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Thomas GM, Wu Y, Leite W, Pingali SV, Weiss KL, Grant AJ, Diggs MW, Schmidt-Krey I, Gutishvili G, Gumbart JC, Urban VS, Lieberman RL. SANS reveals lipid-dependent oligomerization of an intramembrane aspartyl protease from H. volcanii. Biophys J 2024; 123:1846-1856. [PMID: 38824390 PMCID: PMC11267423 DOI: 10.1016/j.bpj.2024.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/05/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024] Open
Abstract
Reactions that occur within the lipid membrane involve, at minimum, ternary complexes among the enzyme, substrate, and lipid. For many systems, the impact of the lipid in regulating activity or oligomerization state is poorly understood. Here, we used small-angle neutron scattering (SANS) to structurally characterize an intramembrane aspartyl protease (IAP), a class of membrane-bound enzymes that use membrane-embedded aspartate residues to hydrolyze transmembrane segments of biologically relevant substrates. We focused on an IAP ortholog from the halophilic archaeon Haloferax volcanii (HvoIAP). HvoIAP purified in n-dodecyl-β-D-maltoside (DDM) fractionates on size-exclusion chromatography (SEC) as two fractions. We show that, in DDM, the smaller SEC fraction is consistent with a compact HvoIAP monomer. Molecular dynamics flexible fitting conducted on an AlphaFold2-generated monomer produces a model in which loops are compact alongside the membrane-embedded helices. In contrast, SANS data collected on the second SEC fraction indicate an oligomer consistent with an elongated assembly of discrete HvoIAP monomers. Analysis of in-line SEC-SANS data of the HvoIAP oligomer, the first such experiment to be conducted on a membrane protein at Oak Ridge National Lab (ORNL), shows a diversity of elongated and spherical species, including one consistent with the tetrameric assembly reported for the Methanoculleus marisnigri JR1 IAP crystal structure not observed previously in solution. Reconstitution of monomeric HvoIAP into bicelles increases enzyme activity and results in the assembly of HvoIAP into a species with similar dimensions as the ensemble of oligomers isolated from DDM. Our study reveals lipid-mediated HvoIAP self-assembly and demonstrates the utility of in-line SEC-SANS in elucidating oligomerization states of small membrane proteins.
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Affiliation(s)
- Gwendell M Thomas
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Yuqi Wu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Wellington Leite
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | | | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Arshay J Grant
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Monneh W Diggs
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Ingeborg Schmidt-Krey
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia; School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | | | - James C Gumbart
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia; School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia.
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2
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Moser C, Muhle-Goll C. Cell-free protein production of a gamma secretase homolog. Protein Expr Purif 2024; 215:106407. [PMID: 38000778 DOI: 10.1016/j.pep.2023.106407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023]
Abstract
Cleavage of the transmembrane domain (TMD) of amyloid-β precursor protein (APP) by γ-secretase, an intramembrane aspartyl protease, generates Aβ peptides of various lengths that form plaques in the brains of Alzheimer's disease patients. Although the debate has not been finally resolved whether these plaques trigger the onset of Alzheimer's or are side products, disease-related mutations suggest their implication in the etiology of the dementia. These occur both in presenilin, the catalytic subunit of γ-secretase, and in the TMD of APP. Despite two seminal cryo-electron microscopy structures that show the complex of γ-secretase with its substrates APP and Notch, the mechanism of γ-secretase is not yet fully understood. Especially on which basis it selects its substrates is still an enigma. The presenilin homolog PSH from the archaeon Methanoculleus marisnigri JR1 (MCMJR1) is catalytically active without accessory proteins in contrast to γ-secretase making it an excellent model for studies of the basic cleavage process. We here focused on the cell-free expression of PSH screening a range of conditions. Cleavage assays to verify the activity show that not only the yield, but mainly the activity of the protease depends on the careful selection of expression conditions. Optimal results were found for a cell-free expression at relatively low temperature, 20 °C, employing cell lysates prepared from E. coli Rosetta cells. To speed up protein preparation for immediate functional assays, a crude purification protocol was developed. This allows to produce ready-made PSH in a fast and efficient manner in less than two days.
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Affiliation(s)
- Celine Moser
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein- Leopoldshafen, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein- Leopoldshafen, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany.
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3
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Höppner S, Schröder B, Fluhrer R. Structure and function of SPP/SPPL proteases: insights from biochemical evidence and predictive modeling. FEBS J 2023; 290:5456-5474. [PMID: 37786993 DOI: 10.1111/febs.16968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/13/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
More than 20 years ago, signal peptide peptidase (SPP) and its homologues, the signal peptide peptidase-like (SPPL) proteases have been identified based on their sequence similarity to presenilins, a related family of intramembrane aspartyl proteases. Other than those for the presenilins, no high-resolution structures for the SPP/SPPL proteases are available. Despite this limitation, over the years bioinformatical and biochemical data have accumulated, which altogether have provided a picture of the overall structure and topology of these proteases, their localization in the cell, the process of substrate recognition, their cleavage mechanism, and their function. Recently, the artificial intelligence-based structure prediction tool AlphaFold has added high-confidence models of the expected fold of SPP/SPPL proteases. In this review, we summarize known structural aspects of the SPP/SPPL family as well as their substrates. Of particular interest are the emerging substrate recognition and catalytic mechanisms that might lead to the prediction and identification of more potential substrates and deeper insight into physiological and pathophysiological roles of proteolysis.
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Affiliation(s)
- Sabine Höppner
- Biochemistry and Molecular Biology, Faculty of Medicine, Institute of Theoretical Medicine, University of Augsburg, Germany
| | - Bernd Schröder
- Institute for Physiological Chemistry, Technische Universität Dresden, Germany
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Faculty of Medicine, Institute of Theoretical Medicine, University of Augsburg, Germany
- Center for Interdisciplinary Health Research, University of Augsburg, Germany
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4
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Wu Y, Thomas GM, Thomsen M, Bahri S, Lieberman RL. Lipid environment modulates processivity and kinetics of a presenilin homolog acting on multiple substrates in vitro. J Biol Chem 2023; 299:105401. [PMID: 38270390 PMCID: PMC10679502 DOI: 10.1016/j.jbc.2023.105401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/12/2023] [Accepted: 10/11/2023] [Indexed: 01/26/2024] Open
Abstract
Intramembrane proteases (IPs) hydrolyze peptides in the lipid membrane. IPs participate in a number of cellular pathways including immune response and surveillance, and cholesterol biosynthesis, and they are exploited by viruses for replication. Despite their broad importance across biology, how activity is regulated in the cell to control protein maturation and release of specific bioactive peptides at the right place and right time remains largely unanswered, particularly for the intramembrane aspartyl protease (IAP) subtype. At a molecular biochemical level, different IAP homologs can cleave non-biological substrates, and there is no sequence recognition motif among the nearly 150 substrates identified for just one IAP, presenilin-1, the catalytic component of γ-secretase known for its involvement in the production of amyloid-β plaques associated with Alzheimer disease. Here we used gel-based assays combined with quantitative mass spectrometry and FRET-based kinetics assays to probe the cleavage profile of the presenilin homolog from the methanogen Methanoculleus marisnigri JR1 as a function of the surrounding lipid-mimicking environment, either detergent micelles or bicelles. We selected four biological IAP substrates that have not undergone extensive cleavage profiling previously, namely, the viral core protein of Hepatitis C virus, the viral core protein of Classical Swine Fever virus, the transmembrane segment of Notch-1, and the tyrosine receptor kinase ErbB4. Our study demonstrates a proclivity toward cleavage of substrates at positions of low average hydrophobicity and a consistent role for the lipid environment in modulating kinetic properties.
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Affiliation(s)
- Yuqi Wu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Gwendell M Thomas
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Max Thomsen
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sara Bahri
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA.
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5
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Kristensen SS, Diep DB, Kjos M, Mathiesen G. The role of site-2-proteases in bacteria: a review on physiology, virulence, and therapeutic potential. MICROLIFE 2023; 4:uqad025. [PMID: 37223736 PMCID: PMC10202637 DOI: 10.1093/femsml/uqad025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/25/2023]
Abstract
Site-2-proteases are a class of intramembrane proteases involved in regulated intramembrane proteolysis. Regulated intramembrane proteolysis is a highly conserved signaling mechanism that commonly involves sequential digestion of an anti-sigma factor by a site-1- and site-2-protease in response to external stimuli, resulting in an adaptive transcriptional response. Variation of this signaling cascade continues to emerge as the role of site-2-proteases in bacteria continues to be explored. Site-2-proteases are highly conserved among bacteria and play a key role in multiple processes, including iron uptake, stress response, and pheromone production. Additionally, an increasing number of site-2-proteases have been found to play a pivotal role in the virulence properties of multiple human pathogens, such as alginate production in Pseudomonas aeruginosa, toxin production in Vibrio cholerae, resistance to lysozyme in enterococci and antimicrobials in several Bacillus spp, and cell-envelope lipid composition in Mycobacterium tuberculosis. The prominent role of site-2-proteases in bacterial pathogenicity highlights the potential of site-2-proteases as novel targets for therapeutic intervention. In this review, we summarize the role of site-2-proteases in bacterial physiology and virulence, as well as evaluate the therapeutic potential of site-2-proteases.
