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Aguayo-Ortiz R, Straub JE, Dominguez L. Influence of membrane lipid composition on the structure and activity of γ-secretase. Phys Chem Chem Phys 2018; 20:27294-27304. [PMID: 30357233 PMCID: PMC11260083 DOI: 10.1039/c8cp04138e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
γ-Secretase (GS) is a multi-subunit membrane-embedded aspartyl protease that cleaves more than 80 integral membrane proteins, including the amyloid precursor protein (APP) to produce the amyloid-β (Aβ) peptide. Oligomerization and aggregation of the 42-amino acid length Aβ isoform in the brain has been associated with the development and progression of Alzheimer's disease (AD). Based on recent experimental structural studies and using multiscale computational modeling approaches, the conformational states and protein-membrane interactions of the GS complex embedded in six homogeneous and six heterogeneous lipid bilayers were characterized. In order to identify potential lipid and cholesterol binding sites, GS regions with high lipid/cholesterol occupancy values were analyzed using atomistic and coarse-grained simulations. Long lipid residence times were observed to be correlated with a large number of hydrogen bonds between the charged headgroups and key GS amino acids. This observation provides a plausible explanation for the inhibition of GS by charged lipids observed in previous experimental studies. Computed lateral pressure profiles suggest that higher transmembrane pressures favor active state conformations of the catalytic subunit. A probable mechanism for the regulation of the local stress response in cholesterol-rich multicomponent lipid bilayers is identified. Finally, it is demonstrated that interactions between the nicastrin extracellular domain and lipid headgroups leads to a compact structural conformation of the GS complex. Overall, this study provides valuable insight into the effect of bilayer lipid composition on the GS structural ensemble and its function.
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
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Popugaeva E, Pchitskaya E, Bezprozvanny I. Dysregulation of Intracellular Calcium Signaling in Alzheimer's Disease. Antioxid Redox Signal 2018; 29:1176-1188. [PMID: 29890840 PMCID: PMC6157344 DOI: 10.1089/ars.2018.7506] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
SIGNIFICANCE Calcium (Ca2+) hypothesis of Alzheimer's disease (AD) gains popularity. It points to new signaling pathways that may underlie AD pathogenesis. Based on calcium hypothesis, novel targets for the development of potential AD therapies are identified. Recent Advances: Recently, the key role of neuronal store-operated calcium entry (nSOCE) in the development of AD has been described. Correct regulation of nSOCE is necessary for the stability of postsynaptic contacts to preserve the memory formation. Molecular identity of hippocampal nSOCE is defined. Perspective nSOCE-activating molecule, prototype of future anti-AD drugs, is described. CRITICAL ISSUES Endoplasmic reticulum Ca2+ overload happens in many but not in all AD models. The nSOCE targeting therapy described in this review may not be universally applicable. FUTURE DIRECTIONS There is a need to determine whether AD is a syndrome with one critical signaling pathway that initiates pathology, or it is a disorder with many different signaling pathways that are disrupted simultaneously or one after each other. It is necessary to validate applicability of nSOCE-activating therapy for the development of anti-AD medication. There is an experimental correlation between downregulated nSOCE and disrupted postsynaptic contacts in AD mouse models. Signaling mechanisms downstream of nSOCE which are responsible for the regulation of stability of postsynaptic contacts have to be discovered. That will bring new targets for the development of AD-preventing therapies. Antioxid. Redox Signal. 29, 1176-1188.
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Affiliation(s)
- Elena Popugaeva
- 1 Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter the Great St.Petersburg Polytechnic University , St.Petersburg, Russian Federation
| | - Ekaterina Pchitskaya
- 1 Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter the Great St.Petersburg Polytechnic University , St.Petersburg, Russian Federation
| | - Ilya Bezprozvanny
- 1 Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter the Great St.Petersburg Polytechnic University , St.Petersburg, Russian Federation.,2 Department of Physiology, UT Southwestern Medical Center at Dallas , Dallas, Texas
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53
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Imai S, Cai T, Yoshida C, Tomita T, Futai E. Specific mutations in presenilin 1 cause conformational changes in γ-secretase to modulate amyloid β trimming. J Biochem 2018; 165:37-46. [DOI: 10.1093/jb/mvy081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/04/2018] [Indexed: 01/08/2023] Open
Affiliation(s)
- So Imai
- Department of Molecular and Cell Biology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiazaaoba, Aobaku, Sendai, Miyagi, Japan
| | - Tetsuo Cai
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Chika Yoshida
- Department of Molecular and Cell Biology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiazaaoba, Aobaku, Sendai, Miyagi, Japan
| | - Taisuke Tomita
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Eugene Futai
- Department of Molecular and Cell Biology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiazaaoba, Aobaku, Sendai, Miyagi, Japan
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54
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Clemente N, Abdine A, Ubarretxena-Belandia I, Wang C. Coupled Transmembrane Substrate Docking and Helical Unwinding in Intramembrane Proteolysis of Amyloid Precursor Protein. Sci Rep 2018; 8:12411. [PMID: 30120254 PMCID: PMC6098081 DOI: 10.1038/s41598-018-30015-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/23/2018] [Indexed: 12/03/2022] Open
Abstract
Intramembrane-cleaving proteases (I-CLiPs) play crucial roles in physiological and pathological processes, such as Alzheimer’s disease and cancer. However, the mechanisms of substrate recognition by I-CLiPs remain poorly understood. The aspartic I-CLiP presenilin is the catalytic subunit of the γ-secretase complex, which releases the amyloid-β peptides (Aβs) through intramembrane proteolysis of the transmembrane domain of the amyloid precursor protein (APPTM). Here we used solution NMR to probe substrate docking of APPTM to the presenilin homologs (PSHs) MCMJR1 and MAMRE50, which cleaved APPTM in the NMR tube. Chemical shift perturbation (CSP) showed juxtamembrane regions of APPTM mediate its docking to MCMJR1. Binding of the substrate to I-CLiP decreased the magnitude of amide proton chemical shifts δH at the C-terminal half of the substrate APPTM, indicating that the docking to the enzyme weakens helical hydrogen bonds and unwinds the substrate transmembrane helix around the initial ε-cleavage site. The APPTM V44M substitution linked to familial AD caused more CSP and helical unwinding around the ε-cleavage site. MAMRE50, which cleaved APPTM at a higher rate, also caused more CSP and helical unwinding in APPTM than MCMJR1. Our data suggest that docking of the substrate transmembrane helix and helical unwinding is coupled in intramembrane proteolysis and FAD mutation modifies enzyme/substrate interaction, providing novel insights into the mechanisms of I-CLiPs and AD drug discovery.
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Affiliation(s)
- Nicolina Clemente
- Biochemistry and Biophysics Graduate Program, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA
| | - Alaa Abdine
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Iban Ubarretxena-Belandia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Biofisika Institute (CSIC, UPV/EHU), Universidad del País Vasco (UPV/EHU), E-48940, Leioa, Spain
| | - Chunyu Wang
- Biochemistry and Biophysics Graduate Program, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA. .,Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA.
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55
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Lichtenthaler SF, Lemberg MK, Fluhrer R. Proteolytic ectodomain shedding of membrane proteins in mammals-hardware, concepts, and recent developments. EMBO J 2018; 37:e99456. [PMID: 29976761 PMCID: PMC6068445 DOI: 10.15252/embj.201899456] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/05/2018] [Accepted: 06/18/2018] [Indexed: 12/14/2022] Open
Abstract
Proteolytic removal of membrane protein ectodomains (ectodomain shedding) is a post-translational modification that controls levels and function of hundreds of membrane proteins. The contributing proteases, referred to as sheddases, act as important molecular switches in processes ranging from signaling to cell adhesion. When deregulated, ectodomain shedding is linked to pathologies such as inflammation and Alzheimer's disease. While proteases of the "a disintegrin and metalloprotease" (ADAM) and "beta-site APP cleaving enzyme" (BACE) families are widely considered as sheddases, in recent years a much broader range of proteases, including intramembrane and soluble proteases, were shown to catalyze similar cleavage reactions. This review demonstrates that shedding is a fundamental process in cell biology and discusses the current understanding of sheddases and their substrates, molecular mechanisms and cellular localizations, as well as physiological functions of protein ectodomain shedding. Moreover, we provide an operational definition of shedding and highlight recent conceptual advances in the field. While new developments in proteomics facilitate substrate discovery, we expect that shedding is not a rare exception, but rather the rule for many membrane proteins, and that many more interesting shedding functions await discovery.
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Affiliation(s)
- Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, Klinikum rechts der Isar, School of Medicine, and Institute for Advanced Study, Technical University Munich, Munich, Germany
- Munich Center for Systems Neurology (SyNergy), Munich, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Regina Fluhrer
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biomedizinisches Centrum (BMC), Ludwig-Maximilians University of Munich, Munich, Germany
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56
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Tong BCK, Wu AJ, Li M, Cheung KH. Calcium signaling in Alzheimer's disease & therapies. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1745-1760. [PMID: 30059692 DOI: 10.1016/j.bbamcr.2018.07.018] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/12/2018] [Accepted: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Alzheimer's disease (AD) is the most common type of dementia and is characterized by the accumulation of amyloid (Aβ) plaques and neurofibrillary tangles in the brain. Much attention has been given to develop AD treatments based on the amyloid cascade hypothesis; however, none of these drugs had good efficacy at improving cognitive functions in AD patients suggesting that Aβ might not be the disease origin. Thus, there are urgent needs for the development of new therapies that target on the proximal cause of AD. Cellular calcium (Ca2+) signals regulate important facets of neuronal physiology. An increasing body of evidence suggests that age-related dysregulation of neuronal Ca2+ homeostasis may play a proximal role in the pathogenesis of AD as disrupted Ca2+ could induce synaptic deficits and promote the accumulation of Aβ plaques and neurofibrillary tangles. Given that Ca2+ disruption is ubiquitously involved in all AD pathologies, it is likely that using chemical agents or small molecules specific to Ca2+ channels or handling proteins on the plasma membrane and membranes of intracellular organelles to correct neuronal Ca2+ dysregulation could open up a new approach to AD prevention and treatment. This review summarizes current knowledge on the molecular mechanisms linking Ca2+ dysregulation with AD pathologies and discusses the possibility of correcting neuronal Ca2+ disruption as a therapeutic approach for AD.
