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Degliesposti G. Probing Protein Complexes Composition, Stoichiometry, and Interactions by Peptide-Based Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:41-57. [PMID: 38507199 DOI: 10.1007/978-3-031-52193-5_4] [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
The characterization of a protein complex by mass spectrometry can be conducted at different levels. Initial steps regard the qualitative composition of the complex and subunit identification. After that, quantitative information such as stoichiometric ratios and copy numbers for each subunit in a complex or super-complex is acquired. Peptide-based LC-MS/MS offers a wide number of methods and protocols for the characterization of protein complexes. This chapter concentrates on the applications of peptide-based LC-MS/MS for the qualitative, quantitative, and structural characterization of protein complexes focusing on subunit identification, determination of stoichiometric ratio and number of subunits per complex as well as on cross-linking mass spectrometry and hydrogen/deuterium exchange as methods for the structural investigation of the biological assemblies.
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2
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Zhu Y, Yun SD, Zhang T, Chang JY, Stover L, Laganowsky A. Native mass spectrometry of proteoliposomes containing integral and peripheral membrane proteins. Chem Sci 2023; 14:14243-14255. [PMID: 38098719 PMCID: PMC10718073 DOI: 10.1039/d3sc04938h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/18/2023] [Indexed: 12/17/2023] Open
Abstract
Cellular membranes are critical to the function of membrane proteins, whether they are associated (peripheral) or embedded (integral) within the bilayer. While detergents have contributed to our understanding of membrane protein structure and function, there remains challenges in characterizing protein-lipid interactions within the context of an intact membrane. Here, we developed a method to prepare proteoliposomes for native mass spectrometry (MS) studies. We first use native MS to detect the encapsulation of soluble proteins within liposomes. We then find the peripheral Gβ1γ2 complex associated with the membrane can be ejected and analyzed using native MS. Four different integral membrane proteins (AmtB, AqpZ, TRAAK, and TREK2), all of which have previously been characterized in detergent, eject from the proteoliposomes as intact complexes bound to lipids that have been shown to tightly associate in detergent, drawing a correlation between the two approaches. We also show the utility of more complex lipid environments, such as a brain polar lipid extract, and show TRAAK ejects from liposomes of this extract bound to lipids. These findings underscore the capability to eject protein complexes from membranes bound to both lipids and metal ions, and this approach will be instrumental in the identification of key protein-lipid interactions.
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Affiliation(s)
- Yun Zhu
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Sangho D Yun
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Jing-Yuan Chang
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Lauren Stover
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
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3
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Panda A, Brown C, Gupta K. Studying Membrane Protein-Lipid Specificity through Direct Native Mass Spectrometric Analysis from Tunable Proteoliposomes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1917-1927. [PMID: 37432128 PMCID: PMC10932607 DOI: 10.1021/jasms.3c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Native mass spectrometry (nMS) has emerged as a key analytical tool to study the organizational states of proteins and their complexes with both endogenous and exogenous ligands. Specifically, for membrane proteins, it provides a key analytical dimension to determine the identity of bound lipids and to decipher their effects on the observed structural assembly. We recently developed an approach to study membrane proteins directly from intact and tunable lipid membranes where both the biophysical properties of the membrane and its lipid compositions can be customized. Extending this, we use our liposome-nMS platform to decipher the lipid specificity of membrane proteins through their multiorganelle trafficking pathways. To demonstrate this, we used VAMP2 and reconstituted it in the endoplasmic reticulum (ER), Golgi, synaptic vesicle (SV), and plasma membrane (PM) mimicking liposomes. By directly studying VAMP2 from these customized liposomes, we show how the same transmembrane protein can bind to different sets of lipids in different organellar-mimicking membranes. Considering that the cellular trafficking pathway of most eukaryotic integral membrane proteins involves residence in multiple organellar membranes, this study highlights how the lipid-specificity of the same integral membrane protein may change depending on the membrane context. Further, leveraging the capability of the platform to study membrane proteins from liposomes with curated biophysical properties, we show how we can disentangle chemical versus biophysical properties, of individual lipids in regulating membrane protein assembly.
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Affiliation(s)
- Aniruddha Panda
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Caroline Brown
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Kallol Gupta
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
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4
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Zhu Y, Odenkirk MT, Qiao P, Zhang T, Schrecke S, Zhou M, Marty MT, Baker ES, Laganowsky A. Combining native mass spectrometry and lipidomics to uncover specific membrane protein-lipid interactions from natural lipid sources. Chem Sci 2023; 14:8570-8582. [PMID: 37593000 PMCID: PMC10430552 DOI: 10.1039/d3sc01482g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023] Open
Abstract
While it is known that lipids play an essential role in regulating membrane protein structure and function, it remains challenging to identify specific protein-lipid interactions. Here, we present an innovative approach that combines native mass spectrometry (MS) and lipidomics to identify lipids retained by membrane proteins from natural lipid extracts. Our results reveal that the bacterial ammonia channel (AmtB) enriches specific cardiolipin (CDL) and phosphatidylethanolamine (PE) from natural headgroup extracts. When the two extracts are mixed, AmtB retains more species, wherein selectivity is tuned to bias headgroup selection. Using a series of natural headgroup extracts, we show TRAAK, a two-pore domain K+ channel (K2P), retains specific acyl chains that is independent of the headgroup. A brain polar lipid extract was then combined with the K2Ps, TRAAK and TREK2, to understand lipid specificity. More than a hundred lipids demonstrated affinity for each protein, and both channels were found to retain specific fatty acids and lysophospholipids known to stimulate channel activity, even after several column washes. Natural lipid extracts provide the unique opportunity to not only present natural lipid diversity to purified membrane proteins but also identify lipids that may be important for membrane protein structure and function.
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Affiliation(s)
- Yun Zhu
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Melanie T Odenkirk
- Department of Chemistry, North Carolina State University Raleigh NC 27695 USA
| | - Pei Qiao
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine Houston TX 77030 USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, The University of Arizona Tucson AZ 85721 USA
| | - Erin S Baker
- Department of Chemistry, University of North Carolina Chapel Hill NC 27514 USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
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5
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Abdul-Khalek N, Wimmer R, Overgaard MT, Gregersen Echers S. Insight on physicochemical properties governing peptide MS1 response in HPLC-ESI-MS/MS: A deep learning approach. Comput Struct Biotechnol J 2023; 21:3715-3727. [PMID: 37560124 PMCID: PMC10407266 DOI: 10.1016/j.csbj.2023.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023] Open
Abstract
Accurate and absolute quantification of peptides in complex mixtures using quantitative mass spectrometry (MS)-based methods requires foreground knowledge and isotopically labeled standards, thereby increasing analytical expenses, time consumption, and labor, thus limiting the number of peptides that can be accurately quantified. This originates from differential ionization efficiency between peptides and thus, understanding the physicochemical properties that influence the ionization and response in MS analysis is essential for developing less restrictive label-free quantitative methods. Here, we used equimolar peptide pool repository data to develop a deep learning model capable of identifying amino acids influencing the MS1 response. By using an encoder-decoder with an attention mechanism and correlating attention weights with amino acid physicochemical properties, we obtain insight on properties governing the peptide-level MS1 response within the datasets. While the problem cannot be described by one single set of amino acids and properties, distinct patterns were reproducibly obtained. Properties are grouped in three main categories related to peptide hydrophobicity, charge, and structural propensities. Moreover, our model can predict MS1 intensity output under defined conditions based solely on peptide sequence input. Using a refined training dataset, the model predicted log-transformed peptide MS1 intensities with an average error of 9.7 ± 0.5% based on 5-fold cross validation, and outperformed random forest and ridge regression models on both log-transformed and real scale data. This work demonstrates how deep learning can facilitate identification of physicochemical properties influencing peptide MS1 responses, but also illustrates how sequence-based response prediction and label-free peptide-level quantification may impact future workflows within quantitative proteomics.
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Affiliation(s)
- Naim Abdul-Khalek
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
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6
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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: 32] [Impact Index Per Article: 32.0] [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.
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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
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7
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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. Presented extensive molecular dynamics (MD) simulation data investigating protein vacuum exposure and rehydration dynamics. Demonstrated that the majority of the protein structure recovers their initial solution conformation after vacuum exposure. Explored the potential gain for structural biology of using MD simulation to refine gas-phase determined protein structures.
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8
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Kumar S, Zhu Y, Stover L, Laganowsky A. Step toward Probing the Nonannular Belt of Membrane Proteins. Anal Chem 2022; 94:13906-13912. [PMID: 36170465 DOI: 10.1021/acs.analchem.2c02811] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Integral membrane proteins are embedded in the biological membrane, where they carry out numerous biological processes. Although lipids present in the membrane are crucial for membrane protein function, it remains difficult to characterize many lipid binding events to membrane proteins, such as those that form the annular belt. Here, we use native mass spectrometry along with the charge-reducing properties of trimethylamine N-oxide (TMAO) to characterize a large number of lipid binding events to the bacterial ammonia channel (AmtB). In the absence of TMAO, significant peak overlap between neighboring charge states is observed, resulting in erroneous abundances for different molecular species. With the addition of TMAO, the weighted average charge state (Zavg) was decreased. In addition, the increased spacing between nearby charge states enabled a higher number of lipid binding species to be observed while minimizing mass spectral peak overlap. These conditions helped us to determine the equilibrium binding constants (Kd) for up to 16 lipid binding events. The binding constants for the first few lipid binding events display the highest affinity, whereas the binding constants for higher lipid binding events converge to a similar value. These findings suggest a transition from nonannular to annular lipid binding to AmtB.
