1
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Yang G, Zhang L, Xie S, Wu J, Khan M, Zhang Y, Liu L, Li J. Protonation State-Induced Unfolding of Protein Secondary Structure in the Gas Phase. J Phys Chem Lett 2024:9374-9379. [PMID: 39240543 DOI: 10.1021/acs.jpclett.4c02103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
The combination of infrared spectroscopy (IR) and ion mobility mass spectrometry (IM-MS) has revealed that protein secondary structures are retained upon transformation from aqueous solution to the gas phase under gentle conditions. Yet the details about where and how these structural elements are embedded in the gas phase remain elusive. In this study, we employ long time scale molecular dynamics (MD) simulations to examine the extent to which proteins retain their solution structures and the impact of protonation state on the stability of secondary structures in the gas phase. Our investigation focuses on two well-studied proteins, myoglobin and β-lactoglobulin, representing typical helical and β-sheet proteins, respectively. Our simulations accurately reproduce the experimental collision cross section (CCS) data measured by IM-MS. Based on accurately reproducing previous experimental collision cross section data and dominant secondary structural species obtained from IM-MS and IR, we confirm that both proteins largely retain their native secondary structural components upon passing from aqueous solution to the gas phase. However, we observe significant reductions in secondary structure contents (19.2 ± 1.2% for myoglobin and 7.3 ± 0.6% for β-lactoglobulin) in specific regions predominantly composed of ionizable residues. Further mechanistic analysis suggests that alterations in protonation states of these residues after phase transition induce changes in their local interaction networks and backbone dihedral angles, which potentially promote the unfolding of secondary structures in the gas phase. We anticipate that similar protonation state induced unfolding may be observed in other proteins possessing distinct secondary structures. Further studies on a broader array of proteins will be essential to refine our understanding of protein structural behavior during the transition to the gas phase.
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Affiliation(s)
- Guiqian Yang
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Lanbi Zhang
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Song Xie
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Juhong Wu
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Majid Khan
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Yongqi Zhang
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Lin Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, People's Republic of China
| | - Jinyu Li
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
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2
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Esser TK, Böhning J, Önür A, Chinthapalli DK, Eriksson L, Grabarics M, Fremdling P, Konijnenberg A, Makarov A, Botman A, Peter C, Benesch JLP, Robinson CV, Gault J, Baker L, Bharat TAM, Rauschenbach S. Cryo-EM of soft-landed β-galactosidase: Gas-phase and native structures are remarkably similar. SCIENCE ADVANCES 2024; 10:eadl4628. [PMID: 38354247 PMCID: PMC10866560 DOI: 10.1126/sciadv.adl4628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
Native mass spectrometry (MS) has become widely accepted in structural biology, providing information on stoichiometry, interactions, homogeneity, and shape of protein complexes. Yet, the fundamental assumption that proteins inside the mass spectrometer retain a structure faithful to native proteins in solution remains a matter of intense debate. Here, we reveal the gas-phase structure of β-galactosidase using single-particle cryo-electron microscopy (cryo-EM) down to 2.6-Å resolution, enabled by soft landing of mass-selected protein complexes onto cold transmission electron microscopy (TEM) grids followed by in situ ice coating. We find that large parts of the secondary and tertiary structure are retained from the solution. Dehydration-driven subunit reorientation leads to consistent compaction in the gas phase. By providing a direct link between high-resolution imaging and the capability to handle and select protein complexes that behave problematically in conventional sample preparation, the approach has the potential to expand the scope of both native mass spectrometry and cryo-EM.
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Affiliation(s)
- Tim K. Esser
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Thermo Fisher Scientific, 1 Boundary Park, Hemel Hempstead, Hertfordshire HP2 7GE, UK
| | - Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alpcan Önür
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Dinesh K. Chinthapalli
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Lukas Eriksson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Marko Grabarics
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Aurelien Botman
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Justin L. P. Benesch
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Lindsay Baker
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephan Rauschenbach
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
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3
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Erba EB, Pastore A. The Complementarity of Nuclear Magnetic Resonance and Native Mass Spectrometry in Probing Protein-Protein Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:109-123. [PMID: 38507203 DOI: 10.1007/978-3-031-52193-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Nuclear magnetic resonance (NMR) and native mass spectrometry (MS) are mature physicochemical techniques with long histories and important applications. NMR spectroscopy provides detailed information about the structure, dynamics, interactions, and chemical environment of biomolecules. MS is an effective approach for determining the mass of biomolecules with high accuracy, sensitivity, and speed. The two techniques offer unique advantages and provide solid tools for structural biology. In the present review, we discuss their individual merits in the context of their applications to structural studies in biology with specific focus on protein interactions and evaluate their limitations. We provide specific examples in which these techniques can complement each other, providing new information on the same scientific case. We discuss how the field may develop and what challenges are expected in the future. Overall, the combination of NMR and MS plays an increasingly important role in integrative structural biology, assisting scientists in deciphering the three-dimensional structure of composite macromolecular assemblies.
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4
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Brodmerkel MN, De Santis E, Caleman C, Marklund EG. Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration. Protein J 2023:10.1007/s10930-023-10110-y. [PMID: 37031302 DOI: 10.1007/s10930-023-10110-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
Proteins can be oriented in the gas phase using strong electric fields, which brings advantages for structure determination using X-ray free electron lasers. Both the vacuum conditions and the electric-field exposure risk damaging the protein structures. Here, we employ molecular dynamics simulations to rehydrate and relax vacuum and electric-field exposed proteins in aqueous solution, which simulates a refinement of structure models derived from oriented gas-phase proteins. We find that the impact of the strong electric fields on the protein structures is of minor importance after rehydration, compared to that of vacuum exposure and ionization in electrospraying. The structures did not fully relax back to their native structure in solution on the simulated timescales of 200 ns, but they recover several features, including native-like intra-protein contacts, which suggests that the structures remain in a state from which the fully native structure is accessible. Our findings imply that the electric fields used in native mass spectrometry are well below a destructive level, and suggest that structures inferred from X-ray diffraction from gas-phase proteins are relevant for solution and in vivo conditions, at least after in silico rehydration.
