1
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Qiu C, Wei R, Bian J, Lin X, Bai T, He J, Guo X, Chu Y. Novel 4-triazole phenyl amide (4-TPA) molecules: Potent promoters of α-synuclein fibril disassembly. Eur J Med Chem 2024; 273:116490. [PMID: 38772136 DOI: 10.1016/j.ejmech.2024.116490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
Parkinson's disease profoundly compromises patients' daily lives, and the disassembly of α-synuclein aggregates, a primary pathological factor, represents a promising therapeutic approach. In this study, we conducted a systematic screening and optimization process to identify the novel scaffold B37, a 4-triazolyl-phenylamine derivative, exhibiting a potent disassembly activity of 1.1 μM against α-synuclein preformed fibrils. Notably, B37 demonstrated significant neuroprotective effects, ameliorated autophagic dysfunction induced by preformed fibrils, mitigated oxidative stress, and restored the co-localization of preformed fibrils with lysosomes. Transmission electron microscopy corroborated its in vitro disassembly function. Pharmacokinetic profiling revealed favorable parameters with a receptible blood-brain barrier permeability. B37 emerges as a promising lead compound for further optimization, aiming to develop a highly effective agent targeting the disassembly of α-synuclein aggregates to treat neurodegenerative diseases like Parkinson's disease.
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Affiliation(s)
- Chenyang Qiu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Ruonan Wei
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jiang Bian
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Xin Lin
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Tengfei Bai
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jie He
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Xiaomin Guo
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yong Chu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China.
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2
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Maurer M, Lazaridis T. Transmembrane β-Barrel Models of α-Synuclein Oligomers. J Chem Inf Model 2023; 63:7171-7179. [PMID: 37963823 DOI: 10.1021/acs.jcim.3c00997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The aggregation of α-synuclein is implicated in a number of neurodegenerative diseases, such as Parkinson's and Multiple System Atrophy, but the role of these aggregates in disease development is not clear. One possible mechanism of cytotoxicity is the disturbance or permeabilization of cell membranes by certain types of oligomers. However, no high-resolution structure of such membrane-embedded complexes has ever been determined. Here we construct and evaluate putative transmembrane β-barrels formed by this protein. Examination of the α-synuclein sequence reveals two regions that could form membrane-embedded β-hairpins: 64-92 (the NAC), and 35-56, which harbors many familial Parkinson's mutations. The stability of β-barrels formed by these hairpins is examined first in implicit membrane pores and then by multimicrosecond all-atom simulations. We find that a NAC region barrel remains stably inserted and hydrated for at least 10 μs. A 35-56 barrel remains stably inserted in the membrane but dehydrates and collapses if all His50 are neutral or if His50 is replaced by Q. If half of the His50 are doubly protonated, the barrel takes an oval shape but remains hydrated for at least 10 μs. Possible implications of these findings for α-synuclein pathology are discussed.
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Affiliation(s)
- Manuela Maurer
- Department of Chemistry & Biochemistry, City College of New York/CUNY, 160 Convent Ave, New York, New York 10031, United States
| | - Themis Lazaridis
- Department of Chemistry & Biochemistry, City College of New York/CUNY, 160 Convent Ave, New York, New York 10031, United States
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3
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Shchukina A, Schwarz TC, Nowakowski M, Konrat R, Kazimierczuk K. Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes. JOURNAL OF BIOMOLECULAR NMR 2023; 77:149-163. [PMID: 37237169 PMCID: PMC10406685 DOI: 10.1007/s10858-023-00418-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]
Abstract
The accelerated acquisition of multidimensional NMR spectra using sparse non-uniform sampling (NUS) has been widely adopted in recent years. The key concept in NUS is that a major part of the data is omitted during measurement, and then reconstructed using, for example, compressed sensing (CS) methods. CS requires spectra to be compressible, that is, they should contain relatively few "significant" points. The more compressible the spectrum, the fewer experimental NUS points needed in order for it to be accurately reconstructed. In this paper we show that the CS processing of similar spectra can be enhanced by reconstructing only the differences between them. Accurate reconstruction can be obtained at lower sampling levels as the difference is sparser than the spectrum itself. In many situations this method is superior to "conventional" compressed sensing. We exemplify the concept of "difference CS" with one such case-the study of alpha-synuclein binding to liposomes and its dependence on temperature. To obtain information on temperature-dependent transitions between different states, we need to acquire several dozen spectra at various temperatures, with and without the presence of liposomes. Our detailed investigation reveals that changes in the binding modes of the alpha-synuclein ensemble are not only temperature-dependent but also show non-linear behavior in their transitions. Our proposed CS processing approach dramatically reduces the number of NUS points required and thus significantly shortens the experimental time.
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Affiliation(s)
- Alexandra Shchukina
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Thomas C Schwarz
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter Campus 5, 1030, Vienna, Austria
| | - Michał Nowakowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter Campus 5, 1030, Vienna, Austria
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4
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Marín I. Emergence of the Synucleins. BIOLOGY 2023; 12:1053. [PMID: 37626939 PMCID: PMC10451939 DOI: 10.3390/biology12081053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
This study establishes the origin and evolutionary history of the synuclein genes. A combination of phylogenetic analyses of the synucleins from twenty-two model species, characterization of local synteny similarities among humans, sharks and lampreys, and statistical comparisons among lamprey and human chromosomes, provides conclusive evidence for the current diversity of synuclein genes arising from the whole-genome duplications (WGDs) that occurred in vertebrates. An ancestral synuclein gene was duplicated in a first WGD, predating the diversification of all living vertebrates. The two resulting genes are still present in agnathan vertebrates. The second WGD, specific to the gnathostome lineage, led to the emergence of the three classical synuclein genes, SNCA, SNCB and SNCG, which are present in all jawed vertebrate lineages. Additional WGDs have added new genes in both agnathans and gnathostomes, while some gene losses have occurred in particular species. The emergence of synucleins through WGDs prevented these genes from experiencing dosage effects, thus avoiding the potential detrimental effects associated with individual duplications of genes that encode proteins prone to aggregation. Additional insights into the structural and functional features of synucleins are gained through the analysis of the highly divergent synuclein proteins present in chondrichthyans and agnathans.
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Affiliation(s)
- Ignacio Marín
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), 46010 Valencia, Spain
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5
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Rajendran M, Queralt-Martín M, Gurnev PA, Rosencrans WM, Rovini A, Jacobs D, Abrantes K, Hoogerheide DP, Bezrukov SM, Rostovtseva TK. Restricting α-synuclein transport into mitochondria by inhibition of α-synuclein-VDAC complexation as a potential therapeutic target for Parkinson's disease treatment. Cell Mol Life Sci 2022; 79:368. [PMID: 35718804 PMCID: PMC11072225 DOI: 10.1007/s00018-022-04389-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 11/03/2022]
Abstract
Involvement of alpha-synuclein (αSyn) in Parkinson's disease (PD) is complicated and difficult to trace on cellular and molecular levels. Recently, we established that αSyn can regulate mitochondrial function by voltage-activated complexation with the voltage-dependent anion channel (VDAC) on the mitochondrial outer membrane. When complexed with αSyn, the VDAC pore is partially blocked, reducing the transport of ATP/ADP and other metabolites. Further, αSyn can translocate into the mitochondria through VDAC, where it interferes with mitochondrial respiration. Recruitment of αSyn to the VDAC-containing lipid membrane appears to be a crucial prerequisite for both the blockage and translocation processes. Here we report an inhibitory effect of HK2p, a small membrane-binding peptide from the mitochondria-targeting N-terminus of hexokinase 2, on αSyn membrane binding, and hence on αSyn complex formation with VDAC and translocation through it. In electrophysiology experiments, the addition of HK2p at micromolar concentrations to the same side of the membrane as αSyn results in a dramatic reduction of the frequency of blockage events in a concentration-dependent manner, reporting on complexation inhibition. Using two complementary methods of measuring protein-membrane binding, bilayer overtone analysis and fluorescence correlation spectroscopy, we found that HK2p induces detachment of αSyn from lipid membranes. Experiments with HeLa cells using proximity ligation assay confirmed that HK2p impedes αSyn entry into mitochondria. Our results demonstrate that it is possible to regulate αSyn-VDAC complexation by a rationally designed peptide, thus suggesting new avenues in the search for peptide therapeutics to alleviate αSyn mitochondrial toxicity in PD and other synucleinopathies.
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Affiliation(s)
- Megha Rajendran
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - María Queralt-Martín
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, Castellón, 12071, Spain
| | - Philip A Gurnev
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - William M Rosencrans
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - Amandine Rovini
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - Daniel Jacobs
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - Kaitlin Abrantes
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - David P Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Sergey M Bezrukov
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA
| | - Tatiana K Rostovtseva
- Section On Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 29B, Room 1G09, Bethesda, MD, 20892, USA.
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6
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Mohapatra A, Bohara VS, Kumar S, Chaudhary N. Polymyxin B accelerates the α-synuclein aggregation. Biophys Chem 2021; 277:106628. [PMID: 34118773 DOI: 10.1016/j.bpc.2021.106628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder caused by the loss of dopaminergic neurons. It is characterised by the deposition of insoluble α-synuclein aggregates in the brain. Constipation is a common PD-associated condition, and the treatment of constipation with certain antibiotics seem to improve the PD symptoms. Polymyxin B, a last resort drug in treating the life-threatening Gram-negative bacterial infections, is one such antibiotic. The administration of polymyxin B in PD patients is known to alleviate the movement disorder symptoms; the mechanism of action, however, remains unclear. We, therefore, wondered if polymyxin B could modulate the aggregation of α-synuclein. We find that the polymyxin B catalyses the aggregation of α-synuclein into amyloid fibrils. At equimolar polymyxin B concentration, the lag phase was reduced to around one-third of that in the absence of polymyxin B.