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Affiliation(s)
- Benjamin Chun-Kit Tong
- School of Chinese Medicine, Hong Kong Baptist University, 7 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong, China
| | - Aston Jiaxi Wu
- School of Chinese Medicine, Hong Kong Baptist University, 7 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong, China
| | - Min Li
- School of Chinese Medicine, Hong Kong Baptist University, 7 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong, China
| | - King-Ho Cheung
- School of Chinese Medicine, Hong Kong Baptist University, 7 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong, China.
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57
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Götz A, Scharnagl C. Dissecting conformational changes in APP's transmembrane domain linked to ε-efficiency in familial Alzheimer's disease. PLoS One 2018; 13:e0200077. [PMID: 29966005 PMCID: PMC6028146 DOI: 10.1371/journal.pone.0200077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/19/2018] [Indexed: 02/02/2023] Open
Abstract
The mechanism by which familial Alzheimer's disease (FAD) mutations within the transmembrane domain (TMD) of the Amyloid Precursor Protein (APP) affect ε-endoproteolysis is only poorly understood. Thereby, mutations in the cleavage domain reduce ε-efficiency of γ-secretase cleavage and some even shift entry into production lines. Since cleavage occurs within the TMD, a relationship between processing and TMD structure and dynamics seems obvious. Using molecular dynamic simulations, we dissect the dynamic features of wild-type and seven FAD-mutants into local and global components. Mutations consistently enhance hydrogen-bond fluctuations upstream of the ε-cleavage sites but maintain strong helicity there. Dynamic perturbation-response scanning reveals that FAD-mutants target backbone motions utilized in the bound state. Those motions, obscured by large-scale motions in the pre-bound state, provide (i) a dynamic mechanism underlying the proposed coupling between binding and ε-cleavage, (ii) key sites consistent with experimentally determined docking sites, and (iii) the distinction between mutants and wild-type.
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Affiliation(s)
- Alexander Götz
- Technical University of Munich, Chair of Physics of Synthetic Biological Systems, Freising, Germany
| | - Christina Scharnagl
- Technical University of Munich, Chair of Physics of Synthetic Biological Systems, Freising, Germany
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58
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Aguayo-Ortiz R, Dominguez L. Simulating the γ-secretase enzyme: Recent advances and future directions. Biochimie 2018; 147:130-135. [DOI: 10.1016/j.biochi.2018.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/27/2018] [Indexed: 11/17/2022]
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59
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Membrane properties that shape the evolution of membrane enzymes. Curr Opin Struct Biol 2018; 51:80-91. [PMID: 29597094 DOI: 10.1016/j.sbi.2018.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/14/2018] [Accepted: 03/15/2018] [Indexed: 02/07/2023]
Abstract
Spectacular recent progress in structural biology has led to determination of the structures of many integral membrane enzymes that catalyze reactions in which at least one substrate also is membrane bound. A pattern of results seems to be emerging in which the active site chemistry of these enzymes is usually found to be analogous to what is observed for water soluble enzymes catalyzing the same reaction types. However, in light of the chemical, structural, and physical complexity of cellular membranes plus the presence of transmembrane gradients and potentials, these enzymes may be subject to membrane-specific regulatory mechanisms that are only now beginning to be uncovered. We review the membrane-specific environmental traits that shape the evolution of membrane-embedded biocatalysts.
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60
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Pchitskaya E, Popugaeva E, Bezprozvanny I. Calcium signaling and molecular mechanisms underlying neurodegenerative diseases. Cell Calcium 2018; 70:87-94. [PMID: 28728834 PMCID: PMC5748019 DOI: 10.1016/j.ceca.2017.06.008] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/22/2017] [Accepted: 06/22/2017] [Indexed: 01/23/2023]
Abstract
Calcium (Ca2+) is a ubiquitous second messenger that regulates various activities in eukaryotic cells. Especially important role calcium plays in excitable cells. Neurons require extremely precise spatial-temporal control of calcium-dependent processes because they regulate such vital functions as synaptic plasticity. Recent evidence indicates that neuronal calcium signaling is abnormal in many of neurodegenerative disorders such as Alzheimer's disease (AD), Huntington's disease (HD) and Parkinson's disease (PD). These diseases represent a major medical, social, financial and scientific problem, but despite enormous research efforts, they are still incurable and only symptomatic relief drugs are available. Thus, new approaches and targets are needed. This review highlight neuronal calcium-signaling abnormalities in these diseases, with particular emphasis on the role of neuronal store-operated Ca2+ entry (SOCE) pathway and its potential relevance as a therapeutic target for treatment of neurodegeneration.
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Affiliation(s)
- Ekaterina Pchitskaya
- Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter The Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation.
| | - Elena Popugaeva
- Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter The Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation.
| | - Ilya Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter The Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation; Department of Physiology, UT Southwestern Medical Center at Dallas, Dallas, TX, USA.
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61
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Cheng G, Han XH, Hao SJ, Nisic M, Zheng SY. In Situ Caging of Biomolecules in Graphene Hybrids for Light Modulated Bioactivity. ACS APPLIED MATERIALS & INTERFACES 2018; 10:3361-3371. [PMID: 29300454 DOI: 10.1021/acsami.7b17544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Remote and noninvasive modulation of protein activity is essential for applications in biotechnology and medicine. Optical control has emerged as the most attractive approach owing to its high spatial and temporal resolutions; however, it is challenging to engineer light responsive proteins. In this work, a near-infrared (NIR) light-responsive graphene-silica-trypsin (GST) nanoreactor is developed for modulating the bioactivity of trypsin molecules. Biomolecules are spatially confined and protected in the rationally designed compartment architecture, which not only reduces the possible interference but also boosts the bioreaction efficiency. Upon NIR irradiation, the photothermal effect of the GST nanoreactor enables the ultrafast in situ heating for remote activation and tuning of the bioactivity. We apply the GST nanoreactor for remote and ultrafast proteolysis of proteins, which remarkably enhances the proteolysis efficiency and reduces the bioreaction time from the overnight of using free trypsin to seconds. We envision that this work not only provides a promising tool of ultrafast and remotely controllable proteolysis for in vivo proteomics in study of tissue microenvironment and other biomedical applications but also paves the way for exploring smart artificial nanoreactors in biomolecular modulation to gain insight in dynamic biological transformation.
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Affiliation(s)
- Gong Cheng
- Department of Biomedical Engineering and ‡Material Research Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Xiao-Hui Han
- Department of Biomedical Engineering and ‡Material Research Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Si-Jie Hao
- Department of Biomedical Engineering and ‡Material Research Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Merisa Nisic
- Department of Biomedical Engineering and ‡Material Research Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Si-Yang Zheng
- Department of Biomedical Engineering and ‡Material Research Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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62
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Naing SH, Kalyoncu S, Smalley DM, Kim H, Tao X, George JB, Jonke AP, Oliver RC, Urban VS, Torres MP, Lieberman RL. Both positional and chemical variables control in vitro proteolytic cleavage of a presenilin ortholog. J Biol Chem 2018; 293:4653-4663. [PMID: 29382721 DOI: 10.1074/jbc.ra117.001436] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/23/2018] [Indexed: 11/06/2022] Open
Abstract
Mechanistic details of intramembrane aspartyl protease (IAP) chemistry, which is central to many biological and pathogenic processes, remain largely obscure. Here, we investigated the in vitro kinetics of a microbial intramembrane aspartyl protease (mIAP) fortuitously acting on the renin substrate angiotensinogen and the C-terminal transmembrane segment of amyloid precursor protein (C100), which is cleaved by the presenilin subunit of γ-secretase, an Alzheimer disease (AD)-associated IAP. mIAP variants with substitutions in active-site and putative substrate-gating residues generally exhibit impaired, but not abolished, activity toward angiotensinogen and retain the predominant cleavage site (His-Thr). The aromatic ring, but not the hydroxyl substituent, within Tyr of the catalytic Tyr-Asp (YD) motif plays a catalytic role, and the hydrolysis reaction incorporates bulk water as in soluble aspartyl proteases. mIAP hydrolyzes the transmembrane region of C100 at two major presenilin cleavage sites, one corresponding to the AD-associated Aβ42 peptide (Ala-Thr) and the other to the non-pathogenic Aβ48 (Thr-Leu). For the former site, we observed more favorable kinetics in lipid bilayer-mimicking bicelles than in detergent solution, indicating that substrate-lipid and substrate-enzyme interactions both contribute to catalytic rates. High-resolution MS analyses across four substrates support a preference for threonine at the scissile bond. However, results from threonine-scanning mutagenesis of angiotensinogen demonstrate a competing positional preference for cleavage. Our results indicate that IAP cleavage is controlled by both positional and chemical factors, opening up new avenues for selective IAP inhibition for therapeutic interventions.
