1
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Miao Y, Wolfe MS. Emerging structures and dynamic mechanisms of γ-secretase for Alzheimer's disease. Neural Regen Res 2025; 20:174-180. [PMID: 38767485 DOI: 10.4103/nrr.nrr-d-23-01781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/11/2024] [Indexed: 05/22/2024] Open
Abstract
γ-Secretase, called "the proteasome of the membrane," is a membrane-embedded protease complex that cleaves 150+ peptide substrates with central roles in biology and medicine, including amyloid precursor protein and the Notch family of cell-surface receptors. Mutations in γ-secretase and amyloid precursor protein lead to early-onset familial Alzheimer's disease. γ-Secretase has thus served as a critical drug target for treating familial Alzheimer's disease and the more common late-onset Alzheimer's disease as well. However, critical gaps remain in understanding the mechanisms of processive proteolysis of substrates, the effects of familial Alzheimer's disease mutations, and allosteric modulation of substrate cleavage by γ-secretase. In this review, we focus on recent studies of structural dynamic mechanisms of γ-secretase. Different mechanisms, including the "Fit-Stay-Trim," "Sliding-Unwinding," and "Tilting-Unwinding," have been proposed for substrate proteolysis of amyloid precursor protein by γ-secretase based on all-atom molecular dynamics simulations. While an incorrect registry of the Notch1 substrate was identified in the cryo-electron microscopy structure of Notch1-bound γ-secretase, molecular dynamics simulations on a resolved model of Notch1-bound γ-secretase that was reconstructed using the amyloid precursor protein-bound γ-secretase as a template successfully captured γ-secretase activation for proper cleavages of both wildtype and mutant Notch, being consistent with biochemical experimental findings. The approach could be potentially applied to decipher the processing mechanisms of various substrates by γ-secretase. In addition, controversy over the effects of familial Alzheimer's disease mutations, particularly the issue of whether they stabilize or destabilize γ-secretase-substrate complexes, is discussed. Finally, an outlook is provided for future studies of γ-secretase, including pathways of substrate binding and product release, effects of modulators on familial Alzheimer's disease mutations of the γ-secretase-substrate complexes. Comprehensive understanding of the functional mechanisms of γ-secretase will greatly facilitate the rational design of effective drug molecules for treating familial Alzheimer's disease and perhaps Alzheimer's disease in general.
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Affiliation(s)
- Yinglong Miao
- Computational Medicine Program and Department of Pharmacology, University of North Carolina - Chapel Hill, Chapel Hill, NC, USA
| | - Michael S Wolfe
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
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2
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Moser C, Guschtschin-Schmidt N, Silber M, Flum J, Muhle-Goll C. Substrate Selection Criteria in Regulated Intramembrane Proteolysis. ACS Chem Neurosci 2024; 15:1321-1334. [PMID: 38525994 DOI: 10.1021/acschemneuro.4c00068] [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] [Indexed: 03/26/2024] Open
Abstract
Alzheimer's disease is the most common form of dementia encountered in an aging population. Characteristic amyloid deposits of Aβ peptides in the brain are generated through cleavage of amyloid precursor protein (APP) by γ-secretase, an intramembrane protease. Cryo-EM structures of substrate γ-secretase complexes revealed details of the process, but how substrates are recognized and enter the catalytic site is still largely ignored. γ-Secretase cleaves a diverse range of substrate sequences without a common consensus sequence, but strikingly, single point mutations within the transmembrane domain (TMD) of specific substrates may greatly affect cleavage efficiencies. Previously, conformational flexibility was hypothesized to be the main criterion for substrate selection. Here we review the 3D structure and dynamics of several γ-secretase substrate TMDs and compare them with mutants shown to affect the cleavage efficiency. In addition, we present structural and dynamic data on ITGB1, a known nonsubstrate of γ-secretase. A comparison of biophysical details between these TMDs and changes generated by introducing crucial mutations allowed us to unravel common principles that differ between substrates and nonsubstrates. We identified three motifs in the investigated substrates: a highly flexible transmembrane domain, a destabilization of the cleavage region, and a basic signature at the end of the transmembrane helix. None of these appears to be exclusive. While conformational flexibility on its own may increase cleavage efficiency in well-known substrates like APP or Notch1, our data suggest that the three motifs seem to be rather variably combined to determine whether a transmembrane helix is efficiently recognized as a γ-secretase substrate.
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Affiliation(s)
- Celine Moser
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Nadja Guschtschin-Schmidt
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Mara Silber
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Julia Flum
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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3
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Hua Z, Watanabe R, Fukunaga T, Matsui Y, Matsuoka M, Yamaguchi S, Tanabe SY, Yamamoto M, Tamura-Kawakami K, Takagi J, Kajita M, Futai E, Shirakabe K. C-terminal amino acids in the type I transmembrane domain of L-type lectin VIP36 affect γ-secretase susceptibility. Biochem Biophys Res Commun 2024; 696:149504. [PMID: 38219489 DOI: 10.1016/j.bbrc.2024.149504] [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: 08/17/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
Regulated intramembrane proteolysis (RIP) is a two-step processing mechanism for transmembrane proteins consisting of ectodomain shedding (shedding), which removes the extracellular domain through juxtamembrane processing and intramembrane proteolysis, which processes membrane-anchored shedding products within the transmembrane domain. RIP irreversibly converts one transmembrane protein into multiple soluble proteins that perform various physiological functions. The only requirement for the substrate of γ-secretase, the major enzyme responsible for intramembrane proteolysis of type I transmembrane proteins, is the absence of a large extracellular domain, and it is thought that γ-secretase can process any type I membrane protein as long as it is shed. In the present study, we showed that the shedding susceptible type I membrane protein VIP36 (36 kDa vesicular integral membrane protein) and its homolog, VIPL, have different γ-secretase susceptibilities in their transmembrane domains. Analysis of the substitution mutants suggested that γ-secretase susceptibility is regulated by C-terminal amino acids in the transmembrane domain. We also compared the transmembrane domains of several shedding susceptible membrane proteins and found that each had a different γ-secretase susceptibility. These results suggest that the transmembrane domain is not simply a stretch of hydrophobic amino acids but is an important element that regulates membrane protein function by controlling the lifetime of the membrane-anchored shedding product.
