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Saurabh A, Prabhu NP. Concerted enhanced-sampling simulations to elucidate the helix-fibril transition pathway of intrinsically disordered α-Synuclein. Int J Biol Macromol 2022; 223:1024-1041. [PMID: 36379279 DOI: 10.1016/j.ijbiomac.2022.11.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/19/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Fibril formation of α-synuclein is linked with Parkinson's disease. The intrinsically disordered nature of α-syn provides extensive conformational plasticity and becomes difficult to characterize its transition pathway from native monomeric to disease-associated fibril form. We implemented different simulation methods such as steered dynamics-umbrella sampling, and replica-exchange and conventional MD simulations to access various conformational states of α-syn. Nineteen distinct intermediate structures were identified by free energy landscape and cluster analysis. They were then sorted based on secondary structure and solvent exposure of fibril-core residues to illustrate the fibril dissociation pathway. The analysis showed that following the initial dissociation of the polypeptide chain from the fibril, α-syn might form either compact-conformations by long-range interactions or extended-conformations stabilized by local interactions. This leads α-syn to adapt two different pathways. The secondary structure, solvation, contact distance, interaction energies and backbone dihedrals of thirty-two selected residues were analyzed for all the 19 intermediates. The results suggested that formation of β-turns, reorganization of salt bridges, and dihedral changes in the hydrophobic regions are the major driving forces for helix-fibril transition. Structural features of the intermediates also correlated with the earlier experimental and computational studies. The study provides critical information on the fibrillation pathway of α-syn.
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Affiliation(s)
- Archi Saurabh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India.
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2
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Xia N, Cabin DE, Fang F, Reijo Pera RA. Parkinson's Disease: Overview of Transcription Factor Regulation, Genetics, and Cellular and Animal Models. Front Neurosci 2022; 16:894620. [PMID: 35600613 PMCID: PMC9115107 DOI: 10.3389/fnins.2022.894620] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/12/2022] [Indexed: 01/21/2023] Open
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative disorders, affecting nearly 7-10 million people worldwide. Over the last decade, there has been considerable progress in our understanding of the genetic basis of PD, in the development of stem cell-based and animal models of PD, and in management of some clinical features. However, there remains little ability to change the trajectory of PD and limited knowledge of the underlying etiology of PD. The role of genetics versus environment and the underlying physiology that determines the trajectory of the disease are still debated. Moreover, even though protein aggregates such as Lewy bodies and Lewy neurites may provide diagnostic value, their physiological role remains to be fully elucidated. Finally, limitations to the model systems for probing the genetics, etiology and biology of Parkinson's disease have historically been a challenge. Here, we review highlights of the genetics of PD, advances in understanding molecular pathways and physiology, especially transcriptional factor (TF) regulators, and the development of model systems to probe etiology and potential therapeutic applications.
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Affiliation(s)
- Ninuo Xia
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
| | - Deborah E. Cabin
- McLaughlin Research Institute for Biomedical Sciences, Inc., Great Falls, MT, United States
| | - Fang Fang
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
| | - Renee A. Reijo Pera
- McLaughlin Research Institute for Biomedical Sciences, Inc., Great Falls, MT, United States
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3
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Whitehead RD, Teschke CM, Alexandrescu AT. Pulse-field gradient nuclear magnetic resonance of protein translational diffusion from native to non-native states. Protein Sci 2022; 31:e4321. [PMID: 35481638 PMCID: PMC9047038 DOI: 10.1002/pro.4321] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/31/2022] [Accepted: 04/12/2022] [Indexed: 01/31/2023]
Abstract
Hydrodynamic radii (Rh -values) calculated from diffusion coefficients measured by pulse-field-gradient nuclear magnetic resonance are compared for folded and unfolded proteins. For native globular proteins, the Rh -values increase as a power of 0.35 with molecular size, close to the scaling factor of 0.33 predicted from polymer theory. Unfolded proteins were studied under four sets of conditions: in the absence of denaturants, in the presence of 6 M urea, in 95% dimethyl sulfoxide (DMSO), and in 40% hexafluoroisopropanol (HFIP). Scaling factors under all four unfolding conditions are similar (0.49-0.53) approaching the theoretical value of 0.60 for a fully unfolded random coil. Persistence lengths are also similar, except smaller in 95% DMSO, suggesting that the polypeptides are more disordered on a local scale with this solvent. Three of the proteins in our unfolded set have an asymmetric sequence-distribution of charged residues. While these proteins behave normally in water and 6 M urea, they give atypically low Rh -values in 40% HFIP and 95% DMSO suggesting they are forming electrostatic hairpins, favored by their asymmetric sequence charge distribution and the low dielectric constants of DMSO and HFIP. While diffusion-ordered NMR spectroscopy can separate small molecules, we show a number of factors combine to make protein-sized molecules much more difficult to resolve in mixtures. Finally, we look at the temperature dependence of apparent diffusion coefficients. Small molecules show a linear temperature response, while large proteins show abnormally large apparent diffusion coefficients at high temperatures due to convection, suggesting diffusion reference standards are only useful near 25°C.