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Affiliation(s)
- Anshuman Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Vijay Singh Bohara
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Nitin Chaudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India.
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7
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Hoogerheide DP, Rostovtseva TK, Bezrukov SM. Exploring lipid-dependent conformations of membrane-bound α-synuclein with the VDAC nanopore. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183643. [PMID: 33971161 PMCID: PMC8255272 DOI: 10.1016/j.bbamem.2021.183643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023]
Abstract
Regulation of VDAC by α-synuclein (αSyn) is a rich and instructive example of protein-protein interactions catalyzed by a lipid membrane surface. αSyn, a peripheral membrane protein involved in Parkinson's disease pathology, is known to bind to membranes in a transient manner. αSyn's negatively charged C-terminal domain is then available to be electromechanically trapped by the VDAC β-barrel, a process that is observed in vitro as the reversible reduction of ion flow through a single voltage-biased VDAC nanopore. Binding of αSyn to the lipid bilayer is a prerequisite of the channel-protein interaction; surprisingly, however, we find that the strength of αSyn binding to the membrane does not correlate in any simple way with its efficiency of blocking VDAC, suggesting that the lipid-dependent conformations of the membrane-bound αSyn control the interaction. Quantitative models of the free energy landscape governing the capture and release processes allow us to discriminate between several αSyn (sub-) conformations on the membrane surface. These results, combined with known structural features of αSyn on anionic lipid membranes, point to a model in which the lipid composition determines the fraction of αSyn molecules for which the charged C terminal domain is constrained to be close, but not tightly bound, to the membrane surface and thus readily captured by the VDAC nanopore. We speculate that changes in the mitochondrial membrane lipid composition may be key regulators of the αSyn-VDAC interaction and consequently of VDAC-facilitated transport of ions and metabolites in and out of mitochondria and, i.e. mitochondrial metabolism.
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Affiliation(s)
- David P Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Tatiana K Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sergey M Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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8
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Nakasone Y, Terazima M. A Time-Resolved Diffusion Technique for Detection of the Conformational Changes and Molecular Assembly/Disassembly Processes of Biomolecules. Front Genet 2021; 12:691010. [PMID: 34276791 PMCID: PMC8278059 DOI: 10.3389/fgene.2021.691010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022] Open
Abstract
Biological liquid-liquid phase separation (LLPS) is driven by dynamic and multivalent interactions, which involves conformational changes and intermolecular assembly/disassembly processes of various biomolecules. To understand the molecular mechanisms of LLPS, kinetic measurements of the intra- and intermolecular reactions are essential. In this review, a time-resolved diffusion technique which has a potential to detect molecular events associated with LLPS is presented. This technique can detect changes in protein conformation and intermolecular interaction (oligomer formation, protein-DNA interaction, and protein-lipid interaction) in time domain, which are difficult to obtain by other methods. After the principle and methods for signal analyses are described in detail, studies on photoreactive molecules (intermolecular interaction between light sensor proteins and its target DNA) and a non-photoreactive molecule (binding and folding reaction of α-synuclein upon mixing with SDS micelle) are presented as typical examples of applications of this unique technique.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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9
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Amos SBA, Schwarz TC, Shi J, Cossins BP, Baker TS, Taylor RJ, Konrat R, Sansom MSP. Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR. J Phys Chem B 2021; 125:2929-2941. [PMID: 33719460 PMCID: PMC8006134 DOI: 10.1021/acs.jpcb.1c01281] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/01/2021] [Indexed: 01/30/2023]
Abstract
α-Synuclein (αS) is a presynaptic protein that binds to cell membranes and is linked to Parkinson's disease (PD). Binding of αS to membranes is a likely first step in the molecular pathophysiology of PD. The αS molecule can adopt multiple conformations, being largely disordered in water, adopting a β-sheet conformation when present in amyloid fibrils, and forming a dynamic multiplicity of α-helical conformations when bound to lipid bilayers and related membrane-mimetic surfaces. Multiscale molecular dynamics simulations in conjunction with nuclear magnetic resonance (NMR) and cross-linking mass spectrometry (XLMS) measurements are used to explore the interactions of αS with an anionic lipid bilayer. The simulations and NMR measurements together reveal a break in the helical structure of the central non-amyloid-β component (NAC) region of αS in the vicinity of residues 65-70, which may facilitate subsequent oligomer formation. Coarse-grained simulations of αS starting from the structure of αS when bound to a detergent micelle reveal the overall pattern of protein contacts to anionic lipid bilayers, while subsequent all-atom simulations provide details of conformational changes upon membrane binding. In particular, simulations and NMR data for liposome-bound αS indicate incipient β-strand formation in the NAC region, which is supported by intramolecular contacts seen via XLMS and simulations. Markov state models based on the all-atom simulations suggest a mechanism of conformational change of membrane-bound αS via a dynamic helix break in the region of residue 65 in the NAC region. The emergent dynamic model of membrane-interacting αS advances our understanding of the mechanism of PD, potentially aiding the design of novel therapeutic approaches.
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Affiliation(s)
- Sarah-Beth
T. A. Amos
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Thomas C. Schwarz
- Department
of Structural and Computational
Biology, Max Perutz Laboratories, University
of Vienna, Campus Vienna
Biocenter 5, Vienna A-1030, Austria
| | - Jiye Shi
- UCB
Pharma, 208 Bath Road, Slough SL1 3WE, U.K.
| | | | | | | | - Robert Konrat
- Department
of Structural and Computational
Biology, Max Perutz Laboratories, University
of Vienna, Campus Vienna
Biocenter 5, Vienna A-1030, Austria
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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10
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Liu J, Bu B, Crowe M, Li D, Diao J, Ji B. Membrane packing defects in synaptic vesicles recruit complexin and synuclein. Phys Chem Chem Phys 2021; 23:2117-2125. [PMID: 33437978 DOI: 10.1039/d0cp03546g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Complexin-1 (Cpx) and α-synuclein (α-Syn) are involved in neurotransmitter release through an interaction with synaptic vesicles (SVs). Recent studies demonstrated that Cpx and α-Syn preferentially associate with highly curved membranes, like SVs, to correctly position them for fusion. Here, based on recent experimental results, to further propose a possible explanation for this mechanism, we performed in silico simulations probing interactions between Cpx or α-Syn and membranes of varying curvature. We found that the preferential association is attributed to smaller, curved membranes containing more packing defects that expose hydrophobic acyl tails, which may favorably interact with hydrophobic residues of Cpx and α-Syn. The number of membrane defects is proportional to the curvature and the size can be regulated by cholesterol.
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Affiliation(s)
- Jie Liu
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing 100081, China
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11
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Takaramoto S, Nakasone Y, Sadakane K, Maruta S, Terazima M. Time-resolved detection of SDS-induced conformational changes in α-synuclein by a micro-stopped-flow system. RSC Adv 2021; 11:1086-1097. [PMID: 35423687 PMCID: PMC8693425 DOI: 10.1039/d0ra09614h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/18/2020] [Indexed: 11/21/2022] Open
Abstract
An intrinsically disordered protein, α-synuclein (αSyn), binds to negatively charged phospholipid membranes and adopts an α-helical structure. This conformational change is also induced by interaction with sodium dodecyl sulfate (SDS), which is an anionic surfactant used in previous studies to mimic membrane binding. However, while the structure of the αSyn and SDS complex has been studied widely by various static measurements, the process of structural change from the denatured state to the folded state remains unclear. In this study, the interaction dynamics between αSyn and SDS micelles was investigated using time-resolved measurements with a micro-stopped-flow system, which has been recently developed. In particular, the time-resolved diffusion based on the transient grating technique in combination with a micro-stopped-flow system revealed the gradual change in diffusion triggered by the presence of SDS micelles. This change is induced not only by binding to SDS micelles, but also by an intramolecular conformational change. It was interesting to find that the diffusion coefficient decreased in an intermediate state and then increased to the final state in the binding reaction. We also carried out stopped-flow-kinetic measurements of circular dichroism and intramolecular fluorescence resonance energy transfer, and the D change was assigned to the formation of a compact structure derived from the helix bending on the micelle. Dynamics of conformation changes of α-synuclein induced by the presence of SDS micelles are revealed using time-resolved diffusion, CD, and FRET measurements combined with a micro-stopped flow system.![]()
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Affiliation(s)
- Shunki Takaramoto
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Yusuke Nakasone
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Kei Sadakane
- Department of Bioinformatics
- Graduate School of Engineering
- Soka University
- Hachioji
- Japan
| | - Shinsaku Maruta
- Department of Bioinformatics
- Graduate School of Engineering
- Soka University
- Hachioji
- Japan
| | - Masahide Terazima
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
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12
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Musteikytė G, Jayaram AK, Xu CK, Vendruscolo M, Krainer G, Knowles TPJ. Interactions of α-synuclein oligomers with lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183536. [PMID: 33373595 DOI: 10.1016/j.bbamem.2020.183536] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 12/24/2022]
Abstract
Parkinson's disease is an increasingly prevalent and currently incurable neurodegenerative disorder. At the molecular level, this disease is characterized by the formation of aberrant intracellular protein deposits known as Lewy bodies. Oligomeric forms of the protein α-synuclein (αS), which are believed to be both intermediates and by-products of Lewy body formation, are considered to be the main pathogenic species. Interactions of such oligomers with lipid membranes are increasingly emerging as a major molecular pathway underpinning their toxicity. Here we review recent progress in our understanding of the interactions of αS oligomers with lipid membranes. We highlight key structural and biophysical features of αS oligomers, the effects of these features on αS oligomer membrane binding properties, and resultant implications for understanding the etiology of Parkinson's disease. We discuss mechanistic modes of αS oligomer-lipid membrane interactions and the effects of environmental factors to such modes. Finally, we provide an overview of the current understanding of the main molecular determinants of αS oligomer toxicity in vivo.