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Affiliation(s)
- Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yun Zhu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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9
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Esser TK, Böhning J, Fremdling P, Agasid MT, Costin A, Fort K, Konijnenberg A, Gilbert JD, Bahm A, Makarov A, Robinson CV, Benesch JLP, Baker L, Bharat TAM, Gault J, Rauschenbach S. Mass-selective and ice-free electron cryomicroscopy protein sample preparation via native electrospray ion-beam deposition. PNAS NEXUS 2022; 1:pgac153. [PMID: 36714824 PMCID: PMC9802471 DOI: 10.1093/pnasnexus/pgac153] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/03/2022] [Indexed: 02/01/2023]
Abstract
Despite tremendous advances in sample preparation and classification algorithms for electron cryomicroscopy (cryo-EM) and single-particle analysis (SPA), sample heterogeneity remains a major challenge and can prevent access to high-resolution structures. In addition, optimization of preparation conditions for a given sample can be time-consuming. In the current work, it is demonstrated that native electrospray ion-beam deposition (native ES-IBD) is an alternative, reliable approach for the preparation of extremely high-purity samples, based on mass selection in vacuum. Folded protein ions are generated by native electrospray ionization, separated from other proteins, contaminants, aggregates, and fragments, gently deposited on cryo-EM grids, frozen in liquid nitrogen, and subsequently imaged by cryo-EM. We demonstrate homogeneous coverage of ice-free cryo-EM grids with mass-selected protein complexes. SPA reveals that the complexes remain folded and assembled, but variations in secondary and tertiary structures are currently limiting information in 2D classes and 3D EM density maps. We identify and discuss challenges that need to be addressed to obtain a resolution comparable to that of the established cryo-EM workflow. Our results show the potential of native ES-IBD to increase the scope and throughput of cryo-EM for protein structure determination and provide an essential link between gas-phase and solution-phase protein structures.
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Affiliation(s)
| | - Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | | | | | - Kyle Fort
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany
| | - Albert Konijnenberg
- Thermo Fisher Scientific, Zwaanstraat 31G/H, 5651 CA Eindhoven, The Netherlands
| | - Joshua D Gilbert
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Alan Bahm
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Alexander Makarov
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | | | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK,Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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10
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van Dyck JF, Burns JR, Le Huray KIP, Konijnenberg A, Howorka S, Sobott F. Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility. Nat Commun 2022; 13:3610. [PMID: 35750666 PMCID: PMC9232653 DOI: 10.1038/s41467-022-31029-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 05/30/2022] [Indexed: 11/09/2022] Open
Abstract
Recent interest in biological and synthetic DNA nanostructures has highlighted the need for methods to comprehensively characterize intermediates and end products of multimeric DNA assembly. Here we use native mass spectrometry in combination with ion mobility to determine the mass, charge state and collision cross section of noncovalent DNA assemblies, and thereby elucidate their structural composition, oligomeric state, overall size and shape. We showcase the approach with a prototypical six-subunit DNA nanostructure to reveal how its assembly is governed by the ionic strength of the buffer, as well as how the mass and mobility of heterogeneous species can be well resolved by careful tuning of instrumental parameters. We find that the assembly of the hexameric, barrel-shaped complex is guided by positive cooperativity, while previously undetected higher-order 12- and 18-mer assemblies are assigned to defined larger-diameter geometric structures. Guided by our insight, ion mobility-mass spectrometry is poised to make significant contributions to understanding the formation and structural diversity of natural and synthetic oligonucleotide assemblies relevant in science and technology.
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Affiliation(s)
- Jeroen F van Dyck
- Biomolecular & Analytical Mass Spectrometry, Chemistry Department, University of Antwerp, Antwerpen, Belgium
| | - Jonathan R Burns
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, London, UK
| | - Kyle I P Le Huray
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry, Chemistry Department, University of Antwerp, Antwerpen, Belgium.,Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Chemistry Department, University of Antwerp, Antwerpen, Belgium. .,School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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11
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Das S, Bhatia R. Liquid extraction surface analysis-mass spectrometry: An advanced and environment-friendly analytical tool in modern analysis. J Sep Sci 2022; 45:2746-2765. [PMID: 35579471 DOI: 10.1002/jssc.202100996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/23/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022]
Abstract
The Liquid Extraction Surface Analysis technique is a new high-throughput instrument for ambient mass spectrometry. The benefits of the Liquid Extraction Surface Analysis-Mass Spectrometry approach are the high throughput screening of samples and the absence of sample preparation. Liquid Extraction Surface Analysis-Mass Spectrometry also consumes less solvent for extraction, making it more environmentally friendly and there is no substrate restriction. It utilizes advanced instrumentation like the use of robotic pipettes, nanoelectrospray systems, electronspray ionization chips which makes it highly efficient. In recent years, Liquid Extraction Surface Analysis-Mass Spectrometry has seen widespread use in a variety of analytical fields including drug metabolite analysis, mapping drug distribution in tissues, protein and lipid characterization etc. In this review, we have summarized the basic working principles of the Liquid Extraction Surface Analysis-Mass Spectrometry approach in detail along with a detailed description of the recently reported applications in the analysis of proteins, lipids, drugs and foods. The investigated analytes along with detection methodologies and significant outcomes of various research reports have been presented with the help of tables. This tool has also been utilized in clinical investigations of biological fluids, fingerprint analysis and authentication of agarwood. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shibam Das
- Department of Pharmaceutical Chemistry & Analysis, ISF College of Pharmacy Moga, Punjab, 142001, India
| | - Rohit Bhatia
- Department of Pharmaceutical Chemistry & Analysis, ISF College of Pharmacy Moga, Punjab, 142001, India
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12
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Giska F, Mariappan M, Bhattacharyya M, Gupta K. Deciphering the molecular organization of GET pathway chaperones through native mass spectrometry. Biophys J 2022; 121:1289-1298. [PMID: 35189106 PMCID: PMC9034188 DOI: 10.1016/j.bpj.2022.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/25/2021] [Accepted: 02/15/2022] [Indexed: 11/02/2022] Open
Abstract
Get3/4/5 chaperone complex is responsible for targeting C-terminal tail-anchored membrane proteins to the endoplasmic reticulum. Despite the availability of several crystal structures of independent proteins and partial structures of subcomplexes, different models of oligomeric states and structural organization have been proposed for the protein complexes involved. Here, using native mass spectrometry (Native-MS), coupled with intact dissociation, we show that Get4/5 exclusively forms a tetramer using both Get5/5 and a novel Get4/4 dimerization interface. Addition of Get3 to this leads to a hexameric (Get3)2-(Get4)2-(Get5)2 complex with closed-ring cyclic architecture. We further validate our claims through molecular modeling and mutational abrogation of the proposed interfaces. Native-MS has become a principal tool to determine the state of oligomeric organization of proteins. The work demonstrates that for multiprotein complexes, native-MS, coupled with molecular modeling and mutational perturbation, can provide an alternative route to render a detailed view of both the oligomeric states as well as the molecular interfaces involved. This is especially useful for large multiprotein complexes with large unstructured domains that make it recalcitrant to conventional structure determination approaches.
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Affiliation(s)
- Fabian Giska
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut; Nanobiology Institute, Yale University, West Haven, Connecticut
| | - Malaiyalam Mariappan
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut; Nanobiology Institute, Yale University, West Haven, Connecticut
| | | | - Kallol Gupta
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut; Nanobiology Institute, Yale University, West Haven, Connecticut.
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13
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Carlo MJ, Patrick AL. Infrared multiple photon dissociation (IRMPD) spectroscopy and its potential for the clinical laboratory. J Mass Spectrom Adv Clin Lab 2022; 23:14-25. [PMID: 34993503 PMCID: PMC8713122 DOI: 10.1016/j.jmsacl.2021.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022] Open
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy is a powerful tool used to probe the vibrational modes-and, by extension, the structure-of an ion within an ion trap mass spectrometer. Compared to traditional FTIR spectroscopy, IRMPD spectroscopy has advantages including its sensitivity and its relative ability to handle complex mixtures. While IRMPD has historically been a technique for fundamental analyses, it is increasingly being applied in a more analytical fashion. Notable recent demonstrations pertinent to the clinical laboratory and adjacent interests include analysis of modified amino acids/residues and carbohydrates, structural elucidation (including isomeric differentiation) of metabolites, identification of novel illicit drugs, and structural studies of various biomolecules and pharmaceuticals. Improvements in analysis time, coupling to commercial instruments, and integration with separations methods are all drivers toward the realization of these analytical applications. Additional improvements in these areas, along with advances in benchtop tunable IR sources and increased cross-discipline collaboration, will continue to drive innovation and widespread adoption. The goal of this tutorial article is to briefly present the fundamentals and instrumentation of IRMPD spectroscopy, as an overview of the utility of this technique for helping to answer questions relevant to clinical analysis, and to highlight limitations to widespread adoption, as well as promising directions in which the field may be heading.
