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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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2
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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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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.
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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
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Bianchi G, Mangiagalli M, Barbiroli A, Longhi S, Grandori R, Santambrogio C, Brocca S. Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins. Biomolecules 2022; 12:biom12040561. [PMID: 35454150 PMCID: PMC9031945 DOI: 10.3390/biom12040561] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/29/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are ensembles of interconverting conformers whose conformational properties are governed by several physico-chemical factors, including their amino acid composition and the arrangement of oppositely charged residues within the primary structure. In this work, we investigate the effects of charge patterning on the average compactness and shape of three model IDPs with different proline content. We model IDP ensemble conformations as ellipsoids, whose size and shape are calculated by combining data from size-exclusion chromatography and native mass spectrometry. For each model IDP, we analyzed the wild-type protein and two synthetic variants with permuted positions of charged residues, where positive and negative amino acids are either evenly distributed or segregated. We found that charge clustering induces remodeling of the conformational ensemble, promoting compaction and/or increasing spherical shape. Our data illustrate that the average shape and volume of the ensembles depend on the charge distribution. The potential effect of other factors, such as chain length, number of proline residues, and secondary structure content, is also discussed. This methodological approach is a straightforward way to model IDP average conformation and decipher the salient sequence attributes influencing IDP structural properties.
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Affiliation(s)
- Greta Bianchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
| | - Alberto Barbiroli
- Departement of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy;
| | - Sonia Longhi
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, 13288 Marseille, France;
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
- Correspondence: (C.S.); (S.B.); Tel.: +39-02-6448-3363 (C.S.); +39-02-6448-3518 (S.B.)
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
- Correspondence: (C.S.); (S.B.); Tel.: +39-02-6448-3363 (C.S.); +39-02-6448-3518 (S.B.)
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Brocca S, Grandori R, Longhi S, Uversky V. Liquid-Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus-Host Interactions. Int J Mol Sci 2020; 21:E9045. [PMID: 33260713 PMCID: PMC7730420 DOI: 10.3390/ijms21239045] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/13/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are unable to adopt a unique 3D structure under physiological conditions and thus exist as highly dynamic conformational ensembles. IDPs are ubiquitous and widely spread in the protein realm. In the last decade, compelling experimental evidence has been gathered, pointing to the ability of IDPs and intrinsically disordered regions (IDRs) to undergo liquid-liquid phase separation (LLPS), a phenomenon driving the formation of membrane-less organelles (MLOs). These biological condensates play a critical role in the spatio-temporal organization of the cell, where they exert a multitude of key biological functions, ranging from transcriptional regulation and silencing to control of signal transduction networks. After introducing IDPs and LLPS, we herein survey available data on LLPS by IDPs/IDRs of viral origin and discuss their functional implications. We distinguish LLPS associated with viral replication and trafficking of viral components, from the LLPS-mediated interference of viruses with host cell functions. We discuss emerging evidence on the ability of plant virus proteins to interfere with the regulation of MLOs of the host and propose that bacteriophages can interfere with bacterial LLPS, as well. We conclude by discussing how LLPS could be targeted to treat phase separation-associated diseases, including viral infections.
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Affiliation(s)
- Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy
| | - Sonia Longhi
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille University and CNRS, 13288 Marseille, France
| | - Vladimir Uversky
- Department of Molecular Medicine, Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33601, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia
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Simon I. Macromolecular Interactions of Disordered Proteins. Int J Mol Sci 2020; 21:ijms21020504. [PMID: 31941113 PMCID: PMC7014052 DOI: 10.3390/ijms21020504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 02/03/2023] Open
Affiliation(s)
- István Simon
- Institute of Enzymology, RCNS, Lorand Eotvos Research Network, Center of Excellence of the Hungarian Academy of Sciences, Magyar Tudósok krt. 2., H-1117 Budapest, Hungary
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