1
|
Wagner WJ, Gross ML. Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta. MASS SPECTROMETRY REVIEWS 2024; 43:782-825. [PMID: 36224716 PMCID: PMC10090239 DOI: 10.1002/mas.21814] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.
Collapse
Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| |
Collapse
|
2
|
Melki R. Disease Mechanisms of Multiple System Atrophy: What a Parallel Between the Form of Pasta and the Alpha-Synuclein Assemblies Involved in MSA and PD Tells Us. CEREBELLUM (LONDON, ENGLAND) 2024; 23:13-21. [PMID: 35657577 PMCID: PMC10864476 DOI: 10.1007/s12311-022-01417-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Intracellular deposits rich in aggregated alpha-synuclein that appear within the central nervous system are intimately associated to Parkinson's disease and multiple system atrophy. While it is understandable that the aggregation of proteins, which share no primary structure identity, such as alpha-synuclein and tau protein, leads to different diseases, that of a given protein yielding distinct pathologies is counterintuitive. This short review relates molecular and mechanistic processes to the observed pathological diversity associated to alpha-synuclein aggregation.
Collapse
Affiliation(s)
- Ronald Melki
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, 18 Route du Panorama, 92265, Fontenay-Aux-Roses, France.
| |
Collapse
|
3
|
Smith JK, Mellick GD, Sykes AM. The role of the endolysosomal pathway in α-synuclein pathogenesis in Parkinson's disease. Front Cell Neurosci 2023; 16:1081426. [PMID: 36704248 PMCID: PMC9871505 DOI: 10.3389/fncel.2022.1081426] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
Parkinson's disease (PD) is a chronic neurodegenerative disease that is characterized by a loss of dopaminergic neurons in the substantia nigra pars compacta of the midbrain (SNpc). Extensive studies into genetic and cellular models of PD implicate protein trafficking as a prominent contributor to the death of these dopaminergic neurons. Considerable evidence also suggests the involvement of α-synuclein as a central component of the characteristic cell death in PD and it is a major structural constituent of proteinaceous inclusion bodies (Lewy bodies; LB). α-synuclein research has been a vital part of PD research in recent years, with newly discovered evidence suggesting that α-synuclein can propagate through the brain via prion-like mechanisms. Healthy cells can internalize toxic α-synuclein species and seed endogenous α-synuclein to form large, pathogenic aggregates and form LBs. A better understanding of how α-synuclein can propagate, enter and be cleared from the cell is vital for therapeutic strategies.
Collapse
|
4
|
Palomino-Hernandez O, Santambrogio C, Rossetti G, Fernandez CO, Grandori R, Carloni P. Molecular Dynamics-Assisted Interpretation of Experimentally Determined Intrinsically Disordered Protein Conformational Components: The Case of Human α-Synuclein. J Phys Chem B 2022; 126:3632-3639. [PMID: 35543707 DOI: 10.1021/acs.jpcb.1c10954] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mass spectrometry and single molecule force microscopy are two experimental approaches able to provide structural information on intrinsically disordered proteins (IDPs). These techniques allow the dissection of conformational ensembles in their main components, although at a low-resolution level. In this work, we interpret the results emerging from these experimental approaches on human alpha synuclein (AS) by analyzing a previously published 73 μs-long molecular-dynamics (MD) simulation of the protein in explicit solvent. We further compare MD-based predictions of single molecule Förster resonance energy transfer (smFRET) data of AS in solution with experimental data. The combined theoretical and experimental data provide a description of AS main conformational ensemble, shedding light into its intramolecular interactions and overall structural compactness. This analysis could be easily transferred to other IDPs.
Collapse
Affiliation(s)
- Oscar Palomino-Hernandez
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany.,Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52425 Aachen, Germany.,Computation-Based Science and Technology Research Center, The Cyprus Institute, 2121 Nicosia, Cyprus.,Institute of Life Science, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany.,Department of Neurology, University Hospital Aachen, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany.,Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Claudio O Fernandez
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPI-NAT). Partner Laboratory of the Max Planck Institute for Biophysical Chemistry (MPI-NAT, MPG). Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario, Argentina S2002LRK Rosario, Argentina
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany.,Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52425 Aachen, Germany.,Institute for Neuroscience and Medicine (INM-11) Forschungszentrum Jülich, 52425 Jülich, Germany
| |
Collapse
|
5
|
Vallejo DD, Rojas Ramírez C, Parson KF, Han Y, Gadkari VV, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
Collapse
Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
6
|
Alpha-Synuclein and Cognitive Decline in Parkinson Disease. Life (Basel) 2021; 11:life11111239. [PMID: 34833115 PMCID: PMC8625417 DOI: 10.3390/life11111239] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022] Open
Abstract
Parkinson disease (PD) is the second most common neurodegenerative disorder in elderly people. It is characterized by the aggregation of misfolded alpha-synuclein throughout the nervous system. Aside from cardinal motor symptoms, cognitive impairment is one of the most disabling non-motor symptoms that occurs during the progression of the disease. The accumulation and spreading of alpha-synuclein pathology from the brainstem to limbic and neocortical structures is correlated with emerging cognitive decline in PD. This review summarizes the genetic and pathophysiologic relationship between alpha-synuclein and cognitive impairment in PD, together with potential areas of biomarker advancement.
Collapse
|
7
|
Lermyte F, Theisen A, O'Connor PB. Solution Condition-Dependent Formation of Gas-Phase Protomers of Alpha-Synuclein in Electrospray Ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:364-372. [PMID: 33237779 DOI: 10.1021/jasms.0c00373] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
One of the main characteristics of biomolecular ions in mass spectrometry is their net charge, and a range of approaches exist to either increase or decrease this quantity in the gas phase. In the context of small molecules, it is well known that, in addition to the charge state, the charge site also has a profound effect on an ion's gas-phase behavior; however, this effect has been far less explored for peptides and intact proteins. Methods exist to determine charge sites of protein ions, and others have observed that the interplay of electrostatic repulsion and inherent basicity leads to different sites gaining or losing a charge depending on the total net charge. Here, we report two distinct protonation site isomers ("protomers") of α-synuclein occurring at the same charge state. The protomers showed important differences in their gas-phase fragmentation behavior and were furthermore distinguishable by ion mobility spectrometry. One protomer was produced under standard electrospray conditions, while the other was observed after addition of 10% dimethyl sulfoxide to the protein solution. Charge sites for both protomers were determined using ultraviolet photodissociation.
Collapse
Affiliation(s)
- Frederik Lermyte
- Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
- School of Engineering, University of Warwick, Coventry CV4 7AL, U.K
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Alina Theisen
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| |
Collapse
|
8
|
Stephens AD, Matak-Vinkovic D, Fernandez-Villegas A, Kaminski Schierle GS. Purification of Recombinant α-synuclein: A Comparison of Commonly Used Protocols. Biochemistry 2020; 59:4563-4572. [PMID: 33237763 PMCID: PMC7818547 DOI: 10.1021/acs.biochem.0c00725] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The initial state of the intrinsically disordered protein α-synuclein (aSyn), e.g., the presence of oligomers and degradation products, or the presence of contaminants and adducts can greatly influence the aggregation kinetics and toxicity of the protein. Here, we compare four commonly used protocols for the isolation of recombinant aSyn from Escherichia coli: boiling, acid precipitation, ammonium sulfate precipitation, and periplasmic lysis followed by ion exchange chromatography and gel filtration. We identified, using nondenaturing electrospray ionization mass spectrometry, that aSyn isolated by acid precipitation and periplasmic lysis was the purest and yielded the highest percentage of monomeric protein, 100% and 96.5%, respectively. We then show that aSyn purified by the different protocols exerts different metabolic stresses in cells, with the more multimeric/degraded and least pure samples leading to a larger increase in cell vitality. However, the percentage of monomeric protein and the purity of the samples did not correlate with aSyn aggregation propensity. This study highlights the importance of characterizing monomeric aSyn after purification, as the choice of purification method can significantly influence the outcome of a subsequent study.
Collapse
Affiliation(s)
- Amberley D. Stephens
- Chemical
Engineering and Biotechnology, University
of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.,
| | - Dijana Matak-Vinkovic
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Ana Fernandez-Villegas
- Chemical
Engineering and Biotechnology, University
of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | | |
Collapse
|
9
|
Lermyte F. Roles, Characteristics, and Analysis of Intrinsically Disordered Proteins: A Minireview. Life (Basel) 2020; 10:E320. [PMID: 33266184 PMCID: PMC7761095 DOI: 10.3390/life10120320] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
In recent years, there has been a growing understanding that a significant fraction of the eukaryotic proteome is intrinsically disordered, and that these conformationally dynamic proteins play a myriad of vital biological roles in both normal and pathological states. In this review, selected examples of intrinsically disordered proteins are highlighted, with particular attention for a few which are relevant in neurological disorders and in viral infection. Next, the underlying causes for the intrinsic disorder are discussed, along with computational methods used to predict whether a given amino acid sequence is likely to adopt a folded or unfolded state in the solution. Finally, biophysical methods for the analysis of intrinsically disordered proteins will be discussed, as well as the unique challenges they pose in this context due to their highly dynamic nature.
