1
|
Xu T, Wang Q, Wang Q, Sun L. Mass spectrometry-intensive top-down proteomics: an update on technology advancements and biomedical applications. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4664-4682. [PMID: 38973469 DOI: 10.1039/d4ay00651h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Proteoforms are all forms of protein molecules from the same gene because of variations at the DNA, RNA, and protein levels, e.g., alternative splicing and post-translational modifications (PTMs). Delineation of proteins in a proteoform-specific manner is crucial for understanding their biological functions. Mass spectrometry (MS)-intensive top-down proteomics (TDP) is promising for comprehensively characterizing intact proteoforms in complex biological systems. It has achieved substantial progress in technological development, including sample preparation, proteoform separations, MS instrumentation, and bioinformatics tools. In a single TDP study, thousands of proteoforms can be identified and quantified from a cell lysate. It has also been applied to various biomedical research to better our understanding of protein function in regulating cellular processes and to discover novel proteoform biomarkers of diseases for early diagnosis and therapeutic development. This review covers the most recent technological development and biomedical applications of MS-intensive TDP.
Collapse
Affiliation(s)
- Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| |
Collapse
|
2
|
Shaw J, Harvey SR, Du C, Xu Z, Edgington RM, Olmedillas E, Saphire EO, Wysocki VH. Protein complex heterogeneity and topology revealed by electron capture charge reduction and surface induced dissociation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583498. [PMID: 38496594 PMCID: PMC10942452 DOI: 10.1101/2024.03.07.583498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
We illustrate the utility of native mass spectrometry (nMS) combined with a fast, tunable gas-phase charge reduction, electron capture charge reduction (ECCR), for the characterization of protein complex topology and glycoprotein heterogeneity. ECCR efficiently reduces the charge states of tetradecameric GroEL, illustrating Orbitrap m/z measurements to greater than 100,000 m/z. For pentameric C-reactive protein and tetradecameric GroEL, our novel device combining ECCR with surface induced dissociation (SID) reduces the charge states and yields more topologically informative fragmentation. This is the first demonstration that ECCR yields more native-like SID fragmentation. ECCR also significantly improved mass and glycan heterogeneity measurements of heavily glycosylated SARS-CoV-2 spike protein trimer and thyroglobulin dimer. Protein glycosylation is important for structural and functional properties and plays essential roles in many biological processes. The immense heterogeneity in glycosylation sites and glycan structure poses significant analytical challenges that hinder a mechanistic understanding of the biological role of glycosylation. Without ECCR, average mass determination of glycoprotein complexes is available only through charge detection mass spectrometry or mass photometry. With narrow m/z selection windows followed by ECCR, multiple glycoform m/z values are apparent, providing quick global glycoform profiling and providing a future path for glycan localization on individual intact glycoforms.
Collapse
Affiliation(s)
- Jared Shaw
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588
| | - Sophie R. Harvey
- Native Mass Spectrometry Guided Structural Biology Center, Ohio State University, Columbus, OH 43210
| | - Chen Du
- Native Mass Spectrometry Guided Structural Biology Center, Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
| | - Zhixin Xu
- Native Mass Spectrometry Guided Structural Biology Center, Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
| | - Regina M. Edgington
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
| | - Eduardo Olmedillas
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Erica Ollmann Saphire
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037
- Department of Medicine, University of California San Diego, La Jolla, CA 92037
| | - Vicki H. Wysocki
- Native Mass Spectrometry Guided Structural Biology Center, Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
| |
Collapse
|
3
|
Bhuvaneshwari RA, Shivamani A, Sengupta I. Line Shape Analysis of 19F NMR-Monitored Chemical Denaturation of a Fold-Switching Protein RfaH Reveals Its Slow Folding Dynamics. J Phys Chem B 2024; 128:465-471. [PMID: 37991741 DOI: 10.1021/acs.jpcb.3c06550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
The recent discovery of metamorphic proteins, which can switch between multiple conformations under native conditions, has challenged the well-established one sequence-one structure paradigm of protein folding. This is exemplified in the C-terminal domain of the multidomain transcription factor RfaH, which converts from an α-helical coiled-coil conformation in its autoinhibited state to a β-barrel conformation upon activation. Here, we use multisite line shape analysis of 19F NMR-monitored equilibrium chemical denaturation measurements of two 19F-labeled variants of full-length RfaH, to show that it folds/unfolds slowly on the NMR time scale, in an apparent all-or-none fashion at physiological pH and room temperature in the 3.3-4.8 M urea concentration range. The significant thermodynamic stability and slow unfolding rate (kinetic stability) are likely responsible for maintaining the closed autoinhibited state of RfaH, preventing spurious interactions with RNA polymerase (RNAP) when not functional. Our results provide a quantitative understanding of the folding-function relationship in the model fold-switching protein RfaH.
