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Sarkar D, Bhunia A. Delineating the Role of GxxxG Motif in Amyloidogenesis: A New Perspective in Targeting Amyloid-Beta Mediated AD Pathogenesis. ACS BIO & MED CHEM AU 2024; 4:4-19. [PMID: 38404748 PMCID: PMC10885112 DOI: 10.1021/acsbiomedchemau.3c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 02/27/2024]
Abstract
The pursuit of a novel structural motif that can shed light on the key functional attributes is a primary focus in the study of protein folding disorders. Decades of research on Alzheimer's disease (AD) have centered on the Amyloid β (Aβ) pathway, highlighting its significance in understanding the disorder. The diversity in the Aβ pathway and the possible silent tracks which are yet to discover, makes it exceedingly intimidating to the interdisciplinary scientific community. Over the course of AD research, Aβ has consistently been at the forefront of scientific inquiry and discussion. In this review, we epitomize the role of a potential structural motif (GxxxG motif) that may provide a new horizon to the Aβ conflict. We emphasize on how comprehensive understanding of this motif from a structure-function perspective may pave the way for designing novel therapeutics intervention in AD and related diseases.
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Affiliation(s)
- Dibakar Sarkar
- Department of Chemical Sciences, Bose Institute, Unified Academic Campus, Sector V, Salt Lake EN
80, Kolkata 700 091, India
| | - Anirban Bhunia
- Department of Chemical Sciences, Bose Institute, Unified Academic Campus, Sector V, Salt Lake EN
80, Kolkata 700 091, India
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2
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Khan A, Killick R, Wirth D, Hoogland D, Hristova K, Ulmschneider JP, King CR, Ulmschneider MB. Masking the transmembrane region of the amyloid β precursor protein as a safe means to lower amyloid β production. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2023; 9:e12428. [PMID: 37954165 PMCID: PMC10632552 DOI: 10.1002/trc2.12428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/19/2023] [Indexed: 11/14/2023]
Abstract
Introduction Reducing brain levels of both soluble and insoluble forms of amyloid beta (Aβ) remains the primary goal of most therapies that target Alzheimer's disease (AD). However, no treatment has so far resulted in patient benefit, and clinical trials of the most promising drug candidates have generally failed due to significant adverse effects. This highlights the need for safer and more selective ways to target and modulate Aβ biogenesis. Methods Peptide technology has advanced to allow reliable synthesis, purification, and delivery of once-challenging hydrophobic sequences. This is opening up new routes to target membrane processes associated with disease. Here we deploy a combination of atomic detail molecular dynamics (MD) simulations, living-cell Förster resonance energy transfer (FRET), and in vitro assays to elucidate the atomic-detail dynamics, molecular mechanisms, and cellular activity and selectivity of a membrane-active peptide that targets the Aβ precursor protein (APP). Results We demonstrate that Aβ biogenesis can be downregulated selectively using an APP occlusion peptide (APPOP). APPOP inhibits Aβ production in a dose-dependent manner, with a mean inhibitory concentration (IC50) of 450 nM toward exogenous APP and 50 nM toward endogenous APP in primary rat cortical neuronal cultures. APPOP does not impact the γ-secretase cleavage of Notch-1, or exhibit toxicity toward cultured primary rat neurons, suggesting that it selectively shields APP from proteolysis. Discussion Drugs targeting AD need to be given early and for very long periods to prevent the onset of clinical symptoms. This necessitates being able to target Aβ production precisely and without affecting the activity of key cellular enzymes such as γ-secretase for other substrates. Peptides offer a powerful way for targeting key pathways precisely, thereby reducing the risk of adverse effects. Here we show that protecting APP from proteolytic processing offers a promising route to safely and specifically lower Aβ burden. In particular, we show that the amyloid pathway can be targeted directly and specificically. This reduces the risk of off-target effects and paves the way for a safe prophylactic treatment.
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Affiliation(s)
| | - Richard Killick
- Living Systems InstituteUniversity of ExeterExeterUK
- King's College LondonMaurice Wohl Clinical Neuroscience InstituteCamberwellLondonUK
| | - Daniel Wirth
- Department of Materials Science and Engineering and Institute for NanoBioTechnologyJohns Hopkins UniversityBaltimoreMarylandUSA
| | | | - Kalina Hristova
- Department of Materials Science and Engineering and Institute for NanoBioTechnologyJohns Hopkins UniversityBaltimoreMarylandUSA
| | | | - Christopher R. King
- National Institutes of HealthNational Institute of Neurological Disorders and StrokeBethesdaMarylandUSA
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Rudajev V, Novotny J. Cholesterol-dependent amyloid β production: space for multifarious interactions between amyloid precursor protein, secretases, and cholesterol. Cell Biosci 2023; 13:171. [PMID: 37705117 PMCID: PMC10500844 DOI: 10.1186/s13578-023-01127-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023] Open
Abstract
Amyloid β is considered a key player in the development and progression of Alzheimer's disease (AD). Many studies investigating the effect of statins on lowering cholesterol suggest that there may be a link between cholesterol levels and AD pathology. Since cholesterol is one of the most abundant lipid molecules, especially in brain tissue, it affects most membrane-related processes, including the formation of the most dangerous form of amyloid β, Aβ42. The entire Aβ production system, which includes the amyloid precursor protein (APP), β-secretase, and the complex of γ-secretase, is highly dependent on membrane cholesterol content. Moreover, cholesterol can affect amyloidogenesis in many ways. Cholesterol influences the stability and activity of secretases, but also dictates their partitioning into specific cellular compartments and cholesterol-enriched lipid rafts, where the amyloidogenic machinery is predominantly localized. The most complicated relationships have been found in the interaction between cholesterol and APP, where cholesterol affects not only APP localization but also the precise character of APP dimerization and APP processing by γ-secretase, which is important for the production of Aβ of different lengths. In this review, we describe the intricate web of interdependence between cellular cholesterol levels, cholesterol membrane distribution, and cholesterol-dependent production of Aβ, the major player in AD.
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Affiliation(s)
- Vladimir Rudajev
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiri Novotny
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
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The Binding of Different Substrate Molecules at the Docking Site and the Active Site of γ-Secretase Can Trigger Toxic Events in Sporadic and Familial Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24031835. [PMID: 36768156 PMCID: PMC9915333 DOI: 10.3390/ijms24031835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Pathogenic changes in γ-secretase activity, along with its response to different drugs, can be affected by changes in the saturation of γ-secretase with its substrate. We analyze the saturation of γ-secretase with its substrate using multiscale molecular dynamics studies. We found that an increase in the saturation of γ-secretase with its substrate could result in the parallel binding of different substrate molecules at the docking site and the active site. The C-terminal domain of the substrate bound at the docking site can interact with the most dynamic presenilin sites at the cytosolic end of the active site tunnel. Such interactions can inhibit the ongoing catalytic activity and increase the production of the longer, more hydrophobic, and more toxic Aβ proteins. Similar disruptions in dynamic presenilin structures can be observed with different drugs and disease-causing mutations. Both, C99-βCTF-APP substrate and its different Aβ products, can support the toxic aggregation. The aggregation depends on the substrate N-terminal domain. Thus, the C99-βCTF-APP substrate and β-secretase path can be more toxic than the C83-αCTF-APP substrate and α-secretase path. Nicastrin can control the toxic aggregation in the closed conformation. The binding of the C99-βCTF-APP substrate to γ-secretase can be controlled by substrate channeling between the nicastrin and β-secretase. We conclude that the presented two-substrate mechanism could explain the pathogenic changes in γ-secretase activity and Aβ metabolism in different sporadic and familial cases of Alzheimer's disease. Future drug-development efforts should target different cellular mechanisms that regulate the optimal balance between γ-secretase activity and amyloid metabolism.
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5
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Formation of extramembrane β-strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proc Natl Acad Sci U S A 2022; 119:e2212207119. [PMID: 36538482 PMCID: PMC9907117 DOI: 10.1073/pnas.2212207119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The 99-residue C-terminal domain of amyloid precursor protein (APP-C99), precursor to amyloid beta (Aβ), is a transmembrane (TM) protein containing intrinsically disordered N- and C-terminal extramembrane domains. Using molecular dynamics (MD) simulations, we show that the structural ensemble of the C99 monomer is best described in terms of thousands of states. The C99 monomer has a propensity to form β-strand in the C-terminal extramembrane domain, which explains the slow spin relaxation times observed in paramagnetic probe NMR experiments. Surprisingly, homodimerization of C99 not only narrows the conformational ensemble from thousands to a few states through the formation of metastable β-strands in extramembrane domains but also stabilizes extramembrane α-helices. The extramembrane domain structure is observed to dramatically impact the homodimerization motif, resulting in the modification of TM domain conformations. Our study provides an atomic-level structural basis for communication between the extramembrane domains of the C99 protein and TM homodimer formation. This finding could serve as a general model for understanding the influence of disordered extramembrane domains on TM protein structure.
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Papadopoulos N, Suelves N, Perrin F, Vadukul DM, Vrancx C, Constantinescu SN, Kienlen-Campard P. Structural Determinant of β-Amyloid Formation: From Transmembrane Protein Dimerization to β-Amyloid Aggregates. Biomedicines 2022; 10:2753. [PMID: 36359274 PMCID: PMC9687742 DOI: 10.3390/biomedicines10112753] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 10/03/2023] Open
Abstract
Most neurodegenerative diseases have the characteristics of protein folding disorders, i.e., they cause lesions to appear in vulnerable regions of the nervous system, corresponding to protein aggregates that progressively spread through the neuronal network as the symptoms progress. Alzheimer's disease is one of these diseases. It is characterized by two types of lesions: neurofibrillary tangles (NFTs) composed of tau proteins and senile plaques, formed essentially of amyloid peptides (Aβ). A combination of factors ranging from genetic mutations to age-related changes in the cellular context converge in this disease to accelerate Aβ deposition. Over the last two decades, numerous studies have attempted to elucidate how structural determinants of its precursor (APP) modify Aβ production, and to understand the processes leading to the formation of different Aβ aggregates, e.g., fibrils and oligomers. The synthesis proposed in this review indicates that the same motifs can control APP function and Aβ production essentially by regulating membrane protein dimerization, and subsequently Aβ aggregation processes. The distinct properties of these motifs and the cellular context regulate the APP conformation to trigger the transition to the amyloid pathology. This concept is critical to better decipher the patterns switching APP protein conformation from physiological to pathological and improve our understanding of the mechanisms underpinning the formation of amyloid fibrils that devastate neuronal functions.