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Affiliation(s)
- Sofie S Kristensen
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), 1433 Ås, Norway
| | | | - Morten Kjos
- Corresponding author. NMBU, P.O. Box 5003, 1433 Ås, Norway. E-mail:
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6
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Schmidt FC, Fitz K, Feilen LP, Okochi M, Steiner H, Langosch D. Different transmembrane domains determine the specificity and efficiency of the cleavage activity of the γ-secretase subunit presenilin. J Biol Chem 2023; 299:104626. [PMID: 36944398 PMCID: PMC10164903 DOI: 10.1016/j.jbc.2023.104626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/07/2023] [Accepted: 03/11/2023] [Indexed: 03/23/2023] Open
Abstract
The γ-secretase complex catalyzes the intramembrane cleavage of C99, a carboxy-terminal fragment of the amyloid precursor protein. Two paralogs of its catalytic subunit presenilin (PS1 and PS2) are expressed which are autocatalytically cleaved into an N-terminal and a C-terminal fragment during maturation of γ-secretase. In this study, we compared the efficiency and specificity of C99 cleavage by PS1- and PS2-containing γ-secretases. Mass spectrometric analysis of cleavage products obtained in cell-free and cell-based assays revealed that the previously described lower amyloid-β (Aβ)38 generation by PS2 is accompanied by a reciprocal increase in Aβ37 production. We further found PS1 and PS2 to show different preferences in the choice of the initial cleavage site of C99. However, the differences in Aβ38 and Aβ37 generation appear to mainly result from altered subsequent stepwise cleavage of Aβ peptides. Apart from these differences in cleavage specificity, we confirmed a lower efficiency of initial C99 cleavage by PS2 using a detergent-solubilized γ-secretase system. By investigating chimeric PS1/2 molecules, we show that the membrane-embedded, nonconserved residues of the N-terminal fragment mainly account for the differential cleavage efficiency and specificity of both presenilins. At the level of individual transmembrane domains (TMDs), TMD3 was identified as a major modulator of initial cleavage site specificity. The efficiency of endoproteolysis strongly depends on nonconserved TMD6 residues at the interface to TMD2, i.e., at a putative gate of substrate entry. Taken together, our results highlight the role of individual presenilin TMDs in the cleavage of C99 and the generation of Aβ peptides.
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Affiliation(s)
- Fabian C Schmidt
- Biopolymer Chemistry, Technical University of Munich, Freising, Germany
| | - Katja Fitz
- Biopolymer Chemistry, Technical University of Munich, Freising, Germany
| | - Lukas P Feilen
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Masayasu Okochi
- Neuropsychiatry, Division of Internal Medicine, Department of Integrated Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Harald Steiner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center (BMC), Ludwig-Maximilians-University, Munich, Germany
| | - Dieter Langosch
- Biopolymer Chemistry, Technical University of Munich, Freising, Germany.
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7
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PSEN2 and ABCA7 variants causing early-onset preclinical pathological changes in Alzheimer's disease: a case report and literature review. Neurol Sci 2023; 44:1987-2001. [PMID: 36701017 DOI: 10.1007/s10072-023-06602-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/04/2023] [Indexed: 01/27/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is a debilitating and highly heritable neurodegenerative disease. Early-onset AD (EOAD) was defined as AD occurring before age 65. Although it has a high genetic risk, EOAD due to PSEN2 variation is very rare. ABCA7 is an important risk gene for AD. Previously reported cases mainly carried variations in a single pathogenic or risk gene. METHODS AND RESULTS: In this study, we report a 35-year-old female carrying variants in both the PSEN2 gene (c.640G > T p.V214L) and ABCA7 gene (c.2848G > A p.V950M). Four previously reported cases carried PSEN2 V214L, and no reported cases carried ABCA7 V950M. She had a history of migraine, patent foramen ovale, spontaneous subarachnoid hemorrhage without aneurysm, and multiple cerebral microhemorrhages. Her MMSE score was 24/30, and her MoCA score was 22/30. The concentration of Aβ42 and the ratio of Aβ42 to Aβ40 in cerebral spinal fluid were obviously decreased. Published variants of PSEN2 and ABCA7 in PubMed were reviewed, and the patients' characteristics were summarized and compared to provide information for the clinical diagnosis of AD. CONCLUSIONS It is necessary to conduct genetic screening in cases with atypical manifestations.
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8
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Eden A, Zhao J, Xiao Y, Gibson J, Wang C. Covalent fragment inhibits intramembrane proteolysis. Front Mol Biosci 2022; 9:958399. [PMID: 36158579 PMCID: PMC9490316 DOI: 10.3389/fmolb.2022.958399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/01/2022] [Indexed: 01/09/2023] Open
Abstract
Alzheimer's disease (AD) is a serious public health crisis with only one current modifying treatment. The reduction of amyloid load by targeting γ-secretase (GS) has been a leading approach in AD drug discovery and development. Despite the focus on GS inhibition, multiple GS inhibitors (GSIs) have failed in clinical trials as a result of side effects including exacerbated cognitive decline. These side effects are largely attributable to inhibition of normal GS function. Standard enzyme inhibitors target catalytic or allosteric sites of the enzyme, including the active site presenilin, as previous GSIs did. To avoid issues observed from broad-spectrum GSIs we discovered that fragment 6H8 that covalently binds to the substrate of GS, the transmembrane domain of amyloid precursor protein (APPTM). Nuclear Magnetic Resonance (NMR) Spectroscopy combined with MALDI-TOF-MS established 6H8 covalently binds to APPTM. 6H8 acts as a Michael acceptor and covalently links to the side chain amines of lysine residues, specifically targeting a cluster of C-terminal lysines K53-K55. Through this modification, 6H8 can inhibit intramembrane proteolysis of an archaeal homolog of presenilin (the active subunit of GS) via substrate binding with a 2-4 μM IC50, determined by a gel-based cleavage assay. 6H8, while too small to be an effective drug candidate, can be combined with a specific non-covalent partner and function as an effective covalent warhead of a targeted covalent inhibitor (TCI). The future development of the 6H8 fragment into the covalent warhead of a TCI is, to our knowledge, a novel approach to AD drug discovery.
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Affiliation(s)
- Angela Eden
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY, United States
- Department of Chemistry and Chemical Biology, Troy, NY, United States
- Department of Biological Sciences, Troy, NY, United States
| | - Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY, United States
| | - Yuanyuan Xiao
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY, United States
| | - James Gibson
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY, United States
- Department of Chemistry and Chemical Biology, Troy, NY, United States
- Department of Biological Sciences, Troy, NY, United States
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9
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De Castro RE, Giménez MI, Cerletti M, Paggi RA, Costa MI. Proteolysis at the Archaeal Membrane: Advances on the Biological Function and Natural Targets of Membrane-Localized Proteases in Haloferax volcanii. Front Microbiol 2022; 13:940865. [PMID: 35814708 PMCID: PMC9263693 DOI: 10.3389/fmicb.2022.940865] [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: 05/10/2022] [Accepted: 06/06/2022] [Indexed: 11/23/2022] Open
Abstract
Proteolysis plays a fundamental role in many processes that occur within the cellular membrane including protein quality control, protein export, cell signaling, biogenesis of the cell envelope among others. Archaea are a distinct and physiologically diverse group of prokaryotes found in all kinds of habitats, from the human and plant microbiomes to those with extreme salt concentration, pH and/or temperatures. Thus, these organisms provide an excellent opportunity to extend our current understanding on the biological functions that proteases exert in cell physiology including the adaptation to hostile environments. This revision describes the advances that were made on archaeal membrane proteases with regard to their biological function and potential natural targets focusing on the model haloarchaeon Haloferax volcanii.
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10
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Feilen LP, Chen SY, Fukumori A, Feederle R, Zacharias M, Steiner H. Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis. eLife 2022; 11:76090. [PMID: 35579427 PMCID: PMC9282858 DOI: 10.7554/elife.76090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cleavage of membrane proteins in the lipid bilayer by intramembrane proteases is crucial for health and disease. Although different lipid environments can potently modulate their activity, how this is linked to their structural dynamics is unclear. Here, we show that the carboxy-peptidase-like activity of the archaeal intramembrane protease PSH, a homolog of the Alzheimer’s disease-associated presenilin/γ-secretase is impaired in micelles and promoted in a lipid bilayer. Comparative molecular dynamics simulations revealed that important elements for substrate binding such as transmembrane domain 6a of PSH are more labile in micelles and stabilized in the lipid bilayer. Moreover, consistent with an enhanced interaction of PSH with a transition-state analog inhibitor, the bilayer promoted the formation of the enzyme’s catalytic active site geometry. Our data indicate that the lipid environment of an intramembrane protease plays a critical role in structural stabilization and active site arrangement of the enzyme-substrate complex thereby promoting intramembrane proteolysis. Cutting proteins into pieces is a crucial process in the cell, allowing several important processes to take place, including cell differentiation (which allows cells to develop into specific types), cell death, protein quality control, or even where in the cell a protein will end up. However, the specialized proteins that carry out this task, known as proteases, can also be involved in the development of disease. For example, in the brain, a protease called γ-secretase cuts up the amyloid-β protein precursor, producing toxic forms of amyloid-β peptides that are widely believed to cause Alzheimer’s disease. Proteases like γ-secretase carry out their role in the membrane, the layer of fats (also known as lipids) that forms the outer boundary of the cell. The environment in this area of the cell can influence the activity of proteases, but it is poorly understood how this happens. One way to address this question would be to compare the activity of γ-secretase in the lipid environment of the membrane to its activity when it is entirely surrounded by different molecules, such as detergent molecules. Unfortunately, γ-secretase is not active when it is removed from its lipid environment by a detergent, making it difficult to perform this comparison. To overcome this issue, Feilen et al. chose to study PSH, a protease similar to γ-secretase that produces the same amyloid-β peptides but remains active in detergent. When Feilen et al. mixed PSH with lipid molecules like those found in the membrane and amyloid-β precursor protein, PSH produced amyloid-β peptides including those that are thought to cause Alzheimer’s. However, when a detergent was substituted for the lipid molecules this led to longer amyloid-β peptides than usual, indicating that PSH was not able to cut proteins as effectively. The change in environment appeared to reduce PSH’s ability to progressively trim small segments from the peptides. Computer modelling of the protease’s structure in lipids versus detergent supported the experimental findings: the model predicted that the areas of PSH important for recognizing and cutting other proteins would be more stable in the membrane compared to the detergent. These results indicate that the cell membrane plays a vital role in the stability of the active regions of proteases that are cleaving in this environment. In the future, this could help to better understand how changes to the lipid molecules in the membrane may contribute to the activity of γ-secretase and its role in Alzheimer’s disease.