Collapse
Affiliation(s)
| | - Anish Shivamani
- Department of Chemistry, IIT Bombay, Powai, Mumbai 400076, India
| | - Ishita Sengupta
- Department of Chemistry, IIT Bombay, Powai, Mumbai 400076, India
| |
Collapse
|
4
|
Zanetti-Polzi L, Daidone I, Iacobucci C, Amadei A. Thermodynamic Evolution of a Metamorphic Protein: A Theoretical-Computational Study of Human Lymphotactin. Protein J 2023:10.1007/s10930-023-10123-7. [PMID: 37233895 DOI: 10.1007/s10930-023-10123-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2023] [Indexed: 05/27/2023]
Abstract
Metamorphic, or fold-switching, proteins feature different folds that are physiologically relevant. The human chemokine XCL1 (or Lymphotactin) is a metamorphic protein that features two native states, an [Formula: see text] and an all[Formula: see text] fold, which have similar stability at physiological condition. Here, extended molecular dynamics (MD) simulations, principal component analysis of atomic fluctuations and thermodynamic modeling based on both the configurational volume and free energy landscape, are used to obtain a detailed characterization of the conformational thermodynamics of human Lymphotactin and of one of its ancestors (as was previously obtained by genetic reconstruction). Comparison of our computational results with the available experimental data show that the MD-based thermodynamics can explain the experimentally observed variation of the conformational equilibrium between the two proteins. In particular, our computational data provide an interpretation of the thermodynamic evolution in this protein, revealing the relevance of the configurational entropy and of the shape of the free energy landscape within the essential space (i.e., the space defined by the generalized internal coordinates providing the largest, typically non-Gaussian, structural fluctuations).
Collapse
Affiliation(s)
- Laura Zanetti-Polzi
- Center S3, CNR-Institute of Nanoscience, Via Campi 213/A, 100190, Modena, Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio (Coppito 1), 67010, L'Aquila, Italy
| | - Claudio Iacobucci
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio (Coppito 1), 67010, L'Aquila, Italy
| | - Andrea Amadei
- Department of Chemical Science and Technology, University of Rome "Tor Vergata", Via Della Ricerca Scientifica 1, 00185, Rome, Italy.
| |
Collapse
|
5
|
Christofi E, Barran P. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chem Rev 2023; 123:2902-2949. [PMID: 36827511 PMCID: PMC10037255 DOI: 10.1021/acs.chemrev.2c00600] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.
Collapse
Affiliation(s)
- Emilia Christofi
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
6
|
Lantz C, Wei B, Zhao B, Jung W, Goring AK, Le J, Miller J, Loo RRO, Loo JA. Native Top-Down Mass Spectrometry with Collisionally Activated Dissociation Yields Higher-Order Structure Information for Protein Complexes. J Am Chem Soc 2022; 144:21826-21830. [PMID: 36441927 PMCID: PMC10017227 DOI: 10.1021/jacs.2c06726] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Native mass spectrometry (MS) of proteins and protein assemblies reveals size and binding stoichiometry, but elucidating structures to understand their function is more challenging. Native top-down MS (nTDMS), i.e., fragmentation of the gas-phase protein, is conventionally used to derive sequence information, locate post-translational modifications (PTMs), and pinpoint ligand binding sites. nTDMS also endeavors to dissociate covalent bonds in a conformation-sensitive manner, such that information about higher-order structure can be inferred from the fragmentation pattern. However, the activation/dissociation method used can greatly affect the resulting information on protein higher-order structure. Methods such as electron capture/transfer dissociation (ECD and ETD, or ExD) and ultraviolet photodissociation (UVPD) can produce product ions that are sensitive to structural features of protein complexes. For multi-subunit complexes, a long-held belief is that collisionally activated dissociation (CAD) induces unfolding and release of a subunit, and thus is not useful for higher-order structure characterization. Here we show not only that sequence information can be obtained directly from CAD of native protein complexes but that the fragmentation pattern can deliver higher-order structural information about their gas- and solution-phase structures. Moreover, CAD-generated internal fragments (i.e., fragments containing neither N-/C-termini) reveal structural aspects of protein complexes.
Collapse
Affiliation(s)
- Carter Lantz
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Benqian Wei
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Boyu Zhao
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Wonhyeuk Jung
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Andrew K Goring
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Jessie Le
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Justin Miller
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Rachel R Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States.,UCLA-DOE Institute, University of California-Los Angeles, Los Angeles, California 90095, United States.,Molecular Biology Institute, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States.,Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States.,UCLA-DOE Institute, University of California-Los Angeles, Los Angeles, California 90095, United States.,Molecular Biology Institute, University of California-Los Angeles, Los Angeles, California 90095, United States
| |
Collapse
|
7
|
Xi K, Hu Z, Wu Q, Wei M, Qian R, Zhu L. Assessing the Performance of Traveling-salesman based Automated Path Searching (TAPS) on Complex Biomolecular Systems. J Chem Theory Comput 2021; 17:5301-5311. [PMID: 34270241 DOI: 10.1021/acs.jctc.1c00182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Though crucial for understanding the function of large biomolecular systems, locating the minimum free energy paths (MFEPs) between their key conformational states is far from trivial due to their high-dimensional nature. Most existing path-searching methods require a static collective variable space as input, encoding intuition or prior knowledge of the transition mechanism. Such information is, however, hardly available a priori and expensive to validate. To alleviate this issue, we have previously introduced a Traveling-salesman based Automated Path Searching method (TAPS) and demonstrated its efficiency on simple peptide systems. Having implemented a parallel version of this method, here we assess the performance of TAPS on three realistic systems (tens to hundreds of residues) in explicit solvents. We show that TAPS successfully located the MFEP for the ground/excited state transition of the T4 lysozyme L99A variant, consistent with previous findings. TAPS also helped identifying the important role of the two polar contacts in directing the loop-in/loop-out transition of the mitogen-activated protein kinase kinase (MEK1), which explained previous mutant experiments. Remarkably, at a minimal cost of 126 ns sampling, TAPS revealed that the Ltn40/Ltn10 transition of lymphotactin needs no complete unfolding/refolding of its β-sheets and that five polar contacts are sufficient to stabilize the various partially unfolded intermediates along the MFEP. These results present TAPS as a general and promising tool for studying the functional dynamics of complex biomolecular systems.