Collapse
Affiliation(s)
- Frederik Lermyte
- Department of Chemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| |
Collapse
|
10
|
Allison TM, Barran P, Benesch JLP, Cianferani S, Degiacomi MT, Gabelica V, Grandori R, Marklund EG, Menneteau T, Migas LG, Politis A, Sharon M, Sobott F, Thalassinos K. Software Requirements for the Analysis and Interpretation of Native Ion Mobility Mass Spectrometry Data. Anal Chem 2020; 92:10881-10890. [PMID: 32649184 DOI: 10.1021/acs.analchem.9b05792] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The past few years have seen a dramatic increase in applications of native mass and ion mobility spectrometry, especially for the study of proteins and protein complexes. This increase has been catalyzed by the availability of commercial instrumentation capable of carrying out such analyses. As in most fields, however, the software to process the data generated from new instrumentation lags behind. Recently, a number of research groups have started addressing this by developing software, but further improvements are still required in order to realize the full potential of the data sets generated. In this perspective, we describe practical aspects as well as challenges in processing native mass spectrometry (MS) and ion mobility-MS data sets and provide a brief overview of currently available tools. We then set out our vision of future developments that would bring the community together and lead to the development of a common platform to expedite future computational developments, provide standardized processing approaches, and serve as a location for the deposition of data for this emerging field. This perspective has been written by members of the European Cooperation in Science and Technology Action on Native MS and Related Methods for Structural Biology (EU COST Action BM1403) as an introduction to the software tools available in this area. It is intended to serve as an overview for newcomers and to stimulate discussions in the community on further developments in this field, rather than being an in-depth review. Our complementary perspective (http://dx.doi.org/10.1021/acs.analchem.9b05791) focuses on computational approaches used in this field.
Collapse
Affiliation(s)
- Timothy M Allison
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Justin L P Benesch
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Matteo T Degiacomi
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom.,Department of Physics, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Valerie Gabelica
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site, 2 Rue Robert Escarpit, 33600 Pessac, France
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Thomas Menneteau
- Division of Biosciences, Institute of Structural and Molecular Biology, University College of London, Gower Street, London WC1E 6BT, United Kingdom
| | - Lukasz G Migas
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium.,School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Konstantinos Thalassinos
- Division of Biosciences, Institute of Structural and Molecular Biology, University College of London, Gower Street, London WC1E 6BT, United Kingdom.,Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, Malet Street, London WC1E 7HX, United Kingdom
| |
Collapse
|
11
|
Österlund N, Lundqvist M, Ilag LL, Gräslund A, Emanuelsson C. Amyloid-β oligomers are captured by the DNAJB6 chaperone: Direct detection of interactions that can prevent primary nucleation. J Biol Chem 2020; 295:8135-8144. [PMID: 32350108 PMCID: PMC7294096 DOI: 10.1074/jbc.ra120.013459] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
A human molecular chaperone protein, DnaJ heat shock protein family (Hsp40) member B6 (DNAJB6), efficiently inhibits amyloid aggregation. This inhibition depends on a unique motif with conserved serine and threonine (S/T) residues that have a high capacity for hydrogen bonding. Global analysis of kinetics data has previously shown that DNAJB6 especially inhibits the primary nucleation pathways. These observations indicated that DNAJB6 achieves this remarkably effective and sub-stoichiometric inhibition by interacting not with the monomeric unfolded conformations of the amyloid-β symbol (Aβ) peptide but with aggregated species. However, these pre-nucleation oligomeric aggregates are transient and difficult to study experimentally. Here, we employed a native MS-based approach to directly detect oligomeric forms of Aβ formed in solution. We found that WT DNAJB6 considerably reduces the signals from the various forms of Aβ (1–40) oligomers, whereas a mutational DNAJB6 variant in which the S/T residues have been substituted with alanines does not. We also detected signals that appeared to represent DNAJB6 dimers and trimers to which varying amounts of Aβ are bound. These data provide direct experimental evidence that it is the oligomeric forms of Aβ that are captured by DNAJB6 in a manner which depends on the S/T residues. We conclude that, in agreement with the previously observed decrease in primary nucleation rate, strong binding of Aβ oligomers to DNAJB6 inhibits the formation of amyloid nuclei.
Collapse
Affiliation(s)
- Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Martin Lundqvist
- Department of Biochemistry and Structural Biology, Lund University, Sweden
| | - Leopold L Ilag
- Department of Materials and Environmental Chemistry, Stockholm University, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | | |
Collapse
|
12
|
Jahan I, Nayeem SM. Effect of Osmolytes on Conformational Behavior of Intrinsically Disordered Protein α-Synuclein. Biophys J 2019; 117:1922-1934. [PMID: 31699336 DOI: 10.1016/j.bpj.2019.09.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/21/2019] [Accepted: 09/30/2019] [Indexed: 11/20/2022] Open
Abstract
α-Synuclein is an intrinsically disordered protein whose function in a healthy brain is poorly understood. It is genetically and neuropathologically linked to Parkinson's disease (PD). PD is manifested after the accumulation of plaques of α-synuclein aggregates in the brain cells. Aggregates of α-synuclein are very toxic and lead to the disruption of cellular homeostasis and neuronal death. α-Synuclein can also contribute to disease propagation as it may exert noxious effects on neighboring cells. Understanding the mechanism of α-synuclein aggregation will facilitate the problem of dealing with neurodegenerative diseases in general and that of PD in particular. Here, we have used molecular dynamics simulations to investigate the behavior of α-synuclein at various temperatures and in different concentrations of urea and trimethyl amine oxide. The residue region from 61 to 95 of α-synuclein is experimentally known as amyloidogenic. In our study, we have identified some other regions, which also have the propensity to form an aggregate besides this known sequence. Urea being a denaturant interacts more with these regions of α-synuclein through hydrogen bond formation and inhibits the β-sheet formation, whereas trimethyl amine oxide itself does not interact much with the protein and stabilizes the protein by preferentially distributing water molecules on the surface of the protein.
Collapse
Affiliation(s)
- Ishrat Jahan
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Shahid M Nayeem
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
| |
Collapse
|
13
|
Depicting Conformational Ensembles of α-Synuclein by Single Molecule Force Spectroscopy and Native Mass Spectroscopy. Int J Mol Sci 2019; 20:ijms20205181. [PMID: 31635031 PMCID: PMC6829300 DOI: 10.3390/ijms20205181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022] Open
Abstract
Description of heterogeneous molecular ensembles, such as intrinsically disordered proteins, represents a challenge in structural biology and an urgent question posed by biochemistry to interpret many physiologically important, regulatory mechanisms. Single-molecule techniques can provide a unique contribution to this field. This work applies single molecule force spectroscopy to probe conformational properties of α-synuclein in solution and its conformational changes induced by ligand binding. The goal is to compare data from such an approach with those obtained by native mass spectrometry. These two orthogonal, biophysical methods are found to deliver a complex picture, in which monomeric α-synuclein in solution spontaneously populates compact and partially compacted states, which are differently stabilized by binding to aggregation inhibitors, such as dopamine and epigallocatechin-3-gallate. Analyses by circular dichroism and Fourier-transform infrared spectroscopy show that these transitions do not involve formation of secondary structure. This comparative analysis provides support to structural interpretation of charge-state distributions obtained by native mass spectrometry and helps, in turn, defining the conformational components detected by single molecule force spectroscopy.
Collapse
|
14
|
Alam P, Bousset L, Melki R, Otzen DE. α-synuclein oligomers and fibrils: a spectrum of species, a spectrum of toxicities. J Neurochem 2019; 150:522-534. [PMID: 31254394 DOI: 10.1111/jnc.14808] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/05/2019] [Accepted: 06/21/2019] [Indexed: 12/14/2022]
Abstract
This review article provides an overview of the different species that α-synuclein aggregates can populate. It also attempts to reconcile conflicting views regarding the cytotoxic roles of oligomers versus fibrils. α-synuclein, while highly dynamic in the monomeric state, can access a large number of different assembly states. Depending on assembly conditions, these states can interconvert over different timescales. The fibrillar state is the most thermodynamically favored due to the many stabilizing interactions formed between each monomeric unit, but different fibrillar types form at different rates. The end distribution is likely to reflect kinetic partitioning as much as thermodynamic equilibra. In addition, metastable oligomeric species, some of which are on-pathway and others off-pathway, can be populated for remarkably long periods of time. Chemical modifications (phosphorylation, oxidation, covalent links to ligands, etc.) perturb these physical interconversions and invariably destabilize the fibrillar state, leading to small prefibrillar assemblies which can coalesce into amorphous states. Both oligomeric and fibrillar species have been shown to be cytotoxic although firm conclusions require very careful evaluation of particle concentrations and is complicated by the great variety and heterogeneity of different experimentally observed states. The mechanistic relationship between oligomers and fibrils remains to be clarified, both in terms of assembly of oligomers into fibrils and potential dissolution of fibrils into oligomers. While oligomers are possibly implicated in the collapse of neuronal homeostasis, the fibrillar state(s) appears to be the most efficient at propagating itself both in vitro and in vivo, pointing to critical roles for multiple different aggregate species in the progression of Parkinson's disease (https://onlinelibrary.wiley.com/page/journal/14714159/homepage/virtual_issues.htm). This article is part of the Special Issue "Synuclein".