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Affiliation(s)
- Maxim N Brodmerkel
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
| | - Emiliano De Santis
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
- Department of Physics and Astronomy, Uppsala University, 75120, Uppsala, Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, 75120, Uppsala, Sweden
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden.
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5
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Brodmerkel MN, De Santis E, Uetrecht C, Caleman C, Marklund EG. Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins. Curr Res Struct Biol 2022; 4:338-348. [PMID: 36440379 PMCID: PMC9685359 DOI: 10.1016/j.crstbi.2022.10.001] [Citation(s) in RCA: 5] [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: 06/27/2022] [Revised: 09/23/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Proteins are innately dynamic, which is important for their functions, but which also poses significant challenges when studying their structures. Gas-phase techniques can utilise separation and a range of sample manipulations to transcend some of the limitations of conventional techniques for structural biology in crystalline or solution phase, and isolate different states for separate interrogation. However, the transfer from solution to the gas phase risks affecting the structures, and it is unclear to what extent different conformations remain distinct in the gas phase, and if resolution in silico can recover the native conformations and their differences. Here, we use extensive molecular dynamics simulations to study the two distinct conformations of dimeric capsid protein of the MS2 bacteriophage. The protein undergoes notable restructuring of its peripheral parts in the gas phase, but subsequent simulation in solvent largely recovers the native structure. Our results suggest that despite some structural loss due to the experimental conditions, gas-phase structural biology techniques provide meaningful data that inform not only about the structures but also conformational dynamics of proteins.
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Affiliation(s)
- Maxim N. Brodmerkel
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, 75123, Sweden
| | - Emiliano De Santis
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, 75123, Sweden
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala, 75120, Sweden
| | - Charlotte Uetrecht
- Leibniz Institute of Virology (LIV), Hamburg, 20251, Germany
- Centre for Structural Systems Biology (CSSB), Deutsches Elektronen-Synchrotron, DESY, Notkestrasse 85, Hamburg, 22607, Germany
- School of Life Sciences, University of Siegen, Siegen, Germany
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala, 75120, Sweden
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Erik G. Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, 75123, Sweden
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6
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Mandl T, Östlin C, Dawod IE, Brodmerkel MN, Marklund EG, Martin AV, Timneanu N, Caleman C. Structural Heterogeneity in Single Particle Imaging Using X-ray Lasers. J Phys Chem Lett 2020; 11:6077-6083. [PMID: 32578996 PMCID: PMC7416308 DOI: 10.1021/acs.jpclett.0c01144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 05/09/2023]
Abstract
One of the challenges facing single particle imaging with ultrafast X-ray pulses is the structural heterogeneity of the sample to be imaged. For the method to succeed with weakly scattering samples, the diffracted images from a large number of individual proteins need to be averaged. The more the individual proteins differ in structure, the lower the achievable resolution in the final reconstructed image. We use molecular dynamics to simulate two globular proteins in vacuum, fully desolvated as well as with two different solvation layers, at various temperatures. We calculate the diffraction patterns based on the simulations and evaluate the noise in the averaged patterns arising from the structural differences and the surrounding water. Our simulations show that the presence of a minimal water coverage with an average 3 Å thickness will stabilize the protein, reducing the noise associated with structural heterogeneity, whereas additional water will generate more background noise.
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Affiliation(s)
- Thomas Mandl
- Department
of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- University
of Applied Sciences Technikum Wien, Höchstädtplatz 6, A-1200 Wien, Austria
| | - Christofer Östlin
- Department
of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Ibrahim E. Dawod
- Department
of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- European
XFEL GmbH, Holzkoppel
4, DE-22869 Schenefeld, Germany
| | - Maxim N. Brodmerkel
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Erik G. Marklund
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Andrew V. Martin
- School
of Science, RMIT University, Melbourne, Victoria 3000, Australia
- ARC Centre
of Excellence for Advanced Molecular Imaging, Clayton, Victoria 3800, Australia
| | - Nicusor Timneanu
- Department
of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Carl Caleman
- Department
of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Center
for Free-Electron Laser Science, Deutsches
Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany
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7
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Allison TM, Barran P, Cianférani S, Degiacomi MT, Gabelica V, Grandori R, Marklund EG, Menneteau T, Migas LG, Politis A, Sharon M, Sobott F, Thalassinos K, Benesch JLP. Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology. Anal Chem 2020; 92:10872-10880. [DOI: 10.1021/acs.analchem.9b05791] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Matteo T. Degiacomi
- Department of Physics, Durham University, South Road, Durham, DH1 3LE, United Kingdom
| | - Valérie 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
- Department of Chemistry, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, Malet Street, London WC1E 7HX, United Kingdom
| | - Justin L. P. Benesch
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom
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8
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Exploring the structure and dynamics of macromolecular complexes by native mass spectrometry. J Proteomics 2020; 222:103799. [DOI: 10.1016/j.jprot.2020.103799] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/23/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
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9
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Vimer S, Ben-Nissan G, Morgenstern D, Kumar-Deshmukh F, Polkinghorn C, Quintyn RS, Vasil’ev YV, Beckman JS, Elad N, Wysocki VH, Sharon M. Comparative Structural Analysis of 20S Proteasome Ortholog Protein Complexes by Native Mass Spectrometry. ACS CENTRAL SCIENCE 2020; 6:573-588. [PMID: 32342007 PMCID: PMC7181328 DOI: 10.1021/acscentsci.0c00080] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Indexed: 05/06/2023]
Abstract
Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental challenges imposed by its niche. This selection pressure leads to structural diversity in protein complexes, which are often difficult to specify, especially in the absence of high-resolution structures. Here, we describe a multilevel experimental approach based on native mass spectrometry (MS) tools for elucidating the structural preservation and variations among highly related protein complexes. The 20S proteasome, an essential protein degradation machinery, served as our model system, wherein we examined five complexes isolated from different organisms. We show that throughout evolution, from the Thermoplasma acidophilum archaeal prokaryotic complex to the eukaryotic 20S proteasomes in yeast (Saccharomyces cerevisiae) and mammals (rat - Rattus norvegicus, rabbit - Oryctolagus cuniculus and human - HEK293 cells), the proteasome increased both in size and stability. Native MS structural signatures of the rat and rabbit 20S proteasomes, which heretofore lacked high-resolution, three-dimensional structures, highly resembled that of the human complex. Using cryoelectron microscopy single-particle analysis, we were able to obtain a high-resolution structure of the rat 20S proteasome, allowing us to validate the MS-based results. Our study also revealed that the yeast complex, and not those in mammals, was the largest in size and displayed the greatest degree of kinetic stability. Moreover, we also identified a new proteoform of the PSMA7 subunit that resides within the rat and rabbit complexes, which to our knowledge have not been previously described. Altogether, our strategy enables elucidation of the unique structural properties of protein complexes that are highly similar to one another, a framework that is valid not only to ortholog protein complexes, but also for other highly related protein assemblies.