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Affiliation(s)
- Zhihai Hua
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Ryoma Watanabe
- Laboratory of Enzymology, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi, 981-8572, Japan
| | - Taku Fukunaga
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Yojiro Matsui
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Mayu Matsuoka
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Shoya Yamaguchi
- Laboratory of Enzymology, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi, 981-8572, Japan
| | - Shun-Ya Tanabe
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Miyu Yamamoto
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Keiko Tamura-Kawakami
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Mihoko Kajita
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Eugene Futai
- Laboratory of Enzymology, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi, 981-8572, Japan
| | - Kyoko Shirakabe
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan; Ritsumeikan Global Innovation Research Institute, Ritsumeikan University, Kusatsu, 525-8577, Japan.
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4
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Aßfalg M, Güner G, Müller SA, Breimann S, Langosch D, Muhle-Goll C, Frishman D, Steiner H, Lichtenthaler SF. Cleavage efficiency of the intramembrane protease γ-secretase is reduced by the palmitoylation of a substrate's transmembrane domain. FASEB J 2024; 38:e23442. [PMID: 38275103 DOI: 10.1096/fj.202302152r] [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: 10/26/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024]
Abstract
The intramembrane protease γ-secretase has broad physiological functions, but also contributes to Notch-dependent tumors and Alzheimer's disease. While γ-secretase cleaves numerous membrane proteins, only few nonsubstrates are known. Thus, a fundamental open question is how γ-secretase distinguishes substrates from nonsubstrates and whether sequence-based features or post-translational modifications of membrane proteins contribute to substrate recognition. Using mass spectrometry-based proteomics, we identified several type I membrane proteins with short ectodomains that were inefficiently or not cleaved by γ-secretase, including 'pituitary tumor-transforming gene 1-interacting protein' (PTTG1IP). To analyze the mechanism preventing cleavage of these putative nonsubstrates, we used the validated substrate FN14 as a backbone and replaced its transmembrane domain (TMD), where γ-cleavage occurs, with the one of nonsubstrates. Surprisingly, some nonsubstrate TMDs were efficiently cleaved in the FN14 backbone, demonstrating that a cleavable TMD is necessary, but not sufficient for cleavage by γ-secretase. Cleavage efficiencies varied by up to 200-fold. Other TMDs, including that of PTTG1IP, were still barely cleaved within the FN14 backbone. Pharmacological and mutational experiments revealed that the PTTG1IP TMD is palmitoylated, which prevented cleavage by γ-secretase. We conclude that the TMD sequence of a membrane protein and its palmitoylation can be key factors determining substrate recognition and cleavage efficiency by γ-secretase.
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Affiliation(s)
- Marlene Aßfalg
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Gökhan Güner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Stephan A Müller
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Stephan Breimann
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Department of Bioinformatics, School of Life Sciences, Technical University of Munich, Freising, Germany
- Biomedical Center (BMC), Division of Metabolic Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
| | | | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Harald Steiner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biomedical Center (BMC), Division of Metabolic Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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5
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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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6
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Ortner M, Guschtschin-Schmidt N, Stelzer W, Muhle-Goll C, Langosch D. Permissive Conformations of a Transmembrane Helix Allow Intramembrane Proteolysis by γ-Secretase. J Mol Biol 2023; 435:168218. [PMID: 37536392 DOI: 10.1016/j.jmb.2023.168218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
The intramembrane protease γ-secretase activates important signaling molecules, such as Notch receptors. It is still unclear, however, how different elements within the primary structure of substrate transmembrane domains (TMDs) contribute to their cleavability. Using a newly developed yeast-based cleavage assay, we identified three crucial regions within the TMDs of the paralogs Notch1 and Notch3 by mutational and gain-of-function approaches. The AAAA or AGAV motifs within the N-terminal half of the TMDs were found to confer strong conformational flexibility to these TMD helices, as determined by mutagenesis coupled to deuterium/hydrogen exchange. Crucial amino acids within the C-terminal half may support substrate docking into the catalytic cleft of presenilin, the enzymatic subunit of γ-secretase. Further, residues close to the C-termini of the TMDs may stabilize a tripartite β-sheet in the substrate/enzyme complex. NMR structures reveal different extents of helix bending as well as an ability to adopt widely differing conformational substates, depending on the sequence of the N-terminal half. The difference in cleavability between Notch1 and Notch3 TMDs is jointly determined by the conformational repertoires of the TMD helices and the sequences of the C-terminal half, as suggested by mutagenesis and building molecular models. In sum, cleavability of a γ-secretase substrate is enabled by different functions of cooperating TMD regions, which deepens our mechanistic understanding of substrate/non-substrate discrimination in intramembrane proteolysis.
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Affiliation(s)
- Martin Ortner
- Chair of Biopolymer Chemistry, Technical University of Munich, Freising, Germany
| | - Nadja Guschtschin-Schmidt
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Walter Stelzer
- Chair of Biopolymer Chemistry, Technical University of Munich, Freising, 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
| | - Dieter Langosch
- Chair of Biopolymer Chemistry, Technical University of Munich, Freising, Germany.