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Affiliation(s)
- Swe-Htet Naing
- School of Chemistry and Biochemistry, Atlanta, Georgia 30332
| | - Sibel Kalyoncu
- School of Chemistry and Biochemistry, Atlanta, Georgia 30332
| | - David M Smalley
- Petit Institute for Bioengineering and Biosciences, Atlanta, Georgia 30332
| | - Hyojung Kim
- School of Chemistry and Biochemistry, Atlanta, Georgia 30332; School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Xingjian Tao
- School of Chemistry and Biochemistry, Atlanta, Georgia 30332
| | - Josh B George
- School of Chemistry and Biochemistry, Atlanta, Georgia 30332
| | - Alex P Jonke
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Ryan C Oliver
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Matthew P Torres
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
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63
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Allosteric Modulation of Intact γ-Secretase Structural Dynamics. Biophys J 2018; 113:2634-2649. [PMID: 29262358 DOI: 10.1016/j.bpj.2017.10.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/26/2017] [Accepted: 10/10/2017] [Indexed: 12/20/2022] Open
Abstract
As a protease complex involved in the cleavage of amyloid precursor proteins that lead to the formation of amyloid β fibrils implicated in Alzheimer's disease, γ-secretase is an important target for developing therapeutics against Alzheimer's disease. γ-secretase is composed of four subunits: nicastrin (NCT) in the extracellular (EC) domain, presenilin-1 (PS1), anterior pharynx defective 1, and presenilin enhancer 2 in the transmembrane (TM) domain. NCT and PS1 play important roles in binding amyloid β precursor proteins and modulating PS1 catalytic activity. Yet, the molecular mechanisms of coupling between substrate/modulator binding and catalytic activity remain to be elucidated. Recent determination of intact human γ-secretase cryo-electron microscopy structure has opened the way for a detailed investigation of the structural dynamics of this complex. Our analysis, based on a membrane-coupled anisotropic network model, reveals two types of NCT motions, bending and twisting, with respect to PS1. These underlie the fluctuations between the "open" and "closed" states of the lid-like NCT with respect to a hydrophilic loop 1 (HL1) on PS1, thus allowing or blocking access of the substrate peptide (EC portion) to HL1 and to the neighboring helix TM2. In addition to this alternating access mechanism, fluctuations in the volume of the PS1 central cavity facilitate the exposure of the catalytic site for substrate cleavage. Druggability simulations show that γ-secretase presents several hot spots for either orthosteric or allosteric inhibition of catalytic activity, consistent with experimental data. In particular, a hinge region at the interface between the EC and TM domains, near the interlobe groove of NCT, emerges as an allo-targeting site that would impact the coupling between HL1/TM2 and the catalytic pocket, opening, to our knowledge, new avenues for structure-based design of novel allosteric modulators of γ-secretase protease activity.
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64
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Yang G, Yu K, Kubicek J, Labahn J. Expression, purification, and preliminary characterization of human presenilin-2. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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65
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Hirano J, Okamoto T, Sugiyama Y, Suzuki T, Kusakabe S, Tokunaga M, Fukuhara T, Sasai M, Tougan T, Matsunaga Y, Yamashita K, Sakai Y, Yamamoto M, Horii T, Standley DM, Moriishi K, Moriya K, Koike K, Matsuura Y. Characterization of SPP inhibitors suppressing propagation of HCV and protozoa. Proc Natl Acad Sci U S A 2017; 114:E10782-E10791. [PMID: 29187532 PMCID: PMC5740650 DOI: 10.1073/pnas.1712484114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Signal peptide peptidase (SPP) is an intramembrane aspartic protease involved in the maturation of the core protein of hepatitis C virus (HCV). The processing of HCV core protein by SPP has been reported to be critical for the propagation and pathogenesis of HCV. Here we examined the inhibitory activity of inhibitors for γ-secretase, another intramembrane cleaving protease, against SPP, and our findings revealed that the dibenzoazepine-type structure in the γ-secretase inhibitors is critical for the inhibition of SPP. The spatial distribution showed that the γ-secretase inhibitor compound YO-01027 with the dibenzoazepine structure exhibits potent inhibiting activity against SPP in vitro and in vivo through the interaction of Val223 in SPP. Treatment with this SPP inhibitor suppressed the maturation of core proteins of all HCV genotypes without the emergence of drug-resistant viruses, in contrast to the treatment with direct-acting antivirals. YO-01027 also efficiently inhibited the propagation of protozoa such as Plasmodium falciparum and Toxoplasma gondii These data suggest that SPP is an ideal target for the development of therapeutics not only against chronic hepatitis C but also against protozoiasis.
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Affiliation(s)
- Junki Hirano
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Toru Okamoto
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan;
| | - Yukari Sugiyama
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Tatsuya Suzuki
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Shinji Kusakabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Makoto Tokunaga
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Takasuke Fukuhara
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Miwa Sasai
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Takahiro Tougan
- Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yasue Matsunaga
- Planning and Promotion Office for University-Industry Collaboration, Osaka University, Osaka 565-0871, Japan
| | | | - Yusuke Sakai
- Department of Veterinary Pathology, Yamaguchi University, Yamaguchi 753-0841, Japan
| | - Masahiro Yamamoto
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Toshihiro Horii
- Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Daron M Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Kohji Moriishi
- Department of Microbiology, Faculty of Medicine, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Kyoji Moriya
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan;
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Johnson DS, Li YM, Pettersson M, St George-Hyslop PH. Structural and Chemical Biology of Presenilin Complexes. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a024067. [PMID: 28320827 PMCID: PMC5710098 DOI: 10.1101/cshperspect.a024067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The presenilin proteins are the catalytic subunits of a tetrameric complex containing presenilin 1 or 2, anterior pharynx defective 1 (APH1), nicastrin, and PEN-2. Other components such as TMP21 may exist in a subset of specialized complexes. The presenilin complex is the founding member of a unique class of aspartyl proteases that catalyze the γ, ɛ, ζ site cleavage of the transmembrane domains of Type I membrane proteins including amyloid precursor protein (APP) and Notch. Here, we detail the structural and chemical biology of this unusual enzyme. Taken together, these studies suggest that the complex exists in several conformations, and subtle long-range (allosteric) shifts in the conformation of the complex underpin substrate access to the catalytic site and the mechanism of action for allosteric inhibitors and modulators. Understanding the mechanics of these shifts will facilitate the design of γ-secretase modulator (GSM) compounds that modulate the relative efficiency of γ, ɛ, ζ site cleavage and/or substrate specificity.
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Affiliation(s)
- Douglas S. Johnson
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Martin Pettersson
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139
| | - Peter H. St George-Hyslop
- Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Addenbrookes Hospital, Cambridge CB2 0XY, United Kingdom,Tanz Centre for Research in Neurodegenerative Diseases and Departments of Medicine, Laboratory Medicine and Pathobiology, and Medical Biophysics, University of Toronto, Toronto, Ontario M5T 2S8, Canada
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67
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Membrane proteins structures: A review on computational modeling tools. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2021-2039. [DOI: 10.1016/j.bbamem.2017.07.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/04/2017] [Accepted: 07/13/2017] [Indexed: 01/02/2023]
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Thai NQ, Nguyen HL, Linh HQ, Li MS. Protocol for fast screening of multi-target drug candidates: Application to Alzheimer's disease. J Mol Graph Model 2017; 77:121-129. [PMID: 28850894 DOI: 10.1016/j.jmgm.2017.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 01/08/2023]
Abstract
The treatment of many diseases may require drugs that are capable to attack multiple targets simultaneously. Obviously, the virtual screening of multi-target drug candidates is much more time consuming compared to the single-target case. This, in particular, concerns the last step of virtual screening where the binding free energy is computed by conventional molecular dynamics simulation. To overcome this difficulty we propose a simple protocol which is relied on the fast steered molecular dynamics simulation and on available experimental data on binding affinity of reference ligand to a given target. Namely, first we compute non-equilibrium works generated during pulling ligands from the binding site using the steered molecular dynamics method. Then as top leads we choose only those compounds that have the non-equilibrium work larger than that of a reference compound for which the binding free energy has been already known from experiment. Despite many efforts no cures for AD (Alzheimer's disease) have been found. One of possible reasons for this failure is that drug candidates were developed for a single target, while there are exist many possible pathways to AD. Applying our new protocol to five targets including amyloid beta fibril, peroxisome proliferator-activated receptor γ, retinoic X receptor α, β- and γ-secretases, we have found two potential drugs (CID 16040294 and CID 9998128) for AD from the large PubChem database. We have also shown that these two ligands can interfere with the activity of popular Acetylcholinesterase target through strong binding towards it.
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Affiliation(s)
- Nguyen Quoc Thai
- Institute for Computational Sciences and Technology,SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Dong Thap University,783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Viet Nam; Biomedical Engineering Department, University of Technology -VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam
| | - Hoang Linh Nguyen
- Institute for Computational Sciences and Technology,SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam
| | - Huynh Quang Linh
- Biomedical Engineering Department, University of Technology -VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam
| | - Mai Suan Li
- Institute for Computational Sciences and Technology,SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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69
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Aguayo-Ortiz R, Chávez-García C, Straub JE, Dominguez L. Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach. Chem Sci 2017; 8:5576-5584. [PMID: 28970936 PMCID: PMC5618787 DOI: 10.1039/c7sc00980a] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/05/2017] [Indexed: 11/21/2022] Open
Abstract
γ-Secretase is an intramembrane-cleaving aspartyl protease that plays an essential role in the processing of a variety of integral membrane proteins. Its role in the ultimate cleavage step in the processing of amyloid precursor protein to form amyloid-β (Aβ) peptide makes it an important therapeutic target in Alzheimer's disease research. Significant recent advances have been made in structural studies of this critical membrane protein complex. However, details of the mechanism of activation of the enzyme complex remain unclear. Using a multiscale computational modeling approach, combining multiple coarse-grained microsecond dynamic trajectories with all-atom models, the structure and two conformational states of the γ-secretase complex were evaluated. The transition between enzymatic state 1 and state 2 is shown to critically depend on the protonation states of the key catalytic residues Asp257 and Asp385 in the active site domain. The active site formation, related to our γ-secretase state 2, is observed to involve a concerted movement of four transmembrane helices from the catalytic subunit, resulting in the required localization of the catalytic residues. Global analysis of the structural ensemble of the enzyme complex was used to identify collective fluctuations important to the mechanism of substrate recognition and demonstrate that the corresponding fluctuations observed were uncorrelated with structural changes associated with enzyme activation. Overall, this computational study provides essential insight into the role of structure and dynamics in the activation and function of γ-secretase.
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Departamento de Fisicoquímica , Facultad de Química , Universidad Nacional Autónoma de México , Mexico City , 04510 , Mexico .
| | - Cecilia Chávez-García
- Departamento de Fisicoquímica , Facultad de Química , Universidad Nacional Autónoma de México , Mexico City , 04510 , Mexico .
| | - John E Straub
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , USA
| | - Laura Dominguez
- Departamento de Fisicoquímica , Facultad de Química , Universidad Nacional Autónoma de México , Mexico City , 04510 , Mexico .
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Abstract
γ-secretase, a membrane-embedded aspartate protease, catalyzes peptide bond hydrolysis of a large variety of type I integral membrane proteins exemplified by amyloid precursor protein (APP). Cleavage of APP leads to formation of β-amyloid plaque, which is a hallmark of Alzheimer's disease (AD). Over 200 AD-associated mutations are mapped to presenilin 1 (PS1), the catalytic component of γ-secretase. In the past three years, several cryo-electron microscopy (cryo-EM) structures of human γ-secretase have been determined at near atomic resolutions. Here we summarize the methods involved and discuss structural features of γ-secretase and the associated functional insights.