Collapse
Affiliation(s)
- Parvez Alam
- iNANO and Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Luc Bousset
- Institute Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-Aux-Roses cedex, France
| | - Ronald Melki
- Institute Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-Aux-Roses cedex, France
| | - Daniel E Otzen
- iNANO and Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| |
Collapse
|
15
|
Xu M, Loa-Kum-Cheung W, Zhang H, Quinn RJ, Mellick GD. Identification of a New α-Synuclein Aggregation Inhibitor via Mass Spectrometry Based Screening. ACS Chem Neurosci 2019; 10:2683-2691. [PMID: 31117342 DOI: 10.1021/acschemneuro.9b00092] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aggregation of disordered α-synuclein protein is pathogenically connected with Parkinson's disease. Therefore, discovering molecules that can inhibit the misfolding and aggregation of α-synuclein is an active research area in PD drug development. A key property of such required therapeutic agents is specific binding to the target protein. Mass spectrometry allows rapid detection of direct interactions between molecules and proteins and is an ideal technique for discovering specific α-synuclein binders. Here, by setting up an automated mass spectrometry-based screening system, we were able to screen over 2500 compounds and identify a new α-synuclein inhibitor, 3-[(3-methoxyphenyl)carbamoyl]-7-[( E)-2-phenylethenyl]-4,7-dihydropyrazolo [1,5- a]pyrimidine-5-carboxylic acid (compound 2). This compound not only significantly inhibits the misfolding and aggregation of α-synuclein and protects neuroblastoma cells from α-synuclein toxicity, but also has a more specific binding site compared with positive controls. Our work for the first time reports the inhibition of compound 2 on α-synuclein aggregation and also consolidates the capability of mass spectrometry to discover α-synuclein aggregation inhibitors.
Collapse
Affiliation(s)
- Mingming Xu
- Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, QLD 4111, Australia
| | - Wendy Loa-Kum-Cheung
- Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, QLD 4111, Australia
| | - Haiyan Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Ronald J. Quinn
- Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, QLD 4111, Australia
| | - George D. Mellick
- Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, QLD 4111, Australia
| |
Collapse
|
16
|
Baul U, Chakraborty D, Mugnai ML, Straub JE, Thirumalai D. Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins. J Phys Chem B 2019; 123:3462-3474. [PMID: 30913885 PMCID: PMC6920032 DOI: 10.1021/acs.jpcb.9b02575] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Intrinsically disordered proteins (IDPs) lack well-defined three-dimensional structures, thus challenging the archetypal notion of structure-function relationships. Determining the ensemble of conformations that IDPs explore under physiological conditions is the first step toward understanding their diverse cellular functions. Here, we quantitatively characterize the structural features of IDPs as a function of sequence and length using coarse-grained simulations. For diverse IDP sequences, with the number of residues ( NT) ranging from 20 to 441, our simulations not only reproduce the radii of gyration ( Rg) obtained from experiments, but also predict the full scattering intensity profiles in excellent agreement with small-angle X-ray scattering experiments. The Rg values are well-described by the standard Flory scaling law, Rg = Rg0 NTν, with ν ≈ 0.588, making it tempting to assert that IDPs behave as polymers in a good solvent. However, clustering analysis reveals that the menagerie of structures explored by IDPs is diverse, with the extent of heterogeneity being highly sequence-dependent, even though ensemble-averaged properties, such as the dependence of Rg on chain length, may suggest synthetic polymer-like behavior in a good solvent. For example, we show that for the highly charged Prothymosin-α, a substantial fraction of conformations is highly compact. Even if the sequence compositions are similar, as is the case for α-Synuclein and a truncated construct from the Tau protein, there are substantial differences in the conformational heterogeneity. Taken together, these observations imply that metrics based on net charge or related quantities alone cannot be used to anticipate the phases of IDPs, either in isolation or in complex with partner IDPs or RNA. Our work sets the stage for probing the interactions of IDPs with each other, with folded protein domains, or with partner RNAs, which are critical for describing the structures of stress granules and biomolecular condensates with important cellular functions.
Collapse
Affiliation(s)
- Upayan Baul
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Mauro L. Mugnai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - D. Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
17
|
Carija A, Pinheiro F, Pujols J, Brás IC, Lázaro DF, Santambrogio C, Grandori R, Outeiro TF, Navarro S, Ventura S. Biasing the native α-synuclein conformational ensemble towards compact states abolishes aggregation and neurotoxicity. Redox Biol 2019; 22:101135. [PMID: 30769283 PMCID: PMC6375061 DOI: 10.1016/j.redox.2019.101135] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/18/2018] [Accepted: 02/04/2019] [Indexed: 01/07/2023] Open
Abstract
The aggregation of α-synuclein (α-syn) into amyloid fibrils is a major pathological hallmark of Parkinson's disease (PD) and other synucleinopathies. The mechanisms underlying the structural transition of soluble and innocuous α-syn to aggregated neurotoxic forms remains largely unknown. The disordered nature of α-syn has hampered the use of structure-based protein engineering approaches to elucidate the molecular determinants of this transition. The recent 3D structure of a pathogenic α-syn fibril provides a template for this kind of studies. The structure supports the NAC domain being a critical element in fibril formation, since it constitutes the core of the fibril, delineating a Greek-key motif. Here, we stapled the ends of this motif with a designed disulfide bond and evaluated its impact on the conformation, aggregation and toxicity of α-syn in different environments. The new covalent link biases the native structural ensemble of α-syn toward compact conformations, reducing the population of fully unfolded species. This conformational bias results in a strongly reduced fibril formation propensity both in the absence and in the presence of lipids and impedes the formation of neurotoxic oligomers. Our study does not support the Greek-key motif being already imprinted in early α-syn assemblies, discarding it as a druggable interface to prevent the initiation of fibrillation. In contrast, it suggests the stabilization of native, compact ensembles as a potential therapeutic strategy to avoid the formation of toxic species and to target the early stages of PD.
Collapse
Affiliation(s)
- Anita Carija
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Francisca Pinheiro
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jordi Pujols
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Inês C Brás
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medicine Göttingen, Waldweg 33, 37073 Göttingen, Germany
| | - Diana Fernandes Lázaro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medicine Göttingen, Waldweg 33, 37073 Göttingen, Germany
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medicine Göttingen, Waldweg 33, 37073 Göttingen, Germany; Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany; Institute of Neuroscience, The Medical School, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH, UK
| | - Susanna Navarro
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| |
Collapse
|
18
|
Theisen A, Black R, Corinti D, Brown JM, Bellina B, Barran PE. Initial Protein Unfolding Events in Ubiquitin, Cytochrome c and Myoglobin Are Revealed with the Use of 213 nm UVPD Coupled to IM-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:24-33. [PMID: 29949061 PMCID: PMC6318241 DOI: 10.1007/s13361-018-1992-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 05/11/2023]
Abstract
The initial stages of protein unfolding may reflect the stability of the entire fold and can also reveal which parts of a protein can be perturbed, without restructuring the rest. In this work, we couple UVPD with activated ion mobility mass spectrometry to measure how three model proteins start to unfold. Ubiquitin, cytochrome c and myoglobin ions produced via nESI from salty solutions are subjected to UV irradiation pre-mobility separation; experiments are conducted with a range of source conditions which alter the conformation of the precursor ion as shown by the drift time profiles. For all three proteins, the compact structures result in less fragmentation than more extended structures which emerge following progressive in-source activation. Cleavage sites are found to differ between conformational ensembles, for example, for the dominant charge state of cytochrome c [M + 7H]7+, cleavage at Phe10, Thr19 and Val20 was only observed in activating conditions whilst cleavage at Ala43 is dramatically enhanced. Mapping the photo-cleaved fragments onto crystallographic structures provides insight into the local structural changes that occur as protein unfolding progresses, which is coupled to global restructuring observed in the drift time profiles. Graphical Abstract.