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Affiliation(s)
- Lukas P Feilen
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Shu-Yu Chen
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Akio Fukumori
- Department of Pharmacotherapeutics II, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Regina Feederle
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Harald Steiner
- Biomedical Center (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
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11
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Olenic S, Heo L, Feig M, Kroos L. Inhibitory proteins block substrate access by occupying the active site cleft of Bacillus subtilis intramembrane protease SpoIVFB. eLife 2022; 11:74275. [PMID: 35471152 PMCID: PMC9042235 DOI: 10.7554/elife.74275] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/25/2022] [Indexed: 12/16/2022] Open
Abstract
Intramembrane proteases (IPs) function in numerous signaling pathways that impact health, but elucidating the regulation of membrane-embedded proteases is challenging. We examined inhibition of intramembrane metalloprotease SpoIVFB by proteins BofA and SpoIVFA. We found that SpoIVFB inhibition requires BofA residues in and near a predicted transmembrane segment (TMS). This segment of BofA occupies the SpoIVFB active site cleft based on cross-linking experiments. SpoIVFB inhibition also requires SpoIVFA. The inhibitory proteins block access of the substrate N-terminal region to the membrane-embedded SpoIVFB active site, based on additional cross-linking experiments; however, the inhibitory proteins did not prevent interaction between the substrate C-terminal region and the SpoIVFB soluble domain. We built a structural model of SpoIVFB in complex with BofA and parts of SpoIVFA and substrate, using partial homology and constraints from cross-linking and co-evolutionary analyses. The model predicts that conserved BofA residues interact to stabilize a TMS and a membrane-embedded C-terminal region. The model also predicts that SpoIVFA bridges the BofA C-terminal region and SpoIVFB, forming a membrane-embedded inhibition complex. Our results reveal a novel mechanism of IP inhibition with clear implications for relief from inhibition in vivo and design of inhibitors as potential therapeutics.
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Affiliation(s)
- Sandra Olenic
- Michigan State University, East Lansing, United States
| | - Lim Heo
- Michigan State University, East Lansing, United States
| | - Michael Feig
- Michigan State University, East Lansing, United States
| | - Lee Kroos
- Michigan State University, East Lansing, United States
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12
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Schwake C, Hyon M, Chishti AH. Signal peptide peptidase: A potential therapeutic target for parasitic and viral infections. Expert Opin Ther Targets 2022; 26:261-273. [PMID: 35235480 DOI: 10.1080/14728222.2022.2047932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Signal peptide peptidase (SPP) is a GxGD-type intramembrane-cleaving aspartyl protease responsible for clearing accumulating signal peptides in the endoplasmic reticulum. SPP is conserved among all kingdoms and is essential for maintaining cell homeostasis. Inhibition of SPP with selective inhibitors and the structurally similar HIV protease inhibitors results in signal peptide accumulation and subsequent cell death. Identification of SPP homologues in major human parasitic infections has opened a new therapeutic opportunity. Moreover, the essentiality of mammalian SPP-mediated viral protein processing during infection is emerging. AREAS COVERED This review introduces the discovery and biological function of human SPP enzymes and identify parasitic homologues as pharmacological targets of both SPP and HIV protease inhibitors. Later, the role of mammalian SPP during viral infection and how disruption of host SPP can be employed as a novel antiviral therapy are examined and discussed. EXPERT OPINION Parasitic and viral infections cause severe health and economic burden, exacerbated by the lack of new therapeutics in the pipeline. SPP has been shown to be essential for malaria parasite growth and encouraging evidence in other parasites demonstrates broad essentiality of these proteases as therapeutic targets. As drug resistant parasite and viruses emerge, SPP inhibition will provide a new generation of compounds to counter the growing threat of antimicrobial resistance.
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Affiliation(s)
- Christopher Schwake
- Department of Developmental, Molecular, and Chemical Biology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Michael Hyon
- Department of Developmental, Molecular, and Chemical Biology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Athar H Chishti
- Department of Developmental, Molecular, and Chemical Biology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
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13
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Conserved Proline Residues of Bacillus subtilis Intramembrane Metalloprotease SpoIVFB Are Important for Substrate Interaction and Cleavage. J Bacteriol 2022; 204:e0038621. [PMID: 35007155 DOI: 10.1128/jb.00386-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intramembrane metalloproteases regulate diverse biological processes by cleaving membrane-associated substrates within the membrane or near its surface. SpoIVFB is an intramembrane metalloprotease of Bacillus subtilis that cleaves Pro-σK during endosporulation. Intramembrane metalloproteases have a broadly conserved NPDG motif, which in the structure of an archaeal enzyme is located in a short loop that interrupts a transmembrane segment facing the active site. The aspartate residue of the NPDG motif acts as a ligand of the zinc ion involved in catalysis. The functions of other residues in the short loop are less well understood. We found that the predicted short loop of SpoIVFB contains two highly conserved proline residues, P132 of the NPDG motif and P135. Mutational analysis revealed that both proline residues are important for Pro-σK cleavage in Escherichia coli engineered to synthesize the proteins. Substitutions for either residue also impaired Pro-σK interaction with SpoIVFB in co-purification assays. Disulfide cross-linking experiments showed that the predicted short loop of SpoIVFB is in proximity to the Proregion of Pro-σK. Alanine substitutions for N129 and P132 of the SpoIVFB NPDG motif reduced cross-linking between its predicted short loop and the Proregion more than a P135A substitution. Conversely, the SpoIVFB P135A substitution reduced Pro-σK cleavage more than the N129A and P132A substitutions during sporulation of B. subtilis. We conclude that all three conserved residues of SpoIVFB are important for substrate interaction and cleavage, and we propose that P135 is necessary to position D137 to act as a zinc ligand. IMPORTANCE Intramembrane metalloproteases (IMMPs) function in numerous signaling pathways. Bacterial IMMPs govern stress responses, including sporulation of some species, thus enhancing the virulence and persistence of pathogens. Knowledge of IMMP-substrate interactions could aid therapeutic design, but structures of IMMP·substrate complexes are unknown. We examined interaction of the IMMP SpoIVFB with its substrate Pro-σK, whose cleavage is required for Bacillus subtilis endosporulation. We found that conserved proline residues in a short loop predicted to interrupt a SpoIVFB transmembrane segment are important for Pro-σK binding and cleavage. Corresponding residues of the Escherichia coli IMMP RseP have also been shown to be important for substrate interaction and cleavage, suggesting this is a broadly conserved feature of IMMPs, potentially suitable as a therapeutic target.
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Linhartová M, Skotnicová P, Hakkila K, Tichý M, Komenda J, Knoppová J, Gilabert JF, Guallar V, Tyystjärvi T, Sobotka R. Mutations Suppressing the Lack of Prepilin Peptidase Provide Insights Into the Maturation of the Major Pilin Protein in Cyanobacteria. Front Microbiol 2021; 12:756912. [PMID: 34712217 PMCID: PMC8546353 DOI: 10.3389/fmicb.2021.756912] [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: 08/11/2021] [Accepted: 09/14/2021] [Indexed: 11/24/2022] Open
Abstract
Type IV pili are bacterial surface-exposed filaments that are built up by small monomers called pilin proteins. Pilins are synthesized as longer precursors (prepilins), the N-terminal signal peptide of which must be removed by the processing protease PilD. A mutant of the cyanobacterium Synechocystis sp. PCC 6803 lacking the PilD protease is not capable of photoautotrophic growth because of the impaired function of Sec translocons. Here, we isolated phototrophic suppressor strains of the original ΔpilD mutant and, by sequencing their genomes, identified secondary mutations in the SigF sigma factor, the γ subunit of RNA polymerase, the signal peptide of major pilin PilA1, and in the pilA1-pilA2 intergenic region. Characterization of suppressor strains suggests that, rather than the total prepilin level in the cell, the presence of non-glycosylated PilA1 prepilin is specifically harmful. We propose that the restricted lateral mobility of the non-glycosylated PilA1 prepilin causes its accumulation in the translocon-rich membrane domains, which attenuates the synthesis of membrane proteins.
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Affiliation(s)
- Markéta Linhartová
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Petra Skotnicová
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Kaisa Hakkila
- Biotechnology/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Martin Tichý
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Josef Komenda
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Knoppová
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | | | - Victor Guallar
- Barcelona Supercomputing Center, Barcelona, Spain.,ICREA: Institucio Catalana de Recerca i Estudis Avançats Passeig Lluis Companys, Barcelona, Spain
| | - Taina Tyystjärvi
- Biotechnology/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Roman Sobotka
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
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15
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Barthelson K, Dong Y, Newman M, Lardelli M. PRESENILIN 1 Mutations Causing Early-Onset Familial Alzheimer's Disease or Familial Acne Inversa Differ in Their Effects on Genes Facilitating Energy Metabolism and Signal Transduction. J Alzheimers Dis 2021; 82:327-347. [PMID: 34024832 DOI: 10.3233/jad-210128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The most common cause of early-onset familial Alzheimer's disease (EOfAD) is mutations in PRESENILIN 1 (PSEN1) allowing production of mRNAs encoding full-length, but mutant, proteins. In contrast, a single known frameshift mutation in PSEN1 causes familial acne inversa (fAI) without EOfAD. The molecular consequences of heterozygosity for these mutation types, and how they cause completely different diseases, remains largely unexplored. OBJECTIVE To analyze brain transcriptomes of young adult zebrafish to identify similarities and differences in the effects of heterozygosity for psen1 mutations causing EOfAD or fAI. METHODS RNA sequencing was performed on mRNA isolated from the brains of a single family of 6-month-old zebrafish siblings either wild type or possessing a single, heterozygous EOfAD-like or fAI-like mutation in their endogenous psen1 gene. RESULTS Both mutations downregulate genes encoding ribosomal subunits, and upregulate genes involved in inflammation. Genes involved in energy metabolism appeared significantly affected only by the EOfAD-like mutation, while genes involved in Notch, Wnt and neurotrophin signaling pathways appeared significantly affected only by the fAI-like mutation. However, investigation of direct transcriptional targets of Notch signaling revealed possible increases in γ-secretase activity due to heterozygosity for either psen1 mutation. Transcriptional adaptation due to the fAI-like frameshift mutation was evident. CONCLUSION We observed both similar and contrasting effects on brain transcriptomes of the heterozygous EOfAD-like and fAI-like mutations. The contrasting effects may illuminate how these mutation types cause distinct diseases.