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Affiliation(s)
- Guanghui Yang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Rui Zhou
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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71
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Li S, Zhang W, Han W. Initial Substrate Binding of γ-Secretase: The Role of Substrate Flexibility. ACS Chem Neurosci 2017; 8:1279-1290. [PMID: 28165225 DOI: 10.1021/acschemneuro.6b00425] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
γ-Secretase cleaves transmembrane domains (TMD) of amyloid precursor protein (APP), producing pathologically relevant amyloid-β proteins. Initial substrate binding represents a key step of the γ-secretase cleavage whose mechanism remains elusive. Through long time scale coarse-grained and atomic simulations, we have found that the APP TMD can bind to the catalytic subunit presenilin 1 (PS1) on an extended surface covering PS1's TMD2/6/9 and PAL motif that are all known to be essential for enzymatic activity. This initial substrate binding could lead to reduction in the vertical gap between APP's ε-cleavage sites and γ-secretase's active center, enhanced flexibility and hydration levels around the ε-sites, and the presentation of these sites to the enzyme. There are heterogeneous substrate binding poses in which the substrate is found to bind to either the N- or C-terminal parts of PS1, or both. Moreover, we also find that the stability of the binding poses can be modulated by the flexibility of substrate TMD. Especially, the APP substrate, when deprived of bending fluctuation, does not bind to TMD9 at PS1's C-terminus. Our simulations have revealed further that another substrate of γ-secretase, namely, notch receptors, though bearing a rigid TMD, can still bind to PS1 TMD9, but by a different mechanism, suggesting that the influence of substrate flexibility is context-dependent. Together, these findings shed light on the mechanism of initial substrate docking of γ-secretase and the role of substrate flexibility in this process.
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Affiliation(s)
- Shu Li
- Key Laboratory of Chemical Genomics, School
of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wan Zhang
- Key Laboratory of Chemical Genomics, School
of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wei Han
- Key Laboratory of Chemical Genomics, School
of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
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72
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Gibson GE, Thakkar A. Interactions of Mitochondria/Metabolism and Calcium Regulation in Alzheimer's Disease: A Calcinist Point of View. Neurochem Res 2017; 42:1636-1648. [PMID: 28181072 DOI: 10.1007/s11064-017-2182-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/12/2017] [Accepted: 01/16/2017] [Indexed: 10/20/2022]
Abstract
Decades of research suggest that alterations in calcium are central to the pathophysiology of Alzheimer's Disease (AD). Highly reproducible changes in calcium dynamics occur in cells from patients with both genetic and non-genetic forms of AD relative to controls. The most robust change is an exaggerated release of calcium from internal stores. Detailed analysis of these changes in animal and cell models of the AD-causing presenilin mutations reveal robust changes in ryanodine receptors, inositol tris-phosphate receptors, calcium leak channels and store activated calcium entry. Similar anomalies in calcium result when AD-like changes in mitochondrial enzymes or oxidative stress are induced experimentally. The calcium abnormalities can be directly linked to the altered tau phosphorylation, amyloid precursor protein processing and synaptic dysfunction that are defining features of AD. A better understanding of these changes is required before using calcium abnormalities as therapeutic targets.
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Affiliation(s)
- Gary E Gibson
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Medical Research Institute, 785 Mamaroneck Avenue, White Plains, NY, 10605, USA.
| | - Ankita Thakkar
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Medical Research Institute, 785 Mamaroneck Avenue, White Plains, NY, 10605, USA
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73
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Verhelst SHL. Intramembrane proteases as drug targets. FEBS J 2017; 284:1489-1502. [PMID: 27889944 DOI: 10.1111/febs.13979] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/14/2016] [Accepted: 11/24/2016] [Indexed: 01/04/2023]
Abstract
Proteases are considered attractive drug targets. Various drugs targeting classical, soluble proteases have been approved for treatment of human disease. Intramembrane proteases (IMPs) are a more recently discovered group of proteolytic enzymes. They are embedded in lipid bilayers and their active sites are located in the plane of a membrane. All four mechanistic families of IMPs have been linked to disease, but currently, no drugs against IMPs have entered the market. In this review, I will outline the function of IMPs with a focus on the ones involved in human disease, which includes Alzheimer's disease, cancer, and infectious diseases by microorganisms. Inhibitors of IMPs are known for all mechanistic classes, but are not yet very potent or selective - aside from those targeting γ-secretase. I will here describe the different features of IMP inhibitors and discuss a list of issues that need attention in the near future in order to improve the drug development for IMPs.
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Affiliation(s)
- Steven H L Verhelst
- Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Belgium.,AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, Dortmund, Germany
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74
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A New Method to Determine the Transmembrane Conformation of Substrates in Intramembrane Proteolysis by Deep-UV Resonance Raman Spectroscopy. Methods Enzymol 2016; 584:207-228. [PMID: 28065264 DOI: 10.1016/bs.mie.2016.10.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We present a new method based on deep-UV resonance Raman spectroscopy to determine the backbone conformation of intramembrane protease substrates. The classical amide vibrational modes reporting on the conformation of just the transmembrane region of the substrate can be resolved from solvent exchangeable regions outside the detergent micelle by partial deuteration of the solvent. In the presence of isotopically triple-labeled intramembrane protease, these amide modes can be accurately measured to monitor the transmembrane conformation of the substrate during intramembrane proteolysis.
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75
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Departamento de Fisicoquímica; Universidad Nacional Autónoma de México; Ciudad de México 04510 México
| | - Laura Dominguez
- Departamento de Fisicoquímica; Universidad Nacional Autónoma de México; Ciudad de México 04510 México
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76
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Abstract
Intramembrane proteases catalyze peptide bond hydrolysis in the lipid bilayer and play a key role in numerous cellular processes. These integral membrane enzymes consist of four classes: site-2 protease (S2P), rhomboid serine protease, Rce1-type glutamyl protease, and aspartyl protease exemplified by presenilin and signal peptide peptidase (SPP). Structural elucidation of these enzymes is important for mechanistic understanding of their functions, particularly their roles in cell signaling and debilitating diseases such as Parkinson's disease and Alzheimer's disease. In the past decade, rigorous effort has led to determination of the crystal structures of S2P from archaebacterium, rhomboid serine protease from E. coli (GlpG), and presenilin/SPP from archaebacterium (PSH). A novel method has been developed to express well-behaved human γ-secretase, which facilitated its structure determination by cryoelectron microscopy (cryo-EM). In this chapter, we will discuss the expression and purification of intramembrane proteases including human γ-secretase and describe the enzymatic activity assays for these intramembrane proteases.
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77
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Ryan NS, Nicholas JM, Weston PSJ, Liang Y, Lashley T, Guerreiro R, Adamson G, Kenny J, Beck J, Chavez-Gutierrez L, de Strooper B, Revesz T, Holton J, Mead S, Rossor MN, Fox NC. Clinical phenotype and genetic associations in autosomal dominant familial Alzheimer's disease: a case series. Lancet Neurol 2016; 15:1326-1335. [PMID: 27777022 DOI: 10.1016/s1474-4422(16)30193-4] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/15/2016] [Accepted: 07/25/2016] [Indexed: 01/09/2023]
Abstract
BACKGROUND The causes of phenotypic heterogeneity in familial Alzheimer's disease with autosomal dominant inheritance are not well understood. We aimed to characterise clinical phenotypes and genetic associations with APP and PSEN1 mutations in symptomatic autosomal dominant familial Alzheimer's disease (ADAD). METHODS We retrospectively analysed genotypic and phenotypic data (age at symptom onset, initial cognitive or behavioural symptoms, and presence of myoclonus, seizures, pyramidal signs, extrapyramidal signs, and cerebellar signs) from all individuals with ADAD due to APP or PSEN1 mutations seen at the Dementia Research Centre in London, UK. We examined the frequency of presenting symptoms and additional neurological features, investigated associations with age at symptom onset, APOE genotype, and mutation position, and explored phenotypic differences between APP and PSEN1 mutation carriers. The proportion of individuals presenting with various symptoms was analysed with descriptive statistics, stratified by mutation type. FINDINGS Between July 1, 1987, and Oct 31, 2015, age at onset was recorded for 213 patients (168 with PSEN1 mutations and 45 with APP mutations), with detailed history and neurological examination findings available for 121 (85 with PSEN1 mutations and 36 with APP mutations). We identified 38 different PSEN1 mutations (four novel) and six APP mutations (one novel). Age at onset differed by mutation, with a younger onset for individuals with PSEN1 mutations than for those with APP mutations (mean age 43·6 years [SD 7·2] vs 50·4 years [SD 5·2], respectively, p<0·0001); within the PSEN1 group, 72% of age at onset variance was explained by the specific mutation. A cluster of five mutations with particularly early onset (mean age at onset <40 years) involving PSEN1's first hydrophilic loop suggests critical functional importance of this region. 71 (84%) individuals with PSEN1 mutations and 35 (97%) with APP mutations presented with amnestic symptoms, making atypical cognitive presentations significantly more common in PSEN1 mutation carriers (n=14; p=0·037). Myoclonus and seizures were the most common additional neurological features; individuals with myoclonus (40 [47%] with PSEN1 mutations and 12 [33%] with APP mutations) were significantly more likely to develop seizures (p=0·001 for PSEN1; p=0·036 for APP), which affected around a quarter of the patients in each group (20 [24%] and nine [25%], respectively). A number of patients with PSEN1 mutations had pyramidal (21 [25%]), extrapyramidal (12 [14%]), or cerebellar (three [4%]) signs. INTERPRETATION ADAD phenotypes are heterogeneous, with both age at onset and clinical features being influenced by mutation position as well as causative gene. This highlights the importance of considering genetic testing in young patients with dementia and additional neurological features in order to appropriately diagnose and treat their symptoms, and of examining different mutation types separately in future research. FUNDING Medical Research Council and National Institute for Health Research.