Collapse
Affiliation(s)
- Alina Theisen
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Rachelle Black
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", 00185, Rome, Italy
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| |
Collapse
|
19
|
Saikusa K, Osakabe A, Kato D, Fuchigami S, Nagadoi A, Nishimura Y, Kurumizaka H, Akashi S. Structural Diversity of Nucleosomes Characterized by Native Mass Spectrometry. Anal Chem 2018; 90:8217-8226. [PMID: 29860831 DOI: 10.1021/acs.analchem.8b01649] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Histone tails, which protrude from nucleosome core particles (NCPs), play crucial roles in the regulation of DNA transcription, replication, and repair. In this study, structural diversity of nucleosomes was investigated in detail by analyzing the observed charge states of nucleosomes reconstituted with various lengths of DNA using positive-mode electrospray ionization mass spectrometry (ESI-MS) and molecular dynamics (MD) simulation. Here, we show that canonical NCPs, having 147 bp DNA closely wrapped around a histone octamer, can be classified into three groups by charge state, with the least-charged group being more populated than the highly charged and intermediate groups. Ions with low charge showed small collision cross sections (CCSs), suggesting that the histone tails are generally compact in the gas phase, whereas the minor populations with higher charges appeared to have more loosened structure. Overlapping dinucleosomes, which contain 14 histone proteins closely packed with 250 bp DNA, showed similar characteristics. In contrast, mononucleosomes reconstituted with a histone octamer and longer DNA (≥250 bp), which have DNA regions uninvolved in the core-structure formation, showed only low-charge ions. This was also true for dinucleosomes with free DNA regions. These results suggest that free DNA regions affect the nucleosome structures. To investigate the possible structures of NCP observed in ESI-MS, computational structural calculations in solution and in vacuo were performed. They suggested that conformers with large CCS values have slightly loosened structure with extended tail regions, which might relate to the biological function of histone tails.
Collapse
Affiliation(s)
- Kazumi Saikusa
- Graduate School of Medical Life Science , Yokohama City University , 1-7-29 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan.,Graduate School of Science , Hiroshima University , 1-3-1 Kagamiyama , Higashi-Hiroshima , Hiroshima 739-8526 , Japan
| | - Akihisa Osakabe
- Graduate School of Advanced Science and Engineering , Waseda University , 2-2 Wakamatsu-cho , Shinjuku-ku, Tokyo 162-8480 , Japan
| | - Daiki Kato
- Graduate School of Advanced Science and Engineering , Waseda University , 2-2 Wakamatsu-cho , Shinjuku-ku, Tokyo 162-8480 , Japan
| | - Sotaro Fuchigami
- Graduate School of Medical Life Science , Yokohama City University , 1-7-29 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| | - Aritaka Nagadoi
- Graduate School of Medical Life Science , Yokohama City University , 1-7-29 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science , Yokohama City University , 1-7-29 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science and Engineering , Waseda University , 2-2 Wakamatsu-cho , Shinjuku-ku, Tokyo 162-8480 , Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science , Yokohama City University , 1-7-29 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| |
Collapse
|
20
|
Morrison LJ, Chai W, Rosenberg JA, Henkelman G, Brodbelt JS. Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry. Phys Chem Chem Phys 2018; 19:20057-20074. [PMID: 28722742 DOI: 10.1039/c7cp04073c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.
Collapse
|
21
|
Kumar H, Singh J, Kumari P, Udgaonkar JB. Modulation of the extent of structural heterogeneity in α-synuclein fibrils by the small molecule thioflavin T. J Biol Chem 2017; 292:16891-16903. [PMID: 28760825 DOI: 10.1074/jbc.m117.795617] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/15/2017] [Indexed: 12/18/2022] Open
Abstract
The transition of intrinsically disordered, monomeric α-synuclein into β-sheet-rich oligomers and fibrils is associated with multiple neurodegenerative diseases. Fibrillar aggregates possessing distinct structures that differ in toxicity have been observed in different pathological phenotypes. Understanding the mechanism of the formation of various fibril polymorphs with differing cytotoxic effects is essential for determining how the aggregation reaction could be modulated to favor nontoxic fibrils over toxic fibrils. In this study, two morphologically different α-synuclein fibrils, one helical and the other ribbon-like, are shown to form together. Surprisingly, a widely used small molecule for probing aggregation reactions, thioflavin T (ThT), was found to tune the structural heterogeneity found in the fibrils. The ribbon-like fibrils formed in the presence of ThT were found to have a longer structural core than the helical fibrils formed in the absence of ThT. The ribbon-like fibrils are also more toxic to cells. By facilitating the formation of ribbon-like fibrils over helical fibrils, ThT reduced the extent of fibril polymorphism. This study highlights the role of a small molecule such as ThT in selectively favoring the formation of a specific type of fibril by binding to aggregates formed early on one of multiple pathways, thereby altering the structural core and external morphology of the fibrils formed.
Collapse
Affiliation(s)
- Harish Kumar
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jogender Singh
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,the Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, and
| | - Pratibha Kumari
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,the Laboratory of Physical Chemistry, Hönggerberg Campus, ETH Zurich, 8093 Zurich, Switzerland
| | - Jayant B Udgaonkar
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India,
| |
Collapse
|
22
|
Natalello A, Santambrogio C, Grandori R. Are Charge-State Distributions a Reliable Tool Describing Molecular Ensembles of Intrinsically Disordered Proteins by Native MS? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:21-28. [PMID: 27730522 DOI: 10.1007/s13361-016-1490-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/13/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution. However, structural rearrangements during electrospray-ionization (ESI) or after the transfer to the gas phase could affect data obtained by native ESI-MS. In particular, charge-state distributions (CSDs) are affected by protein conformation inside ESI droplets, while ion mobility (IM) reflects protein conformation in the gas phase. This review focuses on the available evidence relating IDP solution ensembles with CSDs, trying to summarize cases of apparent consistency or discrepancy. The protein-specificity of ionization patterns and their responses to ligands and buffer conditions suggests that CSDs are imprinted to protein structural features also in the case of IDPs. Nevertheless, it seems that these proteins are more easily affected by electrospray conditions, leading in some cases to rearrangements of the conformational ensembles. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
| |
Collapse
|
23
|
Mason RJ, Paskins AR, Dalton CF, Smith DP. Copper Binding and Subsequent Aggregation of α-Synuclein Are Modulated by N-Terminal Acetylation and Ablated by the H50Q Missense Mutation. Biochemistry 2016; 55:4737-41. [PMID: 27517125 DOI: 10.1021/acs.biochem.6b00708] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Parkinson's disease-associated protein α-synuclein exhibits significant conformational heterogeneity. Bacterially expressed α-synuclein is known to bind to copper, resulting in the formation of aggregation-prone compact conformations. However, in vivo, α-synuclein undergoes acetylation at its N-terminus. Here the effect of this modification and the pathological H50Q mutation on copper binding and subsequent conformational transitions were investigated by electrospray ionization-ion mobility spectrometry-mass spectrometry. We demonstrate that acetylation perturbs the ability of α-synuclein to bind copper and that the H50Q missense mutation in the presence of N-terminal acetylation prevents copper binding. These modifications and mutations prevent the formation of the most compact conformations and inhibit copper-induced aggregation.
Collapse
Affiliation(s)
- Rebecca J Mason
- Biomolecular Sciences Research Centre, Sheffield Hallam University , Sheffield S1 1WB, U.K
| | - Aimee R Paskins
- Biomolecular Sciences Research Centre, Sheffield Hallam University , Sheffield S1 1WB, U.K
| | - Caroline F Dalton
- Biomolecular Sciences Research Centre, Sheffield Hallam University , Sheffield S1 1WB, U.K
| | - David P Smith
- Biomolecular Sciences Research Centre, Sheffield Hallam University , Sheffield S1 1WB, U.K
| |
Collapse
|
24
|
Konijnenberg A, Ranica S, Narkiewicz J, Legname G, Grandori R, Sobott F, Natalello A. Opposite Structural Effects of Epigallocatechin-3-gallate and Dopamine Binding to α-Synuclein. Anal Chem 2016; 88:8468-75. [PMID: 27467405 DOI: 10.1021/acs.analchem.6b00731] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The intrinsically disordered and amyloidogenic protein α-synuclein (AS) has been linked to several neurodegenerative states, including Parkinson's disease. Here, nanoelectrospray-ionization mass spectrometry (nano-ESI-MS), ion mobility (IM), and native top-down electron transfer dissociation (ETD) techniques are employed to study AS interaction with small molecules known to modulate its aggregation, such as epigallocatechin-3-gallate (EGCG) and dopamine (DA). The complexes formed by the two ligands under identical conditions reveal peculiar differences. While EGCG engages AS in compact conformations, DA preferentially binds to the protein in partially extended conformations. The two ligands also have different effects on AS structure as assessed by IM, with EGCG leading to protein compaction and DA to its extension. Native top-down ETD on the protein-ligand complexes shows how the different observed modes of binding of the two ligands could be related to their known opposite effects on AS aggregation. The results also show that the protein can bind either ligand in the absence of any covalent modifications, such as oxidation.