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Affiliation(s)
- Karissa Barthelson
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Yang Dong
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Morgan Newman
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Michael Lardelli
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
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16
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Preparation of a Deuterated Membrane Protein for Small-Angle Neutron Scattering. Methods Mol Biol 2021. [PMID: 33877630 DOI: 10.1007/978-1-0716-1394-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This chapter outlines a protocol developed to prepare a purified deuterated membrane protein for a small-angle neutron scattering (SANS) experiment. SANS is a noninvasive technique well suited to studying membrane protein solution structures, and deuteration enhances the signal from the protein over the background (Breyton et al., Eur Phys J E Soft Matter 36 (7):71, 2013; Garg et al., Biophys J 101 (2):370-377, 2011). We present our workflow: transformation of our plasmid into E. coli, cell growth and expression of our deuterated protein, membrane isolation, detergent solubilization, protein purification, purity assessment, and final preparation for SANS.
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17
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Willumsen N, Poole T, Nicholas JM, Fox NC, Ryan NS, Lashley T. Variability in the type and layer distribution of cortical Aβ pathology in familial Alzheimer's disease. Brain Pathol 2021; 32:e13009. [PMID: 34319632 PMCID: PMC9048809 DOI: 10.1111/bpa.13009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/30/2022] Open
Abstract
Familial Alzheimer's disease (FAD) is caused by autosomal dominant mutations in the PSEN1, PSEN2 or APP genes, giving rise to considerable clinical and pathological heterogeneity in FAD. Here we investigate variability in clinical data and the type and distribution of Aβ pathologies throughout the cortical layers of different FAD mutation cases. Brain tissue from 20 FAD cases [PSEN1 pre-codon 200 (n = 10), PSEN1 post-codon 200 (n = 6), APP (n = 4)] were investigated. Frontal cortex sections were stained immunohistochemically for Aβ, and Nissl to define the cortical layers. The frequency of different amyloid-beta plaque types was graded for each cortical layer and the severity of cerebral amyloid angiopathy (CAA) was determined in cortical and leptomeningeal blood vessels. Comparisons were made between FAD mutations and APOE4 status, with associations between pathology, clinical and genetic data investigated. In this cohort, possession of an APOE4 allele was associated with increased disease duration but not with age at onset, after adjusting for mutation sub-group and sex. We found Aβ pathology to be heterogeneous between cases although Aβ load was highest in cortical layer 3 for all mutation groups and a higher Aβ load was associated with APOE4. The PSEN1 post-codon 200 group had a higher Aβ load in lower cortical layers, with a small number of this group having increased cotton wool plaque pathology in lower layers. Cotton wool plaque frequency was positively associated with the severity of CAA in the whole cohort and in the PSEN1 post-codon 200 group. Carriers of the same PSEN1 mutation can have differing patterns of Aβ deposition, potentially because of differences in risk factors. Our results highlight possible influences of APOE4 genotype, and PSEN1 mutation type on Aβ deposition, which may have effects on the clinical heterogeneity of FAD.
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Affiliation(s)
- Nanet Willumsen
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Teresa Poole
- Department of Medical Statistics, London School of Hygiene & Tropical Medicine, London, UK.,Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Jennifer M Nicholas
- Department of Medical Statistics, London School of Hygiene & Tropical Medicine, London, UK.,Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Nick C Fox
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.,UK Dementia Research Institute at University College London, London, UK
| | - Natalie S Ryan
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.,UK Dementia Research Institute at University College London, London, UK
| | - Tammaryn Lashley
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
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18
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Papadopoulou AA, Fluhrer R. Signaling Functions of Intramembrane Aspartyl-Proteases. Front Cardiovasc Med 2020; 7:591787. [PMID: 33381526 PMCID: PMC7768045 DOI: 10.3389/fcvm.2020.591787] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/16/2020] [Indexed: 01/18/2023] Open
Abstract
Intramembrane proteolysis is more than a mechanism to "clean" the membranes from proteins no longer needed. By non-reversibly modifying transmembrane proteins, intramembrane cleaving proteases hold key roles in multiple signaling pathways and often distinguish physiological from pathological conditions. Signal peptide peptidase (SPP) and signal peptide peptidase-like proteases (SPPLs) recently have been associated with multiple functions in the field of signal transduction. SPP/SPPLs together with presenilins (PSs) are the only two families of intramembrane cleaving aspartyl proteases known in mammals. PS1 or PS2 comprise the catalytic center of the γ-secretase complex, which is well-studied in the context of Alzheimer's disease. The mammalian SPP/SPPL family of intramembrane cleaving proteases consists of five members: SPP and its homologous proteins SPPL2a, SPPL2b, SPPL2c, and SPPL3. Although these proteases were discovered due to their homology to PSs, it became evident in the past two decades that no physiological functions are shared between these two families. Based on studies in cell culture models various substrates of SPP/SPPL proteases have been identified in the past years and recently-developed mouse lines lacking individual members of this protease family, will help to further clarify the physiological functions of these proteases. In this review we concentrate on signaling roles of mammalian intramembrane cleaving aspartyl proteases. In particular, we will highlight the signaling roles of PS via its substrates NOTCH, VEGF, and others, mainly focusing on its involvement in vasculature. Delineating also signaling pathways that are affected and/or controlled by SPP/SPPL proteases. From SPP's participation in tumor progression and survival, to SPPL3's regulation of protein glycosylation and SPPL2c's control over cellular calcium stores, various crossovers between proteolytic activity of intramembrane proteases and cell signaling will be described.
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Affiliation(s)
- Alkmini A. Papadopoulou
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
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19
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A computer-simulated mechanism of familial Alzheimer’s disease: Mutations enhance thermal dynamics and favor looser substrate-binding to γ-secretase. J Struct Biol 2020; 212:107648. [DOI: 10.1016/j.jsb.2020.107648] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/22/2020] [Accepted: 10/09/2020] [Indexed: 11/22/2022]
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20
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Raut P, Glass JB, Lieberman RL. Archaeal roots of intramembrane aspartyl protease siblings signal peptide peptidase and presenilin. Proteins 2020; 89:232-241. [PMID: 32935885 DOI: 10.1002/prot.26009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/27/2020] [Accepted: 09/13/2020] [Indexed: 12/21/2022]
Abstract
Signal peptides help newly synthesized proteins reach the cell membrane or be secreted. As part of a biological process key to immune response and surveillance in humans, and associated with diseases, for example, Alzheimer, remnant signal peptides and other transmembrane segments are proteolyzed by the intramembrane aspartyl protease (IAP) enzyme family. Here, we identified IAP orthologs throughout the tree of life. In addition to eukaryotes, IAPs are encoded in metabolically diverse archaea from a wide range of environments. We found three distinct clades of archaeal IAPs: (a) Euryarchaeota (eg, halophilic Halobacteriales, methanogenic Methanosarcinales and Methanomicrobiales, marine Poseidoniales, acidophilic Thermoplasmatales, hyperthermophilic Archaeoglobus spp.), (b) DPANN, and (c) Bathyarchaeota, Crenarchaeota, and Asgard. IAPs were also present in bacterial genomes from uncultivated members of Candidate Phylum Radiation, perhaps due to horizontal gene transfer from DPANN archaeal lineages. Sequence analysis of the catalytic motif YD…GXGD (where X is any amino acid) in IAPs from archaea and bacteria reveals WD in Lokiarchaeota and many residue types in the X position. Gene neighborhood analysis in halophilic archaea shows IAP genes near corrinoid transporters (btuCDF genes). In marine Euryarchaeota, a putative BtuF-like domain is found in N-terminus of the IAP gene, suggesting a role for these IAPs in metal ion cofactor or other nutrient scavenging. Interestingly, eukaryotic IAP family members appear to have evolved either from Euryarchaeota or from Asgard archaea. Taken together, our phylogenetic and bioinformatics analysis should prompt experiments to probe the biological roles of IAPs in prokaryotic secretomes.
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Affiliation(s)
- Priyam Raut
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jennifer B Glass
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
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21
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Hitzenberger M, Götz A, Menig S, Brunschweiger B, Zacharias M, Scharnagl C. The dynamics of γ-secretase and its substrates. Semin Cell Dev Biol 2020; 105:86-101. [DOI: 10.1016/j.semcdb.2020.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 12/18/2022]
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22
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Escamilla-Ayala A, Wouters R, Sannerud R, Annaert W. Contribution of the Presenilins in the cell biology, structure and function of γ-secretase. Semin Cell Dev Biol 2020; 105:12-26. [DOI: 10.1016/j.semcdb.2020.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/06/2020] [Accepted: 02/17/2020] [Indexed: 01/25/2023]
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23
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Jang DW, Ameer K, Oh JH, Park MK. Optimization and Pretreatment for Hot Water Extraction of Korean Deer ( Cervus canadensis Erxleben) Velvet Antlers. J Microbiol Biotechnol 2020; 30:1116-1123. [PMID: 32423187 PMCID: PMC9728161 DOI: 10.4014/jmb.2004.04009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/03/2020] [Indexed: 12/15/2022]
Abstract
Velvet antler (VA) is a historically traditional medicinal supplement and is well known in Asian countries for its pharmaceutical and health benefits. The objectives for this study were to optimize the hot water extraction (HWE) of VA for the Korean VA industry, and to determine the most effective pretreatment method among microwave (MW), ultrasonication (US), and enzymatic (EZ) techniques. Using response surface methodology, optimum extraction temperatures and times were determined by central composite design configuration based on extraction yield and sialic acid content. Various quality parameters of VA extract including yield, soluble solid, protein, and sialic acid contents were also compared with the conjunction of HWE and pretreatment. The yield and sialic acid content of VA extract were determined to be 40% and 0.73 mg/g, respectively, under an optimum temperature of 100°C at 24 h of extraction time. The yields from VA extracts pretreated with MW, US, and EZ were 17.42%, 19.73%, and 29.15%, respectively. Among the tested commercial enzymes, pepsin was the most effective proteolytic enzyme and led to the highest yield (47.65%), soluble solids (4.03 °brix), protein (1.12 mg/ml), and sialic acid (3.04 mg/ml) contents from VA extract.
