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Cheung See Kit M, Cropley TC, Bleiholder C, Chouinard CD, Sobott F, Webb IK. The role of solvation on the conformational landscape of α-synuclein. Analyst 2023; 149:125-136. [PMID: 37982746 PMCID: PMC10760066 DOI: 10.1039/d3an01680c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Native ion mobility mass spectrometry has been used extensively to characterize ensembles of intrinsically disordered protein (IDP) conformers, but the extent to which the gaseous measurements provide realistic pictures of the solution conformations for such flexible proteins remains unclear. Therefore, we systematically studied the relationship between the solution and gaseous structural ensembles by measuring electrospray charge state and collision cross section (CCS) distributions for cationic and anionic forms of α-synuclein (αSN), an anionic protein in solution, as well as directly probed gas phase residue to residue distances via ion/ion reactions between gaseous α-synuclein cations and disulfonic acid linkers that form strong electrostatic bonds. We also combined results from in-solution protein crosslinking identified from native tandem mass spectrometry (MS/MS) with an initial αSN ensemble generated computationally by IDPConformerGenerator to generate an experimentally restrained solution ensemble of αSN. CCS distributions were directly calculated for the solution ensembles determined by NMR and compared to predicted gaseous conformers. While charge state and collision cross section distributions are useful for qualitatively describing the relative structural dynamics of proteins and major conformational changes induced by changes to solution states, the predicted and measured gas phase conformers include subpopulations that are significantly different than those expected from completely "freezing" solution conformations and preserving them in the gas phase. However, insights were gained on the various roles of solvent in stabilizing various conformers for extremely dynamic proteins like α-synuclein.
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Affiliation(s)
- Melanie Cheung See Kit
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
| | - Tyler C Cropley
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Ian K Webb
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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2
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Heesink G, Marseille MJ, Fakhree MAA, Driver MD, van Leijenhorst-Groener KA, Onck PR, Blum C, Claessens MM. Exploring Intra- and Inter-Regional Interactions in the IDP α-Synuclein Using smFRET and MD Simulations. Biomacromolecules 2023; 24:3680-3688. [PMID: 37407505 PMCID: PMC10428166 DOI: 10.1021/acs.biomac.3c00404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/23/2023] [Indexed: 07/07/2023]
Abstract
Theoretical concepts from polymer physics are often used to describe intrinsically disordered proteins (IDPs). However, amino acid interactions within and between regions of the protein can lead to deviations from typical polymer scaling behavior and even to short-lived secondary structures. To investigate the key interactions in the dynamic IDP α-synuclein (αS) at the amino acid level, we conducted single-molecule fluorescence resonance energy transfer (smFRET) experiments and coarse-grained molecular dynamics (CG-MD) simulations. We find excellent agreement between experiments and simulations. Our results show that a physiological salt solution is a good solvent for αS and that the protein is highly dynamic throughout its entire chain, with local intra- and inter-regional interactions leading to deviations from global scaling. Specifically, we observe expansion in the C-terminal region, compaction in the NAC region, and a slightly smaller distance between the C- and N-termini than expected. Our simulations indicate that the compaction in the NAC region results from hydrophobic aliphatic contacts, mostly between valine and alanine residues, and cation-π interactions between lysine and tyrosine. In addition, hydrogen bonds also seem to contribute to the compaction of the NAC region. The expansion of the C-terminal region is due to intraregional electrostatic repulsion and increased chain stiffness from several prolines. Overall, our study demonstrates the effectiveness of combining smFRET experiments with CG-MD simulations to investigate the key interactions in highly dynamic IDPs at the amino acid level.