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Affiliation(s)
- Nicolas Papadopoulos
- SIGN Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
- Ludwig Institute for Cancer Research Brussels, 1348 Brussels, Belgium
| | - Nuria Suelves
- Aging and Dementia Research Group, Cellular and Molecular (CEMO) Division, Institute of Neuroscience, UCLouvain, 1200 Brussels, Belgium
| | - Florian Perrin
- Memory Disorders Unit, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Devkee M. Vadukul
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London SW7 2BX, UK
| | - Céline Vrancx
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium
- Department of Neurosciences, KU Leuven, 3000 Leuven, Belgium
| | - Stefan N. Constantinescu
- SIGN Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
- Ludwig Institute for Cancer Research Brussels, 1348 Brussels, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, Oxford University, Oxford OX1 2JD, UK
| | - Pascal Kienlen-Campard
- Aging and Dementia Research Group, Cellular and Molecular (CEMO) Division, Institute of Neuroscience, UCLouvain, 1200 Brussels, Belgium
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7
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Lu Y, Salsbury F, Derreumaux P. Impact of A2T and D23N mutations on C99 homodimer conformations. J Chem Phys 2022; 157:085102. [DOI: 10.1063/5.0101622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The proteolytic cleavage of C99 by γ-secretase is the last step in the production of amyloid-β (Aβ) peptides. Previous studies have shown that membrane lipid composition, cholesterol concentration, and mutation in the transmembrane helix modified the structures and fluctuations of C99. In this study, we performed atomistic molecular dynamics simulations of the homodimer of the 55-residue congener of the C-terminal domain of the amyloid protein precursor, C99(1-55), in a POPC-cholesterol lipid bilayer, and we compared the conformational ensemble of WT sequence to those of the A2T and D23N variants. These mutations are particularly interesting as the protective Alzheimer's disease (AD) A2T mutation is known to decrease Aβ production, whereas the early onset AD D23N mutation does not affect Aβ production. We found noticeable differences in the structural ensembles of the three sequences. In particular, A2T varies from both WT and D23N by having long-range effects on the population of the extracellular justamembrane helix, the interface between the G29xxx-G33xxx-G37 motifs and the fluctuations of the transmembrane helical topologies.
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Affiliation(s)
- Yan Lu
- School of Physics, Xidian University, China
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Li CD, Junaid M, Shan X, Wang Y, Wang X, Khan A, Wei DQ. Effect of Cholesterol on C99 Dimerization: Revealed by Molecular Dynamics Simulations. Front Mol Biosci 2022; 9:872385. [PMID: 35928227 PMCID: PMC9343951 DOI: 10.3389/fmolb.2022.872385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/18/2022] [Indexed: 11/28/2022] Open
Abstract
C99 is the immediate precursor for amyloid beta (Aβ) and therefore is a central intermediate in the pathway that is believed to result in Alzheimer’s disease (AD). It has been suggested that cholesterol is associated with C99, but the dynamic details of how cholesterol affects C99 assembly and the Aβ formation remain unclear. To investigate this question, we employed coarse-grained and all-atom molecular dynamics simulations to study the effect of cholesterol and membrane composition on C99 dimerization. We found that although the existence of cholesterol delays C99 dimerization, there is no direct competition between C99 dimerization and cholesterol association. In contrast, the existence of cholesterol makes the C99 dimer more stable, which presents a cholesterol binding C99 dimer model. Cholesterol and membrane composition change the dimerization rate and conformation distribution of C99, which will subsequently influence the production of Aβ. Our results provide insights into the potential influence of the physiological environment on the C99 dimerization, which will help us understand Aβ formation and AD’s etiology.
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Affiliation(s)
- Cheng-Dong Li
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Junaid
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoqi Shan
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjing Wang
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangeng Wang
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, China
- *Correspondence: Dong-Qing Wei,
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9
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Capone R, Tiwari A, Hadziselimovic A, Peskova Y, Hutchison JM, Sanders CR, Kenworthy AK. The C99 domain of the amyloid precursor protein resides in the disordered membrane phase. J Biol Chem 2021; 296:100652. [PMID: 33839158 PMCID: PMC8113881 DOI: 10.1016/j.jbc.2021.100652] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 12/11/2022] Open
Abstract
Processing of the amyloid precursor protein (APP) via the amyloidogenic pathway is associated with the etiology of Alzheimer's disease. The cleavage of APP by β-secretase to generate the transmembrane 99-residue C-terminal fragment (C99) and subsequent processing of C99 by γ-secretase to yield amyloid-β (Aβ) peptides are essential steps in this pathway. Biochemical evidence suggests that amyloidogenic processing of C99 occurs in cholesterol- and sphingolipid-enriched liquid-ordered phase membrane rafts. However, direct evidence that C99 preferentially associates with these rafts has remained elusive. Here, we tested this by quantifying the affinity of C99-GFP for raft domains in cell-derived giant plasma membrane vesicles (GPMVs). We found that C99 was essentially excluded from ordered domains in vesicles from HeLa cells, undifferentiated SH-SY5Y cells, or SH-SY5Y-derived neurons; instead, ∼90% of C99 partitioned into disordered domains. The strong association of C99 with disordered domains occurred independently of its cholesterol-binding activity or homodimerization, or of the presence of the familial Alzheimer disease Arctic mutation (APP E693G). Finally, through biochemical studies we confirmed previous results, which showed that C99 is processed in the plasma membrane by α-secretase, in addition to the well-known γ-secretase. These findings suggest that C99 itself lacks an intrinsic affinity for raft domains, implying that either i) amyloidogenic processing of the protein occurs in disordered regions of the membrane, ii) processing involves a marginal subpopulation of C99 found in rafts, or iii) as-yet-unidentified protein-protein interactions with C99 in living cells drive this protein into membrane rafts to promote its cleavage therein.
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Affiliation(s)
- Ricardo Capone
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Ajit Tiwari
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Yelena Peskova
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
| | - James M Hutchison
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Anne K Kenworthy
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA.
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Kedia S, Ramakrishna P, Netrakanti PR, Singh N, Sisodia SS, Jose M, Kumar S, Mahadevan A, Ramanan N, Nadkarni S, Nair D. Alteration in synaptic nanoscale organization dictates amyloidogenic processing in Alzheimer's disease. iScience 2020; 24:101924. [PMID: 33409475 PMCID: PMC7773964 DOI: 10.1016/j.isci.2020.101924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/22/2020] [Accepted: 12/07/2020] [Indexed: 01/08/2023] Open
Abstract
Despite intuitive insights into differential proteolysis of amyloid precursor protein (APP), the stochasticity behind local product formation through amyloidogenic pathway at individual synapses remain unclear. Here, we show that the major components of amyloidogenic machinery namely, APP and secretases are discretely organized into nanodomains of high local concentration compared to their immediate environment in functional zones of the synapse. Additionally, with the aid of multiple models of Alzheimer's disease (AD), we confirm that this discrete nanoscale chemical map of amyloidogenic machinery is altered at excitatory synapses. Furthermore, we provide realistic models of amyloidogenic processing in unitary vesicles originating from the endocytic zone of excitatory synapses. Thus, we show how an alteration in the stochasticity of synaptic nanoscale organization contributes to the dynamic range of C-terminal fragments β (CTFβ) production, defining the heterogeneity of amyloidogenic processing at individual synapses, leading to long-term synaptic deficits as seen in AD. Components of amyloidogenic machinery are organized into nanodomains Assembly of nanodomains differs between functional zones of the synapse Stochasticity of nanoscale organization dictates dynamic range of APP proteolysis Variability in composition of amyloidogenic machinery is associated with AD
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Affiliation(s)
- Shekhar Kedia
- Centre for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | | | | | - Nivedita Singh
- Centre for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | - Sangram S Sisodia
- Center for Molecular Neurobiology, Department of Neurobiology, The University of Chicago, IL 60637, USA
| | - Mini Jose
- Centre for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | - Sathish Kumar
- Department of Neurology, University of Bonn, Bonn 53127, Germany
| | - Anita Mahadevan
- Department of Neuropathology, NIMHANS, Bangalore 560029, India
| | | | - Suhita Nadkarni
- Indian Institute of Science Education and Research, Pune 411008, India
| | - Deepak Nair
- Centre for Neuroscience, Indian Institute of Science, Bangalore 560012, India
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11
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Gadhave K, Gehi BR, Kumar P, Xue B, Uversky VN, Giri R. The dark side of Alzheimer's disease: unstructured biology of proteins from the amyloid cascade signaling pathway. Cell Mol Life Sci 2020; 77:4163-4208. [PMID: 31894361 PMCID: PMC11104979 DOI: 10.1007/s00018-019-03414-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/17/2019] [Accepted: 12/04/2019] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD) is a leading cause of age-related dementia worldwide. Despite more than a century of intensive research, we are not anywhere near the discovery of a cure for this disease or a way to prevent its progression. Among the various molecular mechanisms proposed for the description of the pathogenesis and progression of AD, the amyloid cascade hypothesis, according to which accumulation of a product of amyloid precursor protein (APP) cleavage, amyloid β (Aβ) peptide, induces pathological changes in the brain observed in AD, occupies a unique niche. Although multiple proteins have been implicated in this amyloid cascade signaling pathway, their structure-function relationships are mostly unexplored. However, it is known that two major proteins related to AD pathology, Aβ peptide, and microtubule-associated protein tau belong to the category of intrinsically disordered proteins (IDPs), which are the functionally important proteins characterized by a lack of fixed, ordered three-dimensional structure. IDPs and intrinsically disordered protein regions (IDPRs) play numerous vital roles in various cellular processes, such as signaling, cell cycle regulation, macromolecular recognition, and promiscuous binding. However, the deregulation and misfolding of IDPs may lead to disturbed signaling, interactions, and disease pathogenesis. Often, molecular recognition-related IDPs/IDPRs undergo disorder-to-order transition upon binding to their biological partners and contain specific disorder-based binding motifs, known as molecular recognition features (MoRFs). Knowing the intrinsic disorder status and disorder-based functionality of proteins associated with amyloid cascade signaling pathway may help to untangle the mechanisms of AD pathogenesis and help identify therapeutic targets. In this paper, we have used multiple computational tools to evaluate the presence of intrinsic disorder and MoRFs in 27 proteins potentially relevant to the amyloid cascade signaling pathway. Among these, BIN1, APP, APOE, PICALM, PSEN1 and CD33 were found to be highly disordered. Furthermore, their disorder-based binding regions and associated short linear motifs have also been identified. These findings represent important foundation for the future research, and experimental characterization of disordered regions in these proteins is required to better understand their roles in AD pathogenesis.
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Affiliation(s)
- Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | | | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33620, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia.
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India.
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12
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Hutchison JM, Shih KC, Scheidt HA, Fantin SM, Parson KF, Pantelopulos GA, Harrington HR, Mittendorf KF, Qian S, Stein RA, Collier SE, Chambers MG, Katsaras J, Voehler MW, Ruotolo BT, Huster D, McFeeters RL, Straub JE, Nieh MP, Sanders CR. Bicelles Rich in both Sphingolipids and Cholesterol and Their Use in Studies of Membrane Proteins. J Am Chem Soc 2020; 142:12715-12729. [PMID: 32575981 DOI: 10.1021/jacs.0c04669] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
How the distinctive lipid composition of mammalian plasma membranes impacts membrane protein structure is largely unexplored, partly because of the dearth of isotropic model membrane systems that contain abundant sphingolipids and cholesterol. This gap is addressed by showing that sphingomyelin and cholesterol-rich (SCOR) lipid mixtures with phosphatidylcholine can be cosolubilized by n-dodecyl-β-melibioside to form bicelles. Small-angle X-ray and neutron scattering, as well as cryo-electron microscopy, demonstrate that these assemblies are stable over a wide range of conditions and exhibit the bilayered-disc morphology of ideal bicelles even at low lipid-to-detergent mole ratios. SCOR bicelles are shown to be compatible with a wide array of experimental techniques, as applied to the transmembrane human amyloid precursor C99 protein in this medium. These studies reveal an equilibrium between low-order oligomer structures that differ significantly from previous experimental structures of C99, providing an example of how ordered membranes alter membrane protein structure.