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Affiliation(s)
- Greta Musteikytė
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Akhila K Jayaram
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom; Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Catherine K Xu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Georg Krainer
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom; Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom.
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13
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Abstract
α-Synuclein is a neuronal protein with an ill-defined biological function that is central to Parkinson’s disease etiology. While considered to be involved in exocytosis, how α-synuclein facilitates synaptic vesicle fusion and release remains an open question. To address this, we investigated α-synuclein–lipid interactions at the plasma membrane through the technique of cellular unroofing, which uncovers an intact basal membrane. We conclusively show that α-synuclein is recruited to exocytic sites, preferring liquid-ordered lipid domains. Importantly, heterogeneous populations of α-synuclein conformers are revealed by measurements of fluorescence lifetime distributions, which are not adequately described by current models of α-synuclein structures. Membrane-bound α-synuclein is conformationally dynamic, exquisitely sensitive to lipid/protein composition, enabling the protein to carry out its function. Parkinson’s disease is associated with α-synuclein (α-syn), a cytosolic protein enriched in presynaptic terminals. The biological function of α-syn remains elusive; however, increasing evidence suggests that the protein is involved in the regulation of synaptic vesicle fusion, signifying the importance of α-syn–lipid interactions. We show that α-syn preferentially binds to GM1-rich, liquid-ordered lipid domains on cytoplasmic membranes by using unroofed cells, which encapsulates lipid complexity and cellular topology. Moreover, proteins (Rab3a, syntaxin-1A, and VAMP2) involved in exocytosis also localize with α-syn, supporting its proposed functional role in exocytosis. To investigate how these lipid/protein interactions influence α-syn at the residue level, α-syn was derivatized with an environmentally sensitive fluorophore (7-nitrobenz-2-oxa-1,3-diazol-4-yl [NBD]) at different N- and C-terminal sites. Measurements of NBD fluorescence lifetime distributions reveal that α-syn adopts a multitude of membrane-bound conformations, which were not recapitulated in simple micelle or vesicle models, indicating an exquisite sensitivity of the protein to the complex lipid environment. Interestingly, these data also suggest the participation of the C terminus in membrane localization, which is generally overlooked and thus emphasize the need to use cellularly derived and biologically relevant membranes for biophysical characterization. Collectively, our results demonstrate that α-syn is more conformationally dynamic at the membrane interface than previously appreciated, which may be important for both its physiological and pathological functions.
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14
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Bhattacharya S, Xu L, Thompson D. Long-range Regulation of Partially Folded Amyloidogenic Peptides. Sci Rep 2020; 10:7597. [PMID: 32371882 PMCID: PMC7200734 DOI: 10.1038/s41598-020-64303-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 04/15/2020] [Indexed: 01/20/2023] Open
Abstract
Neurodegeneration involves abnormal aggregation of intrinsically disordered amyloidogenic peptides (IDPs), usually mediated by hydrophobic protein-protein interactions. There is mounting evidence that formation of α-helical intermediates is an early event during self-assembly of amyloid-β42 (Aβ42) and α-synuclein (αS) IDPs in Alzheimer’s and Parkinson’s disease pathogenesis, respectively. However, the driving force behind on-pathway molecular assembly of partially folded helical monomers into helical oligomers assembly remains unknown. Here, we employ extensive molecular dynamics simulations to sample the helical conformational sub-spaces of monomeric peptides of both Aβ42 and αS. Our computed free energies, population shifts, and dynamic cross-correlation network analyses reveal a common feature of long-range intra-peptide modulation of partial helical folds of the amyloidogenic central hydrophobic domains via concerted coupling with their charged terminal tails (N-terminus of Aβ42 and C-terminus of αS). The absence of such inter-domain fluctuations in both fully helical and completely unfolded (disordered) states suggests that long-range coupling regulates the dynamicity of partially folded helices, in both Aβ42 and αS peptides. The inter-domain coupling suggests a form of intra-molecular allosteric regulation of the aggregation trigger in partially folded helical monomers. This approach could be applied to study the broad range of amyloidogenic peptides, which could provide a new path to curbing pathogenic aggregation of partially folded conformers into oligomers, by inhibition of sites far from the hydrophobic core.
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Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Liang Xu
- Department of Physics, Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland.
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15
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Cholak E, Bugge K, Khondker A, Gauger K, Pedraz-Cuesta E, Pedersen ME, Bucciarelli S, Vestergaard B, Pedersen SF, Rheinstädter MC, Langkilde AE, Kragelund BB. Avidity within the N-terminal anchor drives α-synuclein membrane interaction and insertion. FASEB J 2020; 34:7462-7482. [PMID: 32277854 DOI: 10.1096/fj.202000107r] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 12/25/2022]
Abstract
In the brain, α-synuclein (aSN) partitions between free unbound cytosolic and membrane bound forms modulating both its physiological and pathological role and complicating its study due to structural heterogeneity. Here, we use an interdisciplinary, synergistic approach to characterize the properties of aSN:lipid mixtures, isolated aSN:lipid co-structures, and aSN in mammalian cells. Enabled by the isolation of the membrane-bound state, we show that within the previously described N-terminal membrane anchor, membrane interaction relies both on an N-terminal tail (NTT) head group layer insertion of 14 residues and a folded-upon-binding helix at the membrane surface. Both binding events must be present; if, for example, the NTT insertion is lost, the membrane affinity of aSN is severely compromised and formation of aSN:lipid co-structures hampered. In mammalian cells, compromised cooperativity results in lowered membrane association. Thus, avidity within the N-terminal anchor couples N-terminal insertion and helical surface binding, which is crucial for aSN membrane interaction and cellular localization, and may affect membrane fusion.
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Affiliation(s)
- Ersoy Cholak
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Katrine Bugge
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Adree Khondker
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, Canada
| | - Kimmie Gauger
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Elena Pedraz-Cuesta
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Saskia Bucciarelli
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Stine F Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Annette Eva Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and Department of Biology, University of Copenhagen, Copenhagen, Denmark
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16
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Man WK, De Simone A, Barritt JD, Vendruscolo M, Dobson CM, Fusco G. A Role of Cholesterol in Modulating the Binding of α-Synuclein to Synaptic-Like Vesicles. Front Neurosci 2020; 14:18. [PMID: 32063829 PMCID: PMC7000551 DOI: 10.3389/fnins.2020.00018] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 01/09/2020] [Indexed: 12/15/2022] Open
Abstract
α-Synuclein (αS) is a presynaptic protein whose aggregation is associated with Parkinson's disease (PD). Although the physiological function of αS is still unclear, several lines of evidence indicate that this protein may play a role in the trafficking of synaptic vesicles (SVs) during neurotransmitter release, a task associated with its ability to bind SVs and promote their clustering. It is therefore crucial to identify the cellular factors that modulate this process. To address this question, using nuclear magnetic resonance (NMR) spectroscopy we have characterized the role of cholesterol, a major component of the membrane of SVs, in the binding of αS with synaptic-like vesicles. Our results indicate that cholesterol can act as a modulator of the overall affinity of αS for SVs by reducing the local affinity of the region spanning residues 65-97 in the non-amyloid-β component (NAC) of the protein. The increased population of bound states that expose the region 65-97 to the solvent was found to induce stronger vesicle-vesicle interactions by αS. These results provide evidence that cholesterol modulates the clustering of synaptic vesicles induced by (α)S, and supports the role of the disorder-to-order equilibrium of the NAC region in the modulation of the biological properties of the membrane-bound state of αS.
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Affiliation(s)
- Wing K. Man
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Joseph D. Barritt
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Michele Vendruscolo
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Christopher M. Dobson
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Giuliana Fusco
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
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17
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The N-terminal Acetylation of α-Synuclein Changes the Affinity for Lipid Membranes but not the Structural Properties of the Bound State. Sci Rep 2020; 10:204. [PMID: 31937832 PMCID: PMC6959233 DOI: 10.1038/s41598-019-57023-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/02/2019] [Indexed: 12/29/2022] Open
Abstract
The aggregation of α-synuclein (αS), a protein abundant at presynaptic terminals, is associated with a range of highly debilitating neurodegenerative conditions, including Parkinson’s disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). Emerging evidence indicates that the interaction of αS with lipid membranes defines both its physiological function and pathological effects. The characterisation of the modes of membrane binding by αS is therefore crucial to clarify the balance between normal and aberrant behaviour of this protein. Here we used solid-state nuclear magnetic resonance (ssNMR) spectroscopy to probe the nature of the N-terminally acetylated form of αS (NTAc-αS) bound to synaptic-like lipid vesicles. This post-translational modification is prevalent for the physiological form of αS and modulates the binding to lipid bilayers. By probing the structure, dynamics and membrane topology of NTAc-αS, we found that N-terminal acetylation does not alter significantly the conformational and topological properties of the membrane-bound state of αS, despite increasing its propensity for binding. Taken together, our data and previous characterisations of the cytosolic state of NTAc-αS clarify that the role of the N-terminal acetylation is to regulate the binding affinity of αS for synaptic vesicles without altering the structural properties of the bound state.