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Affiliation(s)
- Dong Wook Jang
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kashif Ameer
- Department of Food Science and Technology and BK 21 Plus Program, Graduate School of Chonnam National University, Gwangju 61186, Republic of Korea,Institute of Food and Nutritional Sciences, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Jun-Hyun Oh
- Department of Plant and Food Sciences, Sangmyung University, Cheonan 31066, Republic of Korea
| | - Mi-Kyung Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea,Food and Bio-Industry Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea,Corresponding author Phone: +82-53-960-5776 Fax: +82-53-950-6772 E-mail:
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24
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Dehury B, Tang N, Mehra R, Blundell TL, Kepp KP. Side-by-side comparison of Notch- and C83 binding to γ-secretase in a complete membrane model at physiological temperature. RSC Adv 2020; 10:31215-31232. [PMID: 35520661 PMCID: PMC9056423 DOI: 10.1039/d0ra04683c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/15/2020] [Indexed: 12/29/2022] Open
Abstract
γ-Secretase cleaves the C99 fragment of the amyloid precursor protein, leading to formation of aggregated β-amyloid peptide central to Alzheimer's disease, and Notch, essential for cell regulation. Recent cryogenic electron microscopy (cryo-EM) structures indicate major changes upon substrate binding, a β-sheet recognition motif, and a possible helix unwinding to expose peptide bonds towards nucleophilic attack. Here we report side-by-side comparison of the 303 K dynamics of the two proteins in realistic membranes using molecular dynamics simulations. Our ensembles agree with the cryo-EM data (full-protein Cα-RMSD = 1.62–2.19 Å) but reveal distinct presenilin helix conformation states and thermal β-strand to coil transitions of C83 and Notch100. We identify distinct 303 K hydrogen bond dynamics and water accessibility of the catalytic sites. The RKRR motif (1758–1761) contributes significantly to Notch binding and serves as a “membrane anchor” that prevents Notch displacement. Water that transiently hydrogen bonds to G1753 and V1754 probably represents the catalytic nucleophile. At 303 K, Notch and C83 binding induce different conformation states, with Notch mostly present in a closed state with shorter Asp–Asp distance. This may explain the different outcome of Notch and C99 cleavage, as the latter is more imprecise with many products. Our identified conformation states may aid efforts to develop conformation-selective drugs that target C99 and Notch cleavage differently, e.g. Notch-sparing γ-secretase modulators. Distinct membrane dynamics and conformations of C83- and Notch-bound γ-secretase may aid the development of Notch-sparing treatments of Alzheimer's disease.![]()
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Affiliation(s)
- Budheswar Dehury
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +45 45252409.,Department of Biochemistry, University of Cambridge Tennis Court Road CB2 1GA UK
| | - Ning Tang
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +45 45252409
| | - Rukmankesh Mehra
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +45 45252409
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge Tennis Court Road CB2 1GA UK
| | - Kasper P Kepp
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +45 45252409
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Signal Peptide Peptidase-Type Proteases: Versatile Regulators with Functions Ranging from Limited Proteolysis to Protein Degradation. J Mol Biol 2020; 432:5063-5078. [DOI: 10.1016/j.jmb.2020.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/02/2020] [Accepted: 05/19/2020] [Indexed: 12/15/2022]
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26
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Mentrup T, Cabrera-Cabrera F, Fluhrer R, Schröder B. Physiological functions of SPP/SPPL intramembrane proteases. Cell Mol Life Sci 2020; 77:2959-2979. [PMID: 32052089 PMCID: PMC7366577 DOI: 10.1007/s00018-020-03470-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/09/2020] [Accepted: 01/22/2020] [Indexed: 01/07/2023]
Abstract
Intramembrane proteolysis describes the cleavage of substrate proteins within their hydrophobic transmembrane segments. Several families of intramembrane proteases have been identified including the aspartyl proteases Signal peptide peptidase (SPP) and its homologues, the SPP-like (SPPL) proteases SPPL2a, SPPL2b, SPPL2c and SPPL3. As presenilin homologues, they employ a similar catalytic mechanism as the well-studied γ-secretase. However, SPP/SPPL proteases cleave transmembrane proteins with a type II topology. The characterisation of SPP/SPPL-deficient mouse models has highlighted a still growing spectrum of biological functions and also promoted the substrate discovery of these proteases. In this review, we will summarise the current hypotheses how phenotypes of these mouse models are linked to the molecular function of the enzymes. At the cellular level, SPP/SPPL-mediated cleavage events rather provide specific regulatory switches than unspecific bulk proteolysis. By this means, a plethora of different cell biological pathways is influenced including signal transduction, membrane trafficking and protein glycosylation.
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Affiliation(s)
- Torben Mentrup
- Institute for Physiological Chemistry, Medizinisch-Theoretisches Zentrum MTZ, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany
| | - Florencia Cabrera-Cabrera
- Institute for Physiological Chemistry, Medizinisch-Theoretisches Zentrum MTZ, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Faculty of Medicine, University of Augsburg, Universitätsstraße 2, 86135, Augsburg, Germany
- Biomedizinisches Centrum (BMC), Ludwig Maximilians University of Munich, Feodor-Lynen-Strasse 17, 81377, Munich, Germany
- DZNE-German Center for Neurodegenerative Diseases, Munich, Feodor-Lynen-Strasse 17, 81377, Munich, Germany
| | - Bernd Schröder
- Institute for Physiological Chemistry, Medizinisch-Theoretisches Zentrum MTZ, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany.
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27
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Substrate-based chemical probes for Alzheimer’s γ-secretase. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02565-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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28
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Bhattarai A, Devkota S, Bhattarai S, Wolfe MS, Miao Y. Mechanisms of γ-Secretase Activation and Substrate Processing. ACS CENTRAL SCIENCE 2020; 6:969-983. [PMID: 32607444 PMCID: PMC7318072 DOI: 10.1021/acscentsci.0c00296] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Indexed: 05/14/2023]
Abstract
Amyloid β-peptide, the principal component of characteristic cerebral plaques of Alzheimer's disease (AD), is produced through intramembrane proteolysis of the amyloid precursor protein (APP) by γ-secretase. Despite the importance in the pathogenesis of AD, the mechanisms of intramembrane proteolysis and substrate processing by γ-secretase remain poorly understood. Here, complementary all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method and biochemical experiments were combined to investigate substrate processing of wildtype and mutant APP by γ-secretase. The GaMD simulations captured spontaneous activation of γ-secretase, with hydrogen bonded catalytic aspartates and water poised for proteolysis of APP at the ε cleavage site. Furthermore, GaMD simulations revealed that familial AD mutations I45F and T48P enhanced the initial ε cleavage between residues Leu49-Val50, while M51F mutation shifted the ε cleavage site to the amide bond between Thr48-Leu49. Detailed analysis of the GaMD simulations allowed us to identify distinct low-energy conformational states of γ-secretase, different secondary structures of the wildtype and mutant APP substrate, and important active-site subpockets for catalytic function of the enzyme. The simulation findings were highly consistent with experimental analyses of APP proteolytic products using mass spectrometry and Western blotting. Taken together, the GaMD simulations and biochemical experiments have enabled us to elucidate the mechanisms of γ-secretase activation and substrate processing, which should facilitate rational computer-aided drug design targeting this functionally important enzyme.
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Affiliation(s)
- Apurba Bhattarai
- Center
for Computational Biology and Department of Molecular Biosciences, and Department of
Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
| | - Sujan Devkota
- Center
for Computational Biology and Department of Molecular Biosciences, and Department of
Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
| | - Sanjay Bhattarai
- Center
for Computational Biology and Department of Molecular Biosciences, and Department of
Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
| | - Michael S. Wolfe
- Center
for Computational Biology and Department of Molecular Biosciences, and Department of
Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
- (M.S.W.)
| | - Yinglong Miao
- Center
for Computational Biology and Department of Molecular Biosciences, and Department of
Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
- (Y.M.)
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29
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Mehra R, Kepp KP. Identification of Structural Calcium Binding Sites in Membrane-Bound Presenilin 1 and 2. J Phys Chem B 2020; 124:4697-4711. [PMID: 32420742 DOI: 10.1021/acs.jpcb.0c01712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Variants of presenilin (PS1 and PS2) are the main genetic risk factors of familial Alzheimer's disease and thus central to the disease etiology. Although mostly studied as catalytic units of γ-secretase controlling Aβ production, presenilins also affect calcium levels, which are disturbed in Alzheimer's disease. We investigated the interaction of calcium with both PS1 and PS2 using all-atom molecular dynamics (MD) simulations in realistic membrane models, with the specific aim to identify any Ca2+ sites. We did not observe any complete Ca2+ leak event, but we identified four persistent Ca2+ sites in membrane-bound PS1 and PS2: One in HL2 near the C-terminal of TM6, one in HL2 toward the N-terminal of TM7, a site at the catalytic aspartate on TM7, and a site at the PALP motif on TM9. The sites feature negatively charged glutamates and aspartates typical of calcium binding. Structural homology to diaspartate calcium transport proteins and mutation studies of calcium efflux support our identified calcium sites. Calcium consistently dampens HL2 motions in all comparisons (PS1, protonated PS1, PS2, protonated PS2). Due to their location in HL2 and the active site, we propose that the calcium sites control autoproteolytic maturation of presenilin by a pH-dependent conformational restriction of the HL2 recognition loop, which also regulates calcium transport proteins such as inositol 1,4,5-triphosphate receptor and ryanodine receptor. Our structural dynamics could provide a possible molecular basis for the need of both calcium and presenilin for lysosome proteolytic function, perhaps relevant also to other protein misfolding diseases.