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Key Words
- 2-AEP, 2-aminoethylphosphonic acid
- 2P1EA, 2-phenyl-1-ethanolamine
- CIVP, cryogenic ion vibrational predissociation spectroscopy
- CLIO, Centre Laser Infrarouge d’Orsay
- DFT, density functional theory
- FA, fluoroamphetamine
- FEL, free electron laser
- FELIX, Free Electron Laser for Infrared eXperiments
- FMA, fluoromethamphetamine
- FTICR, Fourier transform ion cyclotron resonance
- GC–MS, gas chromatography-mass spectrometry
- GSNO, S- nitro glutathione
- GlcNAc, n-Acetylglucosamine
- IR, infrared
- IR2MS3, infrared-infrared double-resonance multi-stage mass spectrometry
- IRMPD, infrared multiple photon dissociation (IRMPD)
- IRMPD-MS, infrared multiple photon dissociation spectroscopy mass spectrometry
- IRPD, infrared predissociation spectroscopy
- IVR, intramolecular vibrational redistribution
- Infrared multiple photon dissociation spectroscopy
- LC, liquid chromatography
- LC-MS, liquid chromatography-mass spectrometry
- LC-MS/MS, liquid chromatography-tandem mass spectrometry
- MDA, methylenedioxyamphetamine
- MDMA, methylenedioxymethamphetamine
- MMC, methylmethcathinone
- MS/MS, tandem mass spectrometry
- MSn, multi-stage mass spectrometry
- Mass spectrometry
- Metabolites
- NANT, N-acetyl-N-nitrosotryptophan
- OPO/A, optical parametric oscillator/amplifier
- PTM, post-translational modification
- Pharmaceuticals
- Post-translational modifications
- SNOCys, S-nitrosocysteine
- UV, ultraviolet
- UV-IR, ultraviolet-infrared
- Vibrational spectroscopy
- cw, continuous wave
- α-PVP, alpha-pyrrolidinovalerophenone
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Affiliation(s)
- Matthew J. Carlo
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Amanda L. Patrick
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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14
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Qiao P, Schrecke S, Walker T, McCabe JW, Lyu J, Zhu Y, Zhang T, Kumar S, Clemmer D, Russell DH, Laganowsky A. Entropy in the Molecular Recognition of Membrane Protein-Lipid Interactions. J Phys Chem Lett 2021; 12:12218-12224. [PMID: 34928154 PMCID: PMC8905501 DOI: 10.1021/acs.jpclett.1c03750] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Understanding the molecular driving forces that underlie membrane protein-lipid interactions requires the characterization of their binding thermodynamics. Here, we employ variable-temperature native mass spectrometry to determine the thermodynamics of lipid binding events to the human G-protein-gated inward rectifier potassium channel, Kir3.2. The channel displays distinct thermodynamic strategies to engage phosphatidylinositol (PI) and phosphorylated forms thereof. The addition of a 4'-phosphate to PI results in an increase in favorable entropy. PI with two or more phosphates exhibits more complex binding, where lipids appear to bind two nonidentical sites on Kir3.2. Remarkably, the interaction of 4,5-bisphosphate PI with Kir3.2 is solely driven by a large, favorable change in entropy. Installment of a 3'-phosphate to PI(4,5)P2 results in an altered thermodynamic strategy. The acyl chain of the lipid has a marked impact on binding thermodynamics and, in some cases, enthalpy becomes favorable.
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Affiliation(s)
- Pei Qiao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yun Zhu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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15
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Abramsson ML, Sahin C, Hopper JTS, Branca RMM, Danielsson J, Xu M, Chandler SA, Österlund N, Ilag LL, Leppert A, Costeira-Paulo J, Lang L, Teilum K, Laganowsky A, Benesch JLP, Oliveberg M, Robinson CV, Marklund EG, Allison TM, Winther JR, Landreh M. Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry. JACS AU 2021; 1:2385-2393. [PMID: 34977906 PMCID: PMC8717373 DOI: 10.1021/jacsau.1c00458] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Indexed: 05/03/2023]
Abstract
In solution, the charge of a protein is intricately linked to its stability, but electrospray ionization distorts this connection, potentially limiting the ability of native mass spectrometry to inform about protein structure and dynamics. How the behavior of intact proteins in the gas phase depends on the presence and distribution of ionizable surface residues has been difficult to answer because multiple chargeable sites are present in virtually all proteins. Turning to protein engineering, we show that ionizable side chains are completely dispensable for charging under native conditions, but if present, they are preferential protonation sites. The absence of ionizable side chains results in identical charge state distributions under native-like and denaturing conditions, while coexisting conformers can be distinguished using ion mobility separation. An excess of ionizable side chains, on the other hand, effectively modulates protein ion stability. In fact, moving a single ionizable group can dramatically alter the gas-phase conformation of a protein ion. We conclude that although the sum of the charges is governed solely by Coulombic terms, their locations affect the stability of the protein in the gas phase.
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Affiliation(s)
- Mia L. Abramsson
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
| | - Cagla Sahin
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
- Linderstrøm-Lang
Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Jonathan T. S. Hopper
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Rui M. M. Branca
- Department
of Oncology-Pathology, Science for Life
Laboratory and Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Jens Danielsson
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Mingming Xu
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Shane A. Chandler
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Nicklas Österlund
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Leopold L. Ilag
- Department
of Material and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Axel Leppert
- Department
of Biosciences and Nutrition, Karolinska
Institutet, Neo, 141 83 Huddinge, Sweden
| | - Joana Costeira-Paulo
- Department
of Chemistry−BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Lisa Lang
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Kaare Teilum
- Linderstrøm-Lang
Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Arthur Laganowsky
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Justin L. P. Benesch
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Mikael Oliveberg
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Carol V. Robinson
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Erik G. Marklund
- Department
of Chemistry−BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Timothy M. Allison
- Biomolecular
Interaction Centre, School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jakob R. Winther
- Linderstrøm-Lang
Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Michael Landreh
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
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16
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Donor MT, Wilson JW, Shepherd SO, Prell JS. Lipid Head Group Adduction to Soluble Proteins Follows Gas-Phase Basicity Predictions: Dissociation Barriers and Charge Abstraction. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 469:116670. [PMID: 34421332 PMCID: PMC8372978 DOI: 10.1016/j.ijms.2021.116670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Native mass spectrometry analysis of membrane proteins has yielded many useful insights in recent years with respect to membrane protein-lipid interactions, including identifying specific interactions and even measuring binding affinities based on observed abundances of lipid-bound ions after collision-induced dissociation (CID). However, the behavior of non-covalent complexes subjected to extensive CID can in principle be affected by numerous factors related to gas-phase chemistry, including gas-phase basicity (GB) and acidity, shared-proton bonds, and other factors. A recent report from our group showed that common lipids span a wide range of GB values. Notably, phosphatidylcholine (PC) and sphingomyelin lipids are more basic than arginine, suggesting they may strip charge upon dissociation in positive ion mode, while phosphoserine lipids are slightly less basic than arginine and may form especially strong shared-proton bonds. Here, we use CID to probe the strength of non-specific gas-phase interactions between lipid head groups and several soluble proteins, used to deliberately avoid possible physiological protein-lipid interactions. The strengths of the protein-head group interactions follow the trend predicted based solely on lipid and amino acid GBs: phosphoserine (PS) head group forms the strongest bonds with these proteins and out-competes the other head groups studied, while glycerophosphocholine (GPC) head groups form the weakest interactions and dissociate carrying away a positive charge. These results indicate that gas-phase thermochemistry can play an important role in determining which head groups remain bound to protein ions with native-like structures and charge states in positive ion mode upon extensive collisional activation.
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Affiliation(s)
- Micah T. Donor
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - Jesse W. Wilson
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - Samantha O. Shepherd
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
- Materials Science Institute, University of Oregon, 1252 University of Oregon, Eugene, OR 97403-1252
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17
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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18
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Otsuka Y. Direct Liquid Extraction and Ionization Techniques for Understanding Multimolecular Environments in Biological Systems (Secondary Publication). Mass Spectrom (Tokyo) 2021; 10:A0095. [PMID: 34249586 PMCID: PMC8246329 DOI: 10.5702/massspectrometry.a0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 11/23/2022] Open
Abstract
A combination of direct liquid extraction using a small volume of solvent and electrospray ionization allows the rapid measurement of complex chemical components in biological samples and visualization of their distribution in tissue sections. This review describes the development of such techniques and their application to biological research since the first reports in the early 2000s. An overview of electrospray ionization, ion suppression in samples, and the acceleration of specific chemical reactions in charged droplets is also presented. Potential future applications for visualizing multimolecular environments in biological systems are discussed.
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Affiliation(s)
- Yoichi Otsuka
- Graduate School of Science, Osaka University, 1–1 Machikaneyama-cho, Toyonaka, Osaka 560–0043, Japan
- JST, PRESTO, 4–1–8 Honcho, Kawaguchi, Saitama 332–0012, Japan
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19
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Chakraborty D, Banerjee A, Wales DJ. Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides. J Phys Chem B 2021; 125:5809-5822. [PMID: 34037392 PMCID: PMC8279551 DOI: 10.1021/acs.jpcb.1c02412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
intrinsic conformational preferences of small peptides may
provide additional insight into the thermodynamics and kinetics of
protein folding. In this study, we explore the underlying energy landscapes
of two model peptides, namely, Ac-Ala-NH2 and Ac-Ser-NH2, using geometry-optimization-based tools developed within
the context of energy landscape theory. We analyze not only how side-chain
polarity influences the structural preferences of the dipeptides,
but also other emergent properties of the landscape, including heat
capacity profiles, and kinetics of conformational rearrangements.