Collapse
Affiliation(s)
- Kun Xi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong 518172, P. R. China.,School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Zhenquan Hu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong 518172, P. R. China.,School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Qiang Wu
- School of Science and Engineering, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong 518172, P. R. China
| | - Meihan Wei
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong 518172, P. R. China
| | - Runtong Qian
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong 518172, P. R. China
| | - Lizhe Zhu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong 518172, P. R. China
| |
Collapse
|
8
|
Madhurima K, Nandi B, Sekhar A. Metamorphic proteins: the Janus proteins of structural biology. Open Biol 2021; 11:210012. [PMID: 33878950 PMCID: PMC8059507 DOI: 10.1098/rsob.210012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The structural paradigm that the sequence of a protein encodes for a unique three-dimensional native fold does not acknowledge the intrinsic plasticity encapsulated in conformational free energy landscapes. Metamorphic proteins are a recently discovered class of biomolecules that illustrate this plasticity by folding into at least two distinct native state structures of comparable stability in the absence of ligands or cofactors to facilitate fold-switching. The expanding list of metamorphic proteins clearly shows that these proteins are not mere aberrations in protein evolution, but may have actually been a consequence of distinctive patterns in selection pressure such as those found in virus–host co-evolution. In this review, we describe the structure–function relationships observed in well-studied metamorphic protein systems, with specific focus on how functional residues are sequestered or exposed in the two folds of the protein. We also discuss the implications of metamorphosis for protein evolution and the efforts that are underway to predict metamorphic systems from sequence properties alone.
Collapse
Affiliation(s)
- Kulkarni Madhurima
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Bodhisatwa Nandi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|
9
|
Lermyte F, Theisen A, O'Connor PB. Solution Condition-Dependent Formation of Gas-Phase Protomers of Alpha-Synuclein in Electrospray Ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:364-372. [PMID: 33237779 DOI: 10.1021/jasms.0c00373] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
One of the main characteristics of biomolecular ions in mass spectrometry is their net charge, and a range of approaches exist to either increase or decrease this quantity in the gas phase. In the context of small molecules, it is well known that, in addition to the charge state, the charge site also has a profound effect on an ion's gas-phase behavior; however, this effect has been far less explored for peptides and intact proteins. Methods exist to determine charge sites of protein ions, and others have observed that the interplay of electrostatic repulsion and inherent basicity leads to different sites gaining or losing a charge depending on the total net charge. Here, we report two distinct protonation site isomers ("protomers") of α-synuclein occurring at the same charge state. The protomers showed important differences in their gas-phase fragmentation behavior and were furthermore distinguishable by ion mobility spectrometry. One protomer was produced under standard electrospray conditions, while the other was observed after addition of 10% dimethyl sulfoxide to the protein solution. Charge sites for both protomers were determined using ultraviolet photodissociation.
Collapse
Affiliation(s)
- Frederik Lermyte
- Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
- School of Engineering, University of Warwick, Coventry CV4 7AL, U.K
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Alina Theisen
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| |
Collapse
|
10
|
Zhou M, Lantz C, Brown KA, Ge Y, Paša-Tolić L, Loo JA, Lermyte F. Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry. Chem Sci 2020; 11:12918-12936. [PMID: 34094482 PMCID: PMC8163214 DOI: 10.1039/d0sc04392c] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
In biology, it can be argued that if the genome contains the script for a cell's life cycle, then the proteome constitutes an ensemble cast of actors that brings these instructions to life. Their interactions with each other, co-factors, ligands, substrates, and so on, are key to understanding nearly any biological process. Mass spectrometry is well established as the method of choice to determine protein primary structure and location of post-translational modifications. In recent years, top-down fragmentation of intact proteins has been increasingly combined with ionisation of noncovalent assemblies under non-denaturing conditions, i.e., native mass spectrometry. Sequence, post-translational modifications, ligand/metal binding, protein folding, and complex stoichiometry can thus all be probed directly. Here, we review recent developments in this new and exciting field of research. While this work is written primarily from a mass spectrometry perspective, it is targeted to all bioanalytical scientists who are interested in applying these methods to their own biochemistry and chemical biology research.