Collapse
Affiliation(s)
- Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry, University of Antwerp , Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Simona Ranica
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Joanna Narkiewicz
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA) and ELETTRA-Sincrotrone Trieste S.C.p.A , 34136 Trieste, Italy
| | - Giuseppe Legname
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA) and ELETTRA-Sincrotrone Trieste S.C.p.A , 34136 Trieste, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, University of Antwerp , Groenenborgerlaan 171, 2020 Antwerp, Belgium.,Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds, LS2 9JT, U.K.,School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy.,Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR of Milano-Bicocca, and Milan Center of Neuroscience (NeuroMI), 20126 Milan, Italy
| |
Collapse
|
25
|
Yu H, Han W, Ma W, Schulten K. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation. J Chem Phys 2015; 143:243142. [PMID: 26723627 PMCID: PMC4684271 DOI: 10.1063/1.4936910] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/18/2015] [Indexed: 12/18/2022] Open
Abstract
Parkinson's disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and (3)J(HNHCα )-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.
Collapse
Affiliation(s)
- Hang Yu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wei Han
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wen Ma
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
26
|
Borysik AJ, Kovacs D, Guharoy M, Tompa P. Ensemble Methods Enable a New Definition for the Solution to Gas-Phase Transfer of Intrinsically Disordered Proteins. J Am Chem Soc 2015; 137:13807-17. [DOI: 10.1021/jacs.5b06027] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Antoni J. Borysik
- King’s College London, Department of Chemistry,
Britannia House, 7 Trinity
Street, London SE1 1DB, U.K
| | - Denes Kovacs
- VIB
Structural Biology Research Centre (SBRC), Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Mainak Guharoy
- VIB
Structural Biology Research Centre (SBRC), Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Peter Tompa
- VIB
Structural Biology Research Centre (SBRC), Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
- Institute
of Enzymology, Research Centre for Natural Sciences of
the Hungarian Academy of Sciences, 1117 Budapest, Hungary
| |
Collapse
|
27
|
van Maarschalkerweerd A, Pedersen MN, Peterson H, Nilsson M, Nguyen T, Skamris T, Rand K, Vetri V, Langkilde AE, Vestergaard B. Formation of covalent di-tyrosine dimers in recombinant α-synuclein. INTRINSICALLY DISORDERED PROTEINS 2015; 3:e1071302. [PMID: 28232892 PMCID: PMC5314896 DOI: 10.1080/21690707.2015.1071302] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/02/2015] [Accepted: 07/02/2015] [Indexed: 11/02/2022]
Abstract
Parkinson's disease is associated with fibril deposition in the diseased brain. Misfolding events of the intrinsically disordered synaptic protein α-synuclein are suggested to lead to the formation of transient oligomeric and cytotoxic species. The etiology of Parkinson's disease is further associated with mitochondrial dysfunction and formation of reactive oxygen species. Oxidative stress causes chemical modification of native α-synuclein, plausibly further influencing misfolding events. Here, we present evidence for the spontaneous formation of covalent di-tyrosine α-synuclein dimers in standard recombinant protein preparations, induced without extrinsic oxidative or nitrative agents. The dimers exhibit no secondary structure but advanced SAXS studies reveal an increased structural definition, resulting in a more hydrophobic micro-environment than the highly disordered monomer. Accordingly, monomers and dimers follow distinct fibrillation pathways.
Collapse
Affiliation(s)
| | - M N Pedersen
- Department of Drug Design and Pharmacology; University of Copenhagen ; Copenhagen, Denmark
| | - H Peterson
- Department of Drug Design and Pharmacology; University of Copenhagen ; Copenhagen, Denmark
| | - M Nilsson
- Department of Drug Design and Pharmacology; University of Copenhagen ; Copenhagen, Denmark
| | - Ttt Nguyen
- Department of Pharmacy; University of Copenhagen ; Copenhagen, Denmark
| | - T Skamris
- Department of Drug Design and Pharmacology; University of Copenhagen ; Copenhagen, Denmark
| | - K Rand
- Department of Pharmacy; University of Copenhagen ; Copenhagen, Denmark
| | - V Vetri
- Dipartimento di Fisica e Chimica; Universitá di Palermo ; Palermo, Italy
| | - A E Langkilde
- Department of Drug Design and Pharmacology; University of Copenhagen ; Copenhagen, Denmark
| | - B Vestergaard
- Department of Drug Design and Pharmacology; University of Copenhagen ; Copenhagen, Denmark
| |
Collapse
|
28
|
Beveridge R, Phillips AS, Denbigh L, Saleem HM, MacPhee CE, Barran PE. Relating gas phase to solution conformations: Lessons from disordered proteins. Proteomics 2015; 15:2872-83. [PMID: 25920945 PMCID: PMC4744708 DOI: 10.1002/pmic.201400605] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/18/2015] [Accepted: 04/24/2015] [Indexed: 01/23/2023]
Abstract
In recent years both mass spectrometry (MS) and ion mobility mass spectrometry (IM‐MS) have been developed as techniques with which to study proteins that lack a fixed tertiary structure but may contain regions that form secondary structure elements transiently, namely intrinsically disordered proteins (IDPs). IM‐MS is a suitable method for the study of IDPs which provides an insight to conformations that are present in solution, potentially enabling the analysis of lowly populated structural forms. Here, we describe the IM‐MS data of two IDPs; α‐Synuclein (α‐Syn) which is implicated in Parkinson's disease, and Apolipoprotein C‐II (ApoC‐II) which is involved in cardiovascular diseases. We report an apparent discrepancy in the way that ApoC‐II behaves in the gas phase. While most IDPs, including α‐Syn, present in many charge states and a wide range of rotationally averaged collision cross sections (CCSs), ApoC‐II presents in just four charge states and a very narrow range of CCSs, independent of solution conditions. Here, we compare MS and IM‐MS data of both proteins, and rationalise the differences between the proteins in terms of different ionisation processes which they may adhere to.
Collapse
Affiliation(s)
- Rebecca Beveridge
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | - Ashley S Phillips
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | | | - Hassan M Saleem
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | - Cait E MacPhee
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Perdita E Barran
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| |
Collapse
|
29
|
Sitkiewicz E, Olędzki J, Poznański J, Dadlez M. Di-tyrosine cross-link decreases the collisional cross-section of aβ peptide dimers and trimers in the gas phase: an ion mobility study. PLoS One 2014; 9:e100200. [PMID: 24945725 PMCID: PMC4063900 DOI: 10.1371/journal.pone.0100200] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/22/2014] [Indexed: 01/04/2023] Open
Abstract
Oligomeric forms of Aβ peptide are most likely the main synaptotoxic and neurotoxic agent in Alzheimer’s disease. Toxicity of various Aβ oligomeric forms has been confirmed in vivo and also in vitro. However, in vitro preparations were found to be orders of magnitude less toxic than oligomers obtained from in vivo sources. This difference can be explained by the presence of a covalent cross-link, which would stabilize the oligomer. In the present work, we have characterized the structural properties of Aβ dimers and trimers stabilized by di- and tri-tyrosine cross-links. Using ion mobility mass spectrometry we have compared the collisional cross-section of non-cross-linked and cross-linked species. We have found that the presence of cross-links does not generate new unique forms but rather shifts the equilibrium towards more compact oligomer types that can also be detected for non-cross-linked peptide. In consequence, more extended forms, probable precursors of off-pathway oligomeric species, become relatively destabilized in cross-linked oligomers and the pathway of oligomer evolution becomes redirected towards fibrillar structures.
Collapse
Affiliation(s)
- Ewa Sitkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Warszawa, Poland
| | - Jacek Olędzki
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Warszawa, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Warszawa, Poland
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Warszawa, Poland
- Institute of Genetics and Biotechnology, Biology Department, Warsaw University, Warszawa, Poland
- * E-mail:
| |
Collapse
|
30
|
The role of initial oligomers in amyloid fibril formation by human stefin B. Int J Mol Sci 2013; 14:18362-84. [PMID: 24013380 PMCID: PMC3794784 DOI: 10.3390/ijms140918362] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 08/21/2013] [Accepted: 08/22/2013] [Indexed: 02/03/2023] Open
Abstract
Oligomers are commonly observed intermediates at the initial stages of amyloid fibril formation. They are toxic to neurons and cause decrease in neural transmission and long-term potentiation. We describe an in vitro study of the initial steps in amyloid fibril formation by human stefin B, which proved to be a good model system. Due to relative stability of the initial oligomers of stefin B, electrospray ionization mass spectrometry (ESI MS) could be applied in addition to size exclusion chromatography (SEC). These two techniques enabled us to separate and detect distinguished oligomers from the monomers: dimers, trimers, tetramers, up to decamers. The amyloid fibril formation process was followed at different pH and temperatures, including such conditions where the process was slow enough to detect the initial oligomeric species at the very beginning of the lag phase and those at the end of the lag phase. Taking into account the results of the lower-order oligomers transformations early in the process, we were able to propose an improved model for the stefin B fibril formation.