The contrasting topographies of the free energy landscape agree with
recent results from Fourier transform microwave spectroscopy experiments,
where Ac-Ala-NH2 was found to exist as a mixture of two
conformers, while Ac-Ser-NH2 remained structurally locked,
despite exhibiting an apparently rich conformational landscape.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Atreyee Banerjee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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20
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What's in a mass? Biochem Soc Trans 2021; 49:1027-1037. [PMID: 33929513 DOI: 10.1042/bst20210288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/27/2021] [Accepted: 03/30/2021] [Indexed: 02/03/2023]
Abstract
This short essay pretends to make the reader reflect on the concept of biological mass and on the added value that the determination of this molecular property of a protein brings to the interpretation of evolutionary and translational snake venomics research. Starting from the premise that the amino acid sequence is the most distinctive primary molecular characteristics of any protein, the thesis underlying the first part of this essay is that the isotopic distribution of a protein's molecular mass serves to unambiguously differentiate it from any other of an organism's proteome. In the second part of the essay, we discuss examples of collaborative projects among our laboratories, where mass profiling of snake venom PLA2 across conspecific populations played a key role revealing dispersal routes that determined the current phylogeographic pattern of the species.
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21
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Abstract
![]()
Previously, we have
demonstrated native mass spectrometry imaging
(native MSI) in which the spatial distribution of proteins maintained
in their native-like, folded conformations was determined using liquid
extraction surface analysis (LESA). While providing an excellent testbed
for proof of principle, the spatial resolution of LESA is currently
limited for imaging primarily by the physical size of the sampling
pipette tip. Here, we report the adoption of nanospray-desorption
electrospray ionization (nano-DESI) for native MSI, delivering substantial
improvements in resolution versus native LESA MSI. In addition, native
nano-DESI may be used for location-targeted top–down proteomics
analysis directly from tissue. Proteins, including a homodimeric complex
not previously detected by native MSI, were identified through a combination
of collisional activation, high-resolution MS and proton transfer
charge reduction.
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Affiliation(s)
- Oliver J Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
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22
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Hammerschmid D, van Dyck JF, Sobott F, Calabrese AN. Interrogating Membrane Protein Structure and Lipid Interactions by Native Mass Spectrometry. Methods Mol Biol 2021; 2168:233-261. [PMID: 33582995 DOI: 10.1007/978-1-0716-0724-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Native mass spectrometry and native ion mobility mass spectrometry are now established techniques in structural biology, with recent work developing these methods for the study of integral membrane proteins reconstituted in both lipid bilayer and detergent environments. Here we show how native mass spectrometry can be used to interrogate integral membrane proteins, providing insights into conformation, oligomerization, subunit composition/stoichiometry, and interactions with detergents/lipids/drugs. Furthermore, we discuss the sample requirements and experimental considerations unique to integral membrane protein native mass spectrometry research.
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Affiliation(s)
- Dietmar Hammerschmid
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.,Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Jeroen F van Dyck
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium.,Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Antonio N Calabrese
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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23
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Anggara K, Zhu Y, Delbianco M, Rauschenbach S, Abb S, Seeberger PH, Kern K. Exploring the Molecular Conformation Space by Soft Molecule-Surface Collision. J Am Chem Soc 2020; 142:21420-21427. [PMID: 33167615 PMCID: PMC7760097 DOI: 10.1021/jacs.0c09933] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 01/08/2023]
Abstract
Biomolecules function by adopting multiple conformations. Such dynamics are governed by the conformation landscape whose study requires characterization of the ground and excited conformation states. Here, the conformational landscape of a molecule is sampled by exciting an initial gas-phase molecular conformer into diverse conformation states, using soft molecule-surface collision (0.5-5.0 eV). The resulting ground and excited molecular conformations, adsorbed on the surface, are imaged at the single-molecule level. This technique permits the exploration of oligosaccharide conformations, until now, limited by the high flexibility of oligosaccharides and ensemble-averaged analytical methods. As a model for cellulose, cellohexaose chains are observed in two conformational extremes, the typical "extended" chain and the atypical "coiled" chain-the latter identified as the gas-phase conformer preserved on the surface. Observing conformations between these two extremes reveals the physical properties of cellohexaose, behaving as a rigid ribbon that becomes flexible when twisted. The conformation space of any molecule that can be electrosprayed can now be explored.
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Affiliation(s)
- Kelvin Anggara
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
| | - Yuntao Zhu
- Max
Planck Institute of Colloids and Interfaces, Am Muhlenberg 1, Potsdam DE-14476, Germany
| | - Martina Delbianco
- Max
Planck Institute of Colloids and Interfaces, Am Muhlenberg 1, Potsdam DE-14476, Germany
| | - Stephan Rauschenbach
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sabine Abb
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
| | - Peter H. Seeberger
- Max
Planck Institute of Colloids and Interfaces, Am Muhlenberg 1, Potsdam DE-14476, Germany
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin DE-14195, Germany
| | - Klaus Kern
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
- Institut
de Physique, École Polytechnique
Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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24
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Hands on Native Mass Spectrometry Analysis of Multi-protein Complexes. Methods Mol Biol 2020. [PMID: 33301118 DOI: 10.1007/978-1-0716-1126-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
By maintaining intact multi-protein complexes in the gas-phase, native mass spectrometry provides their molecular weight with very good accuracy compared to other methods (typically native PAGE or SEC-MALS) (Marcoux and Robinson, Structure 21:1541-1550, 2013). Besides, heterogeneous samples, in terms of both oligomeric states and ligand-bound species can be fully characterized. Here we thoroughly describe the analysis of several oligomeric protein complexes ranging from a 16 = kDa dimer to a 801-kDa tetradecameric complex on different instrumental setups.
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25
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Prabhu GRD, Ponnusamy VK, Witek HA, Urban PL. Sample Flow Rate Scan in Electrospray Ionization Mass Spectrometry Reveals Alterations in Protein Charge State Distribution. Anal Chem 2020; 92:13042-13049. [PMID: 32893617 DOI: 10.1021/acs.analchem.0c01945] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sample flow rate is one of the parameters that influence the sensitivity of electrospray ionization (ESI) mass spectrometry. By varying the sample flow rate, initial droplets of different sizes can be generated. Protein molecules in small droplets may form gas-phase ions earlier than the ones in large droplets. Here, we have systematically studied the influence of sample flow rate on the ESI charge state distributions (CSDs) of model proteins. A dedicated programmable sample flow rate scanner was used to infuse protein samples at different flow rates into a mass spectrometer. The synergistic influence of sample flow rate and various electrolytes (ammonium acetate, ammonium bicarbonate, ammonium formate, and piperidine) was studied. Significant alterations to the CSDs with increasing flow rate were observed. For example, in the presence of ammonium acetate, at low flow rates, lower charge states of proteins showed high intensities, while at high flow rates, ions related to higher charge states of proteins dominated the spectra. On the other hand, in the presence of piperidine, a significant reduction in the ion currents of all charge states was observed during the flow rate scan. Our observations suggest that at low flow rates the protein molecules follow a charged residue model of ionization mechanism, and at high flow rates-due to structural changes in protein molecules in large ESI droplets-the charged residue and chain ejection models can possibly coexist. We propose the use of sample flow rate scan as a way to reveal the influence of flow rate on the CSDs of the studied proteins.
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Affiliation(s)
- Gurpur Rakesh D Prabhu
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan.,Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Vinoth Kumar Ponnusamy
- Department of Medicinal and Applied Chemistry & Research Center for Environmental Medicine, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung 807, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, 100 Shih-Chuan 1st Road, Kaohsiung 807, Taiwan
| | - Henryk A Witek
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan.,Center for Emergent Functional Matter Science, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Pawel L Urban
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
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26
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Wilson JW, Donor MT, Shepherd SO, Prell JS. Increasing Collisional Activation of Protein Complexes Using Smaller Aperture Source Sampling Cones on a Synapt Q-IM-TOF Instrument with a Stepwave Source. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:10.1021/jasms.0c00117. [PMID: 32628844 PMCID: PMC7855748 DOI: 10.1021/jasms.0c00117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Quadrupole ion mobility time-of-flight (Q-IM-TOF) mass spectrometers have revolutionized investigation of native biomolecular complexes. High pressures in the sources of these instruments aid transmission of protein complexes through damping of kinetic energy by collisional cooling. As adducts are removed through collisional heating (declustering), excessive collisional cooling can prevent removal of nonspecific adducts from protein ions, leading to inaccurate mass measurements, broad mass spectral peaks, and obfuscation of ligand binding. We show that reducing the source pressure using smaller aperture source sampling cones (SC) in a Waters Synapt G2-Si instrument increases protein ion heating by decreasing collisional cooling, providing a simple way to enhance removal of adducted salts from soluble proteins (GroEL 14-mer) and detergents from a transmembrane protein complex (heptameric Staphylococcus aureus α-hemolysin, αHL). These experiments are supported by ion heating and cooling simulations which demonstrate reduced collisional cooling at lower source pressures. Using these easily swapped sample cones of different apertures is a facile approach to reproducibly extend the range of activation in Synapt-type instruments.