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Affiliation(s)
- Rukmankesh Mehra
- Technical University of Denmark, DTU Chemistry, DK-2800 Kongens Lyngby, Denmark
| | - Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, DK-2800 Kongens Lyngby, Denmark
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30
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Liu X, Zhao J, Zhang Y, Ubarretxena-Belandia I, Forth S, Lieberman RL, Wang C. Substrate-Enzyme Interactions in Intramembrane Proteolysis: γ-Secretase as the Prototype. Front Mol Neurosci 2020; 13:65. [PMID: 32508589 PMCID: PMC7248309 DOI: 10.3389/fnmol.2020.00065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/03/2020] [Indexed: 11/15/2022] Open
Abstract
Intramembrane-cleaving proteases (I-CLiPs) catalyze the hydrolysis of peptide bonds within the transmembrane regions of membrane protein substrates, releasing bioactive fragments that play roles in many physiological and pathological processes. Based on their catalytic mechanism and nucleophile, I-CLiPs are classified into metallo, serine, aspartyl, and glutamyl proteases. Presenilin is the most prominent among I-CLiPs, as the catalytic subunit of γ-secretase (GS) complex responsible for cleaving the amyloid precursor protein (APP) and Notch, as well as many other membrane substrates. Recent cryo-electron microscopy (cryo-EM) structures of GS provide new details on how presenilin recognizes and cleaves APP and Notch. First, presenilin transmembrane helix (TM) 2 and 6 are dynamic. Second, upon binding to GS, the substrate TM helix is unwound from the C-terminus, resulting in an intermolecular β-sheet between the substrate and presenilin. The transition of the substrate C-terminus from α-helix to β-sheet is proposed to expose the scissile peptide bond in an extended conformation, leaving it susceptible to protease cleavage. Despite the astounding new insights in recent years, many crucial questions remain unanswered regarding the inner workings of γ-secretase, however. Key unanswered questions include how the enzyme recognizes and recruits substrates, how substrates are translocated from an initial docking site to the active site, how active site aspartates recruit and coordinate catalytic water, and the nature of the mechanisms of processive trimming of the substrate and product release. Answering these questions will have important implications for drug discovery aimed at selectively reducing the amyloid load in Alzheimer's disease (AD) with minimal side effects.
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Affiliation(s)
- Xinyue Liu
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, United States
| | - Iban Ubarretxena-Belandia
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Scott Forth
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Raquel L. Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
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31
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Cai T, Tomita T. Structure-activity relationship of presenilin in γ-secretase-mediated intramembrane cleavage. Semin Cell Dev Biol 2020; 105:102-109. [PMID: 32171519 DOI: 10.1016/j.semcdb.2020.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 01/12/2023]
Abstract
Genetic research on familial cases of Alzheimer disease have identified presenilin (PS) as an important membrane protein in the pathomechanism of this disease. PS is the catalytic subunit of γ-secretase, which is responsible for the generation of amyloid-β peptide deposited in the brains of Alzheimer disease patients. γ-Secretase is an atypical protease composed of four membrane proteins (i.e., presenilin, nicastrin, anterior pharynx defective-1 (Aph-1), and presenilin enhancer-2 (Pen-2)) and mediates intramembrane proteolysis. Numerous investigations have been conducted toward understanding the structural features of γ-secretase components as well as the cleavage mechanism of γ-secretase. In this review, we summarize our current understanding of the structure and activity relationship of the γ-secretase complex.
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Affiliation(s)
- Tetsuo Cai
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Taisuke Tomita
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
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32
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Zhang S, Cai F, Wu Y, Bozorgmehr T, Wang Z, Zhang S, Huang D, Guo J, Shen L, Rankin C, Tang B, Song W. A presenilin-1 mutation causes Alzheimer disease without affecting Notch signaling. Mol Psychiatry 2020; 25:603-613. [PMID: 29915376 DOI: 10.1038/s41380-018-0101-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/19/2018] [Accepted: 05/09/2018] [Indexed: 02/01/2023]
Abstract
Presenilin-1 (PSEN1) is the catalytic subunit of the γ-secretase complex, and pathogenic mutations in the PSEN1 gene account for the majority cases of familial AD (FAD). FAD-associated mutant PSEN1 proteins have been shown to affect APP processing and Aβ generation and inhibit Notch1 cleavage and Notch signaling. In this report, we found that a PSEN1 mutation (S169del) altered APP processing and Aβ generation, and promoted neuritic plaque formation as well as learning and memory deficits in AD model mice. However, this mutation did not affect Notch1 cleavage and Notch signaling in vitro and in vivo. Taken together, we demonstrated that PSEN1S169del has distinct effects on APP processing and Notch1 cleavage, suggesting that Notch signaling may not be critical for AD pathogenesis and serine169 could be a critical site as a potential target for the development of novel γ-secretase modulators without affecting Notch1 cleavage to treat AD.
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Affiliation(s)
- Shuting Zhang
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Fang Cai
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Yili Wu
- Department of Psychiatry, Graduate Program in Psychiatry, Jining Medical University, Jining, China
| | - Tahereh Bozorgmehr
- Department of Psychology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Zhe Wang
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Si Zhang
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Daochao Huang
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, 400014, Chongqing, China
| | - Jifeng Guo
- Department of Neurology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lu Shen
- Department of Neurology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Catharine Rankin
- Department of Psychology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Beisha Tang
- Department of Neurology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Weihong Song
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada.
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33
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Zhao J, Xiao Y, Liu X, Kim S, Wu X, Barros M, Zhuang R, Hou X, Zhang Y, Robakis NK, Li YM, Dordick JS, Ubarretxena-Belandia I, Wang C. Substrate interaction inhibits γ-secretase production of amyloid-β peptides. Chem Commun (Camb) 2020; 56:2578-2581. [PMID: 32016207 PMCID: PMC8219260 DOI: 10.1039/c9cc09170j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Combining NMR, mass spectrometry, AlphaLISA and cell assays, we discovered a compound C1 that binds C-terminal juxtamembrane lysines at the transmembrane domain of the amyloid precursor protein (APPTM) and inhibits γ-secretase production of amyloid-β with μM IC50. Our work suggests that targeting APPTM is a novel and viable strategy in AD drug discovery.
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Affiliation(s)
- Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Yuanyuan Xiao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Xinyue Liu
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Soohyun Kim
- Center for Molecular Biology and Genetics of Neurodegeneration, Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xianzhong Wu
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marilia Barros
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ran Zhuang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Nikolaos K Robakis
- Center for Molecular Biology and Genetics of Neurodegeneration, Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jonathan S Dordick
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA. and Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Iban Ubarretxena-Belandia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA and Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, E-48940, Leioa, Spain and Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA. and Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA and Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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34
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Bolla JR, Corey RA, Sahin C, Gault J, Hummer A, Hopper JTS, Lane DP, Drew D, Allison TM, Stansfeld PJ, Robinson CV, Landreh M. A Mass‐Spectrometry‐Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jani Reddy Bolla
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Robin A. Corey
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
- Department of BiologyUniversity of Copenhagen Copenhagen N 2200 Denmark
| | - Joseph Gault
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Alissa Hummer
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
| | - Jonathan T. S. Hopper
- OMass Therapeutics The Oxford Science Park, The Schrödinger Building Kidlington OX4 4GE UK
| | - David P. Lane
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
| | - David Drew
- Department of Biochemistry and BiophysicsStockholm University 10691 Stockholm Sweden
| | - Timothy M. Allison
- Biomolecular Interaction Centre and School of Physical and Chemical SciencesUniversity of Canterbury Christchurch 8140 New Zealand
| | - Phillip J. Stansfeld
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
- School of Life Sciences & Department of ChemistryUniversity of Warwick Coventry CV4 7AL UK
| | - Carol V. Robinson
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
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35
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Bolla JR, Corey RA, Sahin C, Gault J, Hummer A, Hopper JTS, Lane DP, Drew D, Allison TM, Stansfeld PJ, Robinson CV, Landreh M. A Mass-Spectrometry-Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins. Angew Chem Int Ed Engl 2020; 59:3523-3528. [PMID: 31886601 PMCID: PMC7065234 DOI: 10.1002/anie.201914411] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/29/2019] [Indexed: 01/21/2023]
Abstract
Membrane proteins engage in a variety of contacts with their surrounding lipids, but distinguishing between specifically bound lipids, and non-specific, annular interactions is a challenging problem. Applying native mass spectrometry to three membrane protein complexes with different lipid-binding properties, we explore the ability of detergents to compete with lipids bound in different environments. We show that lipids in annular positions on the presenilin homologue protease are subject to constant exchange with detergent. By contrast, detergent-resistant lipids bound at the dimer interface in the leucine transporter show decreased koff rates in molecular dynamics simulations. Turning to the lipid flippase MurJ, we find that addition of the natural substrate lipid-II results in the formation of a 1:1 protein-lipid complex, where the lipid cannot be displaced by detergent from the highly protected active site. In summary, we distinguish annular from non-annular lipids based on their exchange rates in solution.
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Affiliation(s)
- Jani Reddy Bolla
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Robin A. Corey
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet17165SolnaSweden
- Department of BiologyUniversity of CopenhagenCopenhagen N2200Denmark
| | - Joseph Gault
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Alissa Hummer
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Jonathan T. S. Hopper
- OMass TherapeuticsThe Oxford Science Park, The Schrödinger BuildingKidlingtonOX4 4GEUK
| | - David P. Lane
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet17165SolnaSweden
| | - David Drew
- Department of Biochemistry and BiophysicsStockholm University10691StockholmSweden
| | - Timothy M. Allison
- Biomolecular Interaction Centre and School of Physical and Chemical SciencesUniversity of CanterburyChristchurch8140New Zealand
| | - Phillip J. Stansfeld
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
- School of Life Sciences & Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
| | - Carol V. Robinson
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet17165SolnaSweden
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36
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Barniol-Xicota M, Verhelst SHL. Isolation of intramembrane proteases in membrane-like environments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183193. [PMID: 31945321 DOI: 10.1016/j.bbamem.2020.183193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 12/24/2022]
Abstract
Intramembrane proteases (IMPs) are proteolytic enzymes embedded in the lipid bilayer, where they cleave transmembrane substrates. The importance of IMPs relies on their role in a wide variety of cellular processes and diseases. In order to study the activity and function of IMPs, their purified form is often desired. The production of pure and active IMPs has proven to be a challenging task. This process unavoidably requires the use of solubilizing agents that will, to some extent, alter the native environment of these proteases. In this review we present the current solubilization and reconstitution techniques that have been applied to IMPs. In addition, we describe how these techniques had an influence on the activity and structural studies of IMPs, focusing on rhomboid proteases and γ-secretase.