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7
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Chen SY, Feilen LP, Chávez-Gutiérrez L, Steiner H, Zacharias M. Enzyme-substrate hybrid β-sheet controls geometry and water access to the γ-secretase active site. Commun Biol 2023; 6:670. [PMID: 37355752 PMCID: PMC10290658 DOI: 10.1038/s42003-023-05039-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
γ-Secretase is an aspartyl intramembrane protease that cleaves the amyloid precursor protein (APP) involved in Alzheimer's disease pathology and other transmembrane proteins. Substrate-bound structures reveal a stable hybrid β-sheet immediately following the substrate scissile bond consisting of β1 and β2 from the enzyme and β3 from the substrate. Molecular dynamics simulations and enhanced sampling simulations demonstrate that the hybrid β-sheet stability is strongly correlated with the formation of a stable cleavage-compatible active geometry and it also controls water access to the active site. The hybrid β-sheet is only stable for substrates with 3 or more C-terminal residues beyond the scissile bond. The simulation model allowed us to predict the effect of Pro and Phe mutations that weaken the formation of the hybrid β-sheet which were confirmed by experimental testing. Our study provides a direct explanation why γ-secretase preferentially cleaves APP in steps of 3 residues and how the hybrid β-sheet facilitates γ-secretase proteolysis.
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Affiliation(s)
- Shu-Yu Chen
- Center of Functional Protein Assemblies, Technical University of Munich, Garching, Germany
| | - Lukas P Feilen
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Lucía Chávez-Gutiérrez
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven, Leuven, Belgium
| | - Harald Steiner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biomedical Center (BMC), Division of Metabolic Biochemistry, Faculty of Medicine, LMU Munich, Germany
| | - Martin Zacharias
- Center of Functional Protein Assemblies, Technical University of Munich, Garching, Germany.
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8
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Specific Mutations near the Amyloid Precursor Protein Cleavage Site Increase γ-Secretase Sensitivity and Modulate Amyloid-β Production. Int J Mol Sci 2023; 24:ijms24043970. [PMID: 36835396 PMCID: PMC9959964 DOI: 10.3390/ijms24043970] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/16/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Amyloid-β peptides (Aβs) are produced via cleavage of the transmembrane region of the amyloid precursor protein (APP) by γ-secretase and are responsible for Alzheimer's disease. Familial Alzheimer's disease (FAD) is associated with APP mutations that disrupt the cleavage reaction and increase the production of neurotoxic Aβs, i.e., Aβ42 and Aβ43. Study of the mutations that activate and restore the cleavage of FAD mutants is necessary to understand the mechanism of Aβ production. In this study, using a yeast reconstruction system, we revealed that one of the APP FAD mutations, T714I, severely reduced the cleavage, and identified secondary APP mutations that restored the cleavage of APP T714I. Some mutants were able to modulate Aβ production by changing the proportions of Aβ species when introduced into mammalian cells. Secondary mutations include proline and aspartate residues; proline mutations are thought to act through helical structural destabilization, while aspartate mutations are thought to promote interactions in the substrate binding pocket. Our results elucidate the APP cleavage mechanism and could facilitate drug discovery.
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9
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Cooperation of N- and C-terminal substrate transmembrane domain segments in intramembrane proteolysis by γ-secretase. Commun Biol 2023; 6:177. [PMID: 36792683 PMCID: PMC9931712 DOI: 10.1038/s42003-023-04470-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 01/11/2023] [Indexed: 02/17/2023] Open
Abstract
Intramembrane proteases play a pivotal role in biology and medicine, but how these proteases decode cleavability of a substrate transmembrane (TM) domain remains unclear. Here, we study the role of conformational flexibility of a TM domain, as determined by deuterium/hydrogen exchange, on substrate cleavability by γ-secretase in vitro and in cellulo. By comparing hybrid TMDs based on the natural amyloid precursor protein TM domain and an artificial poly-Leu non-substrate, we find that substrate cleavage requires conformational flexibility within the N-terminal half of the TMD helix (TM-N). Robust cleavability also requires the C-terminal TM sequence (TM-C) containing substrate cleavage sites. Since flexibility of TM-C does not correlate with cleavage efficiency, the role of the TM-C may be defined mainly by its ability to form a cleavage-competent state near the active site, together with parts of presenilin, the enzymatic component of γ-secretase. In sum, cleavability of a γ-secretase substrate appears to depend on cooperating TM domain segments, which deepens our mechanistic understanding of intramembrane proteolysis.
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10
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Banerjee A, Saha S, Tvedt NC, Yang LW, Bahar I. Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods. Curr Opin Struct Biol 2023; 78:102517. [PMID: 36587424 PMCID: PMC10038760 DOI: 10.1016/j.sbi.2022.102517] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 12/31/2022]
Abstract
Proteins sample an ensemble of conformers under physiological conditions, having access to a spectrum of modes of motions, also called intrinsic dynamics. These motions ensure the adaptation to various interactions in the cell, and largely assist in, if not determine, viable mechanisms of biological function. In recent years, machine learning frameworks have proven uniquely useful in structural biology, and recent studies further provide evidence to the utility and/or necessity of considering intrinsic dynamics for increasing their predictive ability. Efficient quantification of dynamics-based attributes by recently developed physics-based theories and models such as elastic network models provides a unique opportunity to generate data on dynamics for training ML models towards inferring mechanisms of protein function, assessing pathogenicity, or estimating binding affinities.
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Affiliation(s)
- Anupam Banerjee
- Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261, USA
| | - Satyaki Saha
- Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261, USA
| | - Nathan C Tvedt
- Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261, USA; Computational and Applied Mathematics and Statistics, The College of William and Mary, Williamsburg, VA 23185, USA
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, and PhD Program in Biomedical Artificial Intelligence, National Tsing Hua University, Hsinchu 300044, Taiwan; Physics Division, National Center for Theoretical Sciences, Taipei 106319, Taiwan
| | - Ivet Bahar
- Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261, USA.