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Affiliation(s)
- Jesse W. Wilson
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon Eugene, OR, USA, 97403-1253
| | - Micah T. Donor
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon Eugene, OR, USA, 97403-1253
| | - Samantha O. Shepherd
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon Eugene, OR, USA, 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon Eugene, OR, USA, 97403-1253
- Materials Science Institute, University of Oregon, 1252 University of Oregon, OR, USA, 97403-1252
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27
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Holmquist ML, Ihms EC, Gollnick P, Wysocki VH, Foster MP. Population Distributions from Native Mass Spectrometry Titrations Reveal Nearest-Neighbor Cooperativity in the Ring-Shaped Oligomeric Protein TRAP. Biochemistry 2020; 59:2518-2527. [PMID: 32558551 DOI: 10.1021/acs.biochem.0c00352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Allostery pervades macromolecular function and drives cooperative binding of ligands to macromolecules. To decipher the mechanisms of cooperative ligand binding, it is necessary to define, at a microscopic level, the thermodynamic consequences of binding of each ligand to its energetically coupled site(s). However, extracting these microscopic constants is difficult for macromolecules with more than two binding sites, because the observable [e.g., nuclear magnetic resonance (NMR) chemical shift changes, fluorescence, and enthalpy] can be altered by allostery, thereby distorting its proportionality to site occupancy. Native mass spectrometry (MS) can directly quantify the populations of homo-oligomeric protein species with different numbers of bound ligands, provided the populations are proportional to ion counts and that MS-compatible electrolytes do not alter the overall thermodynamics. These measurements can help decipher allosteric mechanisms by providing unparalleled access to the statistical thermodynamic partition function. We used native MS (nMS) to study the cooperative binding of tryptophan (Trp) to Bacillus stearothermophilus trp RNA binding attenuation protein (TRAP), a ring-shaped homo-oligomeric protein complex with 11 identical binding sites. MS-compatible solutions did not significantly perturb protein structure or thermodynamics as assessed by isothermal titration calorimetry and NMR spectroscopy. Populations of Trpn-TRAP11 states were quantified as a function of Trp concentration by nMS. The population distributions could not be explained by a noncooperative binding model but were described well by a mechanistic nearest-neighbor cooperative model. Nonlinear least-squares fitting yielded microscopic thermodynamic constants that define the interactions between neighboring binding sites. This approach may be applied to quantify thermodynamic cooperativity in other ring-shaped proteins.
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Affiliation(s)
- Melody L Holmquist
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Elihu C Ihms
- VPPL, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 9W. Watkins Mill Road, Suite 250, Gaithersburg, Maryland 20878, United States
| | - Paul Gollnick
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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28
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Evaluation of NHS-Acetate and DEPC labelling for determination of solvent accessible amino acid residues in protein complexes. J Proteomics 2020; 222:103793. [PMID: 32348883 DOI: 10.1016/j.jprot.2020.103793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/27/2020] [Accepted: 04/19/2020] [Indexed: 02/07/2023]
Abstract
The activity of most proteins and protein complexes relies on the formation of defined three-dimensional structures. The analysis of these arrangements is therefore key for understanding their function and regulation in the cell. Besides the traditional structural techniques, structural mass spectrometry delivers insights into the various aspects of protein structure, including stoichiometry, protein-ligand interactions and solvent accessibility. The latter is usually obtained from labelling experiments. In this study, we evaluate two chemical labelling strategies using N-hydroxysuccinimidyl acetate and diethylpyrocarbonate as labelling reagents. We characterised the mass spectra of modified peptides and assessed labelling reactivity of individual amino acid residues in intact proteins. Importantly, we uncovered neutral losses from diethylpyrocarbonate modified amino acids improving the assignments of the peptide fragment spectra. We further established a quantitative labelling workflow to determine labelling percentage and unambiguously distinguish solvent accessible amino acid residues from stochastically labelled residues. Finally, we used ion mobility MS to explore whether labelled proteins maintain their structures and remain stable. We conclude that labelling using N-hydroxysuccinimidyl acetate and diethylpyrocarbonate delivers comparable results, however, N-hydroxysuccinimidyl acetate labelling is compatible with standard proteomic workflows while diethylpyrocarbonate labelling requires specialised experimental conditions and data analysis. SIGNIFICANCE: Covalent labelling is widely used to identify solvent accessible amino acid residues of proteins or protein complexes. However, with increasing sensitivity of available MS instrumentation, a high number of modified residues is usually observed making an unambiguous assignment of solvent accessible residues necessary. In this study, we establish a quantitative labelling workflow for two different labelling strategies to identify accessible amino acid residues. In addition, we characterise observed mass spectra of modified peptides and identified neutral loss of DEPC modified amino acid residues during HCD fragmentation improving their assignments.
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29
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Sever AIM, Konermann L. Gas Phase Protein Folding Triggered by Proton Stripping Generates Inside-Out Structures: A Molecular Dynamics Simulation Study. J Phys Chem B 2020; 124:3667-3677. [DOI: 10.1021/acs.jpcb.0c01934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Alexander I. M. Sever
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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30
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Lin CW, McCabe JW, Russell DH, Barondeau DP. Molecular Mechanism of ISC Iron-Sulfur Cluster Biogenesis Revealed by High-Resolution Native Mass Spectrometry. J Am Chem Soc 2020; 142:6018-6029. [PMID: 32131593 DOI: 10.1021/jacs.9b11454] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous protein cofactors that are required for many important biological processes including oxidative respiration, nitrogen fixation, and photosynthesis. Biosynthetic pathways assemble Fe-S clusters with different iron-to-sulfur stoichiometries and distribute these clusters to appropriate apoproteins. In the ISC pathway, the pyridoxal 5'-phosphate-dependent cysteine desulfurase enzyme IscS provides sulfur to the scaffold protein IscU, which templates the Fe-S cluster assembly. Despite their functional importance, mechanistic details for cluster synthesis have remained elusive. Recent advances in native mass spectrometry (MS) have allowed proteins to be preserved in native-like structures and support applications in the investigation of protein structure, dynamics, ligand interactions, and the identification of protein-associated intermediates. Here, we prepared samples under anaerobic conditions and then applied native MS to investigate the molecular mechanism for Fe-S cluster synthesis. This approach was validated by the high agreement between native MS and traditional visible circular dichroism spectroscopic assays. Time-dependent native MS experiments revealed potential iron- and sulfur-based intermediates that decay as the [2Fe-2S] cluster signal developed. Additional experiments establish that (i) Zn(II) binding stabilizes IscU and protects the cysteine residues from oxidation, weakens the interactions between IscU and IscS, and inhibits Fe-S cluster biosynthesis; and (ii) Fe(II) ions bind to the IscU active site cysteine residues and another lower affinity binding site and promote the intermolecular sulfur transfer reaction from IscS to IscU. Overall, these results support an iron-first model for Fe-S cluster synthesis and highlight the power of native MS in defining protein-associated intermediates and elucidating mechanistic details of enzymatic processes.
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Affiliation(s)
- Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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31
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Zhou M, Liu W, Shaw JB. Charge Movement and Structural Changes in the Gas-Phase Unfolding of Multimeric Protein Complexes Captured by Native Top-Down Mass Spectrometry. Anal Chem 2020; 92:1788-1795. [PMID: 31869201 DOI: 10.1021/acs.analchem.9b03469] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The extent to which noncovalent protein complexes retain native structure in the gas phase is highly dependent on experimental conditions. Energetic collisions with background gas can cause structural changes ranging from unfolding to subunit dissociation. Additionally, recent studies have highlighted the role of charge in such structural changes, but the mechanism is not completely understood. In this study, native top down (native TD) mass spectrometry was used to probe gas-phase structural changes of alcohol dehydrogenase (ADH, 4mer) under varying degrees of in-source activation. Changes in covalent backbone fragments produced by electron capture dissociation (ECD) or 193 nm ultraviolet photodissociation (UVPD) were attributed to structural changes of the ADH 4mer. ECD fragments indicated unfolding started at the N-terminus, and the charge states of UVPD fragments enabled monitoring of charge migration to the unfolded regions. Interestingly, UVPD fragments also indicated that the charge at the "unfolding" N-terminus of ADH decreased at high in-source activation energies after the initial increase. We proposed a possible "refolding-after-unfolding" mechanism, as further supported by monitoring hydrogen elimination from radical a-ions produced by UVPD at the N-terminus of ADH. However, "refolding-after-unfolding" with increasing in-source activation was not observed for charge-reduced ADH, which likely adopted compact structures that are resistant to both charge migration and unfolding. When combined, these results support a charge-directed unfolding mechanism for protein complexes. Overall, an experimental framework was outlined for utilizing native TD to generate structure-informative mass spectral signatures for protein complexes that complement other structure characterization techniques, such as ion mobility and computational modeling.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Boulevard , Richland , Washington 99354 , United States
| | - Weijing Liu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Boulevard , Richland , Washington 99354 , United States
| | - Jared B Shaw
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Boulevard , Richland , Washington 99354 , United States
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32
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Olinares PDB, Chait BT. Native Mass Spectrometry Analysis of Affinity-Captured Endogenous Yeast RNA Exosome Complexes. Methods Mol Biol 2020; 2062:357-382. [PMID: 31768985 DOI: 10.1007/978-1-4939-9822-7_17] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Native mass spectrometry (MS) enables direct mass measurement of intact protein assemblies generating relevant subunit composition and stoichiometry information. Combined with cross-linking and structural data, native MS-derived information is crucial for elucidating the architecture of macromolecular assemblies by integrative structural methods. The exosome complex from budding yeast was among the first endogenous protein complexes to be affinity isolated and subsequently characterized by this technique, providing improved understanding of its composition and structure. We present a protocol that couples efficient affinity capture of yeast exosome complexes and sensitive native MS analysis, including rapid affinity isolation of the endogenous exosome complex from cryolysed yeast cells, elution in nondenaturing conditions by protease cleavage, depletion of the protease, buffer exchange, and native MS measurements using an Orbitrap-based instrument (Exactive Plus EMR).