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18
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Rocha S, Kumar R, Horvath I, Wittung-Stafshede P. Synaptic vesicle mimics affect the aggregation of wild-type and A53T α-synuclein variants differently albeit similar membrane affinity. Protein Eng Des Sel 2019; 32:59-66. [PMID: 31566224 PMCID: PMC6908820 DOI: 10.1093/protein/gzz021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 06/19/2019] [Accepted: 07/01/2019] [Indexed: 11/28/2022] Open
Abstract
α-Synuclein misfolding results in the accumulation of amyloid fibrils in Parkinson's disease. Missense protein mutations (e.g. A53T) have been linked to early onset disease. Although α-synuclein interacts with synaptic vesicles in the brain, it is not clear what role they play in the protein aggregation process. Here, we compare the effect of small unilamellar vesicles (lipid composition similar to synaptic vesicles) on wild-type (WT) and A53T α-synuclein aggregation. Using biophysical techniques, we reveal that binding affinity to the vesicles is similar for the two proteins, and both interact with the helix long axis parallel to the membrane surface. Still, the vesicles affect the aggregation of the variants differently: effects on secondary processes such as fragmentation dominate for WT, whereas for A53T, fibril elongation is mostly affected. We speculate that vesicle interactions with aggregate intermediate species, in addition to monomer binding, vary between WT and A53T, resulting in different consequences for amyloid formation.
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Affiliation(s)
- Sandra Rocha
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Ranjeet Kumar
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Istvan Horvath
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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19
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Cholak E, Bucciarelli S, Bugge K, Johansen NT, Vestergaard B, Arleth L, Kragelund BB, Langkilde AE. Distinct α-Synuclein:Lipid Co-Structure Complexes Affect Amyloid Nucleation through Fibril Mimetic Behavior. Biochemistry 2019; 58:5052-5065. [DOI: 10.1021/acs.biochem.9b00925] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ersoy Cholak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen N, Denmark
| | - Saskia Bucciarelli
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen N, Denmark
| | - Katrine Bugge
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, and REPIN, Department of Biology, Faculty of Science, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Nicolai Tidemand Johansen
- Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen N, Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen N, Denmark
| | - Lise Arleth
- Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen N, Denmark
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, and REPIN, Department of Biology, Faculty of Science, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Annette E. Langkilde
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen N, Denmark
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20
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Rovere M, Powers AE, Jiang H, Pitino JC, Fonseca-Ornelas L, Patel DS, Achille A, Langen R, Varkey J, Bartels T. E46K-like α-synuclein mutants increase lipid interactions and disrupt membrane selectivity. J Biol Chem 2019; 294:9799-9812. [PMID: 31048377 PMCID: PMC6597829 DOI: 10.1074/jbc.ra118.006551] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 05/01/2019] [Indexed: 01/01/2023] Open
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative disorders, and both genetic and histopathological evidence have implicated the ubiquitous presynaptic protein α-synuclein (αSyn) in its pathogenesis. Recent work has investigated how disrupting αSyn's interaction with membranes triggers trafficking defects, cellular stress, and apoptosis. Special interest has been devoted to a series of mutants exacerbating the effects of the E46K mutation (associated with autosomal dominant PD) through homologous Glu-to-Lys substitutions in αSyn's N-terminal region (i.e. E35K and E61K). Such E46K-like mutants have been shown to cause dopaminergic neuron loss and severe but L-DOPA-responsive motor defects in mouse overexpression models, presenting enormous translational potential for PD and other "synucleinopathies." In this work, using a variety of biophysical techniques, we characterize the molecular pathology of E46K-like αSyn mutants by studying their structure and membrane-binding and remodeling abilities. We find that, although a slight increase in the mutants' avidity for synaptic vesicle-like membranes can be detected, most of their deleterious effects are connected to their complete disruption of αSyn's curvature selectivity. Indiscriminate binding can shift αSyn's subcellular localization away from its physiological interactants at the synaptic bouton toward trafficking vesicles and organelles, as observed in E46K-like cellular and murine models, as well as in human pathology. In conclusion, our findings suggest that a loss of curvature selectivity, rather than increased membrane affinity, could be the critical dyshomeostasis in synucleinopathies.
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Affiliation(s)
- Matteo Rovere
- From the Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Alex E Powers
- From the Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Haiyang Jiang
- From the Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Julia C Pitino
- From the Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Luis Fonseca-Ornelas
- From the Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Dushyant S Patel
- From the Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Alessandro Achille
- the Department of Computer Science, University of California, Los Angeles, California 90095
| | - Ralf Langen
- the Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90033, and
| | - Jobin Varkey
- the Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90033, and
| | - Tim Bartels
- From the Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115,
- the Dementia Research Institute, University College London, London WC1E 6BT, United Kingdom
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21
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Bhattacharya S, Xu L, Thompson D. Molecular Simulations Reveal Terminal Group Mediated Stabilization of Helical Conformers in Both Amyloid-β42 and α-Synuclein. ACS Chem Neurosci 2019; 10:2830-2842. [PMID: 30917651 DOI: 10.1021/acschemneuro.9b00053] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The presence of partially structured helices in natively unfolded amyloid-β42 (Aβ42) and α-synuclein (αS) has been shown to accelerate fibrillation in the onset of Alzheimer's and Parkinson's disease, respectively. At the other extreme, folded stable helical conformers have also been reported to resist amyloid formation. Recent studies indicate that amyloidogenic aggregation can be impeded using small molecules that stabilize the α-helical monomers and switch off the neurotoxic pathway. We predict a common intrapeptide route to stabilization based on the plasticity of helical conformations of Aβ42 and αS as assessed through extensive atomistic molecular dynamics (MD) computer simulations (∼36 μs) across ten distinct protein force field and water model combinations. Computed free energies and interaction maps (not obtainable from experiments alone) show that flexible terminal groups (N-terminus of Aβ42 and C-terminus of αS) show a tendency to stabilize folded helical conformations in both peptides via primary hydrophobic interactions with central hydrophobic domains, and secondary salt bridges with other domains. These interactions confer aggregation resistance by decreasing the population of partially structured helices and are absent in control simulations of complete unfolding. Computed helical stability is also significantly reduced in terminal-deleted variants. The models suggest new strategies to tackle neurodegeneration by rationally re-engineering terminal groups to optimize their predicted ability to deactivate helical monomers.
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Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Liang Xu
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
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22
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Ugalde CL, Lawson VA, Finkelstein DI, Hill AF. The role of lipids in α-synuclein misfolding and neurotoxicity. J Biol Chem 2019; 294:9016-9028. [PMID: 31064841 DOI: 10.1074/jbc.rev119.007500] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The misfolding and aggregation of α-synuclein (αsyn) in the central nervous system is associated with a group of neurodegenerative disorders referred to as the synucleinopathies. In addition to being a pathological hallmark of disease, it is now well-established that upon misfolding, αsyn acquires pathogenic properties, such as neurotoxicity, that can contribute to disease development. The mechanisms that produce αsyn misfolding and the molecular events underlying the neuronal damage caused by these misfolded species are not well-defined. A consistent observation that may be relevant to αsyn's pathogenicity is its ability to associate with lipids. This appears important not only to how αsyn aggregates, but also to the mechanism by which the misfolded protein causes intracellular damage. This review discusses the current literature reporting a role of lipids in αsyn misfolding and neurotoxicity in various synucleinopathy disorders and provides an overview of current methods to assess protein misfolding and pathogenicity both in vitro and in vivo.
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Affiliation(s)
- Cathryn L Ugalde
- From the Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia, .,the Departments of Microbiology and Immunology and.,the Howard Florey Institute of Neuroscience and Mental Health, Parkville, Victoria 3052, Australia.,Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3052, Australia, and
| | | | - David I Finkelstein
- the Howard Florey Institute of Neuroscience and Mental Health, Parkville, Victoria 3052, Australia
| | - Andrew F Hill
- From the Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia, .,Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3052, Australia, and
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23
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Ma D, Xu C, Hou W, Zhao C, Ma J, Huang X, Jia Q, Ma L, Diao J, Liu C, Li M, Lu Y. Detecting Single‐Molecule Dynamics on Lipid Membranes with Quenchers‐in‐a‐Liposome FRET. Angew Chem Int Ed Engl 2019; 58:5577-5581. [DOI: 10.1002/anie.201813888] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/11/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Dong‐Fei Ma
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Chun‐Hua Xu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Wen‐Qing Hou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Chun‐Yu Zhao
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of Sciences Shanghai 200032 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jian‐Bing Ma
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Xing‐Yuan Huang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Qi Jia
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Lu Ma
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jiajie Diao
- Department of Cancer BiologyUniversity of Cincinnati School of Medicine Cincinnati OH 45267 USA
| | - Cong Liu
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of Sciences Shanghai 200032 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Songshan Lake Materials Laboratory Dongguan Guangdong 523808 China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Songshan Lake Materials Laboratory Dongguan Guangdong 523808 China
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24
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Ma D, Xu C, Hou W, Zhao C, Ma J, Huang X, Jia Q, Ma L, Diao J, Liu C, Li M, Lu Y. Detecting Single‐Molecule Dynamics on Lipid Membranes with Quenchers‐in‐a‐Liposome FRET. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813888] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Dong‐Fei Ma
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Chun‐Hua Xu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Wen‐Qing Hou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Chun‐Yu Zhao
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of Sciences Shanghai 200032 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jian‐Bing Ma
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Xing‐Yuan Huang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Qi Jia
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Lu Ma
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jiajie Diao
- Department of Cancer BiologyUniversity of Cincinnati School of Medicine Cincinnati OH 45267 USA
| | - Cong Liu
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of Sciences Shanghai 200032 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Songshan Lake Materials Laboratory Dongguan Guangdong 523808 China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Songshan Lake Materials Laboratory Dongguan Guangdong 523808 China
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25
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Abstract
The past few years have resulted in an increased awareness and recognition of the prevalence and roles of intrinsically disordered proteins and protein regions (IDPs and IDRs, respectively) in synaptic vesicle trafficking and exocytosis and in overall synaptic organization. IDPs and IDRs constitute a class of proteins and protein regions that lack stable tertiary structure, but nevertheless retain biological function. Their significance in processes such as cell signaling is now well accepted, but their pervasiveness and importance in other areas of biology are not as widely appreciated. Here, we review the prevalence and functional roles of IDPs and IDRs associated with the release and recycling of synaptic vesicles at nerve terminals, as well as with the architecture of these terminals. We hope to promote awareness, especially among neuroscientists, of the importance of this class of proteins in these critical pathways and structures. The examples discussed illustrate some of the ways in which the structural flexibility conferred by intrinsic protein disorder can be functionally advantageous in the context of cellular trafficking and synaptic function.