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11
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Papadopoulou AA, Stelzer W, Silber M, Schlosser C, Spitz C, Haug-Kröper M, Straub T, Müller SA, Lichtenthaler SF, Muhle-Goll C, Langosch D, Fluhrer R. Helical stability of the GnTV transmembrane domain impacts on SPPL3 dependent cleavage. Sci Rep 2022; 12:20987. [PMID: 36470941 PMCID: PMC9722940 DOI: 10.1038/s41598-022-24772-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Signal-Peptide Peptidase Like-3 (SPPL3) is an intramembrane cleaving aspartyl protease that causes secretion of extracellular domains from type-II transmembrane proteins. Numerous Golgi-localized glycosidases and glucosyltransferases have been identified as physiological SPPL3 substrates. By SPPL3 dependent processing, glycan-transferring enzymes are deactivated inside the cell, as their active site-containing domain is cleaved and secreted. Thus, SPPL3 impacts on glycan patterns of many cellular and secreted proteins and can regulate protein glycosylation. However, the characteristics that make a substrate a favourable candidate for SPPL3-dependent cleavage remain unknown. To gain insights into substrate requirements, we investigated the function of a GxxxG motif located in the transmembrane domain of N-acetylglucosaminyltransferase V (GnTV), a well-known SPPL3 substrate. SPPL3-dependent secretion of the substrate's ectodomain was affected by mutations disrupting the GxxxG motif. Using deuterium/hydrogen exchange and NMR spectroscopy, we studied the effect of these mutations on the helix flexibility of the GnTV transmembrane domain and observed that increased flexibility facilitates SPPL3-dependent shedding and vice versa. This study provides first insights into the characteristics of SPPL3 substrates, combining molecular biology, biochemistry, and biophysical techniques and its results will provide the basis for better understanding the characteristics of SPPL3 substrates with implications for the substrates of other intramembrane proteases.
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Affiliation(s)
- Alkmini A. Papadopoulou
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| | - Walter Stelzer
- grid.6936.a0000000123222966Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Mara Silber
- grid.7892.40000 0001 0075 5874Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany ,grid.7892.40000 0001 0075 5874Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Christine Schlosser
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| | - Charlotte Spitz
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| | - Martina Haug-Kröper
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| | - Tobias Straub
- grid.5252.00000 0004 1936 973XCore Facility Bioinformatics, Biomedical Center, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Stephan A. Müller
- grid.424247.30000 0004 0438 0426DZNE – German Center for Neurodegenerative Diseases, Munich, Germany
| | - Stefan F. Lichtenthaler
- grid.424247.30000 0004 0438 0426DZNE – German Center for Neurodegenerative Diseases, Munich, Germany ,grid.15474.330000 0004 0477 2438Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany ,grid.452617.3Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Claudia Muhle-Goll
- grid.7892.40000 0001 0075 5874Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany ,grid.7892.40000 0001 0075 5874Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Dieter Langosch
- grid.6936.a0000000123222966Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Regina Fluhrer
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
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12
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A thermodynamic investigation of amyloid precursor protein processing by human γ-secretase. Commun Biol 2022; 5:837. [PMID: 35982231 PMCID: PMC9388646 DOI: 10.1038/s42003-022-03818-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/08/2022] [Indexed: 12/14/2022] Open
Abstract
Human γ-secretase cleaves the transmembrane domains (TMDs) of amyloid precursor protein (APP) into pathologically relevant amyloid-β peptides (Aβs). The detailed mechanisms of the unique endoproteolytic cleavage by the presenilin 1 domain (PS1) of γ-secretase are still poorly understood. Herein, we provide thermodynamic insights into how the α-helical APP TMD is processed by γ-secretase and elucidate the specificity of Aβ48/Aβ49 cleavage using unbiased molecular dynamics and bias-exchange metadynamics simulations. The thermodynamic data show that the unwinding of APP TMD is driven by water hydration in the intracellular pocket of PS1, and the scissile bond T32-L33 or L33-V34 of the APP TMD can slide down and up to interact with D257/D385 to achieve endoproteolysis. In the wild-type system, the L33-V34 scissile bond is more easily hijacked by D257/D385 than T32-L33, resulting in higher Aβ49 cleavage, while the T32N mutation on the APP TMD decreases the energy barrier of the sliding of the scissile bonds and increases the hydrogen bond occupancy for Aβ48 cleavage. In summary, the thermodynamic analysis elucidates possible mechanisms of APP TMD processing by PS1, which might facilitate rational drug design targeting γ-secretase. Thermodynamic analysis from unbiased molecular dynamics and bias-exchange metadynamics simulations reveals possible mechanisms on how γ-secretase cleaves the transmembrane domains of amyloid precursor protein into amyloid-β peptides.
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13
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Lu Y, Salsbury F, Derreumaux P. Impact of A2T and D23N mutations on C99 homodimer conformations. J Chem Phys 2022; 157:085102. [DOI: 10.1063/5.0101622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The proteolytic cleavage of C99 by γ-secretase is the last step in the production of amyloid-β (Aβ) peptides. Previous studies have shown that membrane lipid composition, cholesterol concentration, and mutation in the transmembrane helix modified the structures and fluctuations of C99. In this study, we performed atomistic molecular dynamics simulations of the homodimer of the 55-residue congener of the C-terminal domain of the amyloid protein precursor, C99(1-55), in a POPC-cholesterol lipid bilayer, and we compared the conformational ensemble of WT sequence to those of the A2T and D23N variants. These mutations are particularly interesting as the protective Alzheimer's disease (AD) A2T mutation is known to decrease Aβ production, whereas the early onset AD D23N mutation does not affect Aβ production. We found noticeable differences in the structural ensembles of the three sequences. In particular, A2T varies from both WT and D23N by having long-range effects on the population of the extracellular justamembrane helix, the interface between the G29xxx-G33xxx-G37 motifs and the fluctuations of the transmembrane helical topologies.