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Affiliation(s)
- Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA.
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
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33
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Duez Q, Metwally H, Hoyas S, Lemaur V, Cornil J, De Winter J, Konermann L, Gerbaux P. Effects of electrospray mechanisms and structural relaxation on polylactide ion conformations in the gas phase: insights from ion mobility spectrometry and molecular dynamics simulations. Phys Chem Chem Phys 2020; 22:4193-4204. [DOI: 10.1039/c9cp06391a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Gas-phase polymer ions may retain structural features associated with their electrospray formation mechanisms.
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Affiliation(s)
- Quentin Duez
- Organic Synthesis and Mass Spectrometry Laboratory
- Center of Innovation and Research in Materials and Polymers (CIRMAP) – University of Mons (UMONS)
- B-7000 Mons
- Belgium
- Laboratory for Chemistry of Novel Materials
| | - Haidy Metwally
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
| | - Sébastien Hoyas
- Organic Synthesis and Mass Spectrometry Laboratory
- Center of Innovation and Research in Materials and Polymers (CIRMAP) – University of Mons (UMONS)
- B-7000 Mons
- Belgium
- Laboratory for Chemistry of Novel Materials
| | - Vincent Lemaur
- Laboratory for Chemistry of Novel Materials
- Center of Innovation and Research in Materials and Polymers (CIRMAP) – University of Mons (UMONS)
- B-7000 Mons
- Belgium
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials
- Center of Innovation and Research in Materials and Polymers (CIRMAP) – University of Mons (UMONS)
- B-7000 Mons
- Belgium
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory
- Center of Innovation and Research in Materials and Polymers (CIRMAP) – University of Mons (UMONS)
- B-7000 Mons
- Belgium
| | - Lars Konermann
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory
- Center of Innovation and Research in Materials and Polymers (CIRMAP) – University of Mons (UMONS)
- B-7000 Mons
- Belgium
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34
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Hanozin E, Grifnée E, Gattuso H, Matagne A, Morsa D, Pauw ED. Covalent Cross-Linking as an Enabler for Structural Mass Spectrometry. Anal Chem 2019; 91:12808-12818. [PMID: 31490660 DOI: 10.1021/acs.analchem.9b02491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The number of studies referring to the structural elucidation of intact biomolecular systems using mass spectrometry techniques has gradually increased in the post-2000s literature topics. As part of native mass spectrometry, this domain capitalizes on the kinetic trapping of physiological folds in view of probing solution-like conformational properties of isolated molecules or complexes after their electrospray transfer to the gas phase. Despite its efficiency for a wide array of analytes, this approach is expected to be pushed to its limits when considering highly dynamic systems or when dealing with nonideal operating conditions. To circumvent these limitations, we challenge the adequacy of an original strategy based on cross-linkers to improve the gas-phase stability of isolated proteins and ensure the preservation of folded conformations when measuring with strong transmission voltages, by spraying from denaturing solvents, or trapping for extended periods of time. Tested on cytochrome c, myoglobin, and β-lactoglobulin cross-linked using BS3, we validated the process as structurally nonintrusive in solution using far-ultraviolet circular dichroism and unraveled the preservation of folded conformations showing better resilience to denaturation on cross-linked species using ion mobility. The resulting collision cross sections were found in agreement with the native fold, and a preservation of the proteins' secondary and tertiary structures was evidenced using molecular dynamics simulations. Our results provide new insights concerning the fate of electro-sprayed cross-linked conformers in the gas phase, while constituting promising evidence for the validation of this technique as part of future structural mass spectrometry workflows.
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35
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Hanozin E, Morsa D, De Pauw E. Two-Parameter Power Formalism for Structural Screening of Ion Mobility Trends: Applied Study on Artificial Molecular Switches. J Phys Chem A 2019; 123:8043-8052. [PMID: 31449411 DOI: 10.1021/acs.jpca.9b06121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Recent literature provides increasing samples of structural studies relying on ion mobility coupled to mass spectrometry in view of characterizing gas-phase conformation and energetics properties of biomolecular ions. A typical framework consists in experimentally monitoring the collisional cross sections for various experimental conditions and using them as references to select appropriate candidate structures issued from theoretical modeling. Although it has proved successful for structural assignment, this process is resource costly and lengthy, namely due to intricacies in the selection of appropriate input geometries. In the present work, we propose simplified methodologies dedicated to the systematic screening of ion mobility data acquired on systems built from repetitive subunits and detail their application to challenging artificial molecular switch systems. Capitalizing on coarse-grained design, we first demonstrate how the assimilation of subunits into adequately assembled building-blocks can be used for fast assignments of a system topology. Further focusing on topology-specific differential ion mobility trends, we show that the building-block assemblies can be fused into single fully convex solid figure models, i.e., sphere and cylinder, whose projected areas follow a two-parameter power formalism A × nB. We show that the fitting parameters A and B were assigned as structural descriptors respectively associated with the dimensions of each constitutive subunit, i.e., size parameter, and with their assembled tridimensional arrangement, i.e., shape parameter. The present work provides a ready-to-use method for the screening of IM-MS data sets that is expected to facilitate the eventual design of input structures whenever advanced modeling calculations are required.
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Affiliation(s)
- Emeline Hanozin
- Mass Spectrometry Laboratory, MolSys Research Unit , University of Liège , 4000 Liège , Belgium
| | - Denis Morsa
- Mass Spectrometry Laboratory, MolSys Research Unit , University of Liège , 4000 Liège , Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit , University of Liège , 4000 Liège , Belgium
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36
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Seffernick J, Harvey SR, Wysocki VH, Lindert S. Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data. ACS CENTRAL SCIENCE 2019; 5:1330-1341. [PMID: 31482115 PMCID: PMC6716128 DOI: 10.1021/acscentsci.8b00912] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Indexed: 05/23/2023]
Abstract
Recently, mass spectrometry (MS) has become a viable method for elucidation of protein structure. Surface-induced dissociation (SID), colliding multiply charged protein complexes or other ions with a surface, has been paired with native MS to provide useful structural information such as connectivity and topology for many different protein complexes. We recently showed that SID gives information not only on connectivity and topology but also on relative interface strengths. However, SID has not yet been coupled with computational structure prediction methods that could use the sparse information from SID to improve the prediction of quaternary structures, i.e., how protein subunits interact with each other to form complexes. Protein-protein docking, a computational method to predict the quaternary structure of protein complexes, can be used in combination with subunit structures from X-ray crystallography and NMR in situations where it is difficult to obtain an experimental structure of an entire complex. While de novo structure prediction can be successful, many studies have shown that inclusion of experimental data can greatly increase prediction accuracy. In this study, we show that the appearance energy (AE, defined as 10% fragmentation) extracted from SID can be used in combination with Rosetta to successfully evaluate protein-protein docking poses. We developed an improved model to predict measured SID AEs and incorporated this model into a scoring function that combines the RosettaDock scoring function with a novel SID scoring term, which quantifies agreement between experiments and structures generated from RosettaDock. As a proof of principle, we tested the effectiveness of these restraints on 57 systems using ideal SID AE data (AE determined from crystal structures using the predictive model). When theoretical AEs were used, the RMSD of the selected structure improved or stayed the same in 95% of cases. When experimental SID data were incorporated on a different set of systems, the method predicted near-native structures (less than 2 Å root-mean-square deviation, RMSD, from native) for 6/9 tested cases, while unrestrained RosettaDock (without SID data) only predicted 3/9 such cases. Score versus RMSD funnel profiles were also improved when SID data were included. Additionally, we developed a confidence measure to evaluate predicted model quality in the absence of a crystal structure.
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37
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Casañal A, Shakeel S, Passmore LA. Interpretation of medium resolution cryoEM maps of multi-protein complexes. Curr Opin Struct Biol 2019; 58:166-174. [PMID: 31362190 PMCID: PMC6863432 DOI: 10.1016/j.sbi.2019.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 12/20/2022]
Abstract
CryoEM maps at medium (3.5–6 Å) resolution can be challenging to interpret. Integration of multiple methods can inform cryoEM studies. Mass spectrometry and biochemistry facilitate map interpretation and model building.
Electron cryo-microscopy (cryoEM) is used to determine structures of biological molecules, including multi-protein complexes. Maps at better than 3.0 Å resolution are relatively straightforward to interpret since atomic models of proteins and nucleic acids can be built directly. Still, these resolutions are often difficult to achieve, and map quality frequently varies within a structure. This results in data that are challenging to interpret, especially when crystal structures or suitable homology models are not available. Recent advances in mass spectrometry techniques, computational methods and model building tools facilitate subunit/domain fitting into maps, elucidation of protein contacts, and de novo generation of atomic models. Here, we review techniques for map interpretation and provide examples from recent studies of multi-protein complexes.
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Affiliation(s)
- Ana Casañal
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.
| | - Shabih Shakeel
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Lori A Passmore
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.