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Affiliation(s)
- James M Hutchison
- Chemical and Physical Biology Graduate Program and Center for Structural Biology, Vanderbilt University, Nashville 37240, Tennessee, United States
| | - Kuo-Chih Shih
- Polymer Program, Department of Chemical & Biomolecular Engineering, and Department of Biomedical Engineering, University of Connecticut, Storrs 06269, Connecticut, United States
| | - Holger A Scheidt
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig 16-18, 04107, Germany
| | - Sarah M Fantin
- Department of Chemistry, University of Michigan, Ann Arbor 48109, Michigan, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor 48109, Michigan, United States
| | - George A Pantelopulos
- Department of Chemistry, Boston University, Boston 02215, Massachusetts, United States
| | - Haley R Harrington
- Center for Structural Biology and Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville 37240, Tennessee, United States
| | - Kathleen F Mittendorf
- Center for Health Research, Kaiser Permanente, Portland 97227, Oregon, United States
| | - Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge 37831, Tennessee, United States
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville37240, Tennessee, United States
| | - Scott E Collier
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland 97227, Oregon, United States
| | - Melissa G Chambers
- Center for Structural Biology, Vanderbilt University, Nashville 37240, Tennessee, United States
| | - John Katsaras
- Neutron Scattering Division and Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge 37831, Tennessee, United States
| | - Markus W Voehler
- Center for Structural Biology and Department of Chemistry, Vanderbilt University, Nashville 37240, Tennessee, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor 48109, Michigan, United States
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig 16-18, 04107, Germany
| | - Robert L McFeeters
- Department of Chemistry, University of Alabama, Huntsville 35899, Alabama, United States
| | - John E Straub
- Department of Chemistry, Boston University, Boston 02215, Massachusetts, United States
| | - Mu-Ping Nieh
- Polymer Program, Department of Chemical & Biomolecular Engineering, and Department of Biomedical Engineering, University of Connecticut, Storrs 06269, Connecticut, United States
| | - Charles R Sanders
- Center for Structural Biology, Department of Biochemistry, and Department of Medicine, Vanderbilt University School of Medicine, Nashville 37240, Tennessee, United States
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13
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Functions and dysfunctions of nitric oxide in brain. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1949-1967. [DOI: 10.1016/j.bbadis.2018.11.007] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/29/2018] [Accepted: 11/11/2018] [Indexed: 02/06/2023]
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14
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Tang TC, Kienlen-Campard P, Hu Y, Perrin F, Opsomer R, Octave JN, Constantinescu SN, Smith SO. Influence of the familial Alzheimer's disease-associated T43I mutation on the transmembrane structure and γ-secretase processing of the C99 peptide. J Biol Chem 2019; 294:5854-5866. [PMID: 30755484 PMCID: PMC6463720 DOI: 10.1074/jbc.ra118.006061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 02/09/2019] [Indexed: 11/06/2022] Open
Abstract
Extracellular deposition of β-amyloid (Aβ) peptides in the brain is a hallmark of Alzheimer's disease (AD). Upon β-secretase-mediated cleavage of the β C-terminal fragment (β-CTF) from the Aβ precursor protein, the γ-secretase complex produces the Aβ peptides associated with AD. The familial T43I mutation within the transmembrane domain of the β-CTF (also referred to as C99) increases the ratio between the Aβ42 and Aβ40 peptides largely due to a decrease in Aβ40 formation. Aβ42 is the principal component of amyloid deposits within the brain parenchyma, and an increase in the Aβ42/Aβ40 ratio is correlated with early-onset AD. Using NMR and FTIR spectroscopy, here we addressed how the T43I substitution influences the structure of C55, the minimal sequence containing the entire extracellular and transmembrane (TM) domains of C99 needed for γ-secretase processing. 13C NMR chemical shifts indicated that the T43I substitution increases helical structure within the TM domain of C55. These structural changes were associated with a shift of the C55 dimer to the monomer and an increase in the tilt of the TM helix relative to the membrane normal in the T43I mutant compared with that of WT C55. The A21G (Flemish) mutation was previously found to increase secreted Aβ40 levels; here, we combined this mutation in the extracellular domain of C99 with T43I and observed that the T43I/A21G double mutant decreases Aβ40 formation. We discuss how the observed structural changes in the T43I mutant may decrease Aβ40 formation and increase the Aβ42/Aβ40 ratio.
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Affiliation(s)
- Tzu-Chun Tang
- From the Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215
| | | | - Yi Hu
- From the Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215
| | - Florian Perrin
- Ludwig Institute for Cancer Research and de Duve Institute, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Rémi Opsomer
- the Institute of Neuroscience, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Jean-Noël Octave
- the Institute of Neuroscience, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research and de Duve Institute, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Steven O Smith
- From the Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215.
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15
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Abstract
Plasma membrane proteins organize into structures named compartments, microdomains, rafts, phases, crowds, or clusters. These structures are often smaller than 100 nm in diameter. Despite their importance in many cellular functions, little is known about their inner organization. For instance, how densely are molecules packed? Being aware of the protein compaction may contribute to our general understanding of why such structures exist and how they execute their functions. In this study, we have investigated plasma membrane crowds formed by the amyloid precursor protein (APP), a protein well known for its involvement in Alzheimer's disease. By combining biochemical experiments with conventional and super-resolution stimulated emission depletion microscopy, we quantitatively determined the protein packing density within APP crowds. We found that crowds occurring with reasonable frequency contain between 20 and 30 molecules occupying a spherical area with a diameter between 65 and 85 nm. Additionally, we found the vast majority of plasmalemmal APP residing in these crowds. The model suggests a high molecular density of protein material within plasmalemmal APP crowds. This should affect the protein's biochemical accessibility and processing by nonpathological α-secretases. As clustering of APP is a prerequisite for endocytic entry into the pathological processing pathway, elucidation of the packing density also provides a deeper understanding of this part of APP's life cycle.
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16
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Li CD, Junaid M, Chen H, Ali A, Wei DQ. Helix-Switch Enables C99 Dimer Transition between the Multiple Conformations. J Chem Inf Model 2019; 59:339-350. [PMID: 30570254 DOI: 10.1021/acs.jcim.8b00559] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
C99 is the immediate precursor of amyloid-β (Aβ) and therefore is a central intermediate in the pathway that is believed to result in Alzheimer's disease (AD). Recent studies have shown that C99 dimerization changes the Aβ ratio, but the mechanism remains unclear. Previous studies of the C99 dimer have produced controversial structure models. To address these questions, we investigated C99 dimerization using molecular dynamics (MD) simulations. A helix-switch model was revealed in the formation and transition of the C99 dimer, and six types of conformations were identified. The different conformations show differential exposures of γ-cleavage sites and insertion depths in the bilayer, which may modulate γ-cleavage of C99 and lead to different Aβ levels. Our results redefine C99 dimerization, provide a framework to mediate the current controversial results, and give insights into the understanding of the relationship between C99 dimerization and Aβ formation.
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Affiliation(s)
- Cheng-Dong Li
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Minhang District, Shanghai 200240 , China.,Department of Mechanical Engineering and Material Science , Yale University , New Haven , Connecticut 06520-8286 , United States
| | - Muhammad Junaid
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Minhang District, Shanghai 200240 , China
| | - Hui Chen
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Minhang District, Shanghai 200240 , China
| | - Arif Ali
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Minhang District, Shanghai 200240 , China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Minhang District, Shanghai 200240 , China
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17
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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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18
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Hu Y, Kienlen-Campard P, Tang TC, Perrin F, Opsomer R, Decock M, Pan X, Octave JN, Constantinescu SN, Smith SO. β-Sheet Structure within the Extracellular Domain of C99 Regulates Amyloidogenic Processing. Sci Rep 2017; 7:17159. [PMID: 29215043 PMCID: PMC5719365 DOI: 10.1038/s41598-017-17144-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/20/2017] [Indexed: 11/15/2022] Open
Abstract
Familial mutations in C99 can increase the total level of the soluble Aβ peptides produced by proteolysis, as well as the Aβ42/Aβ40 ratio, both of which are linked to the progression of Alzheimer’s disease. We show that the extracellular sequence of C99 forms β-sheet structure upon interaction with membrane bilayers. Mutations that disrupt this structure result in a significant increase in Aβ production and, in specific cases, result in an increase in the amount of Aβ42 relative to Aβ40. Fourier transform infrared and solid-state NMR spectroscopic studies reveal a central β-hairpin within the extracellular sequence comprising Y10-E11-V12 and L17-V18-F19 connected by a loop involving H13-H14-Q15. These results suggest how familial mutations in the extracellular sequence influence C99 processing and provide a structural basis for the development of small molecule modulators that would reduce Aβ production.
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Affiliation(s)
- Yi Hu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | | | - Tzu-Chun Tang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Florian Perrin
- Institute of Neuroscience, Université catholique de Louvain, Brussels, 1200, Belgium.,Ludwig Institute for Cancer Research and de Duve Institute, Université catholique de Louvain, Brussels, 1200, Belgium
| | - Rémi Opsomer
- Institute of Neuroscience, Université catholique de Louvain, Brussels, 1200, Belgium
| | - Marie Decock
- Institute of Neuroscience, Université catholique de Louvain, Brussels, 1200, Belgium
| | - Xiaoshu Pan
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jean-Noel Octave
- Institute of Neuroscience, Université catholique de Louvain, Brussels, 1200, Belgium
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research and de Duve Institute, Université catholique de Louvain, Brussels, 1200, Belgium.
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA.
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19
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Zhou R, Yang G, Shi Y. Dominant negative effect of the loss-of-function γ-secretase mutants on the wild-type enzyme through heterooligomerization. Proc Natl Acad Sci U S A 2017; 114:12731-12736. [PMID: 29078389 PMCID: PMC5715776 DOI: 10.1073/pnas.1713605114] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
γ-secretase is an intramembrane protease complex consisting of nicastrin, presenilin-1/2, APH-1a/b, and Pen-2. Hydrolysis of the 99-residue transmembrane fragment of amyloid precursor protein (APP-C99) by γ-secretase produces β-amyloid (Aβ) peptides. Pathogenic mutations in PSEN1 and PSEN2, which encode the catalytic subunit presenilin-1/2 of γ-secretase, lead to familial Alzheimer's disease in an autosomal dominant manner. However, the underlying mechanism of how the mutant PSEN gene may affect the function of the WT allele remains to be elucidated. Here we report that each of the loss-of-function γ-secretase variants that carries a PSEN1 mutation suppresses the protease activity of the WT γ-secretase on Aβ production. Each of these γ-secretase variants forms a stable oligomer with the WT γ-secretase in vitro in the presence of the detergent CHAPSO {3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate}, but not digitonin. Importantly, robust protease activity of γ-secretase is detectable in the presence of CHAPSO, but not digitonin. These experimental observations suggest a dominant negative effect of the γ-secretase, in which the protease activity of WT γ-secretase is suppressed by the loss-of-function γ-secretase variants through hetero-oligomerization. The relevance of this finding to the genesis of Alzheimer's disease is critically evaluated.