Collapse
|
31
|
Illes-Toth E, Dalton CF, Smith DP. Binding of Dopamine to Alpha-Synuclein is Mediated by Specific Conformational States. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1346-54. [PMID: 23817832 PMCID: PMC3738842 DOI: 10.1007/s13361-013-0676-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 05/11/2023]
Abstract
Parkinson's disease is the second most common neurodegenerative disorder, in which both alpha-synuclein (α-syn) and dopamine (DA) have a critical role. α-Syn is known to be natively unstructured in equilibrium with subpopulations of more compact structures. It is these compact structures that are thought to be linked to amyloid formation. In the presence of DA, α-syn yields a diverse range of SDS-resistant, non-amyloid oligomers, however the precursor state conformation has not been established. Here, three DA molecules have been observed to bind per α-syn monomer by electrospray-ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS). Each of these DA molecules binds exclusively to the extended conformation of α-syn, and binding is not observed in the compact state of the protein. Measurements of collisional cross sectional areas show that the incremental uptake of DA pushes the protein towards a highly extended population, becoming fully populated upon the binding of three DA ligands. Tyrosine (Tyr) as a closely related structural analog, exhibited limited binding to the protein as compared with DA, with a maximum of two ligands being observed. Those Tyr ligands that do bind were observed as adducts to the extended conformation akin to DA. These findings suggest DA is able to modulate α-syn self-assembly by inducing the population of a highly extended state.
Collapse
Affiliation(s)
- Eva Illes-Toth
- Biomedical Research Centre, Sheffield Hallam University, Sheffield, S1 1WB United Kingdom
| | - Caroline F. Dalton
- Biomedical Research Centre, Sheffield Hallam University, Sheffield, S1 1WB United Kingdom
| | - David P. Smith
- Biomedical Research Centre, Sheffield Hallam University, Sheffield, S1 1WB United Kingdom
| |
Collapse
|
32
|
Scarff CA, Sicorello A, Tomé RJ, Macedo-Ribeiro S, Ashcroft AE, Radford SE. A tale of a tail: Structural insights into the conformational properties of the polyglutamine protein ataxin-3. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2013; 345-347:63-70. [PMID: 25844046 PMCID: PMC4375668 DOI: 10.1016/j.ijms.2012.08.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 05/24/2023]
Abstract
Ataxin-3 is the protein responsible for the neurodegenerative polyglutamine disease Spinocerebellar ataxia type 3. Full structural characterisation of ataxin-3 is required to aid in understanding the mechanism of disease. Despite extensive study, little is known about the conformational properties of the full-length protein, in either its non-expanded healthy or expanded pathogenic forms, particularly since its polyglutamine-containing region has denied structural elucidation. In this work, travelling-wave ion mobility spectrometry-mass spectrometry and limited proteolysis have been used to compare the conformational properties of full-length non-expanded ataxin-3 (14Q) and its isolated N-terminal Josephin domain (JD). Limited proteolysis experiments have confirmed that the JD is stable, being extremely resistant to trypsin digestion, with the exception of the α2/α3 hairpin which is flexible and exposed to protease cleavage in solution. The C-terminal region of ataxin-3 which contains the glutamine-rich sequences is largely unstructured, showing little resistance to limited proteolysis. Using ion mobility spectrometry-mass spectrometry we show that ataxin-3 (14Q) adopts a wide range of conformational states in vitro conferred by the flexibility of its C-terminal tail and the α2/α3 hairpin of the N-terminal JD. This study highlights how the power of MS-based approaches to protein structural characterisation can be particularly useful when the target protein is aggregation-prone and has intrinsically unordered regions.
Collapse
Affiliation(s)
- Charlotte A. Scarff
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Alessandro Sicorello
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Ricardo J.L. Tomé
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| |
Collapse
|
33
|
Woods L, Radford S, Ashcroft A. Advances in ion mobility spectrometry-mass spectrometry reveal key insights into amyloid assembly. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1834:1257-68. [PMID: 23063533 PMCID: PMC3787735 DOI: 10.1016/j.bbapap.2012.10.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/27/2012] [Accepted: 10/02/2012] [Indexed: 10/28/2022]
Abstract
Interfacing ion mobility spectrometry to mass spectrometry (IMS-MS) has enabled mass spectrometric analyses to extend into an extra dimension, providing unrivalled separation and structural characterization of lowly populated species in heterogeneous mixtures. One biological system that has benefitted significantly from such advances is that of amyloid formation. Using IMS-MS, progress has been made into identifying transiently populated monomeric and oligomeric species for a number of different amyloid systems and has led to an enhanced understanding of the mechanism by which small molecules modulate amyloid formation. This review highlights recent advances in this field, which have been accelerated by the commercial availability of IMS-MS instruments. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.
Collapse
Affiliation(s)
| | - S.E. Radford
- Astbury Centre for Structural Molecular Biology & School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - A.E. Ashcroft
- Astbury Centre for Structural Molecular Biology & School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| |
Collapse
|
34
|
Testa L, Brocca S, Santambrogio C, D'Urzo A, Habchi J, Longhi S, Uversky VN, Grandori R. Extracting structural information from charge-state distributions of intrinsically disordered proteins by non-denaturing electrospray-ionization mass spectrometry. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25068. [PMID: 28516012 PMCID: PMC5424789 DOI: 10.4161/idp.25068] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/02/2013] [Accepted: 05/16/2013] [Indexed: 11/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) exert key biological functions but tend to escape identification and characterization due to their high structural dynamics and heterogeneity. The possibility to dissect conformational ensembles by electrospray-ionization mass spectrometry (ESI-MS) offers an attracting possibility to develop a signature for this class of proteins based on their peculiar ionization behavior. This review summarizes available data on charge-state distributions (CSDs) obtained for IDPs by non-denaturing ESI-MS, with reference to globular or chemically denatured proteins. The results illustrate the contributions that direct ESI-MS analysis can give to the identification of new putative IDPs and to their conformational investigation.
Collapse
Affiliation(s)
- Lorenzo Testa
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Annalisa D'Urzo
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Johnny Habchi
- Aix-Marseille Université; CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB); Marseille, France
| | - Sonia Longhi
- Aix-Marseille Université; CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB); Marseille, France
| | - Vladimir N Uversky
- Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
| | - Rita Grandori
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| |
Collapse
|
35
|
Kaltashov IA, Bobst CE, Abzalimov RR. Mass spectrometry-based methods to study protein architecture and dynamics. Protein Sci 2013; 22:530-44. [PMID: 23436701 DOI: 10.1002/pro.2238] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 02/11/2013] [Accepted: 02/13/2013] [Indexed: 11/09/2022]
Abstract
Mass spectrometry is now an indispensable tool in the armamentarium of molecular biophysics, where it is used for tasks ranging from protein sequencing and mapping of post-translational modifications to studies of higher order structure, conformational dynamics, and interactions of proteins with small molecule ligands and other biopolymers. This mini-review highlights several popular mass spectrometry-based tools that are now commonly used for structural studies of proteins beyond their covalent structure with a particular emphasis on hydrogen exchange and direct electrospray ionization mass spectrometry.
Collapse
Affiliation(s)
- Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA.
| | | | | |
Collapse
|
36
|
Exploring the accessible conformations of N-terminal acetylated α-synuclein. FEBS Lett 2013; 587:1128-38. [PMID: 23499431 DOI: 10.1016/j.febslet.2013.02.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 02/28/2013] [Accepted: 02/28/2013] [Indexed: 11/21/2022]
Abstract
Alpha synuclein (αsyn) fibrils are found in the Lewy Bodies of patients with Parkinson's disease (PD). The aggregation of the αsyn monomer to soluble oligomers and insoluble fibril aggregates is believed to be one of the causes of PD. Recently, the view of the native state of αsyn as a monomeric ensemble was challenged by a report suggesting that αsyn exists in its native state as a helical tetramer. This review reports on our current understanding of αsyn within the context of these recent developments and describes the work performed by a number of groups to address the monomer/tetramer debate. A number of in depth studies have subsequently shown that both non-acetylated and acetylated αsyn purified under mild conditions are primarily monomer. A description of the accessible states of acetylated αsyn monomer and the ability of αsyn to self-associate is explored.
Collapse
|
37
|
Kang L, Moriarty GM, Woods LA, Ashcroft AE, Radford SE, Baum J. N-terminal acetylation of α-synuclein induces increased transient helical propensity and decreased aggregation rates in the intrinsically disordered monomer. Protein Sci 2012; 21:911-7. [PMID: 22573613 DOI: 10.1002/pro.2088] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 04/27/2012] [Indexed: 12/23/2022]
Abstract
The conformational properties of soluble α-synuclein, the primary protein found in patients with Parkinson's disease, are thought to play a key role in the structural transition to amyloid fibrils. In this work, we report that recombinant 100% N-terminal acetylated α-synuclein purified under mild physiological conditions presents as a primarily monomeric protein, and that the N-terminal acetyl group affects the transient secondary structure and fibril assembly rates of the protein. Residue-specific NMR chemical shift analysis indicates substantial increase in transient helical propensity in the first 9 N-terminal residues, as well as smaller long-range changes in residues 28-31, 43-46, and 50-66: regions in which the three familial mutations currently known to be causative of early onset disease are found. In addition, we show that the N-terminal acetylated protein forms fibrils that are morphologically similar to those formed from nonacetylated α-synuclein, but that their growth rates are slower. Our results highlight that N-terminal acetylation does not form significant numbers of dimers, tetramers, or higher molecular weight species, but does alter the conformational distributions of monomeric α-synuclein species in regions known to be important in metal binding, in association with membranes, and in regions known to affect fibril formation rates.