Collapse
Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Frederik Lermyte
- Department of Chemistry, Institute of Chemistry and Biochemistry, Technical University of Darmstadt 64287 Darmstadt Germany
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège 4000 Liège Belgium
- School of Engineering, University of Warwick Coventry CV4 7AL UK
| |
Collapse
|
11
|
Plant Defensins from a Structural Perspective. Int J Mol Sci 2020; 21:ijms21155307. [PMID: 32722628 PMCID: PMC7432377 DOI: 10.3390/ijms21155307] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 01/12/2023] Open
Abstract
Plant defensins form a family of proteins with a broad spectrum of protective activities against fungi, bacteria, and insects. Furthermore, some plant defensins have revealed anticancer activity. In general, plant defensins are non-toxic to plant and mammalian cells, and interest in using them for biotechnological and medicinal purposes is growing. Recent studies provided significant insights into the mechanisms of action of plant defensins. In this review, we focus on structural and dynamics aspects and discuss structure-dynamics-function relations of plant defensins.
Collapse
|
12
|
Beveridge R, Migas LG, Kriwacki RW, Barran PE. Ion Mobility Mass Spectrometry Measures the Conformational Landscape of p27 and its Domains and how this is Modulated upon Interaction with Cdk2/cyclin A. Angew Chem Int Ed Engl 2019; 58:3114-3118. [PMID: 30570821 PMCID: PMC7122115 DOI: 10.1002/anie.201812697] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/06/2018] [Indexed: 11/09/2022]
Abstract
Intrinsically disordered proteins have been reported to undergo disorder-to-order transitions upon binding to their partners in the cell. The extent of the ordering upon binding and the lack of order prior to binding is difficult to visualize with classical structure determination methods. Binding of p27 to the Cdk2/cyclin A complex is accompanied by partial folding of p27 in the KID domain, with the retention of dynamic behavior for function, particularly in the C-terminal half of the protein. Herein, native ion mobility mass spectrometry (IM-MS) is employed to measure the intrinsic dynamic properties of p27, both in isolation and within the trimeric complex with Cdk2/cyclin A. The trimeric Cdk2/cyclin A/p27-KID complex possesses significant structural heterogeneity compared to Cdk2/cyclin A. These findings support the formation of a fuzzy complex in which both the N- and C-termini of p27 interact with Cdk2/cyclin A in multiple, closely associated states.
Collapse
Affiliation(s)
- Rebecca Beveridge
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | - Lukasz G Migas
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | - Richard W. Kriwacki
- Structural Biology, MS 311, Room D1024F, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678
| | - Perdita E. Barran
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| |
Collapse
|
13
|
Beveridge R, Migas LG, Kriwacki RW, Barran PE. Ion Mobility Mass Spectrometry Measures the Conformational Landscape of p27 and its Domains and how this is Modulated upon Interaction with Cdk2/cyclin A. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rebecca Beveridge
- The Michael Barber Centre for Collaborative Mass SpectrometryThe School of ChemistryManchester Institute for BiotechnologyUniversity of Manchester Manchester UK
| | - Lukasz G. Migas
- The Michael Barber Centre for Collaborative Mass SpectrometryThe School of ChemistryManchester Institute for BiotechnologyUniversity of Manchester Manchester UK
| | - Richard W. Kriwacki
- Structural Biology, MS 311, Room D1024FSt. Jude Children's Research Hospital 262 Danny Thomas Place Memphis TN 38105-3678 USA
| | - Perdita E. Barran
- The Michael Barber Centre for Collaborative Mass SpectrometryThe School of ChemistryManchester Institute for BiotechnologyUniversity of Manchester Manchester UK
| |
Collapse
|
14
|
Stiving AQ, VanAernum ZL, Busch F, Harvey SR, Sarni SH, Wysocki VH. Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure. Anal Chem 2019; 91:190-209. [PMID: 30412666 PMCID: PMC6571034 DOI: 10.1021/acs.analchem.8b05071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Zachary L. VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Samantha H. Sarni
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| |
Collapse
|
15
|
Theisen A, Black R, Corinti D, Brown JM, Bellina B, Barran PE. Initial Protein Unfolding Events in Ubiquitin, Cytochrome c and Myoglobin Are Revealed with the Use of 213 nm UVPD Coupled to IM-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:24-33. [PMID: 29949061 PMCID: PMC6318241 DOI: 10.1007/s13361-018-1992-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 05/11/2023]
Abstract
The initial stages of protein unfolding may reflect the stability of the entire fold and can also reveal which parts of a protein can be perturbed, without restructuring the rest. In this work, we couple UVPD with activated ion mobility mass spectrometry to measure how three model proteins start to unfold. Ubiquitin, cytochrome c and myoglobin ions produced via nESI from salty solutions are subjected to UV irradiation pre-mobility separation; experiments are conducted with a range of source conditions which alter the conformation of the precursor ion as shown by the drift time profiles. For all three proteins, the compact structures result in less fragmentation than more extended structures which emerge following progressive in-source activation. Cleavage sites are found to differ between conformational ensembles, for example, for the dominant charge state of cytochrome c [M + 7H]7+, cleavage at Phe10, Thr19 and Val20 was only observed in activating conditions whilst cleavage at Ala43 is dramatically enhanced. Mapping the photo-cleaved fragments onto crystallographic structures provides insight into the local structural changes that occur as protein unfolding progresses, which is coupled to global restructuring observed in the drift time profiles. Graphical Abstract.