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Affiliation(s)
- Shay Vimer
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| | - David Morgenstern
- Israel
Structural Proteomics Center, Weizmann Institute
of Science, Rehovot, Israel
| | | | - Caley Polkinghorn
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| | - Royston S. Quintyn
- Department
of Chemistry and Biochemistry and Resource for Native Mass Spectrometry
Guided Structural Biology, Ohio State University, Columbus, Ohio 43210, United States
| | - Yury V. Vasil’ev
- e-MSion
Inc., 2121 NE Jack London
Drive, Corvallis, Oregon 97330, United States
| | - Joseph S. Beckman
- e-MSion
Inc., 2121 NE Jack London
Drive, Corvallis, Oregon 97330, United States
- Linus
Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Nadav Elad
- Department
of Chemical Research Support, Weizmann Institute
of Science, Rehovot, Israel
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry and Resource for Native Mass Spectrometry
Guided Structural Biology, Ohio State University, Columbus, Ohio 43210, United States
| | - Michal Sharon
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
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10
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McAlary L, Harrison JA, Aquilina JA, Fitzgerald SP, Kelso C, Benesch JL, Yerbury JJ. Trajectory Taken by Dimeric Cu/Zn Superoxide Dismutase through the Protein Unfolding and Dissociation Landscape Is Modulated by Salt Bridge Formation. Anal Chem 2019; 92:1702-1711. [DOI: 10.1021/acs.analchem.9b01699] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Luke McAlary
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Julian A. Harrison
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - J. Andrew Aquilina
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | | | - Celine Kelso
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Justin L.P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Department, University of Oxford, Oxford OX1 3QZ, U.K
| | - Justin J. Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
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11
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Hospital A, Battistini F, Soliva R, Gelpí JL, Orozco M. Surviving the deluge of biosimulation data. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1449] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Adam Hospital
- Institut de Recerca Biomèdica, IRB Barcelona, The Barcelona Institute of Science and Technology Joint IRB‐BSC Program in Computational Biology Barcelona Spain
| | - Federica Battistini
- Institut de Recerca Biomèdica, IRB Barcelona, The Barcelona Institute of Science and Technology Joint IRB‐BSC Program in Computational Biology Barcelona Spain
| | | | - Josep Lluis Gelpí
- Barcelona Supercomputing Center Join IRB‐BSC Program in Computational Biology Barcelona Spain
- Departament de Bioquímica i Biomedicina Universitat de Barcelona Barcelona Spain
| | - Modesto Orozco
- Institut de Recerca Biomèdica, IRB Barcelona, The Barcelona Institute of Science and Technology Joint IRB‐BSC Program in Computational Biology Barcelona Spain
- Departament de Bioquímica i Biomedicina Universitat de Barcelona Barcelona Spain
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12
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Rolland AD, Prell JS. Computational Insights into Compaction of Gas-Phase Protein and Protein Complex Ions in Native Ion Mobility-Mass Spectrometry. Trends Analyt Chem 2019; 116:282-291. [PMID: 31983791 PMCID: PMC6979403 DOI: 10.1016/j.trac.2019.04.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Native ion mobility-mass spectrometry (IM-MS) is a rapidly growing field for studying the composition and structure of biomolecules and biomolecular complexes using gas-phase methods. Typically, ions are formed in native IM-MS using gentle nanoelectrospray ionization conditions, which in many cases can preserve condensed-phase stoichiometry. Although much evidence shows that large-scale condensed-phase structure, such as quaternary structure and topology, can also be preserved, it is less clear to what extent smaller-scale structure is preserved in native IM-MS. This review surveys computational and experimental efforts aimed at characterizing compaction and structural rearrangements of protein and protein complex ions upon transfer to the gas phase. A brief summary of gas-phase compaction results from molecular dynamics simulations using multiple common force fields and a wide variety of protein ions is presented and compared to literature IM-MS data.
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Affiliation(s)
- Amber D. Rolland
- Department of Chemistry and Biochemistry, 1253 University
of Oregon, Eugene, OR, USA, 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University
of Oregon, Eugene, OR, USA, 97403-1253
- Materials Science Institute, 1252 University of Oregon,
Eugene, OR, USA 97403-1252
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13
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Dyachenko A, Tamara S, Heck AJR. Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:7-15. [PMID: 29736602 PMCID: PMC6318259 DOI: 10.1007/s13361-018-1910-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 05/06/2023]
Abstract
The GroES heptamer is the molecular co-chaperonin that partners with the tetradecamer chaperonin GroEL, which assists in the folding of various nonnative polypeptide chains in Escherichia coli. Gp31 is a structural and functional analogue of GroES encoded by the bacteriophage T4, becoming highly expressed in T4-infected E. coli, taking over the role of GroES, favoring the folding of bacteriophage proteins. Despite being slightly larger, gp31 is quite homologous to GroES in terms of its tertiary and quaternary structure, as well as in its function and mode of interaction with the chaperonin GroEL. Here, we performed a side-by-side comparison of GroES and gp31 heptamer complexes by (ion mobility) tandem mass spectrometry. Surprisingly, we observed quite distinct fragmentation mechanisms for the GroES and gp31 heptamers, whereby GroES displays a unique and unusual bimodal charge distribution in its released monomers. Not only the gas-phase dissociation but also the gas-phase unfolding of GroES and gp31 were found to be very distinct. We rationalize these observations with the similar discrepancies we observed in the thermal unfolding characteristics and surface contacts within GroES and gp31 in the solution. From our data, we propose a model that explains the observed simultaneous dissociation pathways of GroES and the differences between GroES and gp31 gas-phase dissociation and unfolding. We conclude that, although GroES and gp31 exhibit high homology in tertiary and quaternary structure, they are quite distinct in their solution and gas-phase (un)folding characteristics and stability. Graphical Abstract.