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Affiliation(s)
- Natalie S Ryan
- Dementia Research Centre, Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK.
| | - Jennifer M Nicholas
- Dementia Research Centre, Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK; Medical Statistics Unit, Department of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Philip S J Weston
- Dementia Research Centre, Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK
| | - Yuying Liang
- Dementia Research Centre, Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank, University College London Institute of Neurology, London, UK
| | - Rita Guerreiro
- Department of Molecular Neuroscience, University College London Institute of Neurology, London, UK; Department of Medical Sciences, Institute of Biomedicine iBiMED, University of Aveiro, Aveiro Portugal
| | - Gary Adamson
- Medical Research Council Prion Unit, Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK
| | - Janna Kenny
- Medical Research Council Prion Unit, Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK
| | - Jon Beck
- Medical Research Council Prion Unit, Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK
| | - Lucia Chavez-Gutierrez
- VIB Center for the Biology of Disease, Leuven, Belgium; Center for Human Genetics and Leuven Institute for Neurodegenerative Diseases, University of Leuven, Leuven, Belgium
| | - Bart de Strooper
- Department of Molecular Neuroscience, University College London Institute of Neurology, London, UK; VIB Center for the Biology of Disease, Leuven, Belgium; Center for Human Genetics and Leuven Institute for Neurodegenerative Diseases, University of Leuven, Leuven, Belgium
| | - Tamas Revesz
- Queen Square Brain Bank, University College London Institute of Neurology, London, UK
| | - Janice Holton
- Queen Square Brain Bank, University College London Institute of Neurology, London, UK
| | - Simon Mead
- Medical Research Council Prion Unit, Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK
| | - Martin N Rossor
- Dementia Research Centre, Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK
| | - Nick C Fox
- Dementia Research Centre, Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK
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Wojsiat J, Laskowska-Kaszub K, Alquézar C, Białopiotrowicz E, Esteras N, Zdioruk M, Martin-Requero A, Wojda U. Familial Alzheimer's Disease Lymphocytes Respond Differently Than Sporadic Cells to Oxidative Stress: Upregulated p53-p21 Signaling Linked with Presenilin 1 Mutants. Mol Neurobiol 2016; 54:5683-5698. [PMID: 27644130 PMCID: PMC5533859 DOI: 10.1007/s12035-016-0105-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/06/2016] [Indexed: 01/18/2023]
Abstract
Familial (FAD) and sporadic (SAD) Alzheimer's disease do not share all pathomechanisms, but knowledge on their molecular differences is limited. We previously reported that cell cycle control distinguishes lymphocytes from SAD and FAD patients. Significant differences were found in p21 levels of SAD compared to FAD lymphocytes. Since p21 can also regulate apoptosis, the aim of this study was to compare the response of FAD and SAD lymphocytes to oxidative stress like 2-deoxy-D-ribose (2dRib) treatment and to investigate the role of p21 levels in this response. We report that FAD cells bearing seven different PS1 mutations are more resistant to 2dRib-induced cell death than control or SAD cells: FAD cells showed a lower apoptosis rate and a lower depolarization of the mitochondrial membrane. Despite that basal p21 cellular content was lower in FAD than in SAD cells, in response to 2dRib, p21 mRNA and protein levels significantly increased in FAD cells. Moreover, we found a higher cytosolic accumulation of p21 in FAD cells. The transcriptional activation of p21 was shown to be dependent on p53, as it can be blocked by PFT-α, and correlated with the increased phosphorylation of p53 at Serine 15. Our results suggest that in FAD lymphocytes, the p53-mediated increase in p21 transcription, together with a shift in the nucleocytoplasmic localization of p21, confers a survival advantage against 2dRib-induced apoptosis. This compensatory mechanism is absent in SAD cells. Thus, therapeutic and diagnostic designs should take into account possible differential apoptotic responses in SAD versus FAD cells.
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Affiliation(s)
- Joanna Wojsiat
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Pasteur 3, 02-093, Warsaw, Poland
| | - Katarzyna Laskowska-Kaszub
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Pasteur 3, 02-093, Warsaw, Poland
| | - Carolina Alquézar
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
- CIBER de Enfermedades Raras (CIBERER), 28040, Madrid, Spain
| | - Emilia Białopiotrowicz
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Pasteur 3, 02-093, Warsaw, Poland
| | - Noemi Esteras
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
- CIBER de Enfermedades Raras (CIBERER), 28040, Madrid, Spain
| | - Mykola Zdioruk
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Pasteur 3, 02-093, Warsaw, Poland
| | - Angeles Martin-Requero
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
- CIBER de Enfermedades Raras (CIBERER), 28040, Madrid, Spain
| | - Urszula Wojda
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Pasteur 3, 02-093, Warsaw, Poland.
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79
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Popugaeva E, Pchitskaya E, Bezprozvanny I. Dysregulation of neuronal calcium homeostasis in Alzheimer's disease - A therapeutic opportunity? Biochem Biophys Res Commun 2016; 483:998-1004. [PMID: 27641664 DOI: 10.1016/j.bbrc.2016.09.053] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 09/12/2016] [Indexed: 10/21/2022]
Abstract
Alzheimer's disease (AD) is the disease of lost memories. Synaptic loss is a major reason for memory defects in AD. Signaling pathways involved in memory loss in AD are under intense investigation. The role of deranged neuronal calcium (Ca2+) signaling in synaptic loss in AD is described in this review. Familial AD (FAD) mutations in presenilins are linked directly with synaptic Ca2+ signaling abnormalities, most likely by affecting endoplasmic reticulum (ER) Ca2+ leak function of presenilins. Excessive ER Ca2+ release via type 2 ryanodine receptors (RyanR2) is observed in AD spines due to increase in expression and function of RyanR2. Store-operated Ca2+ entry (nSOC) pathway is disrupted in AD spines due to downregulation of STIM2 protein. Because of these Ca2+ signaling abnormalities, a balance in activities of Ca2+-calmodulin-dependent kinase II (CaMKII) and Ca2+-dependent phosphatase calcineurin (CaN) is shifted at the synapse, tilting a balance between long-term potentiation (LTP) and long-term depression (LTD) synaptic mechanisms. As a result, synapses are weakened and eliminated in AD brains by LTD mechanism, causing memory loss. Targeting synaptic calcium signaling pathways offers opportunity for development of AD therapeutic agents.
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Affiliation(s)
- Elena Popugaeva
- Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation.
| | - Ekaterina Pchitskaya
- Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation.
| | - Ilya Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation; Department of Physiology, UT Southwestern Medical Center at Dallas, Dallas, TX, USA.
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80
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Wang HW, Lei J, Shi Y. Biological cryo-electron microscopy in China. Protein Sci 2016; 26:16-31. [PMID: 27534377 PMCID: PMC5192968 DOI: 10.1002/pro.3018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 08/11/2016] [Accepted: 08/11/2016] [Indexed: 12/16/2022]
Abstract
Cryo‐electron microscopy (cryo‐EM) plays an increasingly more important role in structural biology. With the construction of an arm of the Chinese National Protein Science Facility at Tsinghua University, biological cryo‐EM has entered a phase of rapid development in China. This article briefly reviews the history of biological cryo‐EM in China, describes its current status, comments on its impact on the various biological research fields, and presents future outlook.
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Affiliation(s)
- Hong-Wei Wang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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81
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Shinoda T, Shinya N, Ito K, Ishizuka-Katsura Y, Ohsawa N, Terada T, Hirata K, Kawano Y, Yamamoto M, Tomita T, Ishibashi Y, Hirabayashi Y, Kimura-Someya T, Shirouzu M, Yokoyama S. Cell-free methods to produce structurally intact mammalian membrane proteins. Sci Rep 2016; 6:30442. [PMID: 27465719 PMCID: PMC4964339 DOI: 10.1038/srep30442] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/04/2016] [Indexed: 01/19/2023] Open
Abstract
The crystal structures of four membrane proteins, from bacteria or a unicellular alga, have been solved with samples produced by cell-free protein synthesis. In this study, for mammalian membrane protein production, we established the precipitating and soluble membrane fragment methods: membrane proteins are synthesized with the Escherichia coli cell-free system in the presence of large and small membrane fragments, respectively, and are simultaneously integrated into the lipid environments. We applied the precipitating membrane fragment method to produce various mammalian membrane proteins, including human claudins, glucosylceramide synthase, and the γ-secretase subunits. These proteins were produced at levels of about 0.1–1.0 mg per ml cell-free reaction under the initial conditions, and were obtained as precipitates by ultracentrifugation. Larger amounts of membrane proteins were produced by the soluble membrane fragment method, collected in the ultracentrifugation supernatants, and purified directly by column chromatography. For several proteins, the conditions of the membrane fragment methods were further optimized, such as by the addition of specific lipids/detergents. The functional and structural integrities of the purified proteins were confirmed by analyses of their ligand binding activities, size-exclusion chromatography profiles, and/or thermal stabilities. We successfully obtained high-quality crystals of the complex of human claudin-4 with an enterotoxin.
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Affiliation(s)
- Takehiro Shinoda
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Naoko Shinya
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Kaori Ito
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Yoshiko Ishizuka-Katsura
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Noboru Ohsawa
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Takaho Terada
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Structural Biology Laboratory, Yokohama 230-0045, Japan
| | - Kunio Hirata
- RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiaki Kawano
- RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Taisuke Tomita
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yohei Ishibashi
- Laboratory for Molecular Membrane Neuroscience, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Yoshio Hirabayashi
- Laboratory for Molecular Membrane Neuroscience, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Tomomi Kimura-Someya
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Structural Biology Laboratory, Yokohama 230-0045, Japan
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82
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Dow XY, Dettmar CM, DeWalt EL, Newman JA, Dow AR, Roy-Chowdhury S, Coe JD, Kupitz C, Fromme P, Simpson GJ. Second harmonic generation correlation spectroscopy for characterizing translationally diffusing protein nanocrystals. Acta Crystallogr D Struct Biol 2016; 72:849-59. [PMID: 27377382 PMCID: PMC4932918 DOI: 10.1107/s205979831600841x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/24/2016] [Indexed: 11/10/2022] Open
Abstract
Second harmonic generation correlation spectroscopy (SHG-CS) is demonstrated as a new approach to protein nanocrystal characterization. A novel line-scanning approach was performed to enable autocorrelation analysis without sample damage from the intense incident beam. An analytical model for autocorrelation was developed, which includes a correction for the optical scattering forces arising when focusing intense, infrared beams. SHG-CS was applied to the analysis of BaTiO3 nanoparticles ranging from 200 to ∼500 nm and of photosystem I nanocrystals. A size distribution was recovered for each sample and compared with the size histogram measured by scanning electron microscopy (SEM). Good agreement was observed between the two independent measurements. The intrinsic selectivity of the second-order nonlinear optical process provides SHG-CS with the ability to distinguish well ordered nanocrystals from conglomerates and amorphous aggregates. Combining the recovered distribution of particle diameters with the histogram of measured SHG intensities provides the inherent hyperpolarizability per unit volume of the SHG-active nanoparticles. Simulations suggest that the SHG activity per unit volume is likely to exhibit relatively low sensitivity to the subtle distortions within the lattice that contribute to resolution loss in X-ray diffraction, but high sensitivity to the presence of multi-domain crystals.