Collapse
Affiliation(s)
- Alina Theisen
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Rachelle Black
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", 00185, Rome, Italy
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| |
Collapse
|
16
|
Lermyte F, Valkenborg D, Loo JA, Sobott F. Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure. MASS SPECTROMETRY REVIEWS 2018; 37:750-771. [PMID: 29425406 PMCID: PMC6131092 DOI: 10.1002/mas.21560] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 05/11/2023]
Abstract
In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their application in "native" mass spectrometry, their mechanism, determinants of fragmentation behavior, and recent developments in available instrumentation. Although we focus on the two most widely used methods-ECD and ETD-we also discuss the use of other ion/electron, ion/ion, and ion/neutral fragmentation methods, useful for interrogation of a range of classes of biomolecules in positive- and negative-ion mode, and speculate about how this exciting field might evolve in the coming years.
Collapse
Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Dirk Valkenborg
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Agoralaan, Diepenbeek, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| |
Collapse
|
17
|
Schneeberger EM, Breuker K. Replacing H + by Na + or K + in phosphopeptide anions and cations prevents electron capture dissociation. Chem Sci 2018; 9:7338-7353. [PMID: 30542537 PMCID: PMC6237128 DOI: 10.1039/c8sc02470g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/07/2018] [Indexed: 01/29/2023] Open
Abstract
By successively replacing H+ by Na+ or K+ in phosphopeptide anions and cations, we show that the efficiency of fragmentation into c and z˙ or c˙ and z fragments from N-Cα backbone bond cleavage by negative ion electron capture dissociation (niECD) and electron capture dissociation (ECD) substantially decreases with increasing number of alkali ions attached. In proton-deficient phosphopeptide ions with a net charge of 2-, we observed an exponential decrease in electron capture efficiency with increasing number of Na+ or K+ ions attached, suggesting that electrons are preferentially captured at protonated sites. In proton-abundant phosphopeptide ions with a net charge of 3+, the electron capture efficiency was not affected by replacing up to four H+ ions with Na+ or K+ ions, but the yield of c, z˙ and c˙, z fragments from N-Cα backbone bond cleavage generally decreased next to Na+ or K+ binding sites. We interpret the site-specific decrease in fragmentation efficiency as Na+ or K+ binding to backbone amide oxygen in competition with interactions of protonated sites that would otherwise lead to backbone cleavage into c, z˙ or c˙, z fragments. Our findings seriously challenge the hypothesis that the positive charge responsible for ECD into c, z˙ or c˙, z fragments can generally be a sodium or other metal ion instead of a proton.
Collapse
Affiliation(s)
- Eva-Maria Schneeberger
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
| | - Kathrin Breuker
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
| |
Collapse
|
18
|
Gadkari VV, Harvey SR, Raper AT, Chu WT, Wang J, Wysocki VH, Suo Z. Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling. Nucleic Acids Res 2018; 46:3103-3118. [PMID: 29529283 PMCID: PMC5888646 DOI: 10.1093/nar/gky125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/23/2018] [Accepted: 02/12/2018] [Indexed: 12/20/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a trimeric ring-shaped clamp protein that encircles DNA and interacts with many proteins involved in DNA replication and repair. Despite extensive structural work to characterize the monomeric, dimeric, and trimeric forms of PCNA alone and in complex with interacting proteins, no structure of PCNA in a ring-open conformation has been published. Here, we use a multidisciplinary approach, including single-molecule Förster resonance energy transfer (smFRET), native ion mobility-mass spectrometry (IM-MS), and structure-based computational modeling, to explore the conformational dynamics of a model PCNA from Sulfolobus solfataricus (Sso), an archaeon. We found that Sso PCNA samples ring-open and ring-closed conformations even in the absence of its clamp loader complex, replication factor C, and transition to the ring-open conformation is modulated by the ionic strength of the solution. The IM-MS results corroborate the smFRET findings suggesting that PCNA dynamics are maintained in the gas phase and further establishing IM-MS as a reliable strategy to investigate macromolecular motions. Our molecular dynamic simulations agree with the experimental data and reveal that ring-open PCNA often adopts an out-of-plane left-hand geometry. Collectively, these results implore future studies to define the roles of PCNA dynamics in DNA loading and other PCNA-mediated interactions.
Collapse
Affiliation(s)
- Varun V Gadkari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Austin T Raper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, NY 11794-3400, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
19
|
Stuchfield D, Barran P. Unique insights to intrinsically disordered proteins provided by ion mobility mass spectrometry. Curr Opin Chem Biol 2018; 42:177-185. [DOI: 10.1016/j.cbpa.2018.01.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 02/05/2023]
|
20
|
D'Atri V, Causon T, Hernandez-Alba O, Mutabazi A, Veuthey JL, Cianferani S, Guillarme D. Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry? J Sep Sci 2017; 41:20-67. [PMID: 29024509 DOI: 10.1002/jssc.201700919] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).