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Affiliation(s)
- Marta Barniol-Xicota
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49, Box 802, B-3000, Belgium.
| | - Steven H L Verhelst
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49, Box 802, B-3000, Belgium; Leibniz Institute for Analytical Sciences, ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany.
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37
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Popugaeva E, Bezprozvanny I, Chernyuk D. Reversal of Calcium Dysregulation as Potential Approach for Treating Alzheimer's Disease. Curr Alzheimer Res 2020; 17:344-354. [PMID: 32469698 PMCID: PMC8210816 DOI: 10.2174/1567205017666200528162046] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 02/25/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023]
Abstract
Despite decades of research and effort, there is still no effective disease-modifying treatment for Alzheimer's Disease (AD). Most of the recent AD clinical trials were targeting amyloid pathway, but all these trials failed. Although amyloid pathology is a hallmark and defining feature of AD, targeting the amyloid pathway has been very challenging due to low efficacy and serious side effects. Alternative approaches or mechanisms for our understanding of the major cause of memory loss in AD need to be considered as potential therapeutic targets. Increasing studies suggest that Ca2+ dysregulation in AD plays an important role in AD pathology and is associated with other AD abnormalities, such as excessive inflammation, increased ROS, impaired autophagy, neurodegeneration, synapse, and cognitive dysfunction. Ca2+ dysregulation in cytosolic space, Endoplasmic Reticulum (ER) and mitochondria have been reported in the context of various AD models. Drugs or strategies, to correct the Ca2+ dysregulation in AD, have been demonstrated to be promising as an approach for the treatment of AD in preclinical models. This review will discuss the mechanisms of Ca2+ dysregulation in AD and associated pathology and discuss potential approaches or strategies to develop novel drugs for the treatment of AD by targeting Ca2+ dysregulation.
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Affiliation(s)
- Elena Popugaeva
- Department of Medical Physics, Laboratory of Molecular Neurodegeneration, Peter the Great St Petersburg Polytechnic University, St Petersburg, Russia
| | - Ilya Bezprozvanny
- Department of Physiology, UT Southwestern Medical Center, Dallas, USA
| | - Daria Chernyuk
- Department of Medical Physics, Laboratory of Molecular Neurodegeneration, Peter the Great St Petersburg Polytechnic University, St Petersburg, Russia
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38
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Mehra R, Dehury B, Kepp KP. Cryo-temperature effects on membrane protein structure and dynamics. Phys Chem Chem Phys 2020; 22:5427-5438. [DOI: 10.1039/c9cp06723j] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cryo-electron structures revolutionize biology, yet cooling effects are unclear. Using a simulation protocol of hot, cold, and rapidly cooled γ-secretase we identify cryo-contraction and modes relevant to Aβ production and cryo-analysis in general.
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Affiliation(s)
- Rukmankesh Mehra
- DTU Chemistry
- Technical University of Denmark
- DK-2800 Kongens Lyngby
- Denmark
| | - Budheswar Dehury
- DTU Chemistry
- Technical University of Denmark
- DK-2800 Kongens Lyngby
- Denmark
| | - Kasper P. Kepp
- DTU Chemistry
- Technical University of Denmark
- DK-2800 Kongens Lyngby
- Denmark
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39
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Beard HA, Barniol-Xicota M, Yang J, Verhelst SHL. Discovery of Cellular Roles of Intramembrane Proteases. ACS Chem Biol 2019; 14:2372-2388. [PMID: 31287658 DOI: 10.1021/acschembio.9b00404] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intramembrane proteases (IMPs) are localized within lipid bilayers of membranes-either the cell membrane or membranes of various organelles. Cleavage of substrates often results in release from the membrane, leading to a downstream biological effect. This mechanism allows different signaling events to happen through intramembrane proteolysis. Over the years, various mechanistically distinct families of IMPs have been discovered, but the research progress has generally been slower than for soluble proteases due to the challenges associated with membrane proteins. In this review we summarize how each mechanistic family of IMPs was discovered, which chemical tools are available for the study of IMPs, and which techniques have been developed for the discovery of IMP substrates. Finally, we discuss the various roles in cellular physiology of some of these IMPs.
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Affiliation(s)
- Hester A. Beard
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
| | - Marta Barniol-Xicota
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
| | - Jian Yang
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
| | - Steven H. L. Verhelst
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
- Leibniz Institute for Analytical Sciences ISAS, Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
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40
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Glaser T, Arnaud Sampaio VF, Lameu C, Ulrich H. Calcium signalling: A common target in neurological disorders and neurogenesis. Semin Cell Dev Biol 2019; 95:25-33. [DOI: 10.1016/j.semcdb.2018.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022]
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41
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Dehury B, Tang N, Kepp KP. Insights into membrane-bound presenilin 2 from all-atom molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:3196-3210. [PMID: 31405326 DOI: 10.1080/07391102.2019.1655481] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Presenilins 1 and 2 (PS1 or PS2) are main genetic risk factors of familial Alzheimer's disease (AD) that produce the β-amyloid (Aβ) peptides and also have important stand-alone functions related to, e.g. calcium signaling. Most work so far has focused on PS1, but humans carry both PS1 and PS2, and mutations in both cause AD. Here, we develop a computational model of PS2 in the membrane to address the question how pathogenic PS2 mutations affect the membrane-embedded protein. The models are based on cryo-electron microscopy structures of PS1 translated to PS2, augmented with missing residues and a complete all-atom membrane-water system, and equilibrated using three independent 500-ns simulations of molecular dynamics with a structure-balanced force field. We show that the nine-transmembrane channel structure is substantially controlled by major dynamics in the hydrophilic loop bridging TM6 and TM7, which functions as a 'plug' in the PS2 membrane channel. TM2, TM6, TM7 and TM9 flexibility controls the size of this channel. We find that most pathogenic PS2 mutations significantly reduce stability relative to random mutations, using a statistical ANOVA test with all possible mutations in the affected sites as a control. The associated loss of compactness may also impair calcium affinity. Remarkably, similar properties of the open state are known to impair the binding of substrates to γ-secretase, and we thus argue that the two mechanisms could be functionally related.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Budheswar Dehury
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ning Tang
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kasper P Kepp
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
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42
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Kühnle N, Dederer V, Lemberg MK. Intramembrane proteolysis at a glance: from signalling to protein degradation. J Cell Sci 2019; 132:132/16/jcs217745. [DOI: 10.1242/jcs.217745] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ABSTRACT
Over the last two decades, a group of unusual proteases, so-called intramembrane proteases, have become increasingly recognized for their unique ability to cleave peptide bonds within cellular membranes. They are found in all kingdoms of life and fulfil versatile functions ranging from protein maturation, to activation of signalling molecules, to protein degradation. In this Cell Science at a Glance article and the accompanying poster, we focus on intramembrane proteases in mammalian cells. By comparing intramembrane proteases in different cellular organelles, we set out to review their functions within the context of the roles of individual cellular compartments. Additionally, we exemplify their mode of action in relation to known substrates by distinguishing cleavage events that promote degradation of substrate from those that release active domains from the membrane bilayer.
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Affiliation(s)
- Nathalie Kühnle
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Verena Dederer
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Marius K. Lemberg
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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43
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Abstract
γ-Secretase is a membrane-embedded protease complex, with presenilin as the catalytic component containing two transmembrane aspartates in the active site. With more than 90 known substrates, the γ-secretase complex is considered "the proteasome of the membrane", with central roles in biology and medicine. The protease carries out hydrolysis within the lipid bilayer to cleave the transmembrane domain of the substrate multiple times before releasing secreted products. For many years, elucidation of γ-secretase structure and function largely relied on small-molecule probes and mutagenesis. Recently, however, advances in cryo-electron microscopy have led to the first detailed structures of the protease complex. Two new reports of structures of γ-secretase bound to membrane protein substrates provide great insight into the nature of substrate recognition and how Alzheimer's disease-causing mutations in presenilin might alter substrate binding and processing. These new structures offer a powerful platform for elucidating enzyme mechanisms, deciphering effects of disease-causing mutations, and advancing Alzheimer's disease drug discovery.
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Affiliation(s)
- Michael S Wolfe
- Department of Medicinal Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
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44
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Wu HH, Symersky J, Lu M. Structure of an engineered multidrug transporter MdfA reveals the molecular basis for substrate recognition. Commun Biol 2019; 2:210. [PMID: 31240248 PMCID: PMC6572762 DOI: 10.1038/s42003-019-0446-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/30/2019] [Indexed: 02/05/2023] Open
Abstract
MdfA is a prototypical H+-coupled multidrug transporter that is characterized by extraordinarily broad substrate specificity. The involvement of specific H-bonds in MdfA-drug interactions and the simplicity of altering the substrate specificity of MdfA contradict the promiscuous nature of multidrug recognition, presenting a baffling conundrum. Here we show the X-ray structures of MdfA variant I239T/G354E in complexes with three electrically different ligands, determined at resolutions up to 2.2 Å. Our structures reveal that I239T/G354E interacts with these compounds differently from MdfA and that I239T/G354E possesses two discrete, non-overlapping substrate-binding sites. Our results shed new light on the molecular design of multidrug-binding and protonation sites and highlight the importance of often-neglected, long-range charge-charge interactions in multidrug recognition. Beyond helping to solve the ostensible conundrum of multidrug recognition, our findings suggest the mechanistic difference between substrate and inhibitor for any H+-dependent multidrug transporter, which may open new vistas on curtailing efflux-mediated multidrug resistance.