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Affiliation(s)
- David Snead
- From the Department of Biochemistry, Weill Cornell Medicine, New York, New York 10021
| | - David Eliezer
- From the Department of Biochemistry, Weill Cornell Medicine, New York, New York 10021
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26
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Fallah MA, Hauser K. Immobilization approaches can affect protein dynamics: a surface-enhanced infrared spectroscopic study on lipid–protein interactions. Biomater Sci 2019; 7:3204-3212. [DOI: 10.1039/c9bm00140a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Near-field detection of SEIRA reveals that surface immobilization alters conformational properties of α-synuclein.
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Affiliation(s)
| | - Karin Hauser
- Department of Chemistry
- University of Konstanz
- 78457 Konstanz
- Germany
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27
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Xu L, Bhattacharya S, Thompson D. On the ubiquity of helical α-synuclein tetramers. Phys Chem Chem Phys 2019; 21:12036-12043. [DOI: 10.1039/c9cp02464f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The stability of oligomers linearly increases from dimers to octamers, but assembly of oligomers larger than tetramers requires high activation energies.
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Affiliation(s)
- Liang Xu
- Department of Physics
- Bernal Institute
- University of Limerick
- V94 T9PX
- Ireland
| | | | - Damien Thompson
- Department of Physics
- Bernal Institute
- University of Limerick
- V94 T9PX
- Ireland
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28
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Iyer A, Claessens MMAE. Disruptive membrane interactions of alpha-synuclein aggregates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:468-482. [PMID: 30315896 DOI: 10.1016/j.bbapap.2018.10.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/14/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022]
Abstract
Alpha synuclein (αS) is a ~14 kDa intrinsically disordered protein. Decades of research have increased our knowledge on αS yet its physiological function remains largely elusive. The conversion of monomeric αS into oligomers and amyloid fibrils is believed to play a central role of the pathology of Parkinson's disease (PD). It is becoming increasingly clear that the interactions of αS with cellular membranes are important for both αS's functional and pathogenic actions. Therefore, understanding interactions of αS with membranes seems critical to uncover functional or pathological mechanisms. This review summarizes our current knowledge of how physicochemical properties of phospholipid membranes affect the binding and aggregation of αS species and gives an overview of how post-translational modifications and point mutations in αS affect phospholipid membrane binding and protein aggregation. We discuss the disruptive effects resulting from the interaction of αS aggregate species with membranes and highlight current approaches and hypotheses that seek to understand the pathogenic and/or protective role of αS in PD.
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Affiliation(s)
- Aditya Iyer
- Membrane Enzymology Group, University of Groningen, Groningen 9747 AG, The Netherlands
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29
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Rawat A, Langen R, Varkey J. Membranes as modulators of amyloid protein misfolding and target of toxicity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1863-1875. [PMID: 29702073 DOI: 10.1016/j.bbamem.2018.04.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/19/2018] [Accepted: 04/19/2018] [Indexed: 12/15/2022]
Abstract
Abnormal protein aggregation is a hallmark of various human diseases. α-Synuclein, a protein implicated in Parkinson's disease, is found in aggregated form within Lewy bodies that are characteristically observed in the brains of PD patients. Similarly, deposits of aggregated human islet amyloid polypeptide (IAPP) are found in the pancreatic islets in individuals with type 2 diabetes mellitus. Significant number of studies have focused on how monomeric, disaggregated proteins transition into various amyloid structures leading to identification of a vast number of aggregation promoting molecules and processes over the years. Inasmuch as these factors likely enhance the formation of toxic, misfolded species, they might act as risk factors in disease. Cellular membranes, and particularly certain lipids, are considered to be among the major players for aggregation of α-synuclein and IAPP, and membranes might also be the target of toxicity. Past studies have utilized an array of biophysical tools, both in vitro and in vivo, to expound the membrane-mediated aggregation. Here, we focus on membrane interaction of α-synuclein and IAPP, and how various kinds of membranes catalyze or modulate the aggregation of these proteins and how, in turn, these proteins disrupt membrane integrity, both in vitro and in vivo. The membrane interaction and subsequent aggregation has been briefly contrasted to aggregation of α-synuclein and IAPP in solution. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Anoop Rawat
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, United States
| | - Ralf Langen
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, United States.
| | - Jobin Varkey
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, United States.
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30
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Fakhree MA, Nolten IS, Blum C, Claessens MMAE. Different Conformational Subensembles of the Intrinsically Disordered Protein α-Synuclein in Cells. J Phys Chem Lett 2018; 9:1249-1253. [PMID: 29474083 PMCID: PMC5857923 DOI: 10.1021/acs.jpclett.8b00092] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 02/23/2018] [Indexed: 05/27/2023]
Abstract
The intrinsically disordered protein α-synuclein (αS) is thought to play an important role in cellular membrane processes. Although in vitro experiments indicate that this initially disordered protein obtains structure upon membrane binding, NMR and EPR studies in cells could not single out any conformational subensemble. Here we microinjected small amounts of αS, labeled with a Förster resonance energy transfer (FRET) pair, into SH-SY5Y cells to investigate conformational changes upon membrane binding. Our FRET studies show a clear conformational difference between αS in the cytosol and when bound to small vesicles. The identification of these different conformational subensembles inside cells resolves the apparent contradiction between in vitro and in vivo experiments and shows that at least two different conformational subensembles of αS exist in cells. The existence of conformational subensembles supports the idea that αS can obtain different functions which can possibly be dynamically addressed with changing intracellular physicochemical conditions.
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31
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Fusco G, Sanz-Hernandez M, De Simone A. Order and disorder in the physiological membrane binding of α-synuclein. Curr Opin Struct Biol 2017; 48:49-57. [PMID: 29100107 DOI: 10.1016/j.sbi.2017.09.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/21/2017] [Accepted: 09/25/2017] [Indexed: 11/25/2022]
Abstract
α-Synuclein (αS) is a neuronal protein that localises predominantly at the presynaptic terminals, and whose fibrillar aggregates are the major constituents of Lewy bodies in Parkinson's disease. In vivo αS is partitioned between water-soluble and membrane-bound states, and this highly regulated equilibrium influences its biological behaviour under both physiological and pathological conditions. Here we discuss the sequence and structural determinants underlying the transition between the unstructured cytosolic and partially structured membrane-bound states of αS. The balance between order and disorder in this protein system is crucial for the overall regulation of the membrane affinity, the ability to induce the clustering of synaptic vesicles, and the tendency to self assemble into amyloid fibrils at the surface of biological membranes.
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Affiliation(s)
- Giuliana Fusco
- Department of Life Sciences, Imperial College London, South Kensington SW7 2AZ, London, UK
| | - Maximo Sanz-Hernandez
- Department of Life Sciences, Imperial College London, South Kensington SW7 2AZ, London, UK
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington SW7 2AZ, London, UK.
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32
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Fonseca-Ornelas L, Schmidt C, Camacho-Zarco AR, Fernandez CO, Becker S, Zweckstetter M. Small-Molecule-Induced Soluble Oligomers of α-Synuclein with Helical Structure. Chemistry 2017; 23:13010-13014. [PMID: 28763125 DOI: 10.1002/chem.201703001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Indexed: 11/08/2022]
Abstract
Accumulation of α-synuclein (αSyn) aggregates constitutes the hallmark of synucleinopathies including Parkinson's disease. However, many steps from the innocuous, monomeric αSyn toward misfolded oligomers and fibrillar species remain unclear. Here, we show that αSyn can form in solution α-helical oligomers, which are off-pathway to fibrillization, through interaction with the tetrapyrrole phthalocyanine tetrasulfonate. Chemical cross-linking combined with mass spectrometry reveals a large number of intermolecular cross-links along the entire αSyn sequence in the phthalocyanine tetrasulfonate-stabilized αSyn oligomers. Our study suggests that stabilization of structured oligomers by small molecules provides a viable strategy to interfere with αSyn fibrillization.