Collapse
Affiliation(s)
- Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Tim Causon
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU Vienna), Vienna, Austria
| | - Oscar Hernandez-Alba
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Aline Mutabazi
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Jean-Luc Veuthey
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Sarah Cianferani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Abstract
In this review, we focus on an important aspect of ion mobility (IM) research, namely the reporting of quantitative ion mobility measurements in the form of the gas-phase collision cross section (CCS), which has provided a common basis for comparison across different instrument platforms and offers a unique form of structural information, namely size and shape preferences of analytes in the absence of bulk solvent. This review surveys the over 24,000 CCS values reported from IM methods spanning the era between 1975 to 2015, which provides both a historical and analytical context for the contributions made thus far, as well as insight into the future directions that quantitative ion mobility measurements will have in the analytical sciences. The analysis was conducted in 2016, so CCS values reported in that year are purposely omitted. In another few years, a review of this scope will be intractable, as the number of CCS values which will be reported in the next three to five years is expected to exceed the total amount currently published in the literature.
Collapse
Affiliation(s)
- Jody C May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Caleb B Morris
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| |
Collapse
|
23
|
Harvey SR, MacPhee CE, Volkman BF, Barran PE. The association and aggregation of the metamorphic chemokine lymphotactin with fondaparinux: from nm molecular complexes to μm molecular assemblies. Chem Commun (Camb) 2016; 52:394-7. [DOI: 10.1039/c5cc05801e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transmission electron microscopy and drift tube ion mobility-mass spectrometry are used to study the assemblies formed by the metamorphic chemokine lymphotactin in the presence of a model glycosaminoglycan.
Collapse
Affiliation(s)
| | - Cait E. MacPhee
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh
- UK
| | - Brian F. Volkman
- Department of Biochemistry
- Medical College of Wisconsin
- Milwaukee
- USA
| | - Perdita E. Barran
- School of Chemistry
- Manchester Institute of Biotechnology
- University of Manchester
- UK
| |
Collapse
|
24
|
Zhao Y, Li L, Wu C, Jiang X, Ge B, Ren H, Huang F. Stable folding intermediates prevent fast interconversion between the closed and open states of Mad2 through its denatured state. Protein Eng Des Sel 2015; 29:23-9. [PMID: 26489879 DOI: 10.1093/protein/gzv056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 09/25/2015] [Indexed: 01/02/2023] Open
Abstract
Different states of metamorphic proteins can interconvert under physiological conditions to realize corresponding functions. The mechanism behind the conversion is critical for understanding how these proteins work. We report a combined thermodynamic and kinetic study on the folding/unfolding process of the open and closed conformers of mitotic arrest deficient protein 2 (Mad2), a metamorphic protein. It has been observed that open Mad2 (O-Mad2) can convert to closed Mad2 (C-Mad2). Our results show that O-Mad2 and C-Mad2 have similar thermodynamic stability, which explains the presence of metamorphosis. The folding/unfolding kinetics suggest that the conversion between O-Mad2 and C-Mad2 would be much faster than that reported previously if this conversion goes through the denatured state (U) directly, i.e. through an O-Mad2-denatured state (U)-C-Mad2 (O-U-C) pathway. This inconsistency implies that there exist stable intermediates in between the native and denatured states of Mad2, which would either slow down the O-U-C interconversion or prevent it going through the denatured state.
Collapse
Affiliation(s)
- Yuanyuan Zhao
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Huadong), Qingdao 266580, PR China Center for Bioengineering and Biotechnology, China University of Petroleum (Huadong), Qingdao 266580, PR China
| | - Lianghui Li
- Huangdao Community Health Service, Qingdao 266500, PR China
| | - Chunfei Wu
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Huadong), Qingdao 266580, PR China Center for Bioengineering and Biotechnology, China University of Petroleum (Huadong), Qingdao 266580, PR China
| | - Xiaoyong Jiang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Huadong), Qingdao 266580, PR China Center for Bioengineering and Biotechnology, China University of Petroleum (Huadong), Qingdao 266580, PR China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Huadong), Qingdao 266580, PR China Center for Bioengineering and Biotechnology, China University of Petroleum (Huadong), Qingdao 266580, PR China
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Huadong), Qingdao 266580, PR China Center for Bioengineering and Biotechnology, China University of Petroleum (Huadong), Qingdao 266580, PR China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Huadong), Qingdao 266580, PR China Center for Bioengineering and Biotechnology, China University of Petroleum (Huadong), Qingdao 266580, PR China
| |
Collapse
|
25
|
Korkmaz EN, Volkman BF, Cui Q. Interplay of Electrostatics and Hydrophobic Effects in the Metamorphic Protein Human Lymphotactin. J Phys Chem B 2015; 119:9547-58. [PMID: 26134347 DOI: 10.1021/acs.jpcb.5b02810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The human lymphotactin (hLtn) is a protein that features two native states both of which are physiologically relevant: it is a monomer (hLtn10) at 10 °C with 200 mM salt and a dimer (hLtn40) at 40 °C and without salt. Here we focus on the networks of electrostatic and hydrophobic interactions that display substantial changes upon the conversion from hLtn10 to hLtn40 since they are expected to modulate the relative stability of the two folds. In addition to the Arg 23-Arg 43 interaction discussed in previous work, we find several other like-charge pairs that are likely important to the stability of hLtn10. Free energy perturbation calculations are carried out to explicitly evaluate the contribution of the Arg 23-Arg 43 interaction to the hLtn10 stability. hLtn40 features a larger number of salt bridges, and a set of hydrophobic residues undergo major changes in the solvent accessible surface area between hLtn10 and hLtn40, pointing to their importance to the relative stability of the two folds. We also discuss the use of explicit and implicit solvent simulations for characterizing the conformational ensembles under different solution conditions.