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Affiliation(s)
- Richard D Whitehead
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Carolyn M Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.,Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
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Bisi N, Feni L, Peqini K, Pérez-Peña H, Ongeri S, Pieraccini S, Pellegrino S. α-Synuclein: An All-Inclusive Trip Around its Structure, Influencing Factors and Applied Techniques. Front Chem 2021; 9:666585. [PMID: 34307295 PMCID: PMC8292672 DOI: 10.3389/fchem.2021.666585] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022] Open
Abstract
Alpha-synuclein (αSyn) is a highly expressed and conserved protein, typically found in the presynaptic terminals of neurons. The misfolding and aggregation of αSyn into amyloid fibrils is a pathogenic hallmark of several neurodegenerative diseases called synucleinopathies, such as Parkinson’s disease. Since αSyn is an Intrinsically Disordered Protein, the characterization of its structure remains very challenging. Moreover, the mechanisms by which the structural conversion of monomeric αSyn into oligomers and finally into fibrils takes place is still far to be completely understood. Over the years, various studies have provided insights into the possible pathways that αSyn could follow to misfold and acquire oligomeric and fibrillar forms. In addition, it has been observed that αSyn structure can be influenced by different parameters, such as mutations in its sequence, the biological environment (e.g., lipids, endogenous small molecules and proteins), the interaction with exogenous compounds (e.g., drugs, diet components, heavy metals). Herein, we review the structural features of αSyn (wild-type and disease-mutated) that have been elucidated up to present by both experimental and computational techniques in different environmental and biological conditions. We believe that this gathering of current knowledge will further facilitate studies on αSyn, helping the planning of future experiments on the interactions of this protein with targeting molecules especially taking into consideration the environmental conditions.
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Affiliation(s)
- Nicolò Bisi
- BioCIS, CNRS, Université Paris Saclay, Châtenay-Malabry Cedex, France
| | - Lucia Feni
- DISFARM-Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano, Milan, Italy
| | - Kaliroi Peqini
- DISFARM-Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano, Milan, Italy
| | - Helena Pérez-Peña
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
| | - Sandrine Ongeri
- BioCIS, CNRS, Université Paris Saclay, Châtenay-Malabry Cedex, France
| | | | - Sara Pellegrino
- DISFARM-Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano, Milan, Italy
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Bozelli JC, Kamski-Hennekam E, Melacini G, Epand RM. α-Synuclein and neuronal membranes: Conformational flexibilities in health and disease. Chem Phys Lipids 2021; 235:105034. [PMID: 33434528 DOI: 10.1016/j.chemphyslip.2020.105034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 02/08/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease. Currently, PD has no treatment. The neuronal protein α-synuclein (αS) plays an important role in PD. However, the molecular mechanisms governing its physiological and pathological roles are not fully understood. It is becoming widely acknowledged that the biological roles of αS involve interactions with biological membranes. In these biological processes there is a fine-tuned interplay between lipids affecting the properties of αS and αS affecting lipid metabolism, αS binding to membranes, and membrane damage. In this review, the intricate interactions between αS and membranes will be reviewed and a discussion of the relationship between αS and neuronal membrane structural plasticity in health and disease will be made. It is proposed that in healthy neurons the conformational flexibilities of αS and the neuronal membranes are coupled to assist the physiological roles of αS. However, in circumstances where their conformational flexibilities are decreased or uncoupled, there is a shift toward cell toxicity. Strategies to modulate toxic αS-membrane interactions are potential approaches for the development of new therapies for PD. Future work using specific αS molecular species as well as membranes with specific physicochemical properties should widen our understanding of the intricate biological roles of αS which, in turn, would propel the development of new strategies for the treatment of PD.
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Affiliation(s)
- José Carlos Bozelli
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Evelyn Kamski-Hennekam
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada; Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada.
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada.
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Zheng Q, Carty SN, Lazo ND. Helix Dipole and Membrane Electrostatics Delineate Conformational Transitions in the Self-Assembly of Amyloidogenic Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:8389-8397. [PMID: 32628488 PMCID: PMC8095063 DOI: 10.1021/acs.langmuir.0c00723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The self-assembly of amyloidogenic peptides on membrane surfaces is associated with the death of neurons and β-cells in Alzheimer's disease and type 2 diabetes, respectively. The early events of self-assembly in vivo are not known, but there is increasing evidence for the importance of the α-helix. To test the hypothesis that electrostatic interactions involving the helix dipole play a key role in membrane-mediated peptide self-assembly, we studied IAPP[11-25(S20G)-NH2] (R11LANFLVHSGNNFGA25-NH2), which under certain conditions self-assembles in hydro to form β-sheet assemblies through an α-helix-containing intermediate. In the presence of small unilamellar vesicles composed solely of zwitterionic lipids, the peptide does not self-assemble presumably because of the absence of stabilizing electrostatic interactions between the membrane surface and the helix dipole. In the presence of vesicles composed solely of anionic lipids, the peptide forms a long-lived α-helix presumably stabilized by dipole-dipole interactions between adjacent helix dipoles. This helix represents a kinetic trap that inhibits β-sheet formation. Intriguingly, when the amount of anionic lipids was decreased to mimic the ratio of zwitterionic and anionic lipids in cells, the α-helix was short-lived and underwent an α-helix to β-sheet conformational transition. Our work suggests that the helix dipole and membrane electrostatics delineate the conformational transitions occurring along the self-assembly pathway to the amyloid.