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Affiliation(s)
- Ximeng Y. Dow
- Chemistry Department, Purdue University, West Lafayette, IN 47907, USA
| | | | - Emma L. DeWalt
- Chemistry Department, Purdue University, West Lafayette, IN 47907, USA
| | - Justin A. Newman
- Chemistry Department, Purdue University, West Lafayette, IN 47907, USA
| | - Alexander R. Dow
- Chemistry Department, Purdue University, West Lafayette, IN 47907, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Jesse D. Coe
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Christopher Kupitz
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Garth J. Simpson
- Chemistry Department, Purdue University, West Lafayette, IN 47907, USA
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83
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Avci D, Lemberg MK. Clipping or Extracting: Two Ways to Membrane Protein Degradation. Trends Cell Biol 2016; 25:611-622. [PMID: 26410407 DOI: 10.1016/j.tcb.2015.07.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/18/2015] [Accepted: 07/17/2015] [Indexed: 12/20/2022]
Abstract
Protein degradation is a fundamentally important process that allows cells to recognize and remove damaged protein species and to regulate protein abundance according to functional need. A fundamental challenge is to understand how membrane proteins are recognized and removed from cellular organelles. While most of our understanding of this mechanism comes from studies on p97/Cdc48-mediated protein dislocation along the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway, recent studies have revealed intramembrane proteolysis to be an additional mechanism that can extract transmembrane segments. Here, we review these two principles in membrane protein degradation and discuss how intramembrane proteolysis, which introduces an irreversible step in protein dislocation, is used to drive regulated protein turnover.
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Affiliation(s)
- Dönem Avci
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Marius K Lemberg
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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84
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Conformational Changes in Transmembrane Domain 4 of Presenilin 1 Are Associated with Altered Amyloid-β 42 Production. J Neurosci 2016; 36:1362-72. [PMID: 26818522 DOI: 10.1523/jneurosci.5090-14.2016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED γ-Secretase is an intramembrane-cleaving protease that produces amyloid-β peptide 42 (Aβ42), which is the toxic and aggregation-prone species of Aβ that causes Alzheimer's disease. Here, we used the substituted cysteine accessibility method to analyze the structure of transmembrane domains (TMDs) 4 and 5 of human presenilin 1 (PS1), a catalytic subunit of γ-secretase. We revealed that TMD4 and TMD5 face the intramembranous hydrophilic milieu together with TMD1, TMD6, TMD7, and TMD9 of PS1 to form the catalytic pore structure. Notably, we found a correlation in the distance between the cytosolic sides of TMD4/TMD7 and Aβ42 production levels, suggesting that allosteric conformational changes of the cytosolic side of TMD4 affect Aβ42-generating γ-secretase activity. Our results provide new insights into the relationship between the structure and activity of human PS1. SIGNIFICANCE STATEMENT Modulation of γ-secretase activity to reduce toxic amyloid-β peptide species is one plausible therapeutic approaches for Alzheimer's disease. However, precise mechanistic information of γ-secretase still remains unclear. Here we identified the conformational changes in transmembrane domains of presenilin 1 that affect the proteolytic activity of the γ-secretase. Our results highlight the importance of understanding the structural dynamics of presenilin 1 in drug development against Alzheimer's disease.
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85
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Coburger I, Schaub Y, Roeser D, Hardes K, Maeder P, Klee N, Steinmetzer T, Imhof D, Diederich WE, Than ME. Identification of inhibitors of the transmembrane protease FlaK of Methanococcus maripaludis. Microbiologyopen 2016; 5:637-46. [PMID: 27038342 PMCID: PMC4985597 DOI: 10.1002/mbo3.358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/23/2016] [Accepted: 03/07/2016] [Indexed: 01/17/2023] Open
Abstract
GxGD‐type intramembrane cleaving proteases (I‐CLiPs) form a family of proteolytic enzymes that feature an aspartate‐based catalytic mechanism. Yet, they structurally and functionally largely differ from the classical pepsin‐like aspartic proteases. Among them are the archaeal enzyme FlaK, processing its substrate FlaB2 during the formation of flagella and γ‐secretase, which is centrally involved in the etiology of the neurodegenerative Alzheimer's disease. We developed an optimized activity assay for FlaK and based on screening of a small in‐house library and chemical synthesis, we identified compound 9 as the first inhibitor of this enzyme. Our results show that this intramembrane protease differs from classical pepsin‐like aspartic proteases and give insights into the substrate recognition of this enzyme. By providing the needed tools to further study the enzymatic cycle of FlaK, our results also enable further studies towards a functional understanding of other GxGD‐type I‐CLiPs.
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Affiliation(s)
- Ina Coburger
- Leibniz Institute on Aging (FLI), Protein Crystallography Group, Beutenbergstr. 11, Jena, 07745, Germany
| | - Yvonne Schaub
- Leibniz Institute on Aging (FLI), Protein Crystallography Group, Beutenbergstr. 11, Jena, 07745, Germany
| | - Dirk Roeser
- Leibniz Institute on Aging (FLI), Protein Crystallography Group, Beutenbergstr. 11, Jena, 07745, Germany
| | - Kornelia Hardes
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, Marburg, 35032, Germany
| | - Patrick Maeder
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, Marburg, 35032, Germany
| | - Nina Klee
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, Marburg, 35032, Germany
| | - Torsten Steinmetzer
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, Marburg, 35032, Germany
| | - Diana Imhof
- Institute of Pharmacy, Pharmaceutical Chemistry I, University of Bonn, Brühler Str. 7, Bonn, 53119, Germany
| | - Wibke E Diederich
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, Marburg, 35032, Germany
| | - Manuel E Than
- Leibniz Institute on Aging (FLI), Protein Crystallography Group, Beutenbergstr. 11, Jena, 07745, Germany
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86
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Elad N, De Strooper B, Lismont S, Hagen W, Veugelen S, Arimon M, Horré K, Berezovska O, Sachse C, Chávez-Gutiérrez L. The dynamic conformational landscape of gamma-secretase. J Cell Sci 2016; 128:589-98. [PMID: 25501811 PMCID: PMC4311135 DOI: 10.1242/jcs.164384] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The structure and function of the gamma-secretase proteases are of great interest because of their crucial roles in cellular and disease processes. We established a novel purification protocol for the gamma-secretase complex that involves a conformation- and complex-specific nanobody, yielding highly pure and active enzyme. Using single particle electron microscopy, we analyzed the gamma-secretase structure and its conformational variability. Under steady-state conditions, the complex adopts three major conformations, which differ in overall compactness and relative position of the nicastrin ectodomain. Occupancy of the active or substrate-binding sites by inhibitors differentially stabilizes subpopulations of particles with compact conformations, whereas a mutation linked to familial Alzheimer disease results in enrichment of extended-conformation complexes with increased flexibility. Our study presents the csecretase complex as a dynamic population of interconverting conformations, involving rearrangements at the nanometer scale and a high level of structural interdependence between subunits. The fact that protease inhibition or clinical mutations, which affect amyloid beta (Abeta) generation, enrich for particular subpopulations of conformers indicates the functional relevance of the observed dynamic changes, which are likely to be instrumental for highly allosteric behavior of the enzyme.
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Affiliation(s)
- Nadav Elad
- VIB Center for the Biology of Disease, 3000 Leuven, Belgium
- Center of Human Genetics, University Hospitals Leuven & Department of Human Genetics, KU Leuven, and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
| | - Bart De Strooper
- VIB Center for the Biology of Disease, 3000 Leuven, Belgium
- Center of Human Genetics, University Hospitals Leuven & Department of Human Genetics, KU Leuven, and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
- UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
- Authors for correspondence (; ; )
| | - Sam Lismont
- VIB Center for the Biology of Disease, 3000 Leuven, Belgium
- Center of Human Genetics, University Hospitals Leuven & Department of Human Genetics, KU Leuven, and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
| | - Wim Hagen
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse1, 69117 Heidelberg, Germany
| | - Sarah Veugelen
- VIB Center for the Biology of Disease, 3000 Leuven, Belgium
- Center of Human Genetics, University Hospitals Leuven & Department of Human Genetics, KU Leuven, and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
| | - Muriel Arimon
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Katrien Horré
- VIB Center for the Biology of Disease, 3000 Leuven, Belgium
- Center of Human Genetics, University Hospitals Leuven & Department of Human Genetics, KU Leuven, and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
| | - Oksana Berezovska
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse1, 69117 Heidelberg, Germany
| | - Carsten Sachse
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse1, 69117 Heidelberg, Germany
- Authors for correspondence (; ; )
| | - Lucía Chávez-Gutiérrez
- VIB Center for the Biology of Disease, 3000 Leuven, Belgium
- Center of Human Genetics, University Hospitals Leuven & Department of Human Genetics, KU Leuven, and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
- Authors for correspondence (; ; )
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87
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Theobald DL. Presenilin adopts the ClC channel fold. Protein Sci 2016; 25:1363-5. [PMID: 26971579 PMCID: PMC4918416 DOI: 10.1002/pro.2919] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 03/07/2016] [Accepted: 03/07/2016] [Indexed: 01/31/2023]
Abstract
Presenilin is an integral membrane aspartate protease that regulates cellular processes by cleaving proteins within the cell membrane. The recent crystal structure of presenilin reveals a conspicuous pore in a bundle of nine α‐helices, which was originally thought to adopt a novel protein fold. However, here I show that the presenilin fold is a variant of the ClC chloride channel/transporter fold. This observation may have important implications for presenilin's postulated biological role as a calcium leak channel.
