams on rhomboid proteases. This same cavity probably represents the S2' substrate binding site of GlpG. We suggest that the structural changes in β-lactam inhibitor binding reflect the state of the enzyme at an initial stage of substrate binding to the active site. The structural insights from these enzyme-inhibitor complexes provide a starting point for structure-based design for rhomboid inhibitors.
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Affiliation(s)
- Kutti R. Vinothkumar
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Olivier A. Pierrat
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonathan M. Large
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Matthew Freeman
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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41
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Xue Y, Ha Y. Large lateral movement of transmembrane helix S5 is not required for substrate access to the active site of rhomboid intramembrane protease. J Biol Chem 2013; 288:16645-16654. [PMID: 23609444 DOI: 10.1074/jbc.m112.438127] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Rhomboids represent an evolutionarily ancient protease family. Unlike most other proteases, they are polytopic membrane proteins and specialize in cleaving transmembrane protein substrates. The polar active site of rhomboid protease is embedded in the membrane and normally closed. For the bacterial rhomboid GlpG, it has been proposed that one of the transmembrane helices (S5) of the protease can rotate to open a lateral gate, enabling substrate to enter the protease from inside the membrane. Here, we studied the conformational change in GlpG by solving the cocrystal structure of the protease with a mechanism-based inhibitor. We also examined the lateral gating model by cross-linking S5 to a neighboring helix (S2). The crystal structure shows that inhibitor binding displaces a capping loop (L5) from the active site but causes only minor shifts in the transmembrane helices. Cross-linking S5 and S2, which not only restricts the lateral movement of S5 but also prevents substrate from passing between the two helices, does not hinder the ability of the protease to cleave a membrane protein substrate in detergent solution and in reconstituted membrane vesicles. Taken together, these data suggest that a large lateral movement of the S5 helix is not required for substrate access to the active site of rhomboid protease.
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Affiliation(s)
- Yi Xue
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520
| | - Ya Ha
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520.
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42
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Abstract
Rhomboid protease was first discovered in Drosophila. Mutation of the fly gene interfered with growth factor signaling and produced a characteristic phenotype of a pointed head skeleton. The name rhomboid has since been widely used to describe a large family of related membrane proteins that have diverse biological functions but share a common catalytic core domain composed of six membrane-spanning segments. Most rhomboid proteases cleave membrane protein substrates near the N terminus of their transmembrane domains. How these proteases function within the confines of the membrane is not completely understood. Recent progress in crystallographic analysis of the Escherichia coli rhomboid protease GlpG in complex with inhibitors has provided new insights into the catalytic mechanism of the protease and its conformational change. Improved biochemical assays have also identified a substrate sequence motif that is specifically recognized by many rhomboid proteases.
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Affiliation(s)
- Ya Ha
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, USA.
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43
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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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44
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Activity-based probes for rhomboid proteases discovered in a mass spectrometry-based assay. Proc Natl Acad Sci U S A 2013; 110:2472-7. [PMID: 23359682 DOI: 10.1073/pnas.1215076110] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rhomboid proteases are evolutionary conserved intramembrane serine proteases. Because of their emerging role in many important biological pathways, rhomboids are potential drug targets. Unfortunately, few chemical tools are available for their study. Here, we describe a mass spectrometry-based assay to measure rhomboid substrate cleavage and inhibition. We have identified isocoumarin inhibitors and developed activity-based probes for rhomboid proteases. The probes can distinguish between active and inactive rhomboids due to covalent, reversible binding of the active-site serine and stable modification of a histidine residue. Finally, the structure of an isocoumarin-based inhibitor with Escherichia coli rhomboid GlpG uncovers an unusual mode of binding at the active site and suggests that the interactions between the 3-substituent on the isocoumarin inhibitor and hydrophobic residues on the protease reflect S' subsite binding. Overall, these probes represent valuable tools for rhomboid study, and the structural insights may facilitate future inhibitor design.
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45
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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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46
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Sampathkumar P, Mak MW, Fischer-Witholt SJ, Guigard E, Kay CM, Lemieux MJ. Oligomeric state study of prokaryotic rhomboid proteases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:3090-7. [DOI: 10.1016/j.bbamem.2012.08.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 07/25/2012] [Accepted: 08/07/2012] [Indexed: 12/14/2022]
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47
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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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48
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Sherratt AR, Blais DR, Ghasriani H, Pezacki JP, Goto NK. Activity-Based Protein Profiling of the Escherichia coli GlpG Rhomboid Protein Delineates the Catalytic Core. Biochemistry 2012; 51:7794-803. [DOI: 10.1021/bi301087c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Allison R. Sherratt
- Department of Biochemistry,
Microbiology and Immunology, University of Ottawa, Health Sciences Campus, 451 Smyth Road, Ottawa, Canada K1H 8M5
| | - David R. Blais
- Steacie Institute for Molecular
Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Canada K1A 0R6
| | - Houman Ghasriani
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, Canada
K1N 6N5
| | - John Paul Pezacki
- Department of Biochemistry,
Microbiology and Immunology, University of Ottawa, Health Sciences Campus, 451 Smyth Road, Ottawa, Canada K1H 8M5
- Steacie Institute for Molecular
Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Canada K1A 0R6
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, Canada
K1N 6N5
| | - Natalie K. Goto
- Department of Biochemistry,
Microbiology and Immunology, University of Ottawa, Health Sciences Campus, 451 Smyth Road, Ottawa, Canada K1H 8M5
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, Canada
K1N 6N5
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49
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Xue Y, Chowdhury S, Liu X, Akiyama Y, Ellman J, Ha Y. Conformational change in rhomboid protease GlpG induced by inhibitor binding to its S' subsites. Biochemistry 2012; 51:3723-31. [PMID: 22515733 DOI: 10.1021/bi300368b] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhomboid protease conducts proteolysis inside the hydrophobic environment of the membrane. The conformational flexibility of the protease is essential for the enzyme mechanism, but the nature of this flexibility is not completely understood. Here we describe the crystal structure of rhomboid protease GlpG in complex with a phosphonofluoridate inhibitor, which is covalently bonded to the catalytic serine and extends into the S' side of the substrate binding cleft. Inhibitor binding causes subtle but extensive changes in the membrane protease. Many transmembrane helices tilt and shift positions, and the gap between S2 and S5 is slightly widened so that the inhibitor can bind between them. The side chain of Phe-245 from a loop (L5) that acts as a cap rotates and uncovers the opening of the substrate binding cleft to the lipid bilayer. A concurrent turn of the polypeptide backbone at Phe-245 moves the rest of the cap and exposes the catalytic serine to the aqueous solution. This study, together with earlier crystallographic investigation of smaller inhibitors, suggests a simple model for explaining substrate binding to rhomboid protease.
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Affiliation(s)
- Yi Xue
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, USA
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