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Affiliation(s)
- Andrey Dyachenko
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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14
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Porrini M, Rosu F, Rabin C, Darré L, Gómez H, Orozco M, Gabelica V. Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry. ACS CENTRAL SCIENCE 2017; 3:454-461. [PMID: 28573208 PMCID: PMC5445532 DOI: 10.1021/acscentsci.7b00084] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Indexed: 05/25/2023]
Abstract
We report on the fate of nucleic acids conformation in the gas phase as sampled using native mass spectrometry coupled to ion mobility spectrometry. On the basis of several successful reports for proteins and their complexes, the technique has become popular in structural biology, and the conformation survival becomes more and more taken for granted. Surprisingly, we found that DNA and RNA duplexes, at the electrospray charge states naturally obtained from native solution conditions (≥100 mM aqueous NH4OAc), are significantly more compact in the gas phase compared to the canonical solution structures. The compaction is observed for all duplex sizes (gas-phase structures are more compact than canonical B-helices by ∼20% for 12-bp, and by up to ∼30% for 36-bp duplexes), and for DNA and RNA alike. Molecular modeling (density functional calculations on small helices, semiempirical calculations on up to 12-bp, and molecular dynamics on up to 36-bp duplexes) demonstrates that the compaction is due to phosphate group self-solvation prevailing over Coulomb repulsion. Molecular dynamics simulations starting from solution structures do not reproduce the experimental compaction. To be experimentally relevant, molecular dynamics sampling should reflect the progressive structural rearrangements occurring during desolvation. For nucleic acid duplexes, the compaction observed for low charge states results from novel phosphate-phosphate hydrogen bonds formed across both grooves at the very late stages of electrospray.
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Affiliation(s)
- Massimiliano Porrini
- INSERM,
CNRS, Université de Bordeaux, Acides
Nucléiques Régulations Naturelle et Artificielle (ARNA,
U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Frédéric Rosu
- CNRS,
INSERM, Université de Bordeaux, Institut
Européen de Chimie et Biologie (IECB, UMS3033, US001), 2 rue Robert Escarpit, 33607 Pessac, France
| | - Clémence Rabin
- INSERM,
CNRS, Université de Bordeaux, Acides
Nucléiques Régulations Naturelle et Artificielle (ARNA,
U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Leonardo Darré
- The
Barcelona Institute of Science and Technology, Institute for Research in Biomedicine (IRB) Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
- Joint
BSC-CRG-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain
| | - Hansel Gómez
- The
Barcelona Institute of Science and Technology, Institute for Research in Biomedicine (IRB) Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
- Joint
BSC-CRG-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain
| | - Modesto Orozco
- The
Barcelona Institute of Science and Technology, Institute for Research in Biomedicine (IRB) Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
- Joint
BSC-CRG-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain
- Department
of Biochemistry and Biomedicine, University
of Barcelona, Avda Diagonal
647, 08028 Barcelona, Spain
| | - Valérie Gabelica
- INSERM,
CNRS, Université de Bordeaux, Acides
Nucléiques Régulations Naturelle et Artificielle (ARNA,
U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
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15
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Li J, Lyu W, Rossetti G, Konijnenberg A, Natalello A, Ippoliti E, Orozco M, Sobott F, Grandori R, Carloni P. Proton Dynamics in Protein Mass Spectrometry. J Phys Chem Lett 2017; 8:1105-1112. [PMID: 28207277 DOI: 10.1021/acs.jpclett.7b00127] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas phase, and its impact on protein structural determinants, have not been investigated so far. Here, we address this issue by a multistep simulation strategy on a pharmacologically relevant peptide, the N-terminal residues of amyloid-β peptide (Aβ(1-16)). Our calculations reproduce the experimental maximum charge state from ESI-MS and are also in fair agreement with collision cross section (CCS) data measured here by ESI/IM-MS. Although the main structural features are preserved, subtle conformational changes do take place in the first ∼0.1 ms of dynamics. In addition, intramolecular proton dynamics processes occur on the picosecond-time scale in the gas phase as emerging from quantum mechanics/molecular mechanics (QM/MM) simulations at the B3LYP level of theory. We conclude that proton transfer phenomena do occur frequently during fly time in ESI-MS experiments (typically on the millisecond time scale). However, the structural changes associated with the process do not significantly affect the structural determinants.