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Affiliation(s)
- Yan Lu
- School of Physics, Xidian University, China
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14
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Siebert V, Silber M, Heuten E, Muhle-Goll C, Lemberg MK. Cleavage of mitochondrial homeostasis regulator PGAM5 by the intramembrane protease PARL is governed by transmembrane helix dynamics and oligomeric state. J Biol Chem 2022; 298:102321. [PMID: 35921890 PMCID: PMC9436811 DOI: 10.1016/j.jbc.2022.102321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/07/2022] Open
Abstract
The intramembrane protease PARL acts as a crucial mitochondrial safeguard by cleaving the mitophagy regulators PINK1 and PGAM5. Depending on the stress level, PGAM5 can either stimulate cell survival or cell death. In contrast to PINK1, which is constantly cleaved in healthy mitochondria and only active when the inner mitochondrial membrane is depolarized, PGAM5 processing is inversely regulated. However, determinants of PGAM5 that indicate it as a conditional substrate for PARL have not been rigorously investigated, and it is unclear how uncoupling the mitochondrial membrane potential affects its processing compared to that of PINK1. Here, we show that several polar transmembrane residues in PGAM5 distant from the cleavage site serve as determinants for its PARL-catalyzed cleavage. Our NMR analysis indicates that a short N-terminal amphipathic helix, followed by a kink and a C-terminal transmembrane helix harboring the scissile peptide bond are key for a productive interaction with PARL. Furthermore, we also show that PGAM5 is stably inserted into the inner mitochondrial membrane until uncoupling the membrane potential triggers its disassembly into monomers, which are then cleaved by PARL. In conclusion, we propose a model in which PGAM5 is slowly processed by PARL-catalyzed cleavage that is influenced by multiple hierarchical substrate features, including a membrane potential–dependent oligomeric switch.
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15
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Bhattarai A, Devkota S, Do HN, Wang J, Bhattarai S, Wolfe MS, Miao Y. Mechanism of Tripeptide Trimming of Amyloid β-Peptide 49 by γ-Secretase. J Am Chem Soc 2022; 144:6215-6226. [PMID: 35377629 PMCID: PMC9798850 DOI: 10.1021/jacs.1c10533] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The membrane-embedded γ-secretase complex processively cleaves within the transmembrane domain of amyloid precursor protein (APP) to produce 37-to-43-residue amyloid β-peptides (Aβ) of Alzheimer's disease (AD). Despite its importance in pathogenesis, the mechanism of processive proteolysis by γ-secretase remains poorly understood. Here, mass spectrometry and Western blotting were used to quantify the efficiency of tripeptide trimming of wild-type (WT) and familial AD (FAD) mutant Aβ49. In comparison to WT Aβ49, the efficiency of tripeptide trimming was similar for the I45F, A42T, and V46F Aβ49 FAD mutants but substantially diminished for the I45T and T48P mutants. In parallel with biochemical experiments, all-atom simulations using a novel peptide Gaussian accelerated molecular dynamics (Pep-GaMD) method were applied to investigate the tripeptide trimming of Aβ49 by γ-secretase. The starting structure was the active γ-secretase bound to Aβ49 and APP intracellular domain (AICD), as generated from our previous study that captured the activation of γ-secretase for the initial endoproteolytic cleavage of APP (Bhattarai, A., ACS Cent. Sci. 2020, 6, 969-983). Pep-GaMD simulations captured remarkable structural rearrangements of both the enzyme and substrate, in which hydrogen-bonded catalytic aspartates and water became poised for tripeptide trimming of Aβ49 to Aβ46. These structural changes required a positively charged N-terminus of endoproteolytic coproduct AICD, which could dissociate during conformational rearrangements of the protease and Aβ49. The simulation findings were highly consistent with biochemical experimental data. Taken together, our complementary biochemical experiments and Pep-GaMD simulations have enabled elucidation of the mechanism of tripeptide trimming of Aβ49 by γ-secretase.
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Affiliation(s)
- Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Sujan Devkota
- Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
| | - Hung Nguyen Do
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Sanjay Bhattarai
- Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
| | - Michael S. Wolfe
- Corresponding Authors Michael S. Wolfe – Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States; ; Yinglong Miao – Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States;
| | - Yinglong Miao
- Corresponding Authors Michael S. Wolfe – Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States; ; Yinglong Miao – Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States;
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16
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Corin K, Bowie JU. How physical forces drive the process of helical membrane protein folding. EMBO Rep 2022; 23:e53025. [PMID: 35133709 PMCID: PMC8892262 DOI: 10.15252/embr.202153025] [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] [Received: 04/07/2021] [Revised: 07/17/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Protein folding is a fundamental process of life with important implications throughout biology. Indeed, tens of thousands of mutations have been associated with diseases, and most of these mutations are believed to affect protein folding rather than function. Correct folding is also a key element of design. These factors have motivated decades of research on protein folding. Unfortunately, knowledge of membrane protein folding lags that of soluble proteins. This gap is partly caused by the greater technical challenges associated with membrane protein studies, but also because of additional complexities. While soluble proteins fold in a homogenous water environment, membrane proteins fold in a setting that ranges from bulk water to highly charged to apolar. Thus, the forces that drive folding vary in different regions of the protein, and this complexity needs to be incorporated into our understanding of the folding process. Here, we review our understanding of membrane protein folding biophysics. Despite the greater challenge, better model systems and new experimental techniques are starting to unravel the forces and pathways in membrane protein folding.