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Affiliation(s)
- Rui Zhou
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guanghui Yang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310064, Zhejiang Province, China
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20
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Itkin A, Salnikov ES, Aisenbrey C, Raya J, Glattard E, Raussens V, Ruysschaert JM, Bechinger B. Structural Characterization of the Amyloid Precursor Protein Transmembrane Domain and Its γ-Cleavage Site. ACS OMEGA 2017; 2:6525-6534. [PMID: 31457253 PMCID: PMC6645296 DOI: 10.1021/acsomega.7b00619] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/16/2017] [Indexed: 06/10/2023]
Abstract
Alzheimer's disease is the most common form of dementia that affects about 50 million of sufferers worldwide. A major role for the initiation and progression of Alzheimer's disease has been associated with the amyloid β-peptide (Aβ), which is a protease cleavage product of the amyloid precursor protein. The amyloid precursor protein is an integral membrane protein with a single transmembrane domain. Here, we assessed the structural integrity of the transmembrane domain within oriented phosphatidylcholine lipid bilayers and determined the tilt angle distribution and dynamics of various subdomains using solid-state NMR and attenuated total reflectance Fourier transform infrared spectroscopies. Although the overall secondary structure of the transmembrane domain is α-helical, pronounced conformational and topological heterogeneities were observed for the γ- and, to a lesser extent, the ζ-cleavage site, with pronounced implications for the production of Aβ and related peptides, the development of the disease, and pharmaceutical innovation.
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Affiliation(s)
- Anna Itkin
- University
of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics
and NMR, 4, rue Blaise
Pascal, F-67070 Strasbourg, France
- Center
for Structural Biology and Bioinformatics, Laboratory of Structure
and Function of Biological Membranes, Université
Libre de Bruxelles, Campus
Plaine - Acces 2 - Batiment BC - Niveau 4, Boulevard du Triomphe -
CP 206/2, B-1050 Brussels, Belgium
| | - Evgeniy S. Salnikov
- University
of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics
and NMR, 4, rue Blaise
Pascal, F-67070 Strasbourg, France
| | - Christopher Aisenbrey
- University
of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics
and NMR, 4, rue Blaise
Pascal, F-67070 Strasbourg, France
| | - Jesus Raya
- University
of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics
and NMR, 4, rue Blaise
Pascal, F-67070 Strasbourg, France
| | - Elise Glattard
- University
of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics
and NMR, 4, rue Blaise
Pascal, F-67070 Strasbourg, France
| | - Vincent Raussens
- Center
for Structural Biology and Bioinformatics, Laboratory of Structure
and Function of Biological Membranes, Université
Libre de Bruxelles, Campus
Plaine - Acces 2 - Batiment BC - Niveau 4, Boulevard du Triomphe -
CP 206/2, B-1050 Brussels, Belgium
| | - Jean-Marie Ruysschaert
- Center
for Structural Biology and Bioinformatics, Laboratory of Structure
and Function of Biological Membranes, Université
Libre de Bruxelles, Campus
Plaine - Acces 2 - Batiment BC - Niveau 4, Boulevard du Triomphe -
CP 206/2, B-1050 Brussels, Belgium
| | - Burkhard Bechinger
- University
of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics
and NMR, 4, rue Blaise
Pascal, F-67070 Strasbourg, France
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21
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Langosch D, Steiner H. Substrate processing in intramembrane proteolysis by γ-secretase - the role of protein dynamics. Biol Chem 2017; 398:441-453. [PMID: 27845877 DOI: 10.1515/hsz-2016-0269] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/08/2016] [Indexed: 01/31/2023]
Abstract
Intramembrane proteases comprise a number of different membrane proteins with different types of catalytic sites. Their common denominator is cleavage within the plane of the membrane, which usually results in peptide bond scission within the transmembrane helices of their substrates. Despite recent progress in the determination of high-resolution structures, as illustrated here for the γ-secretase complex and its substrate C99, it is still unknown how these enzymes function and how they distinguish between substrates and non-substrates. In principle, substrate/non-substrate discrimination could occur at the level of substrate binding and/or cleavage. Focusing on the γ-secretase/C99 pair, we will discuss recent observations suggesting that global motions within a substrate transmembrane helix may be much more important for defining a substrate than local unraveling at cleavage sites.
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22
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Yan Y, Xu TH, Harikumar KG, Miller LJ, Melcher K, Xu HE. Dimerization of the transmembrane domain of amyloid precursor protein is determined by residues around the γ-secretase cleavage sites. J Biol Chem 2017; 292:15826-15837. [PMID: 28790170 PMCID: PMC5612113 DOI: 10.1074/jbc.m117.789669] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/02/2017] [Indexed: 11/06/2022] Open
Abstract
One of the hallmarks of Alzheimer's disease is the formation of extracellular amyloid plaques that consist mainly of abnormally aggregated forms of amyloid β (Aβ) peptides. These peptides are generated by γ-secretase-catalyzed cleavage of a dimeric membrane-bound C-terminal fragment (C99) of the amyloid precursor protein. Although C99 homodimerization has been linked to Aβ production and changes in the aggregation-determining Aβ42/Aβ40 ratio, the motif through which C99 dimerizes has remained controversial. Here, we have used two independent assays to gain insight into C99 homodimerization in the context of the membrane of live cells: bioluminescence resonance energy transfer and Tango membrane protein-protein interaction assays, which were further confirmed by traditional pull-down assays. Our results indicate a four-amino acid region within the C99 transmembrane helix (43TVIV46) as well as its local secondary structure as critical determinants for homodimerization. These four amino acids are also a hot spot of familial Alzheimer's disease-linked mutations that both decrease C99 homodimerization and γ-secretase cleavage and alter the initial cleavage site to increase the Aβ42/40 ratio.
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Affiliation(s)
- Yan Yan
- From the Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,the University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.,the Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, Michigan 49503, and
| | - Ting-Hai Xu
- From the Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,the University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.,the Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, Michigan 49503, and
| | - Kaleeckal G Harikumar
- the Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona 85259
| | - Laurence J Miller
- the Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona 85259
| | - Karsten Melcher
- the Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, Michigan 49503, and
| | - H Eric Xu
- From the Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China, .,the Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, Michigan 49503, and
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23
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Sun F, Chen L, Wei P, Chai M, Ding X, Xu L, Luo SZ. Dimerization and Structural Stability of Amyloid Precursor Proteins Affected by the Membrane Microenvironments. J Chem Inf Model 2017; 57:1375-1387. [DOI: 10.1021/acs.jcim.7b00196] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fude Sun
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Long Chen
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Peng Wei
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mengya Chai
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiufang Ding
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lida Xu
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shi-Zhong Luo
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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24
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Becker-Pauly C, Pietrzik CU. The Metalloprotease Meprin β Is an Alternative β-Secretase of APP. Front Mol Neurosci 2017; 9:159. [PMID: 28105004 PMCID: PMC5215381 DOI: 10.3389/fnmol.2016.00159] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/09/2016] [Indexed: 01/08/2023] Open
Abstract
The membrane bound metalloprotease meprin β is important for collagen fibril assembly in connective tissue formation and for the detachment of the intestinal mucus layer for proper barrier function. Recent proteomic studies revealed dozens of putative new substrates of meprin β, including the amyloid precursor protein (APP). It was shown that APP is cleaved by meprin β in distinct ways, either at the β-secretase site resulting in increased levels of Aβ peptides, or at the N-terminus releasing 11 kDa, and 20 kDa peptide fragments. The latter event was discussed to be rather neuroprotective, whereas the ectodomain shedding of APP by meprin β reminiscent to BACE-1 is in line with the amyloid hypothesis of Alzheimer's disease, promoting neurodegeneration. The N-terminal 11 kDa and 20 kDa peptide fragments represent physiological cleavage products, since they are found in human brains under different diseased or non-diseased states, whereas these fragments are completely missing in brains of meprin β knock-out animals. Meprin β is not only a sheddase of adhesion molecules, such as APP, but was additionally demonstrated to cleave within the prodomain of ADAM10. Activated ADAM10, the α-secretase of APP, is then able to shed meprin β from the cell surface thereby abolishing the β-secretase activity. All together meprin β seems to be a novel player in APP processing events, even influencing other enzymes involved in APP cleavage.
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Affiliation(s)
- Christoph Becker-Pauly
- Unit for Degradomics of the Protease Web, Institute of Biochemistry, University of Kiel Kiel, Germany
| | - Claus U Pietrzik
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University Mainz Mainz, Germany
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25
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Audagnotto M, Lemmin T, Barducci A, Dal Peraro M. Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer. J Phys Chem Lett 2016; 7:3572-3578. [PMID: 27518597 DOI: 10.1021/acs.jpclett.6b01721] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The proteolytic cleavage of the transmembrane (TM) domain of the amyloid precursor protein (APP) releases amyloid-β (Aβ) peptides, which accumulation in the brain tissue is an early indicator of Alzheimer's disease. We used multiscale molecular dynamics simulations to investigate the stability of APP-TM dimer in realistic models of the synaptic plasma membrane (SPM). Between the two possible dimerization motifs proposed by NMR and EPR, namely G709XXXA713 and G700XXXG704XXXG708, our study revealed that the dimer promoted by the G709XXXA713 motif is not stable in the SPM due to the competition with highly unsaturated lipids that constitute the SPM. Under the same conditions, the dimer promoted by the G700XXXG704XXXG708 motif is instead the most stable species and likely the most biologically relevant. Independently of the dimerization state, both these motifs can be involved in the recruitment of cholesterol molecules.
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Affiliation(s)
- Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics (SIB) , Lausanne 1015, Switzerland
| | - Thomas Lemmin
- Department of Pharmaceutical Chemistry, University of California-San Francisco , San Francisco, California 94143, United States
| | - Alessandro Barducci
- Inserm, U1054 Montpellier, France
- Université de Montpellier, CNRS, UMR 5048 , Centre de Biochimie Structurale, U1054 Montpellier, France
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics (SIB) , Lausanne 1015, Switzerland
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26
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Bocharova OV, Urban AS, Nadezhdin KD, Bocharov EV, Arseniev AS. Cell-free expression of the APP transmembrane fragments with Alzheimer's disease mutations using algal amino acid mixture for structural NMR studies. Protein Expr Purif 2016; 123:105-11. [PMID: 27071311 DOI: 10.1016/j.pep.2016.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 04/07/2016] [Accepted: 04/07/2016] [Indexed: 12/23/2022]
Abstract
Structural investigations need ready supply of the isotope labeled proteins with inserted mutations n the quantities sufficient for the heteronuclear NMR. Though cell-free expression system has been widely used in the past years, high startup cost and complex compound composition prevent many researches from the developing this technique, especially for membrane protein production. Here we demonstrate the utility of a robust, cost-optimized cell-free expression technique for production of the physiologically important transmembrane fragment of amyloid precursor protein, APP686-726, containing Alzheimer's disease mutations in the juxtamembrane (E693G, Arctic form) and the transmembrane parts (V717G, London form, or L723P, Australian form). The protein cost was optimized by varying the FM/RM ratio as well as the amino acid concentration. We obtained the wild-type and mutant transmembrane fragments in the pellet mode of continuous exchange cell-free system consuming only commercial algal mixture of the (13)C,(15)N-labeled amino acids. Scaling up analytical tests, we achieved milligram quantity yields of isotope labeled wild-type and mutant APP686-726 for structural studies by high resolution NMR spectroscopy in membrane mimicking environment. The described approach has from 5 to 23-fold cost advantage over the bacterial expression methods described earlier and 1.5 times exceeds our previous result obtained with the longer APP671-726WT fragment.