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38
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Campuzano IDG, Robinson JH, Hui JO, Shi SDH, Netirojjanakul C, Nshanian M, Egea PF, Lippens JL, Bagal D, Loo JA, Bern M. Native and Denaturing MS Protein Deconvolution for Biopharma: Monoclonal Antibodies and Antibody-Drug Conjugates to Polydisperse Membrane Proteins and Beyond. Anal Chem 2019; 91:9472-9480. [PMID: 31194911 DOI: 10.1021/acs.analchem.9b00062] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) is a ubiquitously used analytical method applied across multiple departments in biopharma, ranging from early research discovery to process development. Accurate, efficient, and consistent protein MS spectral deconvolution across multiple instrument and detector platforms (time-of-flight, Orbitrap, Fourier-transform ion cyclotron resonance) is essential. When proteins are ionized during the ESI process, a distribution of consecutive multiply charged ions are observed on the m/z scale, either positive [M + nH]n+ or negative [M - nH]n- depending on the ionization polarity. The manual calculation of the neutral molecular weight (MW) of single proteins measured by ESI-MS is simple; however, algorithmic deconvolution is required for more complex protein mixtures to derive accurate MWs. Multiple deconvolution algorithms have evolved over the past two decades, all of which have their advantages and disadvantages, in terms of speed, user-input parameters (or ideally lack thereof), and whether they perform optimally on proteins analyzed under denatured or native-MS and solution conditions. Herein, we describe the utility of a parsimonious deconvolution algorithm (explaining the observed spectra with a minimum number of masses) to process a wide range of highly diverse biopharma relevant and research grade proteins and complexes (PEG-GCSF; an IgG1k; IgG1- and IgG2-biotin covalent conjugates; the membrane protein complex AqpZ; a highly polydisperse empty MSP1D1 nanodisc and the tetradecameric chaperone protein complex GroEL) analyzed under native-MS, denaturing LC-MS, and positive and negative modes of ionization, using multiple instruments and therefore multiple data formats. The implementation of a comb filter and peak sharpening option is also demonstrated to be highly effective for deconvolution of highly polydisperse and enhanced separation of a low level lysine glycation post-translational modification (+162.1 Da), partially processed heavy chain lysine residues (+128.1 Da), and loss of N-acetylglucosamine (GlcNAc; -203.1 Da).
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Affiliation(s)
- Iain D G Campuzano
- Discovery Attribute Sciences , Amgen Research , One Amgen Center Drive , Thousand Oaks , California 91320 , United States
| | - John H Robinson
- Discovery Attribute Sciences , Amgen Research , One Amgen Center Drive , Thousand Oaks , California 91320 , United States
| | - John O Hui
- Discovery Attribute Sciences , Amgen Research , One Amgen Center Drive , Thousand Oaks , California 91320 , United States
| | - Stone D-H Shi
- Discovery Attribute Sciences , Amgen Research , One Amgen Center Drive , Thousand Oaks , California 91320 , United States
| | - Chawita Netirojjanakul
- Hybrid Modality Engineering , Amgen Research , One Amgen Center Drive , Thousand Oaks , California 91320 , United States
| | - Michael Nshanian
- Department of Chemistry and Biochemistry , University of California-Los Angeles , Los Angeles , California 90095 , United States
| | - Pascal F Egea
- Department of Biological Chemistry , University of California-Los Angeles , Los Angeles , California 90095 , United States
| | - Jennifer L Lippens
- Discovery Attribute Sciences , Amgen Research , One Amgen Center Drive , Thousand Oaks , California 91320 , United States
| | - Dhanashri Bagal
- Discovery Attribute Sciences , Amgen Research , Veterans Boulevard , South San Francisco , California 94080 , United States
| | - Joseph A Loo
- Department of Biological Chemistry , University of California-Los Angeles , Los Angeles , California 90095 , United States
| | - Marshall Bern
- Protein Metrics , Cupertino , California 95010 , United States
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39
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Patrick JW, Laganowsky A. Probing Heterogeneous Lipid Interactions with Membrane Proteins Using Mass Spectrometry. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 2003:175-190. [PMID: 31218619 DOI: 10.1007/978-1-4939-9512-7_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Native mass spectrometry (Native MS) enables the detection of intact membrane protein complexes in the gas phase. Membrane proteins are encapsulated in nonionic detergent micelles that protect them during transfer into the gas phase and preserves structure and noncovalent interactions. Herein, we describe methods to gently transfer membrane protein complexes bound to a mixture of heterogeneous lipid species into the gas phase. Through careful titrations, equilibrium dissociation constants can be directly determined to elucidate lipid interactions that induce positive, neutral, or negative allostery. These methods can lead to the identification of lipids that modulate membrane protein structure and function.
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Affiliation(s)
- John W Patrick
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
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40
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Österlund N, Moons R, Ilag LL, Sobott F, Gräslund A. Native Ion Mobility-Mass Spectrometry Reveals the Formation of β-Barrel Shaped Amyloid-β Hexamers in a Membrane-Mimicking Environment. J Am Chem Soc 2019; 141:10440-10450. [DOI: 10.1021/jacs.9b04596] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rani Moons
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Leopold L. Ilag
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | - Frank Sobott
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, The United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, The United Kingdom
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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41
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Wang H, Eschweiler J, Cui W, Zhang H, Frieden C, Ruotolo BT, Gross ML. Native Mass Spectrometry, Ion Mobility, Electron-Capture Dissociation, and Modeling Provide Structural Information for Gas-Phase Apolipoprotein E Oligomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:876-885. [PMID: 30887458 PMCID: PMC6504607 DOI: 10.1007/s13361-019-02148-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 05/09/2023]
Abstract
Apolipoprotein E (apoE) is an essential protein in lipid and cholesterol metabolism. Although the three common isoforms in humans differ only at two sites, their consequences in Alzheimer's disease (AD) are dramatically different: only the ε4 allele is a major genetic risk factor for late-onset Alzheimer's disease. The isoforms exist as a mixture of oligomers, primarily tetramer, at low μM concentrations in a lipid-free environment. This self-association is involved in equilibrium with the lipid-free state, and the oligomerization interface overlaps with the lipid-binding region. Elucidation of apoE wild-type (WT) structures at an oligomeric state, however, has not yet been achieved. To address this need, we used native electrospray ionization and mass spectrometry (native MS) coupled with ion mobility (IM) to examine the monomer and tetramer of the three WT isoforms. Although collision-induced unfolding (CIU) cannot distinguish the WT isoforms, the monomeric mutant (MM) of apoE3 shows higher stability when submitted to CIU than the WT monomer. From ion-mobility measurements, we obtained the collision cross section and built a coarse-grained model for the tetramer. Application of electron-capture dissociation (ECD) to the tetramer causes unfolding starting from the C-terminal domain, in good agreement with solution denaturation data, and provides additional support for the C4 symmetry structure of the tetramer.
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Affiliation(s)
- Hanliu Wang
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
- Analytical Research and Development, Pfizer Inc., Chesterfield, MO, 63017, USA
| | - Joseph Eschweiler
- Drug Product Development, Abbvie Inc., North Chicago, IL, 60064, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Weidong Cui
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
- Pivotal Attribute Sciences, Amgen Inc., Cambridge, MA, 02142, USA
| | - Hao Zhang
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
- Pivotal Attribute Sciences, Amgen Inc., Cambridge, MA, 02142, USA
| | - Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA.
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42
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Abstract
Mass spectrometry is one of the key technologies of proteomics, and over the last decade important technical advances in mass spectrometry have driven an increased capability for proteomic discovery. In addition, new methods to capture important biological information have been developed to take advantage of improving proteomic tools.
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Affiliation(s)
- John R Yates
- Molecular Medicine and Neurobiology, Scripps Research, 0550 North Torrey Pines Road, SR302, La Jolla, CA, 92037, USA
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43
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Bults P, Spanov B, Olaleye O, van de Merbel NC, Bischoff R. Intact protein bioanalysis by liquid chromatography – High-resolution mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1110-1111:155-167. [DOI: 10.1016/j.jchromb.2019.01.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/20/2019] [Accepted: 01/31/2019] [Indexed: 02/07/2023]
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44
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Vušurović J, Breuker K. Relative Strength of Noncovalent Interactions and Covalent Backbone Bonds in Gaseous RNA-Peptide Complexes. Anal Chem 2019; 91:1659-1664. [PMID: 30614682 PMCID: PMC6335609 DOI: 10.1021/acs.analchem.8b05387] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Interactions of ribonucleic acids (RNA) with basic ligands such as proteins or aminoglycosides play a key role in fundamental biological processes. Native top-down mass spectrometry (MS) has recently been extended to binding site mapping of RNA-ligand interactions by collisionally activated dissociation, without the need for laborious sample preparation procedures. The technique relies on the preservation of noncovalent interactions at energies that are sufficiently high to cause RNA backbone cleavage. In this study, we address the question of how many and what types of noncovalent interactions allow for binding site mapping by top-down MS. We show that proton transfer from protonated ligand to deprotonated RNA within salt bridges initiates loss of the ligand, but that proton transfer becomes energetically unfavorable in the presence of additional hydrogen bonds such that the noncovalent interactions remain stronger than the covalent RNA backbone bonds.