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Affiliation(s)
- Gobert Heesink
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Mirjam J. Marseille
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Mohammad A. A. Fakhree
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Mark D. Driver
- Micromechanics,
Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Kirsten A. van Leijenhorst-Groener
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Patrick R. Onck
- Micromechanics,
Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Christian Blum
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Mireille M.A.E. Claessens
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
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3
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Appadurai R, Koneru JK, Bonomi M, Robustelli P, Srivastava A. Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding. J Chem Theory Comput 2023; 19:4711-4727. [PMID: 37338049 PMCID: PMC11108026 DOI: 10.1021/acs.jctc.3c00224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Intrinsically disordered proteins (IDPs) populate a range of conformations that are best described by a heterogeneous ensemble. Grouping an IDP ensemble into "structurally similar" clusters for visualization, interpretation, and analysis purposes is a much-desired but formidable task, as the conformational space of IDPs is inherently high-dimensional and reduction techniques often result in ambiguous classifications. Here, we employ the t-distributed stochastic neighbor embedding (t-SNE) technique to generate homogeneous clusters of IDP conformations from the full heterogeneous ensemble. We illustrate the utility of t-SNE by clustering conformations of two disordered proteins, Aβ42, and α-synuclein, in their APO states and when bound to small molecule ligands. Our results shed light on ordered substates within disordered ensembles and provide structural and mechanistic insights into binding modes that confer specificity and affinity in IDP ligand binding. t-SNE projections preserve the local neighborhood information, provide interpretable visualizations of the conformational heterogeneity within each ensemble, and enable the quantification of cluster populations and their relative shifts upon ligand binding. Our approach provides a new framework for detailed investigations of the thermodynamics and kinetics of IDP ligand binding and will aid rational drug design for IDPs.
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Affiliation(s)
- Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | | | - Massimiliano Bonomi
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry. CNRS UMR 3528, C3BI, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Paul Robustelli
- Dartmouth College, Department of Chemistry, Hanover, NH, 03755, USA
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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4
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Savva L, Platts JA. How Cu(II) binding affects structure and dynamics of α-synuclein revealed by molecular dynamics simulations. J Inorg Biochem 2023; 239:112068. [PMID: 36403437 DOI: 10.1016/j.jinorgbio.2022.112068] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
Abstract
We report accelerated molecular dynamics simulations of α-Synuclein and its complex with two Cu(II) ions bound to experimentally determined binding sites. Adding two Cu(II) ions, one bound to the N-terminal region and one to the C-terminus, decreases size and flexibility of the peptide while introducing significant new contacts within and between N-terminus and non-Aβ component (NAC). Cu(II) ions also alter the pattern of secondary structure within the peptide, inducing more and longer-lasting elements of secondary structure such as β-strands and hairpins. Free energy surfaces, obtained from reweighting the accelerated molecular dynamics boost potential, further demonstrate the restriction on size and flexibility that results from binding of copper ions.
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Affiliation(s)
- Loizos Savva
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - James A Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK..
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5
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Santambrogio C, Ponzini E, Grandori R. Native mass spectrometry for the investigation of protein structural (dis)order. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140828. [PMID: 35926718 DOI: 10.1016/j.bbapap.2022.140828] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/24/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
A central challenge in structural biology is represented by dynamic and heterogeneous systems, as typically represented by proteins in solution, with the extreme case of intrinsically disordered proteins (IDPs) [1-3]. These proteins lack a specific three-dimensional structure and have poorly organized secondary structure. For these reasons, they escape structural characterization by conventional biophysical methods. The investigation of these systems requires description of conformational ensembles, rather than of unique, defined structures or bundles of largely superimposable structures. Mass spectrometry (MS) has become a central tool in this field, offering a variety of complementary approaches to generate structural information on either folded or disordered proteins [4-6]. Two main categories of methods can be recognized. On one side, conformation-dependent reactions (such as cross-linking, covalent labeling, H/D exchange) are exploited to label molecules in solution, followed by the characterization of the labeling products by denaturing MS [7-11]. On the other side, non-denaturing ("native") MS can be used to directly explore the different conformational components in terms of geometry and structural compactness [12-16]. All these approaches have in common the capability to conjugate protein structure investigation with the peculiar analytical power of MS measurements, offering the possibility of assessing species distributions for folding and binding equilibria and the combination of both. These methods can be combined with characterization of noncovalent complexes [17, 18] and post-translational modifications [19-23]. This review focuses on the application of native MS to protein structure and dynamics investigation, with a general methodological section, followed by examples on specific proteins from our laboratory.
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Affiliation(s)
- Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
| | - Erika Ponzini
- Materials Science Department, University of Milano-Bicocca, Via R. Cozzi 55, 20125 Milan, Italy; COMiB Research Center, University of Milano-Bicocca, Via R. Cozzi 55, 20125 Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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