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Affiliation(s)
- Jinyu Li
- College of Chemistry, Fuzhou University , 350002 Fuzhou, China
| | - Wenping Lyu
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH-Aachen University , 52056 Aachen, Germany
- Computation-Based Science and Technology Research Center, Cyprus Institute , 2121 Aglantzia, Nicosia, Cyprus
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University , 52062 Aachen, Germany
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich , D-52425 Jülich, Germany
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp , 2000 Antwerpen, Belgium
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Emiliano Ippoliti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
| | - Modesto Orozco
- Joint BSC-IRB Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona , Avgda Diagonal 647, Barcelona 08028, Spain
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp , 2000 Antwerpen, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- JARA-HPC, 52425 Jülich, Germany
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16
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Seddon GM, Bywater RP. The fate of proteins in outer space. INTERNATIONAL JOURNAL OF ASTROBIOLOGY 2017; 16:19-27. [PMID: 29515333 PMCID: PMC5837003 DOI: 10.1017/s1473550415000488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2023]
Abstract
It is well established that any properly conducted biophysical studies of proteins must take appropriate account of solvent. For water-soluble proteins it has been an article of faith that water is largely responsible for stabilizing the fold, a notion that has recently come under increasing scrutiny. Further, there are some instances when proteins are studied experimentally in the absence of solvent, as in matrix-assisted laser desorption/ionization or electrospray mass spectrometry, for example, or in organic solvents for protein engineering purposes. Apart from these considerations, there is considerable speculation as to whether there is life on planets other than Earth, where conditions including the presence of water (both in liquid or vapor form and indeed ice), temperature and pressure may be vastly different from those prevailing on Earth. Mars, for example, has only 0.6% of Earth's mean atmospheric pressure which presents profound problems to protein structures, as this paper and a large corpus of experimental work demonstrate. Similar objections will most likely apply in the case of most exoplanets and other bodies such as comets whose chemistry and climate are still largely unknown. This poses the question, how do proteins survive in these different environments? In order to cast some light on these issues we have conducted a series of molecular dynamics simulations on protein dehydration under a variety of conditions. We find that, while proteins undergoing dehydration can retain their integrity for a short duration they ultimately become disordered, and we further show that the disordering can be retarded if superficial water is kept in place on the surface. These findings are compared with other published results on protein solvation in an astrobiological and astrochemical setting. Inter alia, our results suggest that there are limits as to what to expect in terms of the existence of possible extraterrestrial forms as well to what can be achieved in experimental investigations on living systems despatched from Earth. This finding may appear to undermine currently held hopes that life will be found on nearby planets, but it is important to be aware that the presence of ice and water are by themselves not sufficient; there has to be an atmosphere which includes water vapor at a sufficiently high partial pressure for proteins to be active. A possible scenario in which there has been a history of adequate water vapor pressure which allowed organisms to prepare for a future dessicated state by forming suitable protective capsules cannot of course be ruled out.
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Affiliation(s)
| | - Robert P. Bywater
- Adelard Institute Manchester M29 7FZ UK
- Magdalen College Oxford OX1 4AU UK
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17
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Meyer NA, Root K, Zenobi R, Vidal-de-Miguel G. Gas-Phase Dopant-Induced Conformational Changes Monitored with Transversal Modulation Ion Mobility Spectrometry. Anal Chem 2016; 88:2033-40. [PMID: 26845079 DOI: 10.1021/acs.analchem.5b02750] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The potential of a Transversal Modulation Ion Mobility Spectrometry (TMIMS) instrument for protein analysis applications has been evaluated. The Collision Cross Section (CCS) of cytochrome c measured with the TMIMS is in agreement with values reported in the literature. Additionally, it enables tandem IMS-IMS prefiltration in dry gas and in vapor doped gas. The chemical specificity of the different dopants enables interesting studies on the structure of proteins as CCS changed strongly depending on the specific dopant. Hexane produced an unexpectedly high CCS shift, which can be utilized to evaluate the exposure of hydrophobic parts of the protein. Alcohols produced higher shifts with a dual behavior: an increase in CCS due to vapor uptake at specific absorption sites, followed by a linear shift typical for unspecific and unstable vapor uptake. The molten globule +8 shows a very specific transition. Initially, its CCS follows the trend of the compact folded states, and then it rapidly increases to the levels of the unfolded states. This strong variation suggests that the +8 charge state undergoes a dopant-induced conformational change. Interestingly, more sterically demanding alcohols seem to unfold the protein more effectively also in the gas phase. This study shows the capabilities of the TMIMS device for protein analysis and how tandem IMS-IMS with dopants could provide better understanding of the conformational changes of proteins.
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Affiliation(s)
- Nicole Andrea Meyer
- Department of Chemistry and Applied Biosciences, ETH Zurich , CH-8093, Zurich, Switzerland
| | - Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich , CH-8093, Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich , CH-8093, Zurich, Switzerland
| | - Guillermo Vidal-de-Miguel
- Department of Chemistry and Applied Biosciences, ETH Zurich , CH-8093, Zurich, Switzerland.,Fossil Ion Technology (FIT) , Cipreses 18, 28036, Madrid, Spain
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18
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Li J, Santambrogio C, Brocca S, Rossetti G, Carloni P, Grandori R. Conformational effects in protein electrospray-ionization mass spectrometry. MASS SPECTROMETRY REVIEWS 2016; 35:111-22. [PMID: 25952139 DOI: 10.1002/mas.21465] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/14/2015] [Indexed: 05/11/2023]
Abstract
Electrospray-ionization mass spectrometry (ESI-MS) is a key tool of structural biology, complementing the information delivered by conventional biochemical and biophysical methods. Yet, the mechanism behind the conformational effects in protein ESI-MS is an object of debate. Two parameters-solvent-accessible surface area (As) and apparent gas-phase basicity (GBapp)-are thought to play a role in controlling the extent of protein ionization during ESI-MS experiments. This review focuses on recent experimental and theoretical investigations concerning the influence of these parameters on ESI-MS results and the structural information that can be derived. The available evidence supports a unified model for the ionization mechanism of folded and unfolded proteins. These data indicate that charge-state distribution (CSD) analysis can provide valuable structural information on normally folded, as well as disordered structures.
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Affiliation(s)
- Jinyu Li
- Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, 52057 Aachen, Germany
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Giulia Rossetti
- Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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19
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Boeri Erba E, Petosa C. The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes. Protein Sci 2015; 24:1176-92. [PMID: 25676284 DOI: 10.1002/pro.2661] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/06/2015] [Accepted: 02/06/2015] [Indexed: 12/31/2022]
Abstract
Mass spectrometry (MS) is a powerful tool for determining the mass of biomolecules with high accuracy and sensitivity. MS performed under so-called "native conditions" (native MS) can be used to determine the mass of biomolecules that associate noncovalently. Here we review the application of native MS to the study of protein-ligand interactions and its emerging role in elucidating the structure of macromolecular assemblies, including soluble and membrane protein complexes. Moreover, we discuss strategies aimed at determining the stoichiometry and topology of subunits by inducing partial dissociation of the holo-complex. We also survey recent developments in "native top-down MS", an approach based on Fourier Transform MS, whereby covalent bonds are broken without disrupting non-covalent interactions. Given recent progress, native MS is anticipated to play an increasingly important role for researchers interested in the structure of macromolecular complexes.