Collapse
Affiliation(s)
- Elif Nihal Korkmaz
- †Graduate Program in Biophysics, University of Wisconsin-Madison, 1525 Linden Drive, Madison, Wisconsin 53706, United States
| | - Brian F Volkman
- ‡Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, Wisconsin 53226, United States
| | - Qiang Cui
- †Graduate Program in Biophysics, University of Wisconsin-Madison, 1525 Linden Drive, Madison, Wisconsin 53706, United States.,§Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
26
|
Cammarata MB, Thyer R, Rosenberg J, Ellington A, Brodbelt JS. Structural Characterization of Dihydrofolate Reductase Complexes by Top-Down Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2015; 137:9128-35. [PMID: 26125523 DOI: 10.1021/jacs.5b04628] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The stepwise reduction of dihydrofolate to tetrahydrofolate entails significant conformational changes of dihydrofolate reductase (DHFR). Binary and ternary complexes of DHFR containing cofactor NADPH, inhibitor methotrexate (MTX), or both NADPH and MTX were characterized by 193 nm ultraviolet photodissociation (UVPD) mass spectrometry. UVPD yielded over 80% sequence coverage of DHFR and resulted in production of fragment ions that revealed the interactions between DHFR and each ligand. UVPD of the binary DHFR·NADPH and DHFR·MTX complexes led to an unprecedented number of fragment ions containing either an N- or C-terminal protein fragment still bound to the ligand via retention of noncovalent interactions. In addition, holo-fragments retaining both ligands were observed upon UVPD of the ternary DHFR·NADPH·MTX complex. The combination of extensive holo and apo fragment ions allowed the locations of the NADPH and MTX ligands to be mapped, with NADPH associated with the adenosine binding domain of DHFR and MTX interacting with the loop domain. These findings are consistent with previous crystallographic evidence. Comparison of the backbone cleavage propensities for apo DHFR and its holo counterparts revealed significant variations in UVPD fragmentation in the regions expected to experience conformational changes upon binding NADPH, MTX, or both ligands. In particular, the subdomain rotation and loop movements, which are believed to occur upon formation of the transition state of the ternary complex, are reflected in the UVPD mass spectra. The UVPD spectra indicate enhanced backbone cleavages in regions that become more flexible or show suppressed backbone cleavages for those regions either shielded by the ligand or involved in new intramolecular interactions. This study corroborates the versatility of 193 nm UVPD mass spectrometry as a sensitive technique to track enzymatic cycles that involve conformational rearrangements.
Collapse
Affiliation(s)
- Michael B Cammarata
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ross Thyer
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jake Rosenberg
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew Ellington
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
27
|
D'Atri V, Porrini M, Rosu F, Gabelica V. Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:711-26. [PMID: 26259654 PMCID: PMC4440389 DOI: 10.1002/jms.3590] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 03/04/2015] [Accepted: 03/04/2015] [Indexed: 05/13/2023]
Abstract
Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section Ω(EXP). Molecular modelling is used to visualize what ion three-dimensional structure(s) is(are) compatible with the experiment. The collision cross sections of candidate molecular models have to be calculated, and the resulting Ω(CALC) are compared with the experimental data. Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with Ω(EXP) determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)? (2) How to generate plausible 3D models in the gas phase? (3) Different collision cross section calculation models exist, which have been developed for other analytes than mine. Which one(s) can I apply to my systems? To apply ion mobility spectrometry to nucleic acid structural characterization, we explored each of these questions using a rigid structure which we know is preserved in the gas phase: the tetramolecular G-quadruplex [dTGGGGT]4, and we will present these detailed investigation in this tutorial.