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Affiliation(s)
- Luis Fonseca-Ornelas
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/ Saale, Germany
| | - Aldo R Camacho-Zarco
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - Claudio O Fernandez
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR), Universidad Nacional de Rosario, S2002LRK- Rosario, Argentina, Instituto de Investigaciones para el Descubrimiento de Farmacos de Rosario-IIDEFAR (CONICET-UNR), S2002LRK-, Rosario, Argentina
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Markus Zweckstetter
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany.,Department of Neurology, University Medical Center, University of Göttingen, Waldweg 33, 37073, Göttingen, Germany
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33
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Varkey J, Langen R. Membrane remodeling by amyloidogenic and non-amyloidogenic proteins studied by EPR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 280:127-139. [PMID: 28579098 PMCID: PMC5461824 DOI: 10.1016/j.jmr.2017.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/18/2017] [Accepted: 02/18/2017] [Indexed: 06/07/2023]
Abstract
The advancement in site-directed spin labeling of proteins has enabled EPR studies to expand into newer research areas within the umbrella of protein-membrane interactions. Recently, membrane remodeling by amyloidogenic and non-amyloidogenic proteins has gained a substantial interest in relation to driving and controlling vital cellular processes such as endocytosis, exocytosis, shaping of organelles like endoplasmic reticulum, Golgi and mitochondria, intracellular vesicular trafficking, formation of filopedia and multivesicular bodies, mitochondrial fusion and fission, and synaptic vesicle fusion and recycling in neurotransmission. Misregulation in any of these processes due to an aberrant protein (mutation or misfolding) or alteration of lipid metabolism can be detrimental to the cell and cause disease. Dissection of the structural basis of membrane remodeling by proteins is thus quite necessary for an understanding of the underlying mechanisms, but it remains a formidable task due to the difficulties of various common biophysical tools in monitoring the dynamic process of membrane binding and bending by proteins. This is largely since membranes generally complicate protein structure analysis and this problem is amplified for structural analysis in the presence of different types of membrane curvatures. Recent EPR studies on membrane remodeling by proteins show that a significant structural information can be generated to delineate the role of different protein modules, domains and individual amino acids in the generation of membrane curvature. These studies also show how EPR can complement the data obtained by high resolution techniques such as X-ray and NMR. This perspective covers the application of EPR in recent studies for understanding membrane remodeling by amyloidogenic and non-amyloidogenic proteins that is useful for researchers interested in using or complimenting EPR to gain better understanding of membrane remodeling. We also discuss how a single protein can generate different type of membrane curvatures using specific conformations for specific membrane structures and how EPR is a versatile tool well-suited to analyze subtle alterations in structures under such modifying conditions which otherwise would have been difficult using other biophysical tools.
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Affiliation(s)
- Jobin Varkey
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, United States.
| | - Ralf Langen
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, United States.
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34
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Rostovtseva TK, Hoogerheide DP, Rovini A, Bezrukov SM. Lipids in Regulation of the Mitochondrial Outer Membrane Permeability, Bioenergetics, and Metabolism. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-55539-3_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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35
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Jiang Z, Heinrich F, McGlinchey RP, Gruschus JM, Lee JC. Segmental Deuteration of α-Synuclein for Neutron Reflectometry on Tethered Bilayers. J Phys Chem Lett 2017; 8:29-34. [PMID: 27936328 PMCID: PMC5367044 DOI: 10.1021/acs.jpclett.6b02304] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Neutron reflectometry (NR) is uniquely suited for studying protein interaction with phospholipid bilayers along the bilayer normal on an angstrom scale. However, NR on its own cannot discern specific membrane-bound regions due to a lack of scattering contrast within a protein. Here we report the successful coupling of native chemical ligation (NCL) and NR to study α-synuclein (α-syn), a membrane-binding neuronal protein central in Parkinson's disease. Two α-syn variants were generated where either the first 86 or last 54 residues are deuterated, allowing for region-specific contrast within the protein and the identification of membrane interacting residues by NR. Residues 1-86 are positioned at the hydrocarbon/headgroup interface of the outer leaflet, whereas the density distribution of the 54 C-terminal residues ranges from the hydrocarbon region to the aqueous environment. Coupling of NCL and NR should have broad utility in studies of membrane protein folding.
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Affiliation(s)
- Zhiping Jiang
- Laboratory of Protein Conformation and Dynamics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213 and National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Ryan P. McGlinchey
- Laboratory of Protein Conformation and Dynamics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - James M. Gruschus
- Laboratory of Protein Conformation and Dynamics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jennifer C. Lee
- Laboratory of Protein Conformation and Dynamics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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36
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Sivanesam K, Andersen NH. Modulating the Amyloidogenesis of α-Synuclein. Curr Neuropharmacol 2016; 14:226-37. [PMID: 26517049 PMCID: PMC4857621 DOI: 10.2174/1570159x13666151030103153] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/16/2022] Open
Abstract
Alpha-Synuclein is found in the neuronal cells but its native function is not well known. While α -synuclein is an intrinsically disordered protein that adopts a helical conformation upon membrane binding, numerous studies have shown that oligomeric β-forms of this protein are cytotoxic. This response to misfolded species contributes to Parkinson's Disease etiology and symptoms. The resulting amyloid fibrils are an established diagnostic in Parkinson's Disease. In this review, we focus on strategies that have been used to inhibit the amyloidogenesis of α -synuclein either by stabilizing the native state, or by redirecting the pathway to less toxic aggregates. Small molecules such as polyphenols, peptides as well as large proteins have proven effective at protecting cells against the cytotoxicity of α-synuclein. These strategies may lead to the development of therapeutic agents that could prove useful in combating this disease.
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Affiliation(s)
| | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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37
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Sahay S, Krishnamoorthy G, Maji SK. Site-specific structural dynamics ofα-Synuclein revealed by time-resolved fluorescence spectroscopy: a review. Methods Appl Fluoresc 2016; 4:042002. [DOI: 10.1088/2050-6120/4/4/042002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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38
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Baylon JL, Vermaas JV, Muller MP, Arcario MJ, Pogorelov TV, Tajkhorshid E. Atomic-level description of protein-lipid interactions using an accelerated membrane model. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:1573-83. [PMID: 26940626 PMCID: PMC4877275 DOI: 10.1016/j.bbamem.2016.02.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 02/19/2016] [Accepted: 02/20/2016] [Indexed: 01/03/2023]
Abstract
Peripheral membrane proteins are structurally diverse proteins that are involved in fundamental cellular processes. Their activity of these proteins is frequently modulated through their interaction with cellular membranes, and as a result techniques to study the interfacial interaction between peripheral proteins and the membrane are in high demand. Due to the fluid nature of the membrane and the reversibility of protein-membrane interactions, the experimental study of these systems remains a challenging task. Molecular dynamics simulations offer a suitable approach to study protein-lipid interactions; however, the slow dynamics of the lipids often prevents sufficient sampling of specific membrane-protein interactions in atomistic simulations. To increase lipid dynamics while preserving the atomistic detail of protein-lipid interactions, in the highly mobile membrane-mimetic (HMMM) model the membrane core is replaced by an organic solvent, while short-tailed lipids provide a nearly complete representation of natural lipids at the organic solvent/water interface. Here, we present a brief introduction and a summary of recent applications of the HMMM to study different membrane proteins, complementing the experimental characterization of the presented systems, and we offer a perspective of future applications of the HMMM to study other classes of membrane proteins. This article is part of a Special Issue entitled: Membrane proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Javier L Baylon
- Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology.
| | - Josh V Vermaas
- Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology.
| | - Melanie P Muller
- Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology; College of Medicine.
| | - Mark J Arcario
- Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology; College of Medicine.
| | - Taras V Pogorelov
- Beckman Institute for Advanced Science and Technology; School of Chemical Sciences; Department of Chemistry; National Center for Supercomputing Applications.
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology; College of Medicine; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
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39
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Wang C, Zhao C, Li D, Tian Z, Lai Y, Diao J, Liu C. Versatile Structures of α-Synuclein. Front Mol Neurosci 2016; 9:48. [PMID: 27378848 PMCID: PMC4913103 DOI: 10.3389/fnmol.2016.00048] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/06/2016] [Indexed: 11/20/2022] Open
Abstract
α-Synuclein (α-syn) is an intrinsically disordered protein abundantly distributed in presynaptic terminals. Aggregation of α-syn into Lewy bodies (LB) is a molecular hallmark of Parkinson’s disease (PD). α-Syn features an extreme conformational diversity, which adapts to different conditions and fulfills versatile functions. However, the molecular mechanism of α-syn transformation and the relation between different structural species and their functional and pathogenic roles in neuronal activities and PD remain unknown. In this mini-review, we summarize the recent discoveries of α-syn structures in the membrane-bound state, in cytosol, and in the amyloid state under physiological and pathological conditions. From the current knowledge on different structural species of α-syn, we intend to find a clue about its function and toxicity in normal neurons and under disease conditions, which could shed light on the PD pathogenesis.
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Affiliation(s)
- Chuchu Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai, China
| | - Chunyu Zhao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai, China
| | - Dan Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai, China
| | - Zhiqi Tian
- Department of Cancer Biology, College of Medicine, University of CincinnatiCincinnati, OH, USA; Center for Mitochondrial Biology and Medicine, Key Laboratory of Biomedical Information Engineering of Ministry of the Education School of Life Science, Xi'an Jiaotong UniversityXi'an, China
| | - Ying Lai
- Department of Molecular and Cellular Physiology, Stanford University Stanford, CA, USA
| | - Jiajie Diao
- Department of Cancer Biology, College of Medicine, University of Cincinnati Cincinnati, OH, USA
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai, China
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40
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Structural Ensembles of Membrane-bound α-Synuclein Reveal the Molecular Determinants of Synaptic Vesicle Affinity. Sci Rep 2016; 6:27125. [PMID: 27273030 PMCID: PMC4897633 DOI: 10.1038/srep27125] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/05/2016] [Indexed: 01/05/2023] Open
Abstract
A detailed characterisation of the molecular determinants of membrane binding by α-synuclein (αS), a 140-residue protein whose aggregation is associated with Parkinson's disease, is of fundamental significance to clarify the manner in which the balance between functional and dysfunctional processes are regulated for this protein. Despite its biological relevance, the structural nature of the membrane-bound state αS remains elusive, in part because of the intrinsically dynamic nature of the protein and also because of the difficulties in studying this state in a physiologically relevant environment. In the present study we have used solid-state NMR and restrained MD simulations to refine structure and topology of the N-terminal region of αS bound to the surface of synaptic-like membranes. This region has fundamental importance in the binding mechanism of αS as it acts as to anchor the protein to lipid bilayers. The results enabled the identification of the key elements for the biological properties of αS in its membrane-bound state.