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Affiliation(s)
- Karolina Corin
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
| | - James U Bowie
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
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17
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Structural Studies Providing Insights into Production and Conformational Behavior of Amyloid-β Peptide Associated with Alzheimer's Disease Development. MOLECULES (BASEL, SWITZERLAND) 2021; 26:molecules26102897. [PMID: 34068293 PMCID: PMC8153327 DOI: 10.3390/molecules26102897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022]
Abstract
Alzheimer's disease is the most common type of neurodegenerative disease in the world. Genetic evidence strongly suggests that aberrant generation, aggregation, and/or clearance of neurotoxic amyloid-β peptides (Aβ) triggers the disease. Aβ accumulates at the points of contact of neurons in ordered cords and fibrils, forming the so-called senile plaques. Aβ isoforms of different lengths are found in healthy human brains regardless of age and appear to play a role in signaling pathways in the brain and to have neuroprotective properties at low concentrations. In recent years, different substances have been developed targeting Aβ production, aggregation, interaction with other molecules, and clearance, including peptide-based drugs. Aβ is a product of sequential cleavage of the membrane glycoprotein APP (amyloid precursor protein) by β- and γ-secretases. A number of familial mutations causing an early onset of the disease have been identified in the APP, especially in its transmembrane domain. The mutations are reported to influence the production, oligomerization, and conformational behavior of Aβ peptides. This review highlights the results of structural studies of the main proteins involved in Alzheimer's disease pathogenesis and the molecular mechanisms by which perspective therapeutic substances can affect Aβ production and nucleation.
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18
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Capone R, Tiwari A, Hadziselimovic A, Peskova Y, Hutchison JM, Sanders CR, Kenworthy AK. The C99 domain of the amyloid precursor protein resides in the disordered membrane phase. J Biol Chem 2021; 296:100652. [PMID: 33839158 PMCID: PMC8113881 DOI: 10.1016/j.jbc.2021.100652] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 12/11/2022] Open
Abstract
Processing of the amyloid precursor protein (APP) via the amyloidogenic pathway is associated with the etiology of Alzheimer's disease. The cleavage of APP by β-secretase to generate the transmembrane 99-residue C-terminal fragment (C99) and subsequent processing of C99 by γ-secretase to yield amyloid-β (Aβ) peptides are essential steps in this pathway. Biochemical evidence suggests that amyloidogenic processing of C99 occurs in cholesterol- and sphingolipid-enriched liquid-ordered phase membrane rafts. However, direct evidence that C99 preferentially associates with these rafts has remained elusive. Here, we tested this by quantifying the affinity of C99-GFP for raft domains in cell-derived giant plasma membrane vesicles (GPMVs). We found that C99 was essentially excluded from ordered domains in vesicles from HeLa cells, undifferentiated SH-SY5Y cells, or SH-SY5Y-derived neurons; instead, ∼90% of C99 partitioned into disordered domains. The strong association of C99 with disordered domains occurred independently of its cholesterol-binding activity or homodimerization, or of the presence of the familial Alzheimer disease Arctic mutation (APP E693G). Finally, through biochemical studies we confirmed previous results, which showed that C99 is processed in the plasma membrane by α-secretase, in addition to the well-known γ-secretase. These findings suggest that C99 itself lacks an intrinsic affinity for raft domains, implying that either i) amyloidogenic processing of the protein occurs in disordered regions of the membrane, ii) processing involves a marginal subpopulation of C99 found in rafts, or iii) as-yet-unidentified protein-protein interactions with C99 in living cells drive this protein into membrane rafts to promote its cleavage therein.
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Affiliation(s)
- Ricardo Capone
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Ajit Tiwari
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Yelena Peskova
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
| | - James M Hutchison
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Anne K Kenworthy
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA.
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19
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Spitz C, Schlosser C, Guschtschin-Schmidt N, Stelzer W, Menig S, Götz A, Haug-Kröper M, Scharnagl C, Langosch D, Muhle-Goll C, Fluhrer R. Non-canonical Shedding of TNFα by SPPL2a Is Determined by the Conformational Flexibility of Its Transmembrane Helix. iScience 2020; 23:101775. [PMID: 33294784 PMCID: PMC7689174 DOI: 10.1016/j.isci.2020.101775] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/22/2022] Open
Abstract
Ectodomain (EC) shedding defines the proteolytic removal of a membrane protein EC and acts as an important molecular switch in signaling and other cellular processes. Using tumor necrosis factor (TNF)α as a model substrate, we identify a non-canonical shedding activity of SPPL2a, an intramembrane cleaving aspartyl protease of the GxGD type. Proline insertions in the TNFα transmembrane (TM) helix strongly increased SPPL2a non-canonical shedding, while leucine mutations decreased this cleavage. Using biophysical and structural analysis, as well as molecular dynamic simulations, we identified a flexible region in the center of the TNFα wildtype TM domain, which plays an important role in the processing of TNFα by SPPL2a. This study combines molecular biology, biochemistry, and biophysics to provide insights into the dynamic architecture of a substrate's TM helix and its impact on non-canonical shedding. Thus, these data will provide the basis to identify further physiological substrates of non-canonical shedding in the future.