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Affiliation(s)
- Jovana Vušurović
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI) , Universität Innsbruck , Innrain 80-82 , 6020 Innsbruck , Austria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI) , Universität Innsbruck , Innrain 80-82 , 6020 Innsbruck , Austria
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45
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Peetz O, Hellwig N, Henrich E, Mezhyrova J, Dötsch V, Bernhard F, Morgner N. LILBID and nESI: Different Native Mass Spectrometry Techniques as Tools in Structural Biology. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:181-191. [PMID: 30225732 PMCID: PMC6318263 DOI: 10.1007/s13361-018-2061-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/02/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
Native mass spectrometry is applied for the investigation of proteins and protein complexes worldwide. The challenge in native mass spectrometry is maintaining the features of the proteins of interest, such as oligomeric state, bound ligands, or the conformation of the protein complex, during transfer from solution to gas phase. This is an essential prerequisite to allow conclusions about the solution state protein complex, based on the gas phase measurements. Therefore, soft ionization techniques are required. Widely used for the analysis of protein complexes are nanoelectro spray ionization (nESI) mass spectrometers. A newer ionization method is laser induced liquid bead ion desorption (LILBID), which is based on the release of protein complexes from solution phase via infrared (IR) laser desorption. We use both methods in our lab, depending on the requirements of the biological system we are interested in. Here we benchmark the performance of our LILBID mass spectrometer in comparison to a nESI instrument, regarding sample conditions, buffer and additive tolerances, dissociation mechanism and applicability towards soluble and membrane protein complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Oliver Peetz
- Institute of Physical and Theoretical Chemistry, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Nils Hellwig
- Institute of Physical and Theoretical Chemistry, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Julija Mezhyrova
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, J.W. Goethe-University, Frankfurt am Main, Germany.
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46
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Urner LH, Maier YB, Haag R, Pagel K. Exploring the Potential of Dendritic Oligoglycerol Detergents for Protein Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:174-180. [PMID: 30276626 PMCID: PMC6318253 DOI: 10.1007/s13361-018-2063-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/22/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
The ability to design detergents that are suitable for protein analysis by mass spectrometry (MS) represents an on-going challenge in the field of native MS. Desirable detergent characteristics include charge-reducing properties and low gas-phase stabilities of complexes formed with proteins. In this work, the gas-phase properties of oligoglycerol detergents (OGDs) are optimized by fine tuning of their molecular structure. Furthermore, a tandem mass spectrometry (MS/MS) approach is presented that estimates the gas-phase properties of detergents simply by studying the dissociation behaviour of protein-detergent complexes (PDCs) formed with the soluble protein β-lactoglobulin (BLG). Graphical Abstract ᅟ.
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Affiliation(s)
- Leonhard H Urner
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustraße 3, 14195, Berlin, Germany
| | - Yasmine B Maier
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustraße 3, 14195, Berlin, Germany
| | - Rainer Haag
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustraße 3, 14195, Berlin, Germany
| | - Kevin Pagel
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustraße 3, 14195, Berlin, Germany.
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany.
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47
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Lippens JL, Egea PF, Spahr C, Vaish A, Keener JE, Marty MT, Loo JA, Campuzano ID. Rapid LC-MS Method for Accurate Molecular Weight Determination of Membrane and Hydrophobic Proteins. Anal Chem 2018; 90:13616-13623. [PMID: 30335969 PMCID: PMC6580849 DOI: 10.1021/acs.analchem.8b03843] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Therapeutic target characterization involves many components, including accurate molecular weight (MW) determination. Knowledge of the accurate MW allows one to detect the presence of post-translational modifications, proteolytic cleavages, and importantly, if the correct construct has been generated and purified. Denaturing liquid chromatography-mass spectrometry (LC-MS) can be an attractive method for obtaining this information. However, membrane protein LC-MS methodology has remained relatively under-explored and under-incorporated in comparison to methods for soluble proteins. Here, systematic investigation of multiple gradients and column chemistries has led to the development of a 5 min denaturing LC-MS method for acquiring membrane protein accurate MW measurements. Conditions were interrogated with membrane proteins, such as GPCRs and ion channels, as well as bispecific antibody constructs of variable sizes with the aim to provide the community with rapid LC-MS methods necessary to obtain chromatographic and accurate MW measurements in a medium- to high-throughput manner. The 5 min method detailed has successfully produced MW measurements for hydrophobic proteins with a wide MW range (17.5 to 105.3 kDa) and provided evidence that some constructs indeed contain unexpected modifications or sequence clipping. This rapid LC-MS method is also capable of baseline separating formylated and nonformylated aquaporinZ membrane protein.
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Affiliation(s)
- Jennifer L. Lippens
- Amgen Discovery Research, Amgen, Thousand Oaks, California 91320, United States
| | - Pascal F. Egea
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Chris Spahr
- Amgen Discovery Research, Amgen, Thousand Oaks, California 91320, United States
| | - Amit Vaish
- Amgen Discovery Research, Amgen, Thousand Oaks, California 91320, United States
| | - James E. Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Joseph A. Loo
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Iain D.G. Campuzano
- Amgen Discovery Research, Amgen, Thousand Oaks, California 91320, United States
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48
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Ahdash Z, Lau AM, Martens C, Politis A. Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry. J Vis Exp 2018. [PMID: 30371663 PMCID: PMC6235531 DOI: 10.3791/57966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Proteins are an important class of biological macromolecules that play many key roles in cellular functions including gene expression, catalyzing metabolic reactions, DNA repair and replication. Therefore, a detailed understanding of these processes provides critical information on how cells function. Integrative structural MS methods offer structural and dynamical information on protein complex assembly, complex connectivity, subunit stoichiometry, protein oligomerization and ligand binding. Recent advances in integrative structural MS have allowed for the characterization of challenging biological systems including large DNA binding proteins and membrane proteins. This protocol describes how to integrate diverse MS data such as native MS and ion mobility-mass spectrometry (IM-MS) with molecular dynamics simulations to gain insights into a helicase-nuclease DNA repair protein complex. The resulting approach provides a framework for detailed studies of ligand binding to other protein complexes involved in important biological processes.
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Affiliation(s)
| | - Andy M Lau
- Department of Chemistry, King's College London
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49
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Dong S, Wagner ND, Russell DH. Collision-Induced Unfolding of Partially Metalated Metallothionein-2A: Tracking Unfolding Reactions of Gas-Phase Ions. Anal Chem 2018; 90:11856-11862. [PMID: 30221929 DOI: 10.1021/acs.analchem.8b01622] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metallothioneins (MTs) constitute a group of intrinsically disordered proteins that exhibit extreme diversity in structure, biological functionality, and metal ion specificity. Structures of coordinatively saturated metalated MTs have been extensively studied, but very limited structural information for the partially metalated MTs exists. Here, the conformational preferences from partial metalation of rabbit metallothionein-2A (MT) by Cd2+, Zn2+, and Ag+ are studied using nanoelectrospray ionization ion mobility mass spectrometry. We also employ collision-induced unfolding to probe differences in the gas-phase stabilities of these partially metalated MTs. Our results show that despite their similar ion mobility profiles, Cd4-MT, Zn4-MT, Ag4-MT, and Ag6-MT differ dramatically in their gas-phase stabilities. Furthermore, the sequential addition of each Cd2+ and Zn2+ ion results in the incremental stabilization of unique unfolding intermediates.
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Affiliation(s)
- Shiyu Dong
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Nicole D Wagner
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - David H Russell
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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50
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Beaufour M, Ginguené D, Le Meur R, Castaing B, Cadene M. Liquid Native MALDI Mass Spectrometry for the Detection of Protein-Protein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1981-1994. [PMID: 30066268 PMCID: PMC6153977 DOI: 10.1007/s13361-018-2015-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/14/2018] [Accepted: 06/19/2018] [Indexed: 05/29/2023]
Abstract
Native mass spectrometry (MS) encompasses methods to keep noncovalent interactions of biomolecular complexes intact in the gas phase throughout the instrument and to measure the mass-to-charge ratios of supramolecular complexes directly in the mass spectrometer. Electrospray ionization (ESI) in nondenaturing conditions is now an established method to characterize noncovalent systems. Matrix-assisted laser desorption/ionization (MALDI), on the other hand, consumes low quantities of samples and largely tolerates contaminants, making it a priori attractive for native MS. However, so-called native MALDI approaches have so far been based on solid deposits, where the rapid transition of the sample through a solid state can engender the loss of native conformations. Here we present a new method for native MS based on liquid deposits and MALDI ionization, unambiguously detecting intact noncovalent protein complexes by direct desorption from a liquid spot for the first time. To control for aggregation, we worked with HUαβ, a heterodimer that does not spontaneously rearrange into homodimers in solution. Screening through numerous matrix solutions to observe first the monomeric protein, then the dimer complex, we settled on a nondenaturing binary matrix solution composed of acidic and basic organic matrices in glycerol, which is stable in vacuo. The role of temporal and spatial laser irradiation patterns was found to be critical. Both a protein-protein and a protein-ligand complex could be observed free of aggregation. To minimize gas-phase dissociation, source parameters were optimized to achieve a conservation of complexes above 50% for both systems. Graphical Abstract ᅟ.
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Affiliation(s)
- Martine Beaufour
- Centre de Biophysique Moléculaire, UPR4301, CNRS, affiliated to Université d'Orléans, Rue Charles Sadron, 45071, Orléans Cedex 2, France
| | - David Ginguené
- Centre de Biophysique Moléculaire, UPR4301, CNRS, affiliated to Université d'Orléans, Rue Charles Sadron, 45071, Orléans Cedex 2, France
| | - Rémy Le Meur
- Centre de Biophysique Moléculaire, UPR4301, CNRS, affiliated to Université d'Orléans, Rue Charles Sadron, 45071, Orléans Cedex 2, France
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, UPR4301, CNRS, affiliated to Université d'Orléans, Rue Charles Sadron, 45071, Orléans Cedex 2, France
| | - Martine Cadene
- Centre de Biophysique Moléculaire, UPR4301, CNRS, affiliated to Université d'Orléans, Rue Charles Sadron, 45071, Orléans Cedex 2, France.
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