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Affiliation(s)
- Elisabetta Boeri Erba
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
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20
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Harvey SR, Porrini M, Konijnenberg A, Clarke DJ, Tyler RC, Langridge-Smith PRR, MacPhee CE, Volkman BF, Barran PE. Dissecting the Dynamic Conformations of the Metamorphic Protein Lymphotactin. J Phys Chem B 2014; 118:12348-59. [DOI: 10.1021/jp504997k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | - Massimiliano Porrini
- Institut Européen de Chimie et Biologie (IECB), CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN), 33607 Pessac Cedex, France
| | | | | | - Robert C. Tyler
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | | | | | - Brian F. Volkman
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Perdita E. Barran
- School
of Chemistry,
Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
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21
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Molecular simulation-based structural prediction of protein complexes in mass spectrometry: the human insulin dimer. PLoS Comput Biol 2014; 10:e1003838. [PMID: 25210764 PMCID: PMC4161290 DOI: 10.1371/journal.pcbi.1003838] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 07/26/2014] [Indexed: 01/02/2023] Open
Abstract
Protein electrospray ionization (ESI) mass spectrometry (MS)-based techniques are widely used to provide insight into structural proteomics under the assumption that non-covalent protein complexes being transferred into the gas phase preserve basically the same intermolecular interactions as in solution. Here we investigate the applicability of this assumption by extending our previous structural prediction protocol for single proteins in ESI-MS to protein complexes. We apply our protocol to the human insulin dimer (hIns2) as a test case. Our calculations reproduce the main charge and the collision cross section (CCS) measured in ESI-MS experiments. Molecular dynamics simulations for 0.075 ms show that the complex maximizes intermolecular non-bonded interactions relative to the structure in water, without affecting the cross section. The overall gas-phase structure of hIns2 does exhibit differences with the one in aqueous solution, not inferable from a comparison with calculated CCS. Hence, care should be exerted when interpreting ESI-MS proteomics data based solely on NMR and/or X-ray structural information.
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22
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Abstract
Nucleic acids are diverse polymeric macromolecules that are essential for all life forms. These biomolecules possess a functional three-dimensional structure under aqueous physiological conditions. Mass spectrometry-based approaches have on the other hand opened the possibility to gain structural information on nucleic acids from gas-phase measurements. To correlate gas-phase structural probing results with solution structures, it is therefore important to grasp the extent to which nucleic acid structures are preserved, or altered, when transferred from the solution to a fully anhydrous environment. We will review here experimental and theoretical approaches available to characterize the structure of nucleic acids in the gas phase (with a focus on oligonucleotides and higher-order structures), and will summarize the structural features of nucleic acids that can be preserved in the gas phase on the experiment time scale.
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23
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Aviñó A, Portella G, Ferreira R, Gargallo R, Mazzini S, Gabelica V, Orozco M, Eritja R. Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures. FEBS J 2014; 281:1085-99. [PMID: 24304855 DOI: 10.1111/febs.12670] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/11/2013] [Accepted: 11/27/2013] [Indexed: 01/31/2023]
Abstract
Guanine-rich sequences show large structural variability, with folds ranging from duplex to triplex and quadruplex helices. Quadruplexes are polymorphic, and can show multiple stoichiometries, parallel and antiparallel strand alignments, and different topological arrangements. We analyze here the equilibrium between intramolecular antiparallel and intermolecular parallel G-quadruplexes in the thrombin-binding aptamer (TBA) sequence. Our theoretical and experimental studies demonstrate that an apparently simple modification at the loops of TBA induces a large change in the monomeric antiparallel structure of TBA to yield a parallel G-quadruplex showing a novel T-tetrad. The present results illustrate the extreme polymorphism of G-quadruplexes and the ease with which their conformation in solution can be manipulated by nucleotide modification.
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Affiliation(s)
- Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
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24
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Arcella A, Portella G, Orozco M. Structure of Nucleic Acids in the Gas Phase. PHYSICAL CHEMISTRY IN ACTION 2014. [DOI: 10.1007/978-3-642-54842-0_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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25
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Malevanets A, Consta S. Variation of droplet acidity during evaporation. J Chem Phys 2013; 138:184312. [DOI: 10.1063/1.4804303] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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26
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Zhang H, Cui W, Gross ML, Blankenship RE. Native mass spectrometry of photosynthetic pigment-protein complexes. FEBS Lett 2013; 587:1012-20. [PMID: 23337874 PMCID: PMC3856239 DOI: 10.1016/j.febslet.2013.01.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 12/25/2012] [Accepted: 01/06/2013] [Indexed: 12/16/2022]
Abstract
Native mass spectrometry (MS), or as is sometimes called "native electrospray ionization" allows proteins in their native or near-native states in solution to be introduced into the gas phase and interrogated by mass spectrometry. This approach is now a powerful tool to investigate protein complexes. This article reviews the background of native MS of protein complexes and describes its strengths, taking photosynthetic pigment-protein complexes as examples. Native MS can be utilized in combination with other MS-based approaches to obtain complementary information to that provided by tools such as X-ray crystallography and NMR spectroscopy to understand the structure-function relationships of protein complexes. When additional information beyond that provided by native MS is required, other MS-based strategies can be successfully applied to augment the results of native MS.
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Affiliation(s)
- Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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27
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Meyer T, Gabelica V, Grubmüller H, Orozco M. Proteins in the gas phase. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1130] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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28
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Marchese R, Grandori R, Carloni P, Raugei S. A computational model for protein ionization by electrospray based on gas-phase basicity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1903-10. [PMID: 22993040 DOI: 10.1007/s13361-012-0449-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 07/13/2012] [Accepted: 07/14/2012] [Indexed: 05/11/2023]
Abstract
Identifying the key factor(s) governing the overall protein charge is crucial for the interpretation of electrospray-ionization mass spectrometry data. Current hypotheses invoke different principles for folded and unfolded proteins. Here, first we investigate the gas-phase structure and energetics of several proteins of variable size and different folds. The conformer and protomer space of these proteins ions is explored exhaustively by hybrid Monte-Carlo/molecular dynamics calculations, allowing for zwitterionic states. From these calculations, the apparent gas-phase basicity of desolvated protein ions turns out to be the unifying trait dictating protein ionization by electrospray. Next, we develop a simple, general, adjustable-parameter-free model for the potential energy function of proteins. The model is capable to predict with remarkable accuracy the experimental charge of folded proteins and its well-known correlation with the square root of protein mass.