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Affiliation(s)
- Charlotte Spitz
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Universitätsstrasse 2, 86159 Augsburg, Germany
| | - Christine Schlosser
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Universitätsstrasse 2, 86159 Augsburg, Germany
| | - Nadja Guschtschin-Schmidt
- Karlsruhe Institute of Technology, Institute for Biological Interfaces 4, 76344 Eggenstein- Leopoldshafen, Germany and Karlsruhe Institute of Technology, Institute of Organic Chemistry, 76131 Karlsruhe, Germany
| | - Walter Stelzer
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Simon Menig
- Physics of Synthetic Biological Systems, Technische Universität München, Maximus-von-Imhof Forum 4, 85340 Freising, Germany
| | - Alexander Götz
- Present Address: Leibniz Supercomputing Centre, Boltzmannstr. 1, 85748 Garching, Germany
| | - Martina Haug-Kröper
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Universitätsstrasse 2, 86159 Augsburg, Germany
| | - Christina Scharnagl
- Physics of Synthetic Biological Systems, Technische Universität München, Maximus-von-Imhof Forum 4, 85340 Freising, Germany
| | - Dieter Langosch
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Claudia Muhle-Goll
- Karlsruhe Institute of Technology, Institute for Biological Interfaces 4, 76344 Eggenstein- Leopoldshafen, Germany and Karlsruhe Institute of Technology, Institute of Organic Chemistry, 76131 Karlsruhe, Germany
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Universitätsstrasse 2, 86159 Augsburg, Germany.,DZNE - German Center for Neurodegenerative Diseases, Feodor-Lynen-Str 17, 81377 Munich, Germany
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20
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Silber M, Hitzenberger M, Zacharias M, Muhle-Goll C. Altered Hinge Conformations in APP Transmembrane Helix Mutants May Affect Enzyme-Substrate Interactions of γ-Secretase. ACS Chem Neurosci 2020; 11:4426-4433. [PMID: 33232115 DOI: 10.1021/acschemneuro.0c00640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cleavage of substrates by γ-secretase is an inherently slow process where substrate-enzyme affinities cannot be broken down into specific sequence requirements in contrast to soluble proteases. Nevertheless, despite its apparent sequence tolerance single point mutations in amyloid precursor protein can severely affect cleavage efficiencies and change product line preferences. We have determined by NMR spectroscopy the structures of the transmembrane domain of amyloid precursor protein in TFE/water and compared it to that of four mutants: two FAD mutants, V44M and I45T, and the two diglycine hinge mutants, G38L and G38P. In accordance with previous publications, the transmembrane domain is composed of two helical segments connected by the diglycine hinge. Mutations alter kink angles and structural flexibility. Furthermore, to our surprise, we observe different, but specific mutual orientations of N- and C-terminal helical segments in the four mutants compared to the wildtype. We speculate that the observed orientations for G38L, G38P, V44M, and I45T lead to unfavorable interactions with γ-secretase exosites during substrate movement to the enzyme's active site in presenilin and/or for the accommodation into the substrate-binding cavity of presenilin.
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Affiliation(s)
- Mara Silber
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Manuel Hitzenberger
- Physics Department T38, Technical University of Munich, James-Frank-Str. 1, 85748 Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, James-Frank-Str. 1, 85748 Garching, Germany
| | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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21
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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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22
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Moreira RA, Guzman HV, Boopathi S, Baker JL, Poma AB. Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E5362. [PMID: 33255977 PMCID: PMC7730245 DOI: 10.3390/ma13235362] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 01/27/2023]
Abstract
The novel coronavirus disease 2019 (COVID-19) pandemic has disrupted modern societies and their economies. The resurgence in COVID-19 cases as part of the second wave is observed across Europe and the Americas. The scientific response has enabled a complete structural characterization of the Severe Acute Respiratory Syndrome-novel Coronavirus 2 (SARS-CoV-2). Among the most relevant proteins required by the novel coronavirus to facilitate the cell entry mechanism is the spike protein. This protein possesses a receptor-binding domain (RBD) that binds the cellular angiotensin-converting enzyme 2 (ACE2) and then triggers the fusion of viral and host cell membranes. In this regard, a comprehensive characterization of the structural stability of the spike protein is a crucial step to find new therapeutics to interrupt the process of recognition. On the other hand, it has been suggested that the participation of more than one RBD is a possible mechanism to enhance cell entry. Here, we discuss the protein structural stability based on the computational determination of the dynamic contact map and the energetic difference of the spike protein conformations via the mapping of the hydration free energy by the Poisson-Boltzmann method. We expect our result to foster the discussion of the number of RBD involved during recognition and the repurposing of new drugs to disable the recognition by discovering new hotspots for drug targets apart from the flexible loop in the RBD that binds the ACE2.
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Affiliation(s)
- Rodrigo A. Moreira
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland;
| | - Horacio V. Guzman
- Department of Theoretical Physics, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia;
| | - Subramanian Boopathi
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
| | - Joseph L. Baker
- Department of Chemistry, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, USA;
| | - Adolfo B. Poma
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland;
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23
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Vogel A, Bosse M, Gauglitz M, Wistuba S, Schmidt P, Kaiser A, Gurevich VV, Beck-Sickinger AG, Hildebrand PW, Huster D. The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation. Molecules 2020; 25:E5489. [PMID: 33255213 PMCID: PMC7727705 DOI: 10.3390/molecules25235489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 01/08/2023] Open
Abstract
We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical representative of class A peptide ligand GPCRs, using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were studied using 15N-NMR and quantitative determination of 1H-13C order parameters through the measurement of dipolar couplings in separated-local-field NMR experiments. Order parameters reporting the amplitudes of the molecular motions of the C-H bond vectors of Y1R in DMPC membranes are 0.57 for the Cα sites and lower in the side chains (0.37 for the CH2 and 0.18 for the CH3 groups). Different NMR excitation schemes identify relatively rigid and also dynamic segments of the molecule. In monounsaturated membranes composed of longer lipid chains, Y1R is more rigid, attributed to a higher hydrophobic thickness of the lipid membrane. The presence of an antagonist or NPY has little influence on the amplitude of motions, whereas the addition of agonist and arrestin led to a pronounced rigidization. To investigate Y1R dynamics with site resolution, we conducted extensive all-atom MD simulations of the apo and antagonist-bound state. In each state, three replicas with a length of 20 μs (with one exception, where the trajectory length was 10 μs) were conducted. In these simulations, order parameters of each residue were determined and showed high values in the transmembrane helices, whereas the loops and termini exhibit much lower order. The extracellular helix segments undergo larger amplitude motions than their intracellular counterparts, whereas the opposite is observed for the loops, Helix 8, and termini. Only minor differences in order were observed between the apo and antagonist-bound state, whereas the time scale of the motions is shorter for the apo state. Although these relatively fast motions occurring with correlation times of ns up to a few µs have no direct relevance for receptor activation, it is believed that they represent the prerequisite for larger conformational transitions in proteins.