Collapse
Affiliation(s)
- Lijuan Kang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | | | | | | | | | | |
Collapse
|
38
|
Wilderman PR, Halpert JR. Plasticity of CYP2B enzymes: structural and solution biophysical methods. Curr Drug Metab 2012; 13:167-76. [PMID: 22208531 DOI: 10.2174/138920012798918417] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 06/21/2011] [Accepted: 06/22/2011] [Indexed: 01/05/2023]
Abstract
In the past three years, major advances in understanding cytochrome P450 2B (CYP2B) structure-function relationships have been made through determination of multiple ligand-bound and one ligand-free X-ray crystal structure of CYP2B4 and one ligand-bound X-ray crystal structure of CYP2B6. These structures have provided insight into the features that provide the high degree of plasticity of the enzymes. A combination of a phenylalanine cluster that allows for concerted movement of helices F through G and a conserved set of electrostatic interactions involving Arg(262) facilitates movement of this region to accommodate binding of ligands of various sizes without perturbing most of the P450 fold. Integrating solution based techniques such as NMR or deuterium exchange mass spectrometry (DXMS) with computational methods including molecular docking has provided further insight into enzyme behavior upon ligand binding. In addition, extended molecular dynamics simulations have provided a link between an open and a closed conformation of ligand-free CYP2B4 found in crystal structures. Other studies revealed the utility of rational engineering in improving stability of P450s to facilitate structural studies. The solution and computational results combined with the X-ray crystal structures yield a comprehensive picture of how these enzymes adopt different conformations to bind various ligands.
Collapse
Affiliation(s)
- P Ross Wilderman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, 92093-0703, USA.
| | | |
Collapse
|
39
|
Sjoelund V, Kaltashov IA. Modification of the zonal elution method for detection of transient protein-protein interactions involving ligand exchange. Anal Chem 2012; 84:4608-12. [PMID: 22500549 PMCID: PMC3352988 DOI: 10.1021/ac300104d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A new affinity chromatography method was developed by modifying a zonal elution method. The new method targets transient protein-protein interactions, such as those encountered during direct ligand transfer between the ligand transporter and its cognate receptor. A ligand-loaded transport protein is immobilized on the solid support, and a plug containing a putative receptor is flowed through the column. Elution profiles of proteins not interacting with the immobilized transporter can be approximated with a simple Gaussian curve, while the elution profiles of cognate receptors show significant delay and exhibit complex shape. Ligand transfer from the immobilized transporter molecules to the receptors is verified by both UV absorbance measurements and mass spectrometry. The sensitivity of the method is demonstrated using retinoic acid (RA) transfer from various isoforms of cellular RA binding proteins (CRABPs) and RA receptor γ (RARγ). Although these interactions have been hypothesized long ago to proceed via direct mechanism (i.e., via transient docking of the receptor and the transporter), the existing biophysical techniques failed to detect the presence of the transporter-receptor complexes. However, the modified zonal elution method provides unequivocal evidence of direct interaction between RARγ and one of the CRABP isoforms (CRABP II) during the ligand transfer to the receptor.
Collapse
Affiliation(s)
- Virginie Sjoelund
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA
| |
Collapse
|
40
|
Fauerbach JA, Yushchenko DA, Shahmoradian SH, Chiu W, Jovin TM, Jares-Erijman EA. Supramolecular non-amyloid intermediates in the early stages of α-synuclein aggregation. Biophys J 2012; 102:1127-36. [PMID: 22404935 DOI: 10.1016/j.bpj.2012.01.051] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/05/2012] [Accepted: 01/26/2012] [Indexed: 10/28/2022] Open
Abstract
The aggregation of α-synuclein is associated with progression of Parkinson's disease. We have identified submicrometer supramolecular structures that mediate the early stages of the overall mechanism. The sequence of structural transformations between metastable intermediates were captured and characterized by atomic force microscopy guided by a fluorescent probe sensitive to preamyloid species. A novel ~0.3-0.6 μm molecular assembly, denoted the acuna, nucleates, expands, and liberates fibers with distinctive segmentation and a filamentous fuzzy fringe. These fuzzy fibers serve as precursors of mature amyloid fibrils. Cryo-electron tomography resolved the acuna inner structure as a scaffold of highly condensed colloidal masses interlinked by thin beaded threads, which were perceived as fuzziness by atomic force microscopy. On the basis of the combined data, we propose a sequential mechanism comprising molecular, colloidal, and fibrillar stages linked by reactions with disparate temperature dependencies and distinct supramolecular forms. We anticipate novel diagnostic and therapeutic approaches to Parkinson's and related neurodegenerative diseases based on these new insights into the aggregation mechanism of α-synuclein and intermediates, some of which may act to cause and/or reinforce neurotoxicity.
Collapse
Affiliation(s)
- Jonathan A Fauerbach
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), CIHIDECAR CONICET, Buenos Aires, Argentina
| | | | | | | | | | | |
Collapse
|
41
|
Aggregation of α-synuclein is kinetically controlled by intramolecular diffusion. Proc Natl Acad Sci U S A 2012; 109:2336-41. [PMID: 22308332 DOI: 10.1073/pnas.1109526109] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We hypothesize that the first step of aggregation of disordered proteins, such as α-synuclein, is controlled by the rate of backbone reconfiguration. When reconfiguration is fast, bimolecular association is not stable, but as reconfiguration slows, association is more stable and subsequent aggregation is faster. To investigate this hypothesis, we have measured the rate of intramolecular diffusion in α-synuclein, a protein involved in Parkinson's disease, under solvent conditions that accelerate or decelerate aggregation. Using the method of tryptophan-cysteine (Trp-Cys) quenching, the rate of intramolecular contact is measured in four different loops along the chain length. This intrinsically disordered protein is highly diffusive at low temperature at neutral pH, when aggregation is slow, and compacts and diffuses more slowly at high temperature or low pH, when aggregation is rapid. Diffusion also slows with the disease mutation A30P. This work provides unique insights into the earliest steps of α-synuclein aggregation pathway and should provide the basis for the development of drugs that can prevent aggregation at the initial stage.
Collapse
|
42
|
Ullman O, Fisher CK, Stultz CM. Explaining the structural plasticity of α-synuclein. J Am Chem Soc 2011; 133:19536-46. [PMID: 22029383 PMCID: PMC3227348 DOI: 10.1021/ja208657z] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Indexed: 01/10/2023]
Abstract
Given that α-synuclein has been implicated in the pathogenesis of several neurodegenerative disorders, deciphering the structure of this protein is of particular importance. While monomeric α-synuclein is disordered in solution, it can form aggregates rich in cross-β structure, relatively long helical segments when bound to micelles or lipid vesicles, and a relatively ordered helical tetramer within the native cell environment. To understand the physical basis underlying this structural plasticity, we generated an ensemble for monomeric α-synuclein using a Bayesian formalism that combines data from NMR chemical shifts, RDCs, and SAXS with molecular simulations. An analysis of the resulting ensemble suggests that a non-negligible fraction of the ensemble (0.08, 95% confidence interval 0.03-0.12) places the minimal toxic aggregation-prone segment in α-synuclein, NAC(8-18), in a solvent exposed and extended conformation that can form cross-β structure. Our data also suggest that a sizable fraction of structures in the ensemble (0.14, 95% confidence interval 0.04-0.23) contains long-range contacts between the N- and C-termini. Moreover, a significant fraction of structures that contain these long-range contacts also place the NAC(8-18) segment in a solvent exposed orientation, a finding in contrast to the theory that such long-range contacts help to prevent aggregation. Lastly, our data suggest that α-synuclein samples structures with amphipathic helices that can self-associate via hydrophobic contacts to form tetrameric structures. Overall, these observations represent a comprehensive view of the unfolded ensemble of monomeric α-synuclein and explain how different conformations can arise from the monomeric protein.