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29
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Hensen U, Meyer T, Haas J, Rex R, Vriend G, Grubmüller H. Exploring protein dynamics space: the dynasome as the missing link between protein structure and function. PLoS One 2012; 7:e33931. [PMID: 22606222 PMCID: PMC3350514 DOI: 10.1371/journal.pone.0033931] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 02/20/2012] [Indexed: 12/25/2022] Open
Abstract
Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs. The complete set of these patterns, which we tentatively call the dynasome, spans a multi-dimensional space with axes, the dynasome descriptors, characterizing different aspects of protein dynamics. The unique dynamic fingerprint of each protein is represented as a vector in the dynasome space. The difference between any two vectors, consequently, gives a reliable measure of the difference between the corresponding protein dynamics. We characterize the properties of the dynasome by comparing the dynamics fingerprints obtained from molecular dynamics simulations of 112 proteins but our approach is, in principle, not restricted to any specific source of data of protein dynamics. We conclude that: 1. the dynasome consists of a continuum of proteins, rather than well separated classes. 2. For the majority of proteins we observe strong correlations between structure and dynamics. 3. Proteins with similar function carry out similar dynamics, which suggests a new method to improve protein function annotation based on protein dynamics.
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Affiliation(s)
- Ulf Hensen
- Theoretische und computergestützte Biophysik, Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany
| | - Tim Meyer
- Theoretische und computergestützte Biophysik, Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany
| | - Jürgen Haas
- Theoretische und computergestützte Biophysik, Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany
| | - René Rex
- Theoretische und computergestützte Biophysik, Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany
| | - Gert Vriend
- CMBI, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Helmut Grubmüller
- Theoretische und computergestützte Biophysik, Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany
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30
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Hilton GR, Benesch JLP. Two decades of studying non-covalent biomolecular assemblies by means of electrospray ionization mass spectrometry. J R Soc Interface 2012; 9:801-16. [PMID: 22319100 PMCID: PMC3306659 DOI: 10.1098/rsif.2011.0823] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 01/16/2012] [Indexed: 12/31/2022] Open
Abstract
Mass spectrometry (MS) is a recognized approach for characterizing proteins and the complexes they assemble into. This application of a long-established physico-chemical tool to the frontiers of structural biology has stemmed from experiments performed in the early 1990s. While initial studies focused on the elucidation of stoichiometry by means of simple mass determination, developments in MS technology and methodology now allow researchers to address questions of shape, inter-subunit connectivity and protein dynamics. Here, we chart the remarkable rise of MS and its application to biomolecular complexes over the last two decades.
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Affiliation(s)
| | - Justin L. P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX3 1QZ, UK
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31
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Arcella A, Portella G, Ruiz ML, Eritja R, Vilaseca M, Gabelica V, Orozco M. Structure of Triplex DNA in the Gas Phase. J Am Chem Soc 2012; 134:6596-606. [DOI: 10.1021/ja209786t] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Annalisa Arcella
- Joint IRB BSC Research Program
in Computational Biology, Institute for Research in Biomedicine, Baldiri Reixach 10, Barcelona 08028, Spain
| | - Guillem Portella
- Joint IRB BSC Research Program
in Computational Biology, Institute for Research in Biomedicine, Baldiri Reixach 10, Barcelona 08028, Spain
| | - Maria Luz Ruiz
- Chemistry and Molecular Pharmacology
Program, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN, Barcelona 08028, Spain
| | - Ramon Eritja
- Chemistry and Molecular Pharmacology
Program, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN, Barcelona 08028, Spain
| | - Marta Vilaseca
- Mass Spectrometry Core Facility, Institute for Research in Biomedicine, Barcelona 08028,
Spain
| | - Valérie Gabelica
- Department of Chemistry, University of Liège, Allée de la Chimie,
Building B6c, B-4000 Liège, Belgium
| | - Modesto Orozco
- Joint IRB BSC Research Program
in Computational Biology, Institute for Research in Biomedicine, Baldiri Reixach 10, Barcelona 08028, Spain
- Departament de Bioquímica
i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Avgda Diagonal 645, Barcelona
08028, Spain
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32
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Hall Z, Politis A, Bush MF, Smith LJ, Robinson CV. Charge-State Dependent Compaction and Dissociation of Protein Complexes: Insights from Ion Mobility and Molecular Dynamics. J Am Chem Soc 2012; 134:3429-38. [DOI: 10.1021/ja2096859] [Citation(s) in RCA: 206] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Zoe Hall
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry
Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Argyris Politis
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry
Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Matthew F. Bush
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry
Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Lorna J. Smith
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory,
South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry
Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
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33
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Bernadó P. Low‐resolution structural approaches to study biomolecular assemblies. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Pau Bernadó
- Institute for Research in Biomedicine, Barcelona, Spain
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34
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Faustino I, Pérez A, Orozco M. Toward a consensus view of duplex RNA flexibility. Biophys J 2011; 99:1876-85. [PMID: 20858433 DOI: 10.1016/j.bpj.2010.06.061] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 06/22/2010] [Accepted: 06/25/2010] [Indexed: 11/25/2022] Open
Abstract
The structure and flexibility of the RNA duplex has been studied using extended molecular dynamics simulations on four diverse 18-mer oligonucleotides designed to contain many copies of the 10 unique dinucleotide steps in different sequence environments. Simulations were performed using the two most popular force fields for nucleic acids simulations (AMBER and CHARMM) in their latest versions, trying to arrive to a consensus picture of the RNA flexibility. Contrary to what was found for DNA duplex (DNA(2)), no clear convergence is found for the RNA duplex (RNA(2)), but one of the force field seems to agree better with experimental data. MD simulations performed with this force field were used to fully characterize, for the first time to our knowledge, the sequence-dependent elastic properties of RNA duplexes at different levels of resolutions. The flexibility pattern of RNA(2) shows similarities with DNA(2), but also surprising differences, which help us to understand the different biological functions of both molecules. A full mesoscopic model of RNA duplex at different resolution levels is derived to be used for genome-wide description of the flexibility of double-helical fragments of RNA.