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Affiliation(s)
- Alexander Vogel
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Mathias Bosse
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Marcel Gauglitz
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Sarah Wistuba
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Peter Schmidt
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Anette Kaiser
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Brüderstr. 34, D-04103 Leipzig, Germany; (A.K.); (A.G.B.-S.)
| | - Vsevolod V. Gurevich
- Vanderbilt University Medical Center, 2200 Pierce Avenue, Nashville, TN 37232, USA;
| | - Annette G. Beck-Sickinger
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Brüderstr. 34, D-04103 Leipzig, Germany; (A.K.); (A.G.B.-S.)
| | - Peter W. Hildebrand
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
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24
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Substrate recruitment by γ-secretase. Semin Cell Dev Biol 2020; 105:54-63. [DOI: 10.1016/j.semcdb.2020.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 12/27/2022]
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25
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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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26
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Steiner A, Schlepckow K, Brunner B, Steiner H, Haass C, Hagn F. γ-Secretase cleavage of the Alzheimer risk factor TREM2 is determined by its intrinsic structural dynamics. EMBO J 2020; 39:e104247. [PMID: 32830336 PMCID: PMC7560206 DOI: 10.15252/embj.2019104247] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/14/2022] Open
Abstract
Sequence variants of the microglial expressed TREM2 (triggering receptor expressed on myeloid cells 2) are a major risk factor for late onset Alzheimer's disease. TREM2 requires a stable interaction with DAP12 in the membrane to initiate signaling, which is terminated by TREM2 ectodomain shedding and subsequent intramembrane cleavage by γ‐secretase. To understand the structural basis for the specificity of the intramembrane cleavage event, we determined the solution structure of the TREM2 transmembrane helix (TMH). Caused by the presence of a charged amino acid in the membrane region, the TREM2‐TMH adopts a kinked structure with increased flexibility. Charge removal leads to TMH stabilization and reduced dynamics, similar to its structure in complex with DAP12. Strikingly, these dynamical features match with the site of the initial γ‐secretase cleavage event. These data suggest an unprecedented cleavage mechanism by γ‐secretase where flexible TMH regions act as key determinants of substrate cleavage specificity.
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Affiliation(s)
- Andrea Steiner
- Bavarian NMR Center at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kai Schlepckow
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
| | - Bettina Brunner
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
| | - Harald Steiner
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany.,Biomedical Center (BMC), Chair of Metabolic Biochemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany.,Biomedical Center (BMC), Chair of Metabolic Biochemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Franz Hagn
- Bavarian NMR Center at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
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27
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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: 20] [Impact Index Per Article: 5.0] [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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28
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Zhou R, Yang G, Shi Y. Macromolecular complex in recognition and proteolysis of amyloid precursor protein in Alzheimer's disease. Curr Opin Struct Biol 2019; 61:1-8. [PMID: 31629221 DOI: 10.1016/j.sbi.2019.09.004] [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: 08/24/2019] [Accepted: 09/07/2019] [Indexed: 12/31/2022]
Abstract
Proteolysis of amyloid precursor protein (APP), first extracellularly by β-secretase and then within the membrane by γ-secretase, produces β-amyloid peptides (Aβ). Aβ accumulates in the brain to form amyloid plaques, a hallmark of Alzheimer's disease (AD). Mutations in APP and presenilin (the catalytic subunit of γ-secretase) result in early onset of AD. Cryogenic electron microscopy (cryo-EM) structures of substrate-free and substrate-bound γ-secretase, determined at atomic resolutions, reveal the physical basis of distinct substrate specificity. These advances, together with the discovery and characterization of multiple proteins that interact with APP or presenilin, have given rise to an optimistic scenario for future mechanistic understanding of AD.
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Affiliation(s)
- Rui Zhou
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Guanghui Yang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou 310024, Zhejiang Province, China.
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29
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Stelzer W, Langosch D. Conformationally Flexible Sites within the Transmembrane Helices of Amyloid Precursor Protein and Notch1 Receptor. Biochemistry 2019; 58:3065-3068. [PMID: 31264841 DOI: 10.1021/acs.biochem.9b00505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Intramembrane proteases typically cleave multiple substrates within their transmembrane domains (TMDs). Because substrate TMDs lack a consensus sequence around their scissile sites, it remains unclear how the enzyme discriminates substrates from nonsubstrates at the level of their TMDs. Here, we compare the previously well investigated TMDs of γ-secretase substrates C99 and Notch1 in terms of helix flexibility. Our results reveal that the low-stability site neigboring a functionally relevant diglycine hinge of C99 has an equivalent in the Notch1 TMD. This suggests that the tetra-alanine motif of Notch1 also functions as a hinge which may facilitate its cleavage.
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Affiliation(s)
- Walter Stelzer
- Lehrstuhl Chemie der Biopolymere , Technische Universität München , Weihenstephaner Berg 3 , 85354 Freising , Germany.,Munich Center For Integrated Protein Science (CIPSM) , Munich Germany
| | - Dieter Langosch
- Lehrstuhl Chemie der Biopolymere , Technische Universität München , Weihenstephaner Berg 3 , 85354 Freising , Germany.,Munich Center For Integrated Protein Science (CIPSM) , Munich Germany
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