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Affiliation(s)
- Olga V Bocharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
| | - Anatoly S Urban
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia; Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., 141700, Dolgoprudny, Russia
| | - Kirill D Nadezhdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia; Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., 141700, Dolgoprudny, Russia
| | - Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia; National Research Centre "Kurchatov Institute", Dept. Complex NBIC-technologies, Akad. Kurchatova pl. 1, 123182, Moscow, Russia
| | - Alexander S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia; Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., 141700, Dolgoprudny, Russia
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27
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Chen W, Gamache E, Rosenman DJ, Xie J, Lopez MM, Li YM, Wang C. Familial Alzheimer's mutations within APPTM increase Aβ42 production by enhancing accessibility of ε-cleavage site. Nat Commun 2015; 5:3037. [PMID: 24390130 DOI: 10.1038/ncomms4037] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/29/2013] [Indexed: 02/08/2023] Open
Abstract
The high Aβ42/Aβ40 production ratio is a hallmark of familial Alzheimer's disease, which can be caused by mutations in the amyloid precursor protein (APP). The C-terminus of Aβ is generated by γ-secretase cleavage within the transmembrane domain of APP (APPTM), a process that is primed by an initial ε-cleavage at either T48 or L49, resulting in subsequent production of Aβ42 or Aβ40, respectively. Here we solve the dimer structures of wild-type APPTM (AAPTM WT) and mutant APPTM (FAD mutants V44M) with solution NMR. The right-handed APPTM helical dimer is mediated by GXXXA motif. From the NMR structural and dynamic data, we show that the V44M and V44A mutations can selectively expose the T48 site by weakening helical hydrogen bonds and increasing hydrogen-deuterium exchange rate (kex). We propose a structural model in which FAD mutations (V44M and V44A) can open the T48 site γ-secretase for the initial ε-cleavage, and consequently shift cleavage preference towards Aβ42.
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Affiliation(s)
- Wen Chen
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
| | - Eric Gamache
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
| | - David J Rosenman
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
| | - Jian Xie
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
| | - Maria M Lopez
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
| | - Yue-Ming Li
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
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Viswanath S, Dominguez L, Foster LS, Straub JE, Elber R. Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization. Proteins 2015; 83:2170-85. [PMID: 26404856 DOI: 10.1002/prot.24934] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/13/2015] [Accepted: 09/17/2015] [Indexed: 12/13/2022]
Abstract
Novel adjustments are introduced to the docking algorithm, DOCK/PIERR, for the purpose of predicting structures of transmembrane protein complexes. Incorporating knowledge about the membrane environment is shown to significantly improve docking accuracy. The extended version of DOCK/PIERR is shown to perform comparably to other leading docking packages. This membrane version of DOCK/PIERR is applied to the prediction of coiled-coil homodimer structures of the transmembrane region of the C-terminal peptide of amyloid precursor protein (C99). Results from MD simulation of the C99 homodimer in POPC bilayer and docking are compared. Docking results are found to capture key aspects of the homodimer ensemble, including the existence of three topologically distinct conformers. Furthermore, the extended version of DOCK/PIERR is successful in capturing the effects of solvation in membrane and micelle. Specifically, DOCK/PIERR reproduces essential differences in the homodimer ensembles simulated in POPC bilayer and DPC micelle, where configurational entropy and surface curvature effects bias the handedness and topology of the homodimer ensemble.
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Affiliation(s)
- Shruthi Viswanath
- Department of Computer Science, University of Texas at Austin, Austin, Texas, 78712.,Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas, 78712
| | - Laura Dominguez
- Department of Chemistry, Boston University, Boston, Massachusetts, 02215
| | - Leigh S Foster
- Department of Chemistry, Boston University, Boston, Massachusetts, 02215
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts, 02215
| | - Ron Elber
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas, 78712.,Department of Chemistry, University of Texas at Austin, Austin, Texas, 78712
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29
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Winkler E, Julius A, Steiner H, Langosch D. Homodimerization Protects the Amyloid Precursor Protein C99 Fragment from Cleavage by γ-Secretase. Biochemistry 2015; 54:6149-52. [DOI: 10.1021/acs.biochem.5b00986] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Edith Winkler
- BMC-Biomedical
Center, Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany
| | - Ayse Julius
- Lehrstuhl
Chemie der Biopolymere, Technische Universität München, Weihenstephaner
Berg 3, 85354 Freising, Germany
- Munich Center For Integrated Protein Science (CIPSM), Munich, Germany
| | - Harald Steiner
- BMC-Biomedical
Center, Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany
- DZNE-German Center for Neurodegenerative Diseases, Munich, Germany
| | - Dieter Langosch
- Lehrstuhl
Chemie der Biopolymere, Technische Universität München, Weihenstephaner
Berg 3, 85354 Freising, Germany
- Munich Center For Integrated Protein Science (CIPSM), Munich, Germany
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30
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Decock M, El Haylani L, Stanga S, Dewachter I, Octave JN, Smith SO, Constantinescu SN, Kienlen-Campard P. Analysis by a highly sensitive split luciferase assay of the regions involved in APP dimerization and its impact on processing. FEBS Open Bio 2015; 5:763-73. [PMID: 26500837 PMCID: PMC4588712 DOI: 10.1016/j.fob.2015.09.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/07/2015] [Accepted: 09/01/2015] [Indexed: 12/27/2022] Open
Abstract
Amyloid precursor protein (APP) dimerizes more than its C-terminal fragments in cells. Mutations of membrane GXXXG motifs affect Aβ production but not APP dimerization. Deletion of the APP intracellular domain increases APP dimerization.
Alzheimer’s disease (AD) is a neurodegenerative disease that causes progressive loss of cognitive functions, leading to dementia. Two types of lesions are found in AD brains: neurofibrillary tangles and senile plaques. The latter are composed mainly of the β-amyloid peptide (Aβ) generated by amyloidogenic processing of the amyloid precursor protein (APP). Several studies have suggested that dimerization of APP is closely linked to Aβ production. Nevertheless, the mechanisms controlling APP dimerization and their role in APP function are not known. Here we used a new luciferase complementation assay to analyze APP dimerization and unravel the involvement of its three major domains: the ectodomain, the transmembrane domain and the intracellular domain. Our results indicate that within cells full-length APP dimerizes more than its α and β C-terminal fragments, confirming the pivotal role of the ectodomain in this process. Dimerization of the APP transmembrane (TM) domain has been reported to regulate processing at the γ-cleavage site. We show that both non-familial and familial AD mutations in the TM GXXXG motifs strongly modulate Aβ production, but do not consistently change dimerization of the C-terminal fragments. Finally, we found for the first time that removal of intracellular domain strongly increases APP dimerization. Increased APP dimerization is linked to increased non-amyloidogenic processing.
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Key Words
- AD, Alzheimer’s disease
- AICD, APP intracellular domain
- APP
- APP, amyloid precursor protein
- Alzheimer disease
- Amyloid beta peptide
- Aβ, β-amyloid peptide
- CHO, chinese hamster ovary
- CTF, C-terminal fragment
- DAPT, N-[N-(3,5-difluorophenacetyl)-l-alanyl]-S-phenylglycine t-butyl ester
- DTT, dithiothreitol
- Dimerization
- ECL, enzymatic chemi-luminescence
- ECLIA, electro-chemiluminescence immuno-assay
- FBS, fetal bovine serum
- FRET, fluorescence resonance energy transfer
- GXXXG motifs
- KPI, Kunitz-type protease inhibitor
- NSAIDs, nonsteroidal anti-inflammatory drugs
- PBS, phosphate buffered saline
- PS1/PS2, presenilin1/presenilin2
- RLU, relative light unit
- SP, signal peptide
- Split luciferase
- TM, transmembrane
- YFP, yellow fluorescent protein
- sAPPα, soluble APPα
- sAPPβ, soluble APPβ
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Affiliation(s)
- Marie Decock
- Institute of Neuroscience, Université catholique de Louvain, Brussels 1200, Belgium
| | - Laetitia El Haylani
- Institute of Neuroscience, Université catholique de Louvain, Brussels 1200, Belgium
| | - Serena Stanga
- Institute of Neuroscience, Université catholique de Louvain, Brussels 1200, Belgium
| | - Ilse Dewachter
- Institute of Neuroscience, Université catholique de Louvain, Brussels 1200, Belgium
| | - Jean-Noël Octave
- Institute of Neuroscience, Université catholique de Louvain, Brussels 1200, Belgium
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Stefan N Constantinescu
- de Duve Institute and Ludwig Institute for Cancer Research, Université catholique de Louvain, Brussels 1200, Belgium
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31
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Svedružić ŽM, Popović K, Šendula-Jengić V. Decrease in catalytic capacity of γ-secretase can facilitate pathogenesis in sporadic and Familial Alzheimer's disease. Mol Cell Neurosci 2015; 67:55-65. [PMID: 26051801 DOI: 10.1016/j.mcn.2015.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/13/2015] [Accepted: 06/01/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Alzheimer's disease can be a result of an age-induced disparity between increase in cellular metabolism of Aβ peptides and decrease in maximal activity of a membrane-embedded protease γ-secretase. RESULTS We compared activity of WT γ-secretase with the activity of 6 FAD mutants in its presenilin-1 component and 5 FAD mutants in Aβ-part of its APP substrate (Familial Alzheimer's disease). All 11 FAD mutations show linear correlation between the decrease in maximal activity and the clinically observed age-of-onset and age-of-death. Biphasic-inhibitors showed that a higher ratio between physiological Aβ-production and the maximal activity of γ-secretase can be observed in cells that can facilitate pathogenic changes in Aβ-products. For example, Aβ production in cells with WT γ-secretase is at 11% of its maximal activity, with delta-exon-9 mutant at 26%, while with M139V mutant is at 28% of the maximal activity. In the same conditions, G384A mutant is fully saturated and at its maximal activity. Similarly, Aβ production in cells with γ-secretase complex carrying Aph1AL component is 12% of its maximal activity, while in cells with Aph1B complex is 26% of its maximal activity. Similar to the cell-based studies, clinical studies of biphasic dose-response in plasma samples of 54 healthy individuals showed variable ratios between physiological Aβ production and the maximal activity of γ-secretase. CONCLUSIONS The increase in the ratio between physiological Aβ production and maximal activity of γ-secretase can be an early sign of pathogenic processes in enzyme-based, cell-based, and clinical studies of sporadic and Familiar Alzheimer's disease.