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Affiliation(s)
- Douglas L Theobald
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, 02453
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88
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Radchenko M, Nie R, Lu M. Disulfide Cross-linking of a Multidrug and Toxic Compound Extrusion Transporter Impacts Multidrug Efflux. J Biol Chem 2016; 291:9818-26. [PMID: 26975373 DOI: 10.1074/jbc.m116.715227] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Indexed: 01/12/2023] Open
Abstract
Multidrug and toxic compound extrusion (MATE) transporters contribute to multidrug resistance by extruding different drugs across cell membranes. The MATE transporters alternate between their extracellular and intracellular facing conformations to propel drug export, but how these structural changes occur is unclear. Here we combine site-specific cross-linking and functional studies to probe the movement of transmembrane helices in NorM from Neiserria gonorrheae (NorM-NG), a MATE transporter with known extracellular facing structure. We generated an active, cysteine-less NorM-NG and conducted pairwise cysteine mutagenesis on this variant. We found that copper phenanthroline catalyzed disulfide bond formation within five cysteine pairs and increased the electrophoretic mobility of the corresponding mutants. Furthermore, copper phenanthroline abolished the activity of the five paired cysteine mutants, suggesting that these substituted amino acids come in spatial proximity during transport, and the proximity changes are functionally indispensable. Our data also implied that the substrate-binding transmembrane helices move up to 10 Å in NorM-NG during transport and afforded distance restraints for modeling the intracellular facing transporter, thereby casting new light on the underlying mechanism.
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Affiliation(s)
- Martha Radchenko
- From the Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois 60064
| | - Rongxin Nie
- From the Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois 60064
| | - Min Lu
- From the Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois 60064
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89
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Zhang Y, Halder S, Kerr RA, Parrell D, Ruotolo B, Kroos L. Complex Formed between Intramembrane Metalloprotease SpoIVFB and Its Substrate, Pro-σK. J Biol Chem 2016; 291:10347-62. [PMID: 26953342 DOI: 10.1074/jbc.m116.715508] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 11/06/2022] Open
Abstract
Intramembrane metalloproteases (IMMPs) are conserved from bacteria to humans and control many important signaling pathways, but little is known about how IMMPs interact with their substrates. SpoIVFB is an IMMP that cleaves Pro-σ(K) during Bacillus subtilis endospore formation. When catalytically inactive SpoIVFB was coexpressed with C-terminally truncated Pro-σ(K)(1-126) (which can be cleaved by active SpoIVFB) in Escherichia coli, the substrate dramatically improved solubilization of the enzyme from membranes with mild detergents. Both the Pro(1-20) and σ(K)(21-126) parts contributed to improving SpoIVFB solubilization from membranes, but only the σ(K) part was needed to form a stable complex with SpoIVFB in a pulldown assay. The last 10 residues of SpoIVFB were required for improved solubilization from membranes by Pro-σ(K)(1-126) and for normal interaction with the substrate. The inactive SpoIVFB·Pro-σ(K)(1-126)-His6 complex was stable during affinity purification and gel filtration chromatography. Disulfide cross-linking of the purified complex indicated that it resembled the complex formed in vivo Ion mobility-mass spectrometry analysis resulted in an observed mass consistent with a 4:2 SpoIVFB·Pro-σ(K)(1-126)-His6 complex. Stepwise photobleaching of SpoIVFB fused to a fluorescent protein supported the notion that the enzyme is tetrameric during B. subtilis sporulation. The results provide the first evidence that an IMMP acts as a tetramer, give new insights into how SpoIVFB interacts with its substrate, and lay the foundation for further biochemical analysis of the enzyme·substrate complex and future structural studies.
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Affiliation(s)
- Yang Zhang
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and
| | - Sabyasachi Halder
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and
| | - Richard A Kerr
- the Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Daniel Parrell
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and
| | - Brandon Ruotolo
- the Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Lee Kroos
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and
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90
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Somavarapu AK, Kepp KP. The dynamic mechanism of presenilin-1 function: Sensitive gate dynamics and loop unplugging control protein access. Neurobiol Dis 2016; 89:147-56. [PMID: 26852951 DOI: 10.1016/j.nbd.2016.02.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 12/20/2022] Open
Abstract
There is no molecular explanation for the many presenilin 1 (PSEN1) mutations causing Alzheimer's disease, but both gain of function relating to amyloid production and loss of isolated PSEN1 function have been implied. We report here the first detailed dynamic all-atom model of mature PSEN1 from molecular dynamics in an explicit membrane with particular account of the as yet unexplored loop dynamics. We find that mature PSEN1 contains multiple distinct conformational states whereas non-mature PSEN1 is a typical one-state protein. We confirm a previously suggested gating mechanism, and find that the 106-131 loop acts as a "hinge" for the TM2 and TM6 "doors". More importantly, we identify an unplugging mechanism of the Exon 9 loop associated only with mature PSEN1. Proper opening of both the "gate" and "plug" in the membrane produces channel-like morphologies and access to the catalytic aspartates. Dynamically, these features seem linked. The long-range sensitivity of this gate-plug system to subtle conformational changes can explain why so many PSEN1 mutants cause disease. Reduced access and imprecise substrate cleavage associated with impaired gate-plug dynamics is directly illustrated by the effect of maturation in our work and could explain the overall reduction in Aβ levels upon PSEN1 mutation and the increase in the Aβ 42/40 ratio. Yet, our PSEN1-only dynamics are particularly insightful in revealing PSEN1-only dynamics relating to e.g. its role as membrane channel. Thus, our identified gate-plug mechanism is relevant for designing PSEN1 modulating therapies for treatment of Alzheimer's disease within both the amyloid/γ-secretase hypothesis and within the PSEN1 loss of function paradigm.
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Affiliation(s)
| | - Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, DK-2800 Kongens Lyngby, Denmark.
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91
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Structural biology of intramembrane proteases: mechanistic insights from rhomboid and S2P to γ-secretase. Curr Opin Struct Biol 2016; 37:97-107. [PMID: 26811996 DOI: 10.1016/j.sbi.2015.12.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/14/2015] [Accepted: 12/28/2015] [Indexed: 12/21/2022]
Abstract
Intramembrane proteases catalyze hydrolysis of peptide bond within the lipid bilayer and play a key role in a variety of cellular processes. These membrane-embedded enzymes comprise four major classes: rhomboid serine proteases, site-2 metalloproteases, Rce1-type glutamyl proteases, and aspartyl proteases exemplified by signal peptide peptidase and γ-secretase. In the past several years, three-dimensional structures of representative members of these four classes of intramembrane protease have been reported at atomic resolutions, which reveal distinct protein folds and active site configurations. These structures, together with structure-guided biochemical analyses, shed light on the working mechanisms of water access and substrate entry. In this review, we discuss the shared as well as unique features of these intramembrane proteases, with a focus on presenilin-the catalytic component of γ-secretase.
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92
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Abstract
Symmetry is a common feature among natural systems, including protein structures. A strong propensity toward symmetric architectures has long been recognized for water-soluble proteins, and this propensity has been rationalized from an evolutionary standpoint. Proteins residing in cellular membranes, however, have traditionally been less amenable to structural studies, and thus the prevalence and significance of symmetry in this important class of molecules is not as well understood. In the past two decades, researchers have made great strides in this area, and these advances have provided exciting insights into the range of architectures adopted by membrane proteins. These structural studies have revealed a similarly strong bias toward symmetric arrangements, which were often unexpected and which occurred despite the restrictions imposed by the membrane environment on the possible symmetry groups. Moreover, membrane proteins disproportionately contain internal structural repeats resulting from duplication and fusion of smaller segments. This article discusses the types and origins of symmetry in membrane proteins and the implications of symmetry for protein function.
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Affiliation(s)
- Lucy R Forrest
- Computational Structural Biology Group, Porter Neuroscience Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20852;
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93
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Futai E, Osawa S, Cai T, Fujisawa T, Ishiura S, Tomita T. Suppressor Mutations for Presenilin 1 Familial Alzheimer Disease Mutants Modulate γ-Secretase Activities. J Biol Chem 2016; 291:435-46. [PMID: 26559975 PMCID: PMC4697183 DOI: 10.1074/jbc.m114.629287] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 11/07/2015] [Indexed: 12/27/2022] Open
Abstract
γ-Secretase is a multisubunit membrane protein complex containing presenilin (PS1) as a catalytic subunit. Familial Alzheimer disease (FAD) mutations within PS1 were analyzed in yeast cells artificially expressing membrane-bound substrate, amyloid precursor protein, or Notch fused to Gal4 transcriptional activator. The FAD mutations, L166P and G384A (Leu-166 to Pro and Gly-384 to Ala substitution, respectively), were loss-of-function in yeast. We identified five amino acid substitutions that suppress the FAD mutations. The cleavage of amyloid precursor protein or Notch was recovered by the secondary mutations. We also found that secondary mutations alone activated the γ-secretase activity. FAD mutants with suppressor mutations, L432M or S438P within TMD9 together with a missense mutation in the second or sixth loops, regained γ-secretase activity when introduced into presenilin null mouse fibroblasts. Notably, the cells with suppressor mutants produced a decreased amount of Aβ42, which is responsible for Alzheimer disease. These results indicate that the yeast system is useful to screen for mutations and chemicals that modulate γ-secretase activity.