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41
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Tuttle MD, Comellas G, Nieuwkoop AJ, Covell DJ, Berthold DA, Kloepper KD, Courtney JM, Kim JK, Barclay AM, Kendall A, Wan W, Stubbs G, Schwieters CD, Lee VMY, George JM, Rienstra CM. Solid-state NMR structure of a pathogenic fibril of full-length human α-synuclein. Nat Struct Mol Biol 2016; 23:409-15. [PMID: 27018801 PMCID: PMC5034296 DOI: 10.1038/nsmb.3194] [Citation(s) in RCA: 707] [Impact Index Per Article: 88.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 02/25/2016] [Indexed: 12/17/2022]
Abstract
Misfolded α-synuclein amyloid fibrils are the principal components of Lewy bodies and neurites, hallmarks of Parkinson's disease (PD). We present a high-resolution structure of an α-synuclein fibril, in a form that induces robust pathology in primary neuronal culture, determined by solid-state NMR spectroscopy and validated by EM and X-ray fiber diffraction. Over 200 unique long-range distance restraints define a consensus structure with common amyloid features including parallel, in-register β-sheets and hydrophobic-core residues, and with substantial complexity arising from diverse structural features including an intermolecular salt bridge, a glutamine ladder, close backbone interactions involving small residues, and several steric zippers stabilizing a new orthogonal Greek-key topology. These characteristics contribute to the robust propagation of this fibril form, as supported by the structural similarity of early-onset-PD mutants. The structure provides a framework for understanding the interactions of α-synuclein with other proteins and small molecules, to aid in PD diagnosis and treatment.
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Affiliation(s)
- Marcus D Tuttle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gemma Comellas
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Andrew J Nieuwkoop
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Dustin J Covell
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
- Institute on Aging, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Deborah A Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kathryn D Kloepper
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joseph M Courtney
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jae K Kim
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alexander M Barclay
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Amy Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - William Wan
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Gerald Stubbs
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland, USA
| | - Virginia M Y Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
- Institute on Aging, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Julia M George
- Department of Biological and Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Chad M Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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42
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Eichmann C, Campioni S, Kowal J, Maslennikov I, Gerez J, Liu X, Verasdonck J, Nespovitaya N, Choe S, Meier BH, Picotti P, Rizo J, Stahlberg H, Riek R. Preparation and Characterization of Stable α-Synuclein Lipoprotein Particles. J Biol Chem 2016; 291:8516-27. [PMID: 26846854 DOI: 10.1074/jbc.m115.707968] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Indexed: 01/11/2023] Open
Abstract
Multiple neurodegenerative diseases are caused by the aggregation of the human α-Synuclein (α-Syn) protein. α-Syn possesses high structural plasticity and the capability of interacting with membranes. Both features are not only essential for its physiological function but also play a role in the aggregation process. Recently it has been proposed that α-Syn is able to form lipid-protein particles reminiscent of high-density lipoproteins. Here, we present a method to obtain a stable and homogeneous population of nanometer-sized particles composed of α-Syn and anionic phospholipids. These particles are called α-Syn lipoprotein (nano)particles to indicate their relationship to high-density lipoproteins formed by human apolipoproteins in vivo and of in vitro self-assembling phospholipid bilayer nanodiscs. Structural investigations of the α-Syn lipoprotein particles by circular dichroism (CD) and magic angle solid-state nuclear magnetic resonance (MAS SS-NMR) spectroscopy establish that α-Syn adopts a helical secondary structure within these particles. Based on cryo-electron microscopy (cryo-EM) and dynamic light scattering (DLS) α-Syn lipoprotein particles have a defined size with a diameter of ∼23 nm. Chemical cross-linking in combination with solution-state NMR and multiangle static light scattering (MALS) of α-Syn particles reveal a high-order protein-lipid entity composed of ∼8-10 α-Syn molecules. The close resemblance in size between cross-linked in vitro-derived α-Syn lipoprotein particles and a cross-linked species of endogenous α-Syn from SH-SY5Y human neuroblastoma cells indicates a potential functional relevance of α-Syn lipoprotein nanoparticles.
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Affiliation(s)
| | | | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | | | - Juan Gerez
- Institute of Biochemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Xiaoxia Liu
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | | | | | - Senyon Choe
- Structural Biology Laboratory, The Salk Institute, La Jolla, California 92037 and
| | | | - Paola Picotti
- Institute of Biochemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Roland Riek
- From the Laboratory of Physical Chemistry and Structural Biology Laboratory, The Salk Institute, La Jolla, California 92037 and
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43
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Kumar P, Segers-Nolten IMJ, Schilderink N, Subramaniam V, Huber M. Parkinson's Protein α-Synuclein Binds Efficiently and with a Novel Conformation to Two Natural Membrane Mimics. PLoS One 2015; 10:e0142795. [PMID: 26588454 PMCID: PMC4654490 DOI: 10.1371/journal.pone.0142795] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/27/2015] [Indexed: 01/11/2023] Open
Abstract
Binding of human α-Synuclein, a protein associated with Parkinson’s disease, to natural membranes is thought to be crucial in relation to its pathological and physiological function. Here the binding of αS to small unilamellar vesicles mimicking the inner mitochondrial and the neuronal plasma membrane is studied in situ by continuous wave and pulsed electron paramagnetic resonance. Local binding information of αS spin labeled by MTSL at positions 56 and 69 respectively shows that also helix 2 (residues 50–100) binds firmly to both membranes. By double electron-electron resonance (DEER) on the mutant spin labeled at positions 27 and 56 (αS 27/56) a new conformation on the membrane is found with a distance of 3.6 nm/ 3.7 nm between residues 27 and 56. In view of the low negative charge density of these membranes, the strong interaction is surprising, emphasizing that function and pathology of αS could involve synaptic vesicles and mitochondria.
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Affiliation(s)
- Pravin Kumar
- Department of Physics, Huygens-Kammerlingh-Onnes Laboratory, Leiden University, Leiden, The Netherlands
| | - Ine M. J. Segers-Nolten
- Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands
| | - Nathalie Schilderink
- Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands
| | - Vinod Subramaniam
- Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands
- FOM Institute AMOLF, Amsterdam, The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kammerlingh-Onnes Laboratory, Leiden University, Leiden, The Netherlands
- * E-mail:
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44
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Vermaas JV, Baylon JL, Arcario MJ, Muller MP, Wu Z, Pogorelov TV, Tajkhorshid E. Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution. J Membr Biol 2015; 248:563-82. [PMID: 25998378 PMCID: PMC4490090 DOI: 10.1007/s00232-015-9806-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/30/2015] [Indexed: 12/24/2022]
Abstract
Biological membranes constitute a critical component in all living cells. In addition to providing a conducive environment to a wide range of cellular processes, including transport and signaling, mounting evidence has established active participation of specific lipids in modulating membrane protein function through various mechanisms. Understanding lipid-protein interactions underlying these mechanisms at a sufficiently high resolution has proven extremely challenging, partly due to the semi-fluid nature of the membrane. In order to address this challenge computationally, multiple methods have been developed, including an alternative membrane representation termed highly mobile membrane mimetic (HMMM) in which lateral lipid diffusion has been significantly enhanced without compromising atomic details. The model allows for efficient sampling of lipid-protein interactions at atomic resolution, thereby significantly enhancing the effectiveness of molecular dynamics simulations in capturing membrane-associated phenomena. In this review, after providing an overview of HMMM model development, we will describe briefly successful application of the model to study a variety of membrane processes, including lipid-dependent binding and insertion of peripheral proteins, the mechanism of phospholipid insertion into lipid bilayers, and characterization of optimal tilt angle of transmembrane helices. We conclude with practical recommendations for proper usage of the model in simulation studies of membrane processes.
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Affiliation(s)
- Josh V. Vermaas
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
| | - Javier L. Baylon
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
| | - Mark J. Arcario
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
| | - Melanie P. Muller
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
| | - Zhe Wu
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
| | - Taras V. Pogorelov
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
| | - Emad Tajkhorshid
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
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45
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Jiang Z, Hess SK, Heinrich F, Lee JC. Molecular details of α-synuclein membrane association revealed by neutrons and photons. J Phys Chem B 2015; 119:4812-23. [PMID: 25790164 DOI: 10.1021/jp512499r] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
α-Synuclein (α-syn) is an abundant neuronal protein associated with Parkinson's disease that is disordered in solution, but it exists in equilibrium between a bent-helix and an elongated-helix on negatively charged membranes. Here, neutron reflectometry (NR) and fluorescence spectroscopy were employed to uncover molecular details of the interaction between α-syn and two anionic lipids, phosphatidic acid (PA) and phosphatidylserine (PS). Both NR and site-specific Trp measurements indicate that penetration depth of α-syn is similar for either PA- or PS-containing membranes (∼9-11 Å from bilayer center) even though there is a preference for α-syn binding to PA. However, closer examination of the individual Trp quenching profiles by brominated lipids reveals differences into local membrane interactions especially at position 39 where conformational heterogeneity was observed. The data also indicate that while W94 penetrates the bilayer as deeply as W4, W94 resides in a more polar surrounding. Taken together, we suggest the N- and C-terminal regions near positions 4 and 94 are anchored to the membrane, while the putative linker spanning residue 39 samples multiple conformations, which are sensitive to the chemical nature of the membrane surface. This flexibility may enable α-syn to bind diverse biomembranes in vivo.