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Affiliation(s)
- Željko M Svedružić
- Medical Biochemistry, PB Rab, Faculty of Medicine, University of Rijeka, Rab, Croatia; Department of Biotechnology, University of Rijeka, Rijeka, Croatia.
| | - Katarina Popović
- Neurology and Geriatrics, PB Rab, Faculty of Medicine, University of Rijeka, Rab, Croatia
| | - Vesna Šendula-Jengić
- Medical Biochemistry, PB Rab, Faculty of Medicine, University of Rijeka, Rab, Croatia; Neurology and Geriatrics, PB Rab, Faculty of Medicine, University of Rijeka, Rab, Croatia
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32
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Oestereich F, Bittner HJ, Weise C, Grohmann L, Janke LK, Hildebrand PW, Multhaup G, Munter LM. Impact of amyloid precursor protein hydrophilic transmembrane residues on amyloid-beta generation. Biochemistry 2015; 54:2777-84. [PMID: 25875527 DOI: 10.1021/acs.biochem.5b00217] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Amyloid-β (Aβ) peptides are likely the molecular cause of neurodegeneration observed in Alzheimer's disease. In the brain, Aβ42 and Aβ40 are toxic and the most important proteolytic fragments generated through sequential processing of the amyloid precursor protein (APP) by β- and γ-secretases. Impeding the generation of Aβ42 and Aβ40 is thus considered as a promising strategy to prevent Alzheimer's disease. We therefore wanted to determine key parameters of the APP transmembrane sequence enabling production of these Aβ species. Here we show that the hydrophilicity of amino acid residues G33, T43, and T48 critically determines the generation of Aβ42 and Aβ40 peptides (amino acid numbering according to Aβ nomenclature starting with aspartic acid 1). First, we performed a comprehensive mutational analysis of glycine residue G33 positioned within the N-terminal half of the APP transmembrane sequence by exchanging it against the 19 other amino acids. We found that hydrophilicity of the residue at position 33 positively correlated with Aβ42 and Aβ40 generation. Second, we analyzed two threonine residues at positions T43 and T48 in the C-terminal half of the APP-transmembrane sequence. Replacement of single threonine residues by hydrophobic valines inversely affected Aβ42 and Aβ40 generation. We observed that threonine mutants affected the initial γ-secretase cut, which is associated with levels of Aβ42 or Aβ40. Overall, hydrophilic residues of the APP transmembrane sequence decide on the exact initial γ-cut and the amounts of Aβ42 and Aβ40.
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Affiliation(s)
- Felix Oestereich
- †Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, H3G 1Y6 Montréal, Canada.,‡Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany.,∥Integrated Program in Neuroscience, McGill University, Montréal, Canada
| | - Heiko J Bittner
- §Institut für Medizinische Physik und Biophysik, Charité, Charitéplatz 1, 10117 Berlin, Germany
| | - Christoph Weise
- ‡Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Lisa Grohmann
- ‡Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Lisa-Kristin Janke
- ‡Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Peter W Hildebrand
- §Institut für Medizinische Physik und Biophysik, Charité, Charitéplatz 1, 10117 Berlin, Germany
| | - Gerhard Multhaup
- †Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, H3G 1Y6 Montréal, Canada.,‡Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Lisa-Marie Munter
- †Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, H3G 1Y6 Montréal, Canada.,‡Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
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33
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Stangl M, Schneider D. Functional competition within a membrane: Lipid recognition vs. transmembrane helix oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1886-96. [PMID: 25791349 DOI: 10.1016/j.bbamem.2015.03.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/09/2015] [Accepted: 03/09/2015] [Indexed: 12/27/2022]
Abstract
Binding of specific lipids to large, polytopic membrane proteins is well described, and it is clear that such lipids are crucial for protein stability and activity. In contrast, binding of defined lipid species to individual transmembrane helices and regulation of transmembrane helix monomer-oligomer equilibria by binding of distinct lipids is a concept, which has emerged only lately. Lipids bind to single-span membrane proteins, both in the juxta-membrane region as well as in the hydrophobic membrane core. While some interactions counteract transmembrane helix oligomerization, in other cases lipid binding appears to enhance oligomerization. As reversible oligomerization is involved in activation of many membrane proteins, binding of defined lipids to single-span transmembrane proteins might be a mechanism to regulate and/or fine-tune the protein activity. But how could lipid binding trigger the activity of a protein? How can binding of a single lipid molecule to a transmembrane helix affect the structure of a transmembrane helix oligomer, and consequently its signaling state? These questions are discussed in the present article based on recent results obtained with simple, single-span transmembrane proteins. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- Michael Stangl
- Department of Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany.
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34
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Urban S, Moin SM. A subset of membrane-altering agents and γ-secretase modulators provoke nonsubstrate cleavage by rhomboid proteases. Cell Rep 2014; 8:1241-7. [PMID: 25159145 DOI: 10.1016/j.celrep.2014.07.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/05/2014] [Accepted: 07/22/2014] [Indexed: 01/04/2023] Open
Abstract
Rhomboid proteases are integral membrane enzymes that regulate cell signaling, adhesion, and organelle homeostasis pathways, making substrate specificity a key feature of their function. Interestingly, we found that perturbing the membrane pharmacologically in living cells had little effect on substrate processing but induced inappropriate cleavage of nonsubstrates by rhomboid proteases. A subclass of drugs known to modulate γ-secretase activity acted on the membrane directly and induced nonsubstrate cleavage by rhomboid proteases but left true substrate cleavage sites unaltered. These observations highlight an active role for the membrane in guiding rhomboid selectivity and caution that membrane-targeted drugs should be evaluated for cross-activity against membrane-resident enzymes that are otherwise unrelated to the intended drug target. Furthermore, some γ-secretase-modulating activity or toxicity could partly result from global membrane effects.
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Affiliation(s)
- Siniša Urban
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Syed M Moin
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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35
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Dominguez L, Foster L, Meredith SC, Straub JE, Thirumalai D. Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection. J Am Chem Soc 2014; 136:9619-26. [PMID: 24926593 PMCID: PMC4105063 DOI: 10.1021/ja503150x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The 99 amino acid C-terminal fragment of amyloid precursor protein (C99), consisting of a single transmembrane (TM) helix, is known to form homodimers. Homodimers can be processed by γ-secretase to produce amyloid-β (Aβ) protein, which is implicated in Alzheimer's disease (AD). While knowledge of the structure of C99 homodimers is of great importance, experimental NMR studies and simulations have produced varying structural models, including right-handed and left-handed coiled-coils. In order to investigate the structure of this critical protein complex, simulations of the C99(15-55) homodimer in POPC membrane bilayer and DPC surfactant micelle environments were performed using a multiscale approach that blends atomistic and coarse-grained models. The C99(15-55) homodimer adopts a dominant right-handed coiled-coil topology consisting of three characteristic structural states in a bilayer, only one of which is dominant in the micelle. Our structural study, which provides a self-consistent framework for understanding a number of experiments, shows that the energy landscape of the C99 homodimer supports a variety of slowly interconverting structural states. The relative importance of any given state can be modulated through environmental selection realized by altering the membrane or micelle characteristics.
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Affiliation(s)
- Laura Dominguez
- Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States
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36
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Song Y, Hustedt EJ, Brandon S, Sanders CR. Competition between homodimerization and cholesterol binding to the C99 domain of the amyloid precursor protein. Biochemistry 2013; 52:5051-64. [PMID: 23865807 DOI: 10.1021/bi400735x] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The 99-residue transmembrane C-terminal domain (C99, also known as β-CTF) of the amyloid precursor protein (APP) is the product of the β-secretase cleavage of the full-length APP and is the substrate for γ-secretase cleavage. The latter cleavage releases the amyloid-β polypeptides that are closely associated with Alzheimer's disease. C99 is thought to form homodimers; however, the free energy in favor of dimerization has not previously been quantitated. It was also recently documented that cholesterol forms a 1:1 complex with monomeric C99 in bicelles. Here, the affinities for both homodimerization and cholesterol binding to C99 were measured in bilayered lipid vesicles using both electron paramagnetic resonance (EPR) and Förster resonance energy transfer (FRET) methods. Homodimerization and cholesterol binding were seen to be competitive processes that center on the transmembrane G₇₀₀XXXG₇₀₄XXXG₇₀₈ glycine-zipper motif and adjacent Gly709. On one hand, the observed Kd for cholesterol binding (Kd = 2.7 ± 0.3 mol %) is on the low end of the physiological cholesterol concentration range in mammalian cell membranes. On the other hand, the observed K(d) for homodimerization (K(d) = 0.47 ± 0.15 mol %) likely exceeds the physiological concentration range for C99. These results suggest that the 1:1 cholesterol/C99 complex will be more highly populated than C99 homodimers under most physiological conditions. These observations are of relevance for understanding the γ-secretase cleavage of C99.
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Affiliation(s)
- Yuanli Song
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
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Cho H, Wu M, Bilgin B, Walton SP, Chan C. Latest developments in experimental and computational approaches to characterize protein-lipid interactions. Proteomics 2013; 12:3273-85. [PMID: 22997137 DOI: 10.1002/pmic.201200255] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 08/30/2012] [Accepted: 09/05/2012] [Indexed: 12/16/2022]
Abstract
Understanding the functional roles of all the molecules in cells is an ultimate goal of modern biology. An important facet is to understand the functional contributions from intermolecular interactions, both within a class of molecules (e.g. protein-protein) or between classes (e.g. protein-DNA). While the technologies for analyzing protein-protein and protein-DNA interactions are well established, the field of protein-lipid interactions is still relatively nascent. Here, we review the current status of the experimental and computational approaches for detecting and analyzing protein-lipid interactions. Experimental technologies fall into two principal categories, namely solution-based and array-based methods. Computational methods include large-scale data-driven analyses and predictions/dynamic simulations based on prior knowledge of experimentally identified interactions. Advances in the experimental technologies have led to improved computational analyses and vice versa, thereby furthering our understanding of protein-lipid interactions and their importance in biological systems.
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Affiliation(s)
- Hyunju Cho
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
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So PP, Khodr CE, Chen CD, Abraham CR. Comparable dimerization found in wildtype and familial Alzheimer's disease amyloid precursor protein mutants. AMERICAN JOURNAL OF NEURODEGENERATIVE DISEASE 2013; 2:15-28. [PMID: 23515184 PMCID: PMC3601467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 02/06/2013] [Indexed: 06/01/2023]
Abstract
Alzheimer's disease (AD) is a progressive and fatal neurodegenerative disorder marked by memory impairment and cognitive deficits. A major component of AD pathology is the accumulation of amyloid plaques in the brain, which are comprised of amyloid beta (Aβ) peptides derived from the amyloidogenic processing of the amyloid precursor protein (AβPP) by β- and γ-secretases. In a subset of patients, inheritance of mutations in the AβPP gene is responsible for altering Aβ production, leading to early onset disease. Interestingly, many of these familial mutations lie within the transmembrane domain of the protein near the GxxxG and GxxxA dimerization motifs that are important for transmembrane interactions. As AβPP dimerization has been linked to changes in Aβ production, it is of interest to know whether familial AβPP mutations affect full-length APP dimerization. Using bimolecular fluorescence complementation (BiFC), blue native gel electrophoresis, and live cell chemical cross-linking, we found that familial Alzheimer's disease (FAD) mutations do not affect full-length AβPP dimerization in transfected HEK293 and COS7 cells. It follows that changes in AβPP dimerization are not necessary for altered Aβ production, and in FAD mutations, changes in Aβ levels are more likely a result of alternative proteolytic processing.