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Affiliation(s)
- Eugene Futai
- From the Department of Molecular and Cell Biology, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi 981-8555, the Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902,
| | - Satoko Osawa
- the Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences and
| | - Tetsuo Cai
- the Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences and Laboratory of Neuropathology and Neuroscience, Faculty of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomoya Fujisawa
- From the Department of Molecular and Cell Biology, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi 981-8555
| | - Shoichi Ishiura
- the Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902
| | - Taisuke Tomita
- the Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences and Laboratory of Neuropathology and Neuroscience, Faculty of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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94
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Johnson JL, Kalyoncu S, Lieberman RL. Lessons from an α-Helical Membrane Enzyme: Expression, Purification, and Detergent Optimization for Biophysical and Structural Characterization. Methods Mol Biol 2016; 1432:281-301. [PMID: 27485343 DOI: 10.1007/978-1-4939-3637-3_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This chapter outlines the protocol developed in our lab to produce a multipass α-helical membrane protein. We present our work flow, from ortholog selection to protein purification, including molecular biology for plasmid construction, protein expression in E. coli, membrane isolation and detergent solubilization, protein purification and tag removal, biophysical assessment of protein stability in different detergents, and detergent concentration determination using thin-layer chromatography. We focus on results from our ongoing work with intramembrane aspartyl proteases from archaeal organisms.
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Affiliation(s)
- Jennifer L Johnson
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA, 30332-0400, USA
| | - Sibel Kalyoncu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA, 30332-0400, USA
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA, 30332-0400, USA.
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95
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Nicastrin functions to sterically hinder γ-secretase-substrate interactions driven by substrate transmembrane domain. Proc Natl Acad Sci U S A 2015; 113:E509-18. [PMID: 26699478 DOI: 10.1073/pnas.1512952113] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
γ-Secretase is an intramembrane-cleaving protease that processes many type-I integral membrane proteins within the lipid bilayer, an event preceded by shedding of most of the substrate's ectodomain by α- or β-secretases. The mechanism by which γ-secretase selectively recognizes and recruits ectodomain-shed substrates for catalysis remains unclear. In contrast to previous reports that substrate is actively recruited for catalysis when its remaining short ectodomain interacts with the nicastrin component of γ-secretase, we find that substrate ectodomain is entirely dispensable for cleavage. Instead, γ-secretase-substrate binding is driven by an apparent tight-binding interaction derived from substrate transmembrane domain, a mechanism in stark contrast to rhomboid--another family of intramembrane-cleaving proteases. Disruption of the nicastrin fold allows for more efficient cleavage of substrates retaining longer ectodomains, indicating that nicastrin actively excludes larger substrates through steric hindrance, thus serving as a molecular gatekeeper for substrate binding and catalysis.
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96
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Nguyen MTN, Kersavond TV, Verhelst SHL. Chemical Tools for the Study of Intramembrane Proteases. ACS Chem Biol 2015; 10:2423-34. [PMID: 26473325 DOI: 10.1021/acschembio.5b00693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intramembrane proteases (IMPs) reside inside lipid bilayers and perform peptide hydrolysis in transmembrane or juxtamembrane regions of their substrates. Many IMPs are involved in crucial regulatory pathways and human diseases, including Alzheimer's disease, Parkinson's disease, and diabetes. In the past, chemical tools have been instrumental in the study of soluble proteases, enabling biochemical and biomedical research in complex environments such as tissue lysates or living cells. However, IMPs place special challenges on probe design and applications, and progress has been much slower than for soluble proteases. In this review, we will give an overview of the available chemical tools for IMPs, including activity-based probes, affinity-based probes, and synthetic substrates. We will discuss how these have been used to increase our structural and functional understanding of this fascinating group of enzymes, and how they might be applied to address future questions and challenges.
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Affiliation(s)
- Minh T. N. Nguyen
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Tim Van Kersavond
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Steven H. L. Verhelst
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
- KU Leuven − University of Leuven, Department
of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49 Box 802, 3000 Leuven, Belgium
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97
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Duggan SP, McCarthy JV. Beyond γ-secretase activity: The multifunctional nature of presenilins in cell signalling pathways. Cell Signal 2015; 28:1-11. [PMID: 26498858 DOI: 10.1016/j.cellsig.2015.10.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/19/2015] [Indexed: 01/24/2023]
Abstract
The presenilins are the catalytic subunit of the membrane-embedded tetrameric γ-secretase protease complexes. More that 90 transmembrane proteins have been reported to be γ-secretase substrates, including the widely studied amyloid precursor protein (APP) and the Notch receptor, which are precursors for the generation of amyloid-β peptides and biologically active APP intracellular domain (AICD) and Notch intracellular domain (NICD). The diversity of γ-secretase substrates highlights the importance of presenilin-dependent γ-secretase protease activities as a regulatory mechanism in a range of biological systems. However, there is also a growing body of evidence that supports the existence of γ-secretase-independent functions for the presenilins in the regulation and progression of an array of cell signalling pathways. In this review, we will present an overview of current literature that proposes evolutionarily conserved presenilin functions outside of the γ-secretase complex, with a focus on the suggested role of the presenilins in the regulation of Wnt/β-catenin signalling, protein trafficking and degradation, calcium homeostasis and apoptosis.
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Affiliation(s)
- Stephen P Duggan
- Signal Transduction Laboratory, School of Biochemistry & Cell Biology, ABCRF, Western Gateway Building, University College Cork, Cork, Ireland
| | - Justin V McCarthy
- Signal Transduction Laboratory, School of Biochemistry & Cell Biology, ABCRF, Western Gateway Building, University College Cork, Cork, Ireland.
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98
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Popugaeva E, Vlasova OL, Bezprozvanny I. Restoring calcium homeostasis to treat Alzheimer's disease: a future perspective. Neurodegener Dis Manag 2015; 5:395-8. [PMID: 26477700 DOI: 10.2217/nmt.15.36] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder that primarily compromises memory formation and storage. Several hypotheses regarding the pathogenesis of AD have been proposed; however, no cure is available to date. Here we describe the calcium hypothesis of AD, which is gaining popularity. We present data supporting this hypothesis and focus on a recently discovered calcium-signaling pathway that is dysregulated in AD and propose targets for the development of disease-modifying therapies.
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Affiliation(s)
- Elena Popugaeva
- Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter the Great St Petersburg Polytechnic University, St Petersburg, Russian Federation
| | - Olga L Vlasova
- Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter the Great St Petersburg Polytechnic University, St Petersburg, Russian Federation
| | - Ilya Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter the Great St Petersburg Polytechnic University, St Petersburg, Russian Federation.,Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
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99
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The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility. Proc Natl Acad Sci U S A 2015; 112:12390-5. [PMID: 26392539 DOI: 10.1073/pnas.1513782112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Regulated intramembrane proteolysis (RIP) is a conserved mechanism crucial for numerous cellular processes, including signaling, transcriptional regulation, axon guidance, cell adhesion, cellular stress responses, and transmembrane protein fragment degradation. Importantly, it is relevant in various diseases including Alzheimer's disease, cardiovascular diseases, and cancers. Even though a number of structures of different intramembrane proteases have been solved recently, fundamental questions concerning mechanistic underpinnings of RIP and therapeutic interventions remain. In particular, this includes substrate recognition, what properties render a given substrate amenable for RIP, and how the lipid environment affects the substrate cleavage. Members of the sterol regulatory element-binding protein (SREBP) family of transcription factors are critical regulators of genes involved in cholesterol/lipid homeostasis. After site-1 protease cleavage of the inactive SREBP transmembrane precursor protein, RIP of the anchor intermediate by site-2 protease generates the mature transcription factor. In this work, we have investigated the labile anchor intermediate of SREBP-1 using NMR spectroscopy. Surprisingly, NMR chemical shifts, site-resolved solvent exposure, and relaxation studies show that the cleavage site of the lipid-signaling protein intermediate bears rigid α-helical topology. An evolutionary conserved motif, by contrast, interrupts the secondary structure ∼9-10 residues C-terminal of the scissile bond and acts as an inducer of conformational flexibility within the carboxyl-terminal transmembrane region. These results are consistent with molecular dynamics simulations. Topology, stability, and site-resolved dynamics data suggest that the cleavage of the α-helical substrate in the case of RIP may be associated with a hinge motion triggered by the molecular environment.
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100
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Naing SH, Vukoti KM, Drury JE, Johnson JL, Kalyoncu S, Hill SE, Torres MP, Lieberman RL. Catalytic Properties of Intramembrane Aspartyl Protease Substrate Hydrolysis Evaluated Using a FRET Peptide Cleavage Assay. ACS Chem Biol 2015; 10:2166-74. [PMID: 26118406 DOI: 10.1021/acschembio.5b00305] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical details of intramembrane proteolysis remain elusive despite its prevalence throughout biology. We developed a FRET peptide assay for the intramembrane aspartyl protease (IAP) from Methanoculleus marisnigri JR1 in combination with quantitative mass spectrometry cleavage site analysis. IAP can hydrolyze the angiotensinogen sequence, a substrate for the soluble aspartyl protease renin, at a predominant cut site, His-Thr. Turnover is slow (min(-1) × 10(-3)), affinity and Michaelis constant (Km) values are in the low micromolar range, and both catalytic rates and cleavage sites are the same in detergent as reconstituted into bicelles. Three well-established, IAP-directed inhibitors were directly confirmed as competitive, albeit with modest inhibitor constant (Ki) values. Partial deletion of the first transmembrane helix results in a biophysically similar but less active enzyme than full-length IAP, indicating a catalytic role. Our study demonstrates previously unappreciated similarities with soluble aspartyl proteases, provides new biochemical features of IAP and inhibitors, and offers tools to study other intramembrane protease family members in molecular detail.
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Affiliation(s)
- Swe-Htet Naing
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic
Drive Northwest, Atlanta, Georgia 30332-0400, United States
| | - Krishna M. Vukoti
- School
of Biology, Georgia Institute of Technology, 310 Ferst Drive Northwest, Atlanta, Georgia 30332-0230, United States
| | - Jason E. Drury
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic
Drive Northwest, Atlanta, Georgia 30332-0400, United States
| | - Jennifer L. Johnson
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic
Drive Northwest, Atlanta, Georgia 30332-0400, United States
| | - Sibel Kalyoncu
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic
Drive Northwest, Atlanta, Georgia 30332-0400, United States
| | - Shannon E. Hill
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic
Drive Northwest, Atlanta, Georgia 30332-0400, United States
| | - Matthew P. Torres
- School
of Biology, Georgia Institute of Technology, 310 Ferst Drive Northwest, Atlanta, Georgia 30332-0230, United States
| | - Raquel L. Lieberman
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic
Drive Northwest, Atlanta, Georgia 30332-0400, United States
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