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Affiliation(s)
- Zhiping Jiang
- †Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Sara K Hess
- †Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Frank Heinrich
- ‡Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.,§Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jennifer C Lee
- †Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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46
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Burré J, Sharma M, Südhof TC. Definition of a molecular pathway mediating α-synuclein neurotoxicity. J Neurosci 2015; 35:5221-32. [PMID: 25834048 PMCID: PMC4380997 DOI: 10.1523/jneurosci.4650-14.2015] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/17/2015] [Accepted: 02/20/2015] [Indexed: 01/06/2023] Open
Abstract
α-Synuclein physiologically chaperones SNARE-complex assembly at the synapse but pathologically misfolds into neurotoxic aggregates that are characteristic for neurodegenerative disorders, such as Parkinson's disease, and that may spread from one neuron to the next throughout the brain during Parkinson's disease pathogenesis. In normal nerve terminals, α-synuclein is present in an equilibrium between a cytosolic form that is natively unfolded and monomeric and a membrane-bound form that is composed of an α-helical multimeric species that chaperones SNARE-complex assembly. Although the neurotoxicity of α-synuclein is well established, the relationship between the native conformations of α-synuclein and its pathological aggregation remain incompletely understood; most importantly, it is unclear whether α-synuclein aggregation originates from its monomeric cytosolic or oligomeric membrane-bound form. Here, we address this question by introducing into α-synuclein point mutations that block membrane binding and by then assessing the effect of blocking membrane binding on α-synuclein aggregation and neurotoxicity. We show that membrane binding inhibits α-synuclein aggregation; conversely, blocking membrane binding enhances α-synuclein aggregation. Stereotactic viral expression of wild-type and mutant α-synuclein in the substantia nigra of mice demonstrated that blocking α-synuclein membrane binding significantly enhanced its neurotoxicity in vivo. Our data delineate a folding pathway for α-synuclein that ranges from a physiological multimeric, α-helical, and membrane-bound species that acts as a SNARE-complex chaperone over a monomeric, natively unfolded form to an amyloid-like aggregate that is neurotoxic in vivo.
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Affiliation(s)
- Jacqueline Burré
- Departments of Molecular and Cellular Physiology and Appel Institute for Alzheimer's Disease Research, Brain and Mind Research Institute, Weill Cornell Medical College, New York, New York 10021
| | - Manu Sharma
- Departments of Molecular and Cellular Physiology and Appel Institute for Alzheimer's Disease Research, Brain and Mind Research Institute, Weill Cornell Medical College, New York, New York 10021
| | - Thomas C Südhof
- Departments of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University Medical School, Stanford, California 94305, and
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47
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Basak S, Prasad GVRK, Varkey J, Chattopadhyay K. Early sodium dodecyl sulfate induced collapse of α-synuclein correlates with its amyloid formation. ACS Chem Neurosci 2015; 6:239-46. [PMID: 25369246 DOI: 10.1021/cn500168x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The aggregation of α-synuclein (A-syn) has been implicated strongly in Parkinson's disease (PD). In vitro studies established A-syn to be a member of the intrinsically disordered protein (IDP) family. This protein undergoes structural interconversion between an extended and a compact state, and this equilibrium influences the mechanism of its aggregation. A combination of fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) has been used to study the membrane induced conformational reorganization and aggregation of A-syn. Different structural and conformational events, including the early collapse, the formation of the secondary structure, and aggregation have been identified and characterized using FCS and other biophysical methods. In addition, the concentrations of glycerol and urea have been varied to study the effect of solution conditions on the above conformational events. Further, we have extended this study on a number of A-syn mutants, namely, A30P, A53T, and E46K. These mutants are chosen because of their known implications in the disease pathology. The variation of solution conditions and mutational analyses suggest a strong correlation between the extent of early collapse and the onset of aggregation in PD.
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Affiliation(s)
- Sujit Basak
- Protein
Folding and Dynamics Laboratory Structural Biology and Bioinformatics
Division CSIR-Indian Institute of Chemical Biology (IICB) 4, Raja
S.C. Mullick Road, Kolkata-700032, India
| | - G. V. R Krishna Prasad
- Department
of Biological Sciences, Indian Institute of Science Education and Research, Sec 81, SAS Nagar, Mohali, Punjab-140306, India
| | - Jobin Varkey
- Centre
for Converging Technologies, University of Rajasthan, Jaipur-3002004, India
| | - Krishnananda Chattopadhyay
- Protein
Folding and Dynamics Laboratory Structural Biology and Bioinformatics
Division CSIR-Indian Institute of Chemical Biology (IICB) 4, Raja
S.C. Mullick Road, Kolkata-700032, India
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48
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Sivanesam K, Byrne A, Bisaglia M, Bubacco L, Andersen N. Binding Interactions of Agents That Alter α-Synuclein Aggregation. RSC Adv 2015; 5:11577-11590. [PMID: 25705374 DOI: 10.1039/c5ra00325c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Further examination of peptides with well-folded antiparallel β strands as inhibitors of amyloid formation from α-synuclein has resulted in more potent inhibitors. Several of these had multiple Tyr residues and represent a new lead for inhibitor design by small peptides that do not divert α-synuclein to non-amyloid aggregate formation. The most potent inhibitor obtained in this study is a backbone cyclized version of a previously studied β hairpin, designated as WW2, with a cross-strand Trp/Trp cluster. The cyclization was accomplished by adding a d-Pro-l-Pro turn locus across strand termini. At a 2:1 peptide to α-synuclein ratio, cyclo-WW2 displays complete inhibition of β-structure formation. Trp-bearing antiparallel β-sheets held together by a disulphide bond are also potent inhibitors. 15N HSQC spectra of α-synuclein provided new mechanistic details. The time course of 15N HSQC spectral changes observed during β-oligomer formation has revealed which segments of the structure become part of the rigid core of an oligomer at early stages of amyloidogenesis and that the C-terminus remains fully flexible throughout the process. All of the effective peptide inhibitors display binding-associated titration shifts in 15N HSQC spectra of α-synuclein in the C-terminal Q109-E137 segment. Cyclo-WW2, the most potent inhibitor, also displays titration shifts in the G41-T54 span of α-synuclein, an additional binding site. The earliest aggregation event appears to be centered about H50 which is also a binding site for our most potent inhibitor.
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Affiliation(s)
- K Sivanesam
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - A Byrne
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - M Bisaglia
- Department of Biology, University of Padua, 35121 Padova, Italy
| | - L Bubacco
- Department of Biology, University of Padua, 35121 Padova, Italy
| | - N Andersen
- Department of Chemistry, University of Washington, Seattle, WA 98195
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49
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Vermaas JV, Tajkhorshid E. Conformational heterogeneity of α-synuclein in membrane. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1838:3107-17. [PMID: 25135664 PMCID: PMC4194229 DOI: 10.1016/j.bbamem.2014.08.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 08/09/2014] [Accepted: 08/11/2014] [Indexed: 12/13/2022]
Abstract
α-Synuclein (αS) is a natively disordered protein in solution, thought to be involved in the fusion of neurotransmitter vesicles to cellular membranes during neurotransmission. Monomeric αS has been previously characterized in two distinct membrane-associated conformations: a broken-helix structure, and an extended helix. By employing atomistic molecular dynamics and a novel membrane representation with significantly enhanced lipid mobility (HMMM), we investigate the process of spontaneous membrane binding of αS and the conformational dynamics of monomeric αS in its membrane-bound form. By repeatedly placing helical αS monomers in solution above a planar lipid bilayer and observing their spontaneous association and its spontaneous insertion into the membrane during twenty independent unbiased simulations, we are able to characterize αS in its membrane-bound state, suggesting that αS has a highly variable membrane insertion depth at equilibrium. Our simulations also capture two distinct states of αS, the starting broken-helix conformation seen in the micelle bound NMR structures, and a semi-extended helix. Analysis of lipid distributions near αS monomers indicates that the transition to a semi-extended helix is facilitated by concentration of phosphatidyl-serine headgroups along the inner edge of the protein. Such a lipid-mediated transition between helix-turn-helix and extended conformations of αS may also occur in vivo, and may be important for the physiological function of αS.
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Affiliation(s)
- Josh V Vermaas
- Beckman Institute for Advanced Science and Technology, Department of Biochemistry, College of Medicine, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, Department of Biochemistry, College of Medicine, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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50
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Snead D, Eliezer D. Alpha-synuclein function and dysfunction on cellular membranes. Exp Neurobiol 2014; 23:292-313. [PMID: 25548530 PMCID: PMC4276801 DOI: 10.5607/en.2014.23.4.292] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/15/2014] [Accepted: 11/16/2014] [Indexed: 11/19/2022] Open
Abstract
Alpha-synuclein is a small neuronal protein that is closely associated with the etiology of Parkinson's disease. Mutations in and alterations in expression levels of alpha-synuclein cause autosomal dominant early onset heredity forms of Parkinson's disease, and sporadic Parkinson's disease is defined in part by the presence of Lewy bodies and Lewy neurites that are composed primarily of alpha-synuclein deposited in an aggregated amyloid fibril state. The normal function of alpha-synuclein is poorly understood, and the precise mechanisms by which it leads to toxicity and cell death are also unclear. Although alpha-synuclein is a highly soluble, cytoplasmic protein, it binds to a variety of cellular membranes of different properties and compositions. These interactions are considered critical for at least some normal functions of alpha-synuclein, and may well play critical roles in both the aggregation of the protein and its mechanisms of toxicity. Here we review the known features of alpha-synuclein membrane interactions in the context of both the putative functions of the protein and of its pathological roles in disease.
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Affiliation(s)
- David Snead
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
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