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Affiliation(s)
- Ignacio Faustino
- Joint Institute of IRB/BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona, Spain
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35
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Ben-Nissan G, Sharon M. Capturing protein structural kinetics by mass spectrometry. Chem Soc Rev 2011; 40:3627-37. [DOI: 10.1039/c1cs15052a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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36
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van der Spoel D, Marklund EG, Larsson DSD, Caleman C. Proteins, Lipids, and Water in the Gas Phase. Macromol Biosci 2010; 11:50-9. [DOI: 10.1002/mabi.201000291] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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37
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Michaelevski I, Eisenstein M, Sharon M. Gas-Phase Compaction and Unfolding of Protein Structures. Anal Chem 2010; 82:9484-91. [DOI: 10.1021/ac1021419] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Izhak Michaelevski
- Departments of Biological Chemistry and Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miriam Eisenstein
- Departments of Biological Chemistry and Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Sharon
- Departments of Biological Chemistry and Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
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38
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Dynameomics: a comprehensive database of protein dynamics. Structure 2010; 18:423-35. [PMID: 20399180 DOI: 10.1016/j.str.2010.01.012] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 01/17/2010] [Accepted: 01/21/2010] [Indexed: 12/15/2022]
Abstract
The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 2000 protein/peptide systems (approximately 11,000 independent simulations) representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through http://www.dynameomics.org.
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39
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Atmanene C, Chaix D, Bessin Y, Declerck N, Van Dorsselaer A, Sanglier-Cianferani S. Combination of Noncovalent Mass Spectrometry and Traveling Wave Ion Mobility Spectrometry Reveals Sugar-Induced Conformational Changes of Central Glycolytic Genes Repressor/DNA Complex. Anal Chem 2010; 82:3597-605. [DOI: 10.1021/ac902784n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Cédric Atmanene
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 STRASBOURG, France, CNRS UMR7178, 67087 Strasbourg, France and INSERM U554, Centre de Biochimie Structurale, CNRS UMR5048 and Université Montpellier 1, 29 rue de Navacelles, F-34090 Montpellier, France
| | - Denix Chaix
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 STRASBOURG, France, CNRS UMR7178, 67087 Strasbourg, France and INSERM U554, Centre de Biochimie Structurale, CNRS UMR5048 and Université Montpellier 1, 29 rue de Navacelles, F-34090 Montpellier, France
| | - Yannick Bessin
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 STRASBOURG, France, CNRS UMR7178, 67087 Strasbourg, France and INSERM U554, Centre de Biochimie Structurale, CNRS UMR5048 and Université Montpellier 1, 29 rue de Navacelles, F-34090 Montpellier, France
| | - Nathalie Declerck
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 STRASBOURG, France, CNRS UMR7178, 67087 Strasbourg, France and INSERM U554, Centre de Biochimie Structurale, CNRS UMR5048 and Université Montpellier 1, 29 rue de Navacelles, F-34090 Montpellier, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 STRASBOURG, France, CNRS UMR7178, 67087 Strasbourg, France and INSERM U554, Centre de Biochimie Structurale, CNRS UMR5048 and Université Montpellier 1, 29 rue de Navacelles, F-34090 Montpellier, France
| | - Sarah Sanglier-Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 STRASBOURG, France, CNRS UMR7178, 67087 Strasbourg, France and INSERM U554, Centre de Biochimie Structurale, CNRS UMR5048 and Université Montpellier 1, 29 rue de Navacelles, F-34090 Montpellier, France
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40
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D’Abramo M, Meyer T, Bernadó P, Pons C, Recio JF, Orozco M. On the Use of low-resolution Data to Improve Structure Prediction of Proteins and Protein Complexes. J Chem Theory Comput 2009; 5:3129-37. [DOI: 10.1021/ct900305m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Marco D’Abramo
- Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain and Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Structural and Computational Biology Program, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain, Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Departament de
| | - Tim Meyer
- Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain and Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Structural and Computational Biology Program, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain, Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Departament de
| | - Pau Bernadó
- Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain and Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Structural and Computational Biology Program, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain, Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Departament de
| | - Carles Pons
- Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain and Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Structural and Computational Biology Program, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain, Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Departament de
| | - Juan Fernández Recio
- Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain and Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Structural and Computational Biology Program, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain, Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Departament de
| | - Modesto Orozco
- Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain and Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Structural and Computational Biology Program, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain, Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Departament de
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41
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Marklund EG, Larsson DSD, van der Spoel D, Patriksson A, Caleman C. Structural stability of electrosprayed proteins: temperature and hydration effects. Phys Chem Chem Phys 2009; 11:8069-78. [PMID: 19727514 DOI: 10.1039/b903846a] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Electrospray ionization is a gentle method for sample delivery, routinely used in gas-phase studies of proteins. It is crucial for structural investigations that the protein structure is preserved, and a good understanding of how structure is affected by the transition to the gas phase is needed for the tuning of experiments to meet that requirement. Small amounts of residual solvent have been shown to protect the protein, but temperature is important too, although it is not well understood how the latter affects structural details. Using molecular dynamics we have simulated four sparingly hydrated globular proteins (Trp-cage; Ctf, a C-terminal fragment of a bacterial ribosomal protein; ubiquitin; and lysozyme) in vacuum starting at temperatures ranging from 225 K to 425 K. For three of the proteins, our simulations show that a water layer corresponding to 3 A preserves the protein structure in vacuum, up to starting temperatures of 425 K. Only Ctf shows minor secondary structural changes at lower starting temperatures. The structural conservation stems mainly from interactions with the surrounding water. Temperature scales in simulations are not directly translatable into experiments, but the wide temperature range in which we find the proteins to be stable is reassuring for the success of future single particle imaging experiments. The water molecules aggregate in clusters and form patterns on the protein surface, maintaining a reproducible hydrogen bonding network. The simulations were performed mainly using OPLS-AA/L, with cross checks using AMBER03 and GROMOS96 53a6. Only minor differences between the results from the three different force fields were observed.
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Affiliation(s)
- Erik G Marklund
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124, Uppsala, Sweden
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