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Affiliation(s)
- Pauline Pl So
- Department of Medicine Graduate Program in Molecular Medicine, Boston University School of Medicine 72 East Concord Street, K-304, Boston, MA, 02118, USA
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39
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Pester O, Barrett PJ, Hornburg D, Hornburg P, Pröbstle R, Widmaier S, Kutzner C, Dürrbaum M, Kapurniotu A, Sanders CR, Scharnagl C, Langosch D. The backbone dynamics of the amyloid precursor protein transmembrane helix provides a rationale for the sequential cleavage mechanism of γ-secretase. J Am Chem Soc 2013; 135:1317-29. [PMID: 23265086 PMCID: PMC3560327 DOI: 10.1021/ja3112093] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The etiology of Alzheimer's disease depends on the relative abundance of different amyloid-β (Aβ) peptide species. These peptides are produced by sequential proteolytic cleavage within the transmembrane helix of the 99 residue C-terminal fragment of the amyloid precursor protein (C99) by the intramembrane protease γ-secretase. Intramembrane proteolysis is thought to require local unfolding of the substrate helix, which has been proposed to be cleaved as a homodimer. Here, we investigated the backbone dynamics of the substrate helix. Amide exchange experiments of monomeric recombinant C99 and of synthetic transmembrane domain peptides reveal that the N-terminal Gly-rich homodimerization domain exchanges much faster than the C-terminal cleavage region. MD simulations corroborate the differential backbone dynamics, indicate a bending motion at a diglycine motif connecting dimerization and cleavage regions, and detect significantly different H-bond stabilities at the initial cleavage sites. Our results are consistent with the following hypotheses about cleavage of the substrate: First, the GlyGly hinge may precisely position the substrate within γ-secretase such that its catalytic center must start proteolysis at the known initial cleavage sites. Second, the ratio of cleavage products formed by subsequent sequential proteolysis could be influenced by differential extents of solvation and by the stabilities of H-bonds at alternate initial sites. Third, the flexibility of the Gly-rich domain may facilitate substrate movement within the enzyme during sequential proteolysis. Fourth, dimerization may affect substrate processing by decreasing the dynamics of the dimerization region and by increasing that of the C-terminal part of the cleavage region.
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Affiliation(s)
- Oxana Pester
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Paul J. Barrett
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee USA 37232-8725
| | - Daniel Hornburg
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Philipp Hornburg
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Rasmus Pröbstle
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Simon Widmaier
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Christoph Kutzner
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Milena Dürrbaum
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Aphrodite Kapurniotu
- Fachgebiet Peptidbiochemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Charles R. Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee USA 37232-8725
| | - Christina Scharnagl
- Fakultät für Physik E14, Technische Universität München, Maximus-von-Imhof-Forum 4, 85354 Freising, Germany
| | - Dieter Langosch
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
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40
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Sykes AM, Palstra N, Abankwa D, Hill JM, Skeldal S, Matusica D, Venkatraman P, Hancock JF, Coulson EJ. The effects of transmembrane sequence and dimerization on cleavage of the p75 neurotrophin receptor by γ-secretase. J Biol Chem 2012; 287:43810-24. [PMID: 23105112 DOI: 10.1074/jbc.m112.382903] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cleavage of transmembrane receptors by γ-secretase is the final step in the process of regulated intramembrane proteolysis (RIP) and has a significant impact on receptor function. Although relatively little is known about the molecular mechanism of γ-secretase enzymatic activity, it is becoming clear that substrate dimerization and/or the α-helical structure of the substrate can regulate the site and rate of γ-secretase activity. Here we show that the transmembrane domain of the pan-neurotrophin receptor p75(NTR), best known for regulating neuronal death, is sufficient for its homodimerization. Although the p75(NTR) ligands NGF and pro-NGF do not induce homerdimerization or RIP, homodimers of p75(NTR) are γ-secretase substrates. However, dimerization is not a requirement for p75(NTR) cleavage, suggesting that γ-secretase has the ability to recognize and cleave each receptor molecule independently. The transmembrane cysteine 257, which mediates covalent p75(NTR) interactions, is not crucial for homodimerization, but this residue is required for normal rates of γ-secretase cleavage. Similarly, mutation of the residues alanine 262 and glycine 266 of an AXXXG dimerization motif flanking the γ-secretase cleavage site within the p75(NTR) transmembrane domain alters the orientation of the domain and inhibits γ-secretase cleavage of p75(NTR). Nonetheless, heteromer interactions of p75(NTR) with TrkA increase full-length p75(NTR) homodimerization, which in turn potentiates the rate of γ-cleavage following TrkA activation independently of rates of α-cleavage. These results provide support for the idea that the helical structure of the p75(NTR) transmembrane domain, which may be affected by co-receptor interactions, is a key element in γ-secretase-catalyzed cleavage.
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Affiliation(s)
- Alex M Sykes
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
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Devauges V, Marquer C, Lécart S, Cossec JC, Potier MC, Fort E, Suhling K, Lévêque-Fort S. Homodimerization of amyloid precursor protein at the plasma membrane: a homoFRET study by time-resolved fluorescence anisotropy imaging. PLoS One 2012; 7:e44434. [PMID: 22973448 PMCID: PMC3433432 DOI: 10.1371/journal.pone.0044434] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 08/03/2012] [Indexed: 11/18/2022] Open
Abstract
Classical FRET (Förster Resonance Energy Transfer) using two fluorescent labels (one for the donor and another one for the acceptor) is not efficient for studying the homodimerization of a protein as only half of the homodimers formed can be identified by this technique. We thus resorted to homoFRET detected by time-resolved Fluorescence Anisotropy IMaging (tr-FAIM). To specifically image the plasma membrane of living cells, an original combination of tr-FAIM and Total Internal Reflection Fluorescence Lifetime Imaging Microscope (TIRFLIM) was implemented. The correcting factor accounting for the depolarization due to the high numerical aperture (NA) objective, mandatory for TIRF microscopy, was quantified on fluorescein solutions and on HEK293 cells expressing enhanced Green Fluorescence Protein (eGFP). Homodimerization of Amyloid Precursor Protein (APP), a key mechanism in the etiology of Alzheimer’s disease, was measured on this original set-up. We showed, both in epifluorescence and under TIRF excitation, different energy transfer rates associated with the homodimerization of wild type APP-eGFP or of a mutated APP-eGFP, which forms constitutive dimers. This original set-up thus offers promising prospects for future studies of protein homodimerization in living cells in control and pathological conditions.
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Affiliation(s)
- Viviane Devauges
- Institut des Sciences Moléculaires d’Orsay, CNRS UMR 8214, Univ. Paris Sud, Orsay, France
- Laboratoire Charles Fabry, CNRS UMR 8501, Institut d’Optique, Univ. Paris Sud, Palaiseau, France
- Centre de Photonique Biomédicale, Univ. Paris Sud, CLUPS/LUMAT FR2764, Orsay, France
| | | | - Sandrine Lécart
- Centre de Photonique Biomédicale, Univ. Paris Sud, CLUPS/LUMAT FR2764, Orsay, France
| | | | | | - Emmanuel Fort
- Institut Langevin, ESPCI ParisTech, Univ. Paris Diderot, UMR 7587, Paris, France
| | - Klaus Suhling
- Department of Physics, King’s College London, Strand, London, United Kingdom
| | - Sandrine Lévêque-Fort
- Institut des Sciences Moléculaires d’Orsay, CNRS UMR 8214, Univ. Paris Sud, Orsay, France
- Centre de Photonique Biomédicale, Univ. Paris Sud, CLUPS/LUMAT FR2764, Orsay, France
- * E-mail:
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Svedružić ZM, Popović K, Smoljan I, Sendula-Jengić V. Modulation of γ-secretase activity by multiple enzyme-substrate interactions: implications in pathogenesis of Alzheimer's disease. PLoS One 2012; 7:e32293. [PMID: 22479317 PMCID: PMC3316526 DOI: 10.1371/journal.pone.0032293] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 01/24/2012] [Indexed: 11/19/2022] Open
Abstract
Background We describe molecular processes that can facilitate pathogenesis of Alzheimer's disease (AD) by analyzing the catalytic cycle of a membrane-imbedded protease γ-secretase, from the initial interaction with its C99 substrate to the final release of toxic Aβ peptides. Results The C-terminal AICD fragment is cleaved first in a pre-steady-state burst. The lowest Aβ42/Aβ40 ratio is observed in pre-steady-state when Aβ40 is the dominant product. Aβ42 is produced after Aβ40, and therefore Aβ42 is not a precursor for Aβ40. The longer more hydrophobic Aβ products gradually accumulate with multiple catalytic turnovers as a result of interrupted catalytic cycles. Saturation of γ-secretase with its C99 substrate leads to 30% decrease in Aβ40 with concomitant increase in the longer Aβ products and Aβ42/Aβ40 ratio. To different degree the same changes in Aβ products can be observed with two mutations that lead to an early onset of AD, ΔE9 and G384A. Four different lines of evidence show that γ-secretase can bind and cleave multiple substrate molecules in one catalytic turnover. Consequently depending on its concentration, NotchΔE substrate can activate or inhibit γ-secretase activity on C99 substrate. Multiple C99 molecules bound to γ-secretase can affect processive cleavages of the nascent Aβ catalytic intermediates and facilitate their premature release as the toxic membrane-imbedded Aβ-bundles. Conclusions Gradual saturation of γ-secretase with its substrate can be the pathogenic process in different alleged causes of AD. Thus, competitive inhibitors of γ-secretase offer the best chance for a successful therapy, while the noncompetitive inhibitors could even facilitate development of the disease by inducing enzyme saturation at otherwise sub-saturating substrate. Membrane-imbedded Aβ-bundles generated by γ-secretase could be neurotoxic and thus crucial for our understanding of the amyloid hypothesis and AD pathogenesis.
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Affiliation(s)
- Zeljko M Svedružić
- Medical Biochemistry, Faculty of Medicine, University of Rijeka, Rab, Croatia.
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43
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Moraes CF, Lins TC, Carmargos EF, Naves JOS, Pereira RW, Nóbrega OT. Lessons from genome-wide association studies findings in Alzheimer's disease. Psychogeriatrics 2012; 12:62-73. [PMID: 22416831 DOI: 10.1111/j.1479-8301.2011.00378.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder with a complex genetic background. Recent genome-wide association studies (GWAS) have placed important new contributors into the genetic framework of early- and late-onset forms of this dementia. Besides confirming the major role of classic allelic variants (e.g. apolipoprotein E) in the development of AD, GWAS have thus far implicated over 20 single nucleotide polymorphisms in AD. In this review, we summarize the findings of 16 AD-based GWAS performed to date whose public registries are available at the National Human Genome Research Institute, with an emphasis on understanding whether the polymorphic markers under consideration support functional implications to the pathophysiological role of the major genetic risk factors unraveled by GWAS.