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Affiliation(s)
- Hsin-Hui Wu
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064 USA
| | - Jindrich Symersky
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064 USA
| | - Min Lu
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064 USA
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45
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Aguayo‐Ortiz R, Guzmán‐Ocampo DC, Dominguez L. Toward the Characterization of DAPT Interactions with γ‐Secretase. ChemMedChem 2019; 14:1005-1010. [DOI: 10.1002/cmdc.201900106] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/26/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Rodrigo Aguayo‐Ortiz
- Facultad de QuímicaDepartamento de FisicoquímicaUniversidad Nacional Autónoma de México Mexico City 04510 Mexico
| | - Dulce C. Guzmán‐Ocampo
- Facultad de QuímicaDepartamento de FisicoquímicaUniversidad Nacional Autónoma de México Mexico City 04510 Mexico
| | - Laura Dominguez
- Facultad de QuímicaDepartamento de FisicoquímicaUniversidad Nacional Autónoma de México Mexico City 04510 Mexico
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46
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Brown MC, Abdine A, Chavez J, Schaffner A, Torres-Arancivia C, Lada B, JiJi RD, Osman R, Cooley JW, Ubarretxena-Belandia I. Unwinding of the Substrate Transmembrane Helix in Intramembrane Proteolysis. Biophys J 2019; 114:1579-1589. [PMID: 29642028 DOI: 10.1016/j.bpj.2018.01.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/19/2017] [Accepted: 01/08/2018] [Indexed: 10/17/2022] Open
Abstract
Intramembrane-cleaving proteases (I-CLiPs) activate pools of single-pass helical membrane protein signaling precursors that are key in the physiology of prokaryotic and eukaryotic cells. Proteases typically cleave peptide bonds within extended or flexible regions of their substrates, and thus the mechanism underlying the ability of I-CLiPs to hydrolyze the presumably α-helical transmembrane domain (TMD) of these membrane proteins is unclear. Using deep-ultraviolet resonance Raman spectroscopy in combination with isotopic labeling, we show that although predominantly in canonical α-helical conformation, the TMD of the established I-CLiP substrate Gurken displays 310-helical geometry. As measured by microscale thermophoresis, this substrate binds with high affinity to the I-CLiPs GlpG rhomboid and MCMJR1 presenilin homolog in detergent micelles. Binding results in deep-ultraviolet resonance Raman spectra, indicating conformational changes consistent with unwinding of the 310-helical region of the substrate's TMD. This 310-helical conformation is key for intramembrane proteolysis, as the substitution of a single proline residue in the TMD of Gurken by alanine suppresses 310-helical content in favor of α-helical geometry and abolishes cleavage without affecting binding to the I-CLiP. Complemented by molecular dynamics simulations of the TMD of Gurken, our vibrational spectroscopy data provide biophysical evidence in support of a model in which the transmembrane region of cleavable I-CLiP substrates displays local deviations in canonical α-helical conformation characterized by chain flexibility, and binding to the enzyme results in conformational changes that facilitate local unwinding of the transmembrane helix for cleavage.
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Affiliation(s)
- Mia C Brown
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - Alaa Abdine
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jose Chavez
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Adam Schaffner
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Celia Torres-Arancivia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brian Lada
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - Renee D JiJi
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - Roman Osman
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jason W Cooley
- Department of Chemistry, University of Missouri, Columbia, Missouri.
| | - Iban Ubarretxena-Belandia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain.
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47
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Naing SH, Oliver RC, Weiss KL, Urban VS, Lieberman RL. Solution Structure of an Intramembrane Aspartyl Protease via Small Angle Neutron Scattering. Biophys J 2019; 114:602-608. [PMID: 29414706 DOI: 10.1016/j.bpj.2017.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/04/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022] Open
Abstract
Intramembrane aspartyl proteases (IAPs) comprise one of four families of integral membrane proteases that hydrolyze substrates within the hydrophobic lipid bilayer. IAPs include signal peptide peptidase, which processes remnant signal peptides from nascent polypeptides in the endoplasmic reticulum, and presenilin, the catalytic component of the γ-secretase complex that processes Notch and amyloid precursor protein. Despite their broad biomedical reach, basic structure-function relationships of IAPs remain active areas of research. Characterization of membrane-bound proteins is notoriously challenging due to their inherently hydrophobic character. For IAPs, oligomerization state in solution is one outstanding question, with previous proposals for monomer, dimer, tetramer, and octamer. Here we used small angle neutron scattering (SANS) to characterize n-dodecyl-β-D-maltopyranoside (DDM) detergent solutions containing and absent a microbial IAP ortholog. A unique feature of SANS is the ability to modulate the solvent composition to mask all but the enzyme of interest. The signal from the IAP was enhanced by deuteration and, uniquely, scattering from DDM and buffers were matched by the use of both tail-deuterated DDM and D2O. The radius of gyration calculated for IAP and the corresponding ab initio consensus model are consistent with a monomer. The model is slightly smaller than the crystallographic IAP monomer, suggesting a more compact protein in solution compared with the crystal lattice. Our study provides direct insight into the oligomeric state of purified IAP in surfactant solution, and demonstrates the utility of fully contrast-matching the detergent in SANS to characterize other intramembrane proteases and their membrane-bound substrates.
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Affiliation(s)
- Swe-Htet Naing
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Ryan C Oliver
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia.
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48
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Quantifying correlations between mutational sites in the catalytic subunit of γ-secretase. J Mol Graph Model 2019; 88:221-227. [PMID: 30772652 DOI: 10.1016/j.jmgm.2019.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/17/2019] [Accepted: 02/01/2019] [Indexed: 11/22/2022]
Abstract
Presenilin 1 (PS1) is the catalytic subunit of the γ-secretase complex which is involved in the generation of amyloid-β peptides (Aβ). Single point mutations in PS1 alter the cleavage pattern of the amyloid precursor protein (APP) and lead to the formation of aberrant Aβ peptides. To date, more than two hundred mutations distributed among almost a third of PS1's amino acids have been associated to the development of Alzheimer's disease (AD). Nevertheless, the mechanism by which mutations far from the catalytic site alter the γ-secretase's cleavage pattern remains unclear. In this work we analyzed correlated motions between amino acids in the wild type (WT) enzyme and 13 γ-secretase mutant models employing a multi-scale molecular dynamics approach. The effect of the protonation state of key catalytic residue Asp385 on the correlation networks was also evaluated. We observed that the strength and number of correlations is highly influenced in all mutant models in both protonation state models. The biggest changes were observed in mutants I83T, W165G, H214Y and L435F; the latest has been proved to drastically reduce γ-secretase activity. Finally, we made a classification of the studied mutations according to their correlation networks with amino acids at: (1) the interfaces with the other γ-secretase components, (2) the catalytic site, (3) the substrate entry site and (4) the substrate recognition site. Overall, this work provides insight into the allosteric communication networks of PS1.
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49
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Schaduangrat N, Prachayasittikul V, Choomwattana S, Wongchitrat P, Phopin K, Suwanjang W, Malik AA, Vincent B, Nantasenamat C. Multidisciplinary approaches for targeting the secretase protein family as a therapeutic route for Alzheimer's disease. Med Res Rev 2019; 39:1730-1778. [PMID: 30628099 DOI: 10.1002/med.21563] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 11/21/2018] [Accepted: 12/24/2018] [Indexed: 12/27/2022]
Abstract
The continual increase of the aging population worldwide renders Alzheimer's disease (AD) a global prime concern. Several attempts have been focused on understanding the intricate complexity of the disease's development along with the on- andgoing search for novel therapeutic strategies. Incapability of existing AD drugs to effectively modulate the pathogenesis or to delay the progression of the disease leads to a shift in the paradigm of AD drug discovery. Efforts aimed at identifying AD drugs have mostly focused on the development of disease-modifying agents in which effects are believed to be long lasting. Of particular note, the secretase enzymes, a group of proteases responsible for the metabolism of the β-amyloid precursor protein (βAPP) and β-amyloid (Aβ) peptides production, have been underlined for their promising therapeutic potential. This review article attempts to comprehensively cover aspects related to the identification and use of drugs targeting the secretase enzymes. Particularly, the roles of secretases in the pathogenesis of AD and their therapeutic modulation are provided herein. Moreover, an overview of the drug development process and the contribution of computational (in silico) approaches for facilitating successful drug discovery are also highlighted along with examples of relevant computational works. Promising chemical scaffolds, inhibitors, and modulators against each class of secretases are also summarized herein. Additionally, multitarget secretase modulators are also taken into consideration in light of the current growing interest in the polypharmacology of complex diseases. Finally, challenging issues and future outlook relevant to the discovery of drugs targeting secretases are also discussed.
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Affiliation(s)
- Nalini Schaduangrat
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Veda Prachayasittikul
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Saowapak Choomwattana
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Prapimpun Wongchitrat
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Kamonrat Phopin
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Wilasinee Suwanjang
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Aijaz Ahmad Malik
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Bruno Vincent
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand.,Centre National de la Recherche Scientifique, Paris, France
| | - Chanin Nantasenamat
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
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50
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Proteolytic systems of archaea: slicing, dicing, and mincing in the extreme. Emerg Top Life Sci 2018; 2:561-580. [PMID: 32953999 DOI: 10.1042/etls20180025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Archaea are phylogenetically distinct from bacteria, and some of their proteolytic systems reflect this distinction. Here, the current knowledge of archaeal proteolysis is reviewed as it relates to protein metabolism, protein homeostasis, and cellular regulation including targeted proteolysis by proteasomes associated with AAA-ATPase networks and ubiquitin-like modification. Proteases and peptidases that facilitate the recycling of peptides to amino acids as well as membrane-associated and integral membrane proteases are also reviewed.
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