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Affiliation(s)
- Qiuchen Zheng
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
| | - Senegal N Carty
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
| | - Noel D Lazo
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
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Lucas HR, Fernández RD. Navigating the dynamic landscape of alpha-synuclein morphology: a review of the physiologically relevant tetrameric conformation. Neural Regen Res 2020; 15:407-415. [PMID: 31571649 PMCID: PMC6921358 DOI: 10.4103/1673-5374.265792] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
N-acetylated α-synuclein (αSyn) has long been established as an intrinsically disordered protein associated with a dysfunctional role in Parkinson's disease. In recent years, a physiologically relevant, higher order conformation has been identified as a helical tetramer that is tailored by buried hydrophobic interactions and is distinctively aggregation resistant. The canonical mechanism by which the tetramer assembles remains elusive. As novel biochemical approaches, computational methods, pioneering purification platforms, and powerful imaging techniques continue to develop, puzzling information that once sparked debate as to the veracity of the tetramer has now shed light upon this new counterpart in αSyn neurobiology. Nuclear magnetic resonance and computational studies on multimeric αSyn structure have revealed that the protein folding propensity is controlled by small energy barriers that enable large scale reconfiguration. Alternatively, familial mutations ablate tetramerization and reconfigure polymorphic fibrillization. In this review, we will discuss the dynamic landscape of αSyn quaternary structure with a focus on the tetrameric conformation.
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Affiliation(s)
- Heather R Lucas
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Ricardo D Fernández
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
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Afrose F, McKay MJ, Mortazavi A, Suresh Kumar V, Greathouse DV, Koeppe RE. Transmembrane Helix Integrity versus Fraying To Expose Hydrogen Bonds at a Membrane-Water Interface. Biochemistry 2019; 58:633-645. [PMID: 30565458 DOI: 10.1021/acs.biochem.8b01119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Transmembrane helices dominate the landscape for many membrane proteins. Often flanked by interfacial aromatic residues, these transmembrane helices also contain loops and interhelix segments, which could help in stabilizing a transmembrane orientation. Using 2H nuclear magnetic resonance spectroscopy to monitor bilayer-incorporated model GWALP23 family peptides, we address systematically the issue of helix fraying in relation to the dynamics and orientation of highly similar individual transmembrane helices. We inserted aromatic (Phe, Trp, Tyr, and His) or non-aromatic residues (Ala and Gly) into positions 4 and 5 adjacent to a core transmembrane helix to examine the side-chain dependency of the transmembrane orientation, dynamics, and helix integrity (extent and location of unraveling). Incorporation of [2H]alanine labels enables one to assess the helicity of the core sequence and the peptide termini. For most of the helices, we observed substantial unwinding involving at least three residues at both ends. For the unique case of histidine at positions 4 and 5, an extended N-terminal unwinding was observed up to residue 7. For further investigation of the onset of fraying, we employed A4,5GWALP23 with 2H labels at residues 4 and 5 and found that the number of terminal residues involved in the unwinding depends on bilayer thicknesses and helps to govern the helix dynamics. The combined results enable us to compare and contrast the extent of fraying for each related helix, as reflected by the deviation of experimental 2H quadrupolar splitting magnitudes of juxta-terminal alanines A3 and A21 from those represented by an ideal helix geometry.
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Affiliation(s)
- Fahmida Afrose
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Matthew J McKay
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Armin Mortazavi
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Vasupradha Suresh Kumar
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
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Das T, Eliezer D. Probing Structural Changes in Alpha-Synuclein by Nuclear Magnetic Resonance Spectroscopy. Methods Mol Biol 2019; 1948:157-181. [PMID: 30771177 PMCID: PMC8193918 DOI: 10.1007/978-1-4939-9124-2_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Alpha-synuclein, the principal protein involved in the pathogenesis of Parkinson's disease, has been shown to exchange between multiple conformational states, with hitherto unclear physiological role of such conformational changes. Due to its ability to provide rich structural information for proteins in their near-native environment, nuclear magnetic resonance (NMR) spectroscopy has been a valuable tool to study these conformational states. In this review we describe the application of model systems and NMR methods to the study of membrane-bound states of alpha-synuclein. We provide a detailed description, primarily meant for someone new to the field, of how to prepare the necessary samples, perform the basic experiments, and obtain an initial interpretation of the results.
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