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Affiliation(s)
- Clayton F Moraes
- Geriatric Service, Hospital of the Catholic University of Brasília, Graduate Program in Medical Sciences, University of Brasília, Brasília - DF, Brazil
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44
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So PP, Zeldich E, Seyb KI, Huang MM, Concannon JB, King GD, Chen CD, Cuny GD, Glicksman MA, Abraham CR. Lowering of amyloid beta peptide production with a small molecule inhibitor of amyloid-β precursor protein dimerization. AMERICAN JOURNAL OF NEURODEGENERATIVE DISEASE 2012; 1:75-87. [PMID: 22822474 PMCID: PMC3560454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 04/22/2012] [Indexed: 06/01/2023]
Abstract
The amyloid β precursor protein (APP) is a single-pass transmembrane glycoprotein that is ubiquitously expressed in many cell types, including neurons. Amyloidogenic processing of APP by β- and γ-secretases leads to the production of amyloid-β (Aβ) peptides that can oligomerize and aggregate into amyloid plaques, a characteristic hallmark of Alzheimer's disease (AD) brains. Multiple reports suggest that dimerization of APP may play a role in Aβ production; however, it is not yet clear whether APP dimers increase or decrease Aβ and the mechanism is not fully understood. To better understand the relationship between APP dimerization and production of Aβ, a high throughput screen for small molecule modulators of APP dimerization was conducted using APP-Firefly luciferase enzyme complementation to detect APP dimerization. Selected modulators identified from a compound library of 77,440 compounds were tested for their effects on Aβ generation. Two molecules that inhibited APP dimerization produced a reduction in Aβ levels as measured by ELISA. The inhibitors did not change sAPPα or γ-CTF levels, but lowered sAPPβ levels, suggesting that blocking the dimerization is preventing the cleavage by β-secretase in the amyloidogenic processing of APP. To our knowledge, this is the first High Throughput Screen (HTS) effort to identify small molecule modulators of APP dimerization. Inhibition of APP dimerization has previously been suggested as a therapeutic target in AD. The findings reported here further support that modulation of APP dimerization may be a viable means of reducing the production of Aβ.
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Affiliation(s)
- Pauline Pl So
- Department of Medicine Graduate Program in Molecular Medicine, Boston University School of Medicine, Boston, MA, USA
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45
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Zhuang T, Jap BK, Sanders CR. Solution NMR approaches for establishing specificity of weak heterodimerization of membrane proteins. J Am Chem Soc 2011; 133:20571-80. [PMID: 22084929 DOI: 10.1021/ja208972h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solution NMR provides a powerful approach for detecting complex formation involving weak to moderate intermolecular affinity. However, solution NMR has only rarely been used to detect complex formation between two membrane proteins in model membranes. The impact of specific binding on the NMR spectrum of a membrane protein can be difficult to distinguish from spectral changes that are induced by nonspecific binding and/or by changes that arise from forced cohabitation of the two proteins in a single model membrane assembly. This is particularly the case when solubility limits make it impossible to complete a titration to the point of near saturation of complex formation. In this work experiments are presented that provide the basis for establishing whether specific complex formation occurs between two membrane proteins under conditions where binding is not of high avidity. Application of these methods led to the conclusion that the membrane protein CD147 (also known as EMMPRIN or basigin) forms a specific heterodimeric complex in the membrane with the 99-residue transmembrane C-terminal fragment of the amyloid precursor protein (C99 or APP-βCTF), the latter being the immediate precursor of the amyloid-β polypeptides that are closely linked to the etiology of Alzheimer's disease.
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Affiliation(s)
- Tiandi Zhuang
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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46
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Isbert S, Wagner K, Eggert S, Schweitzer A, Multhaup G, Weggen S, Kins S, Pietrzik CU. APP dimer formation is initiated in the endoplasmic reticulum and differs between APP isoforms. Cell Mol Life Sci 2011; 69:1353-75. [PMID: 22105709 PMCID: PMC3314181 DOI: 10.1007/s00018-011-0882-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 10/25/2011] [Accepted: 10/27/2011] [Indexed: 12/30/2022]
Abstract
The amyloid precursor protein (APP) is part of a larger gene family, which has been found to form homo- or heterotypic complexes with its homologues, whereby the exact molecular mechanism and origin of dimer formation remains elusive. In order to assess the cellular location of dimerization, we have generated a cell culture model system in CHO-K1 cells, stably expressing human APP, harboring dilysine-based organelle sorting motifs [KKAA-endoplasmic reticulum (ER); KKFF-Golgi], accomplishing retention within early secretory compartments. We show that APP exists as disulfide-bonded dimers upon ER retention after it was isolated from cells, and analyzed by SDS-polyacrylamide gel electrophoresis under non-reducing conditions. In contrast, strong denaturing and reducing conditions, or deletion of the E1 domain, resulted in the disappearance of those dimers. Thus we provide first evidence that a fraction of APP can associate via intermolecular disulfide bonds, likely generated between cysteines located in the extracellular E1 domain. We particularly visualize APP dimerization itself and identified the ER as subcellular compartment of its origin using biochemical or split GFP approaches. Interestingly, we also found that minor amounts of SDS-resistant APP dimers were located to the cell surface, revealing that once generated in the oxidative environment of the ER, dimers remained stably associated during transport. In addition, we show that APP isoforms encompassing the Kunitz-type protease inhibitor (KPI) domain exhibit a strongly reduced ability to form cis-directed dimers in the ER, whereas trans-mediated cell aggregation of Drosophila Schneider S2-cells was isoform independent. Thus, suggesting that steric properties of KPI-APP might be the cause for weaker cis-interaction in the ER, compared to APP695. Finally, we provide evidence that APP/APLP1 heterointeractions are likewise initiated in the ER.
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Affiliation(s)
- Simone Isbert
- Department of Pathobiochemistry, Molecular Neurodegeneration, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
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47
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Asada-Utsugi M, Uemura K, Noda Y, Kuzuya A, Maesako M, Ando K, Kubota M, Watanabe K, Takahashi M, Kihara T, Shimohama S, Takahashi R, Berezovska O, Kinoshita A. N-cadherin enhances APP dimerization at the extracellular domain and modulates Aβ production. J Neurochem 2011; 119:354-63. [PMID: 21699541 DOI: 10.1111/j.1471-4159.2011.07364.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Sequential processing of amyloid precursor protein (APP) by β- and γ-secretase leads to the generation of amyloid-β (Aβ) peptides, which plays a central role in Alzheimer's disease pathogenesis. APP is capable of forming a homodimer through its extracellular domain as well as transmembrane GXXXG motifs. A number of reports have shown that dimerization of APP modulates Aβ production. On the other hand, we have previously reported that N-cadherin-based synaptic contact is tightly linked to Aβ production. In the present report, we investigated the effect of N-cadherin expression on APP dimerization and metabolism. Here, we demonstrate that N-cadherin expression facilitates cis-dimerization of APP. Moreover, N-cadherin expression led to increased production of Aβ as well as soluble APPβ, indicating that β-secretase-mediated cleavage of APP is enhanced. Interestingly, N-cadherin expression affected neither dimerization of C99 nor Aβ production from C99, suggesting that the effect of N-cadherin on APP metabolism is mediated through APP extracellular domain. We confirmed that N-cadherin enhances APP dimerization by a novel luciferase-complementation assay, which could be a platform for drug screening on a high-throughput basis. Taken together, our results suggest that modulation of APP dimerization state could be one of mechanisms, which links synaptic contact and Aβ production.
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Affiliation(s)
- Megumi Asada-Utsugi
- School of Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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48
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Kim J, Lee J, Kwon D, Lee H, Grailhe R. A comparative analysis of resonance energy transfer methods for Alzheimer related protein-protein interactions in living cells. MOLECULAR BIOSYSTEMS 2011; 7:2991-6. [PMID: 21909576 DOI: 10.1039/c1mb05279a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fluorescence resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET) are extensively used to analyze protein interactions occurring in living cells. Although these two techniques are broadly applied in cellular biology, comparative analysis of their strengths and limitations is lacking. To this end, we analyzed a small network of proteins involved in the amyloidogenic processing of the Alzheimer β-amyloid precursor using FRET based cytometry, BRET, and fluorescence lifetime imaging microscopy (FLIM). Using all three methods, we were able to detect the interactions of the amyloid precursor protein with APBB1, APBB2, and APP itself. And we found an unreported interacting pair, APP-APH1A. In addition, we show that these four interacting pairs exhibit a strong FRET correlation with the acceptor/donor expression ratios. Overall the FRET based cytometry was the most sensitive and reliable approach to screen for new interacting proteins. Therefore, we applied FRET based cytometry to study competitive binding of two proteins, APBB1 and APBB2, with the same APP target.
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Affiliation(s)
- Jiho Kim
- Neurodegeneration and Applied Microscopy, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, 463-400, South Korea
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49
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Ng DP, Poulsen BE, Deber CM. Membrane protein misassembly in disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1115-22. [PMID: 21840297 DOI: 10.1016/j.bbamem.2011.07.046] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 11/19/2022]
Abstract
Helix-helix interactions play a central role in the folding and assembly of integral α-helical membrane proteins and are fundamentally dictated by the amino acid sequence of the TM domain. It is not surprising then that missense mutations that target these residues are often linked to disease. In this review, we focus on the molecular mechanisms through which missense mutations lead to aberrant folding and/or assembly of these proteins, and then discuss pharmacological approaches that may potentially mitigate or reverse the negative effects of these mutations. Improving our understanding of how missense mutations affect the interactions between TM α-helices will increase our capability to develop effective therapeutic approaches to counter the misassembly of these proteins and, ultimately, disease. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Affiliation(s)
- Derek P Ng
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
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50
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Lu JX, Yau WM, Tycko R. Evidence from solid-state NMR for nonhelical conformations in the transmembrane domain of the amyloid precursor protein. Biophys J 2011; 100:711-719. [PMID: 21281586 DOI: 10.1016/j.bpj.2010.12.3696] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 10/22/2010] [Accepted: 12/08/2010] [Indexed: 02/03/2023] Open
Abstract
The amyloid precursor protein (APP) is subject to proteolytic processing by γ-secretase within neuronal membranes, leading to Alzheimer's disease-associated β-amyloid peptide production by cleavage near the midpoint of the single transmembrane (TM) segment of APP. Conformational properties of the TM segment may affect its susceptibility to γ-secretase cleavage, but these properties have not been established definitively, especially in bilayer membranes with physiologically relevant lipid compositions. In this article, we report an investigation of the APP-TM conformation, using (13)C chemical shifts obtained with two-dimensional solid-state NMR spectroscopy as site-specific conformational probes. We find that the APP-TM conformation is not a simple α-helix, particularly at 37°C in multilamellar vesicles with compositions that mimic the composition of neuronal cell membranes. Instead, we observe a mixture of helical and nonhelical conformations at the N- and C-termini and in the vicinity of the γ-cleavage site. Conformational plasticity of the TM segment of APP may be an important factor in the γ-secretase cleavage mechanism.
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Affiliation(s)
- Jun-Xia Lu
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.
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