Collapse
Affiliation(s)
- Orly Ullman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Charles K. Fisher
- Committee on Higher Degrees in Biophysics, Harvard University Cambridge, Massachusetts 02139-4307, United States
| | - Collin M. Stultz
- Committee on Higher Degrees in Biophysics, Harvard University Cambridge, Massachusetts 02139-4307, United States
- Harvard-MIT Division of Health Sciences and Technology, Department of Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| |
Collapse
|
43
|
Clarke DJ, Murray E, Hupp T, Mackay CL, Langridge-Smith PRR. Mapping a noncovalent protein-peptide interface by top-down FTICR mass spectrometry using electron capture dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1432-40. [PMID: 21953198 DOI: 10.1007/s13361-011-0155-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 04/13/2011] [Accepted: 04/15/2011] [Indexed: 05/11/2023]
Abstract
Noncovalent protein-ligand and protein-protein complexes are readily detected using electrospray ionization mass spectrometry (ESI MS). Furthermore, recent reports have demonstrated that careful use of electron capture dissociation (ECD) fragmentation allows covalent backbone bonds of protein complexes to be dissociated without disruption of noncovalent protein-ligand interactions. In this way the site of protein-ligand interfaces can be identified. To date, protein-ligand complexes, which have proven tractable to this technique, have been mediated by ionic electrostatic interactions, i.e., ion pair interactions or salt bridging. Here we extend this methodology by applying ECD to study a protein-peptide complex that contains no electrostatics interactions. We analyzed the complex between the 21 kDa p53-inhibitor protein anterior gradient-2 and its hexapeptide binding ligand (PTTIYY). ECD fragmentation of the 1:1 complex occurs with retention of protein-peptide binding and analysis of the resulting fragments allows the binding interface to be localized to a C-terminal region between residues 109 and 175. These finding are supported by a solution-phase competition assay, which implicates the region between residues 108 and 122 within AGR2 as the PTTIYY binding interface. Our study expands previous findings by demonstrating that top-down ECD mass spectrometry can be used to determine directly the sites of peptide-protein interfaces. This highlights the growing potential of using ECD and related top-down fragmentation techniques for interrogation of protein-protein interfaces.
Collapse
Affiliation(s)
- David J Clarke
- SIRCAMS, EastChem School of Chemistry, University of Edinburgh, Edinburgh, UK
| | | | | | | | | |
Collapse
|
44
|
Abstract
Proteins provide much of the scaffolding for life, as well as undertaking a variety of essential catalytic reactions. These characteristic functions have led us to presuppose that proteins are in general functional only when well structured and correctly folded. As we begin to explore the repertoire of possible protein sequences inherent in the human and other genomes, two stark facts that belie this supposition become clear: firstly, the number of apparent open reading frames in the human genome is significantly smaller than appears to be necessary to code for all of the diverse proteins in higher organisms, and secondly that a significant proportion of the protein sequences that would be coded by the genome would not be expected to form stable three-dimensional (3D) structures. Clearly the genome must include coding for a multitude of alternative forms of proteins, some of which may be partly or fully disordered or incompletely structured in their functional states. At the same time as this likelihood was recognized, experimental studies also began to uncover examples of important protein molecules and domains that were incompletely structured or completely disordered in solution, yet remained perfectly functional. In the ensuing years, we have seen an explosion of experimental and genome-annotation studies that have mapped the extent of the intrinsic disorder phenomenon and explored the possible biological rationales for its widespread occurrence. Answers to the question 'why would a particular domain need to be unstructured?' are as varied as the systems where such domains are found. This review provides a survey of recent new directions in this field, and includes an evaluation of the role not only of intrinsically disordered proteins but also of partially structured and highly dynamic members of the disorder-order continuum.
Collapse
|
45
|
Wilderman PR, Shah MB, Liu T, Li S, Hsu S, Roberts AG, Goodlett DR, Zhang Q, Woods VL, Stout CD, Halpert JR. Plasticity of cytochrome P450 2B4 as investigated by hydrogen-deuterium exchange mass spectrometry and X-ray crystallography. J Biol Chem 2010; 285:38602-11. [PMID: 20880847 DOI: 10.1074/jbc.m110.180646] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Crystal structures of the xenobiotic metabolizing cytochrome P450 2B4 have demonstrated markedly different conformations in the presence of imidazole inhibitors or in the absence of ligand. However, knowledge of the plasticity of the enzyme in solution has remained scant. Thus, hydrogen-deuterium exchange mass spectrometry (DXMS) was utilized to probe the conformations of ligand-free P450 2B4 and the complex with 4-(4-chlorophenyl)imidazole (4-CPI) or 1-biphenyl-4-methyl-1H-imidazole (1-PBI). The results of DXMS indicate that the binding of 4-CPI slowed the hydrogen-deuterium exchange rate over the B'- and C-helices and portions of the F-G-helix cassette compared with P450 2B4 in the absence of ligands. In contrast, there was little difference between the ligand-free and 1-PBI-bound exchange sets. In addition, DXMS suggests that the ligand-free P450 2B4 is predominantly open in solution. Interestingly, a new high resolution structure of ligand-free P450 2B4 was obtained in a closed conformation very similar to the 4-CPI complex. Molecular dynamics simulations performed with the closed ligand-free structure as the starting point were used to probe the energetically accessible conformations of P450 2B4. The simulations were found to equilibrate to a conformation resembling the 1-PBI-bound P450 2B4 crystal structure. The results indicate that conformational changes observed in available crystal structures of the promiscuous xenobiotic metabolizing cytochrome P450 2B4 are consistent with its solution structural behavior.
Collapse
Affiliation(s)
- P Ross Wilderman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Uversky VN, Dunker AK. Understanding protein non-folding. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1804:1231-64. [PMID: 20117254 PMCID: PMC2882790 DOI: 10.1016/j.bbapap.2010.01.017] [Citation(s) in RCA: 895] [Impact Index Per Article: 63.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2009] [Revised: 01/09/2010] [Accepted: 01/21/2010] [Indexed: 02/07/2023]
Abstract
This review describes the family of intrinsically disordered proteins, members of which fail to form rigid 3-D structures under physiological conditions, either along their entire lengths or only in localized regions. Instead, these intriguing proteins/regions exist as dynamic ensembles within which atom positions and backbone Ramachandran angles exhibit extreme temporal fluctuations without specific equilibrium values. Many of these intrinsically disordered proteins are known to carry out important biological functions which, in fact, depend on the absence of a specific 3-D structure. The existence of such proteins does not fit the prevailing structure-function paradigm, which states that a unique 3-D structure is a prerequisite to function. Thus, the protein structure-function paradigm has to be expanded to include intrinsically disordered proteins and alternative relationships among protein sequence, structure, and function. This shift in the paradigm represents a major breakthrough for biochemistry, biophysics and molecular biology, as it opens new levels of understanding with regard to the complex life of proteins. This review will try to answer the following questions: how were intrinsically disordered proteins discovered? Why don't these proteins fold? What is so special about intrinsic disorder? What are the functional advantages of disordered proteins/regions? What is the functional repertoire of these proteins? What are the relationships between intrinsically disordered proteins and human diseases?
Collapse
Affiliation(s)
- Vladimir N Uversky
- Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | | |
Collapse
|
47
|
Nath S, Meuvis J, Hendrix J, Carl SA, Engelborghs Y. Early aggregation steps in alpha-synuclein as measured by FCS and FRET: evidence for a contagious conformational change. Biophys J 2010; 98:1302-11. [PMID: 20371330 PMCID: PMC2849099 DOI: 10.1016/j.bpj.2009.12.4290] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 12/01/2009] [Accepted: 12/02/2009] [Indexed: 11/30/2022] Open
Abstract
The kinetics of aggregation of alpha-synuclein are usually studied by turbidity or Thio-T fluorescence. Here we follow the disappearance of monomers and the formation of early oligomers using fluorescence correlation spectroscopy. Alexa488-labeled A140C-synuclein was used as a fluorescent probe in trace amounts in the presence of excess unlabeled alpha-synuclein. Repeated short measurements produce a distribution of diffusion coefficients. Initially, a sharp peak is obtained corresponding to monomers, followed by a distinct transient population and the gradual formation of broader-sized distributions of higher oligomers. The kinetics of aggregation can be followed by the decreasing number of fast-diffusing species. Both the disappearance of fast-diffusing species and the appearance of turbidity can be fitted to the Finke-Watzky equation, but the apparent rate constants obtained are different. This reflects the fact that the disappearance of fast species occurs largely during the lag phase of turbidity development, due to the limited sensitivity of turbidity to the early aggregation process. The nucleation of the early oligomers is concentration-dependent and accompanied by a conformational change that precedes beta-structure formation, and can be visualized using fluorescence resonance energy transfer between the donor-labeled N-terminus and the acceptor-labeled cysteine in the mutant A140C.
Collapse
Affiliation(s)
- Sangeeta Nath
- Laboratory of Biomolecular Dynamics, Department of Chemistry & BioSCENTer, University of Leuven, Leuven, Belgium
| | - Jessika Meuvis
- Laboratory of Biomolecular Dynamics, Department of Chemistry & BioSCENTer, University of Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Laboratory of Biomolecular Dynamics, Department of Chemistry & BioSCENTer, University of Leuven, Leuven, Belgium
| | - Shaun A. Carl
- Laboratory of Quantum and Physical Chemistry, Department of Chemistry, University of Leuven, Leuven, Belgium
| | - Yves Engelborghs
- Laboratory of Biomolecular Dynamics, Department of Chemistry & BioSCENTer, University of Leuven, Leuven, Belgium
| |
Collapse
|