Collapse
Affiliation(s)
- Valentina D'Atri
- Univ. Bordeaux, IECB, ARNA laboratoryPessac, F-33600, France
- INSERM, U869, ARNA laboratoryBordeaux, F-33000, France
| | - Massimiliano Porrini
- Univ. Bordeaux, IECB, ARNA laboratoryPessac, F-33600, France
- INSERM, U869, ARNA laboratoryBordeaux, F-33000, France
| | | | - Valérie Gabelica
- Univ. Bordeaux, IECB, ARNA laboratoryPessac, F-33600, France
- INSERM, U869, ARNA laboratoryBordeaux, F-33000, France
| |
Collapse
|
28
|
Durbin KR, Skinner OS, Fellers RT, Kelleher NL. Analyzing internal fragmentation of electrosprayed ubiquitin ions during beam-type collisional dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:782-7. [PMID: 25716753 PMCID: PMC4401654 DOI: 10.1007/s13361-015-1078-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/31/2014] [Accepted: 12/31/2014] [Indexed: 05/11/2023]
Abstract
Gaseous fragmentation of intact proteins is multifaceted and can be unpredictable by current theories in the field. Contributing to the complexity is the multitude of precursor ion states and fragmentation channels. Terminal fragment ions can be re-fragmented, yielding product ions containing neither terminus, termed internal fragment ions. In an effort to better understand and capitalize upon this fragmentation process, we collisionally dissociated the high (13+), middle (10+), and low (7+) charge states of electrosprayed ubiquitin ions. Both terminal and internal fragmentation processes were quantified through step-wise increases of voltage potential in the collision cell. An isotope fitting algorithm matched observed product ions to theoretical terminal and internal fragment ions. At optimal energies for internal fragmentation of the 10+, nearly 200 internal fragments were observed; on average each of the 76 residues in ubiquitin was covered by 24.1 internal fragments. A pertinent finding was that formation of internal ions occurs at similar energy thresholds as terminal b- and y-ion types in beam-type activation. This large amount of internal fragmentation is frequently overlooked during top-down mass spectrometry. As such, we present several new approaches to visualize internal fragments through modified graphical fragment maps. With the presented advances of internal fragment ion accounting and visualization, the total percentage of matched fragment ions increased from approximately 40% to over 75% in a typical beam-type MS/MS spectrum. These sequence coverage improvements offer greater characterization potential for whole proteins with no needed experimental changes and could be of large benefit for future high-throughput intact protein analysis.
Collapse
Affiliation(s)
- Kenneth R Durbin
- Departments of Chemistry and Molecular Biosciences, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | | | | | | |
Collapse
|
29
|
Harvey SR, Porrini M, Tyler RC, MacPhee CE, Volkman BF, Barran PE. Electron capture dissociation and drift tube ion mobility-mass spectrometry coupled with site directed mutations provide insights into the conformational diversity of a metamorphic protein. Phys Chem Chem Phys 2015; 17:10538-50. [DOI: 10.1039/c4cp05136j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ion mobility mass spectrometry can be combined with data from top-down sequencing to discern adopted conformations of proteins in the absence of solvent.
Collapse
Affiliation(s)
| | - Massimiliano Porrini
- Institut Européen de Chimie et Biologie (IECB)
- U869 ARNA – Inserm 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
- USA
| | - Cait E. MacPhee
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh
- UK
| | - Brian F. Volkman
- Department of Biochemistry
- Medical College of Wisconsin
- Milwaukee
- USA
| | - Perdita E. Barran
- School of Chemistry
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| |
Collapse
|
30
|
Katari M, Payen de la Garanderie E, Nicol E, Steinmetz V, van der Rest G, Carmichael D, Frison G. Combining gas phase electron capture and IRMPD action spectroscopy to probe the electronic structure of a metastable reduced organometallic complex containing a non-innocent ligand. Phys Chem Chem Phys 2015; 17:25689-92. [DOI: 10.1039/c5cp01501d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Gas-phase reduction of a Zn(ii) complex followed by IR spectroscopy shows that the incoming electron is localized on the metal rather than on the ligand.
Collapse
Affiliation(s)
- Madanakrishna Katari
- Laboratoire de Chimie Moléculaire
- Ecole polytechnique and CNRS
- 91128 Palaiseau Cedex
- France
| | | | - Edith Nicol
- Laboratoire de Chimie Moléculaire
- Ecole polytechnique and CNRS
- 91128 Palaiseau Cedex
- France
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique
- Université Paris Sud
- CNRS
- 91405 Orsay
- France
| | | | - Duncan Carmichael
- Laboratoire de Chimie Moléculaire
- Ecole polytechnique and CNRS
- 91128 Palaiseau Cedex
- France
| | - Gilles Frison
- Laboratoire de Chimie Moléculaire
- Ecole polytechnique and CNRS
- 91128 Palaiseau Cedex
- France
| |
Collapse
|
31
|
Beveridge R, Covill S, Pacholarz KJ, Kalapothakis JMD, MacPhee CE, Barran PE. A Mass-Spectrometry-Based Framework To Define the Extent of Disorder in Proteins. Anal Chem 2014; 86:10979-91. [DOI: 10.1021/ac5027435] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rebecca Beveridge
- Manchester
Institute of Biotechnology, Michael Barber Centre for Collaborative
Mass Spectrometry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Sam Covill
- School
of Chemistry, University of Edinburgh, Joseph Black Building, West Mains
Road, Edinburgh EH9 3JJ, United Kingdom
| | - Kamila J. Pacholarz
- School
of Chemistry, University of Edinburgh, Joseph Black Building, West Mains
Road, Edinburgh EH9 3JJ, United Kingdom
| | - Jason M. D. Kalapothakis
- School
of Chemistry, University of Edinburgh, Joseph Black Building, West Mains
Road, Edinburgh EH9 3JJ, United Kingdom
- School
of Physics and Astronomy, University of Edinburgh, James Clerk
Maxwell Building, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - Cait E. MacPhee
- School
of Physics and Astronomy, University of Edinburgh, James Clerk
Maxwell Building, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - Perdita E. Barran
- Manchester
Institute of Biotechnology, Michael Barber Centre for Collaborative
Mass Spectrometry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| |
Collapse
|