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Snijder J, Heck AJR. Analytical approaches for size and mass analysis of large protein assemblies. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:43-64. [PMID: 25014341 DOI: 10.1146/annurev-anchem-071213-020015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Analysis of the size and mass of nanoparticles, whether they are natural biomacromolecular or synthetic supramolecular assemblies, is an important step in the characterization of such molecular species. In recent years, electrospray ionization (ESI) has emerged as a technology through which particles with masses up to 100 MDa can be ionized and transferred into the gas phase, preparing them for accurate mass analysis. Here we review currently used methodologies, with a clear focus on native mass spectrometry (MS). Additional complementary methodologies are also covered, including ion-mobility analysis, nanomechanical mass sensors, and charge-detection MS. The literature discussed clearly demonstrates the great potential of ESI-based methodologies for the size and mass analysis of nanoparticles, including very large naturally occurring protein assemblies. The analytical approaches discussed are powerful tools in not only structural biology, but also nanotechnology.
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Affiliation(s)
- Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands; ,
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52
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Thompson NJ, Merdanovic M, Ehrmann M, van Duijn E, Heck AJR. Substrate occupancy at the onset of oligomeric transitions of DegP. Structure 2013; 22:281-90. [PMID: 24373769 DOI: 10.1016/j.str.2013.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 11/14/2013] [Accepted: 11/20/2013] [Indexed: 01/06/2023]
Abstract
The protease-chaperone DegP undergoes secondary through quaternary structural changes, regulating function and preventing indiscriminate proteolysis. Several structures of DegP oligomers have been observed, including the resting state 6-mer and the 12-mer and 24-mer active states. However, the precise events of the transition between the resting and active states still need to be elucidated. We used native mass spectrometry to demonstrate that binding of multiple substrate-mimicking peptide ligands to the DegP resting state occurs prior to the transition to an active conformation. This transition occurred at a 6-mer occupancy of 40% for each peptide ligand. We observed ligand-specific 9-mer formation with a maximum load of 9 peptides, whereas other substrates led to 12-mers accommodating 24 peptides. Based on these data, we present a model for the initial steps of substrate-induced transitions from the resting to active states of DegP.
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Affiliation(s)
- Natalie J Thompson
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Melisa Merdanovic
- Faculty of Biology, Center for Medical Biotechnology, University Duisburg-Essen, 45117 Essen, Germany
| | - Michael Ehrmann
- Faculty of Biology, Center for Medical Biotechnology, University Duisburg-Essen, 45117 Essen, Germany; School of Biosciences, Cardiff University, Cardiff CF10 3US, UK
| | - Esther van Duijn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands.
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53
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Sizing up large protein complexes by electrospray ionisation-based electrophoretic mobility and native mass spectrometry: morphology selective binding of Fabs to hepatitis B virus capsids. Anal Bioanal Chem 2013; 406:1437-46. [PMID: 24357008 DOI: 10.1007/s00216-013-7548-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 11/29/2013] [Accepted: 12/02/2013] [Indexed: 12/29/2022]
Abstract
The capsid of hepatitis B virus (HBV) is a major viral antigen and important diagnostic indicator. HBV capsids have prominent protrusions ('spikes') on their surface and are unique in having either T = 3 or T = 4 icosahedral symmetry. Mouse monoclonal and also human polyclonal antibodies bind either near the spike apices (historically the 'α-determinant') or in the 'floor' regions between them (the 'β-determinant'). Native mass spectrometry (MS) and gas-phase electrophoretic mobility molecular analysis (GEMMA) were used to monitor the titration of HBV capsids with the antigen-binding domain (Fab) of mAb 3120, which has long defined the β-determinant. Both methods readily distinguished Fab binding to the two capsid morphologies and could provide accurate masses and dimensions for these large immune complexes, which range up to ~8 MDa. As such, native MS and GEMMA provide valuable alternatives to a more time-consuming cryo-electron microscopy analysis for preliminary characterisation of virus-antibody complexes.
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54
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Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus. Mol Cell 2013; 52:135-145. [PMID: 24119403 DOI: 10.1016/j.molcel.2013.09.013] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/30/2013] [Accepted: 09/12/2013] [Indexed: 12/26/2022]
Abstract
The CRISPR-Cas system is a prokaryotic host defense system against genetic elements. The Type III-B CRISPR-Cas system of the bacterium Thermus thermophilus, the TtCmr complex, is composed of six different protein subunits (Cmr1-6) and one crRNA with a stoichiometry of Cmr112131445361:crRNA1. The TtCmr complex copurifies with crRNA species of 40 and 46 nt, originating from a distinct subset of CRISPR loci and spacers. The TtCmr complex cleaves the target RNA at multiple sites with 6 nt intervals via a 5' ruler mechanism. Electron microscopy revealed that the structure of TtCmr resembles a "sea worm" and is composed of a Cmr2-3 heterodimer "tail," a helical backbone of Cmr4 subunits capped by Cmr5 subunits, and a curled "head" containing Cmr1 and Cmr6. Despite having a backbone of only four Cmr4 subunits and being both longer and narrower, the overall architecture of TtCmr resembles that of Type I Cascade complexes.
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55
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The role of initial oligomers in amyloid fibril formation by human stefin B. Int J Mol Sci 2013; 14:18362-84. [PMID: 24013380 PMCID: PMC3794784 DOI: 10.3390/ijms140918362] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 08/21/2013] [Accepted: 08/22/2013] [Indexed: 02/03/2023] Open
Abstract
Oligomers are commonly observed intermediates at the initial stages of amyloid fibril formation. They are toxic to neurons and cause decrease in neural transmission and long-term potentiation. We describe an in vitro study of the initial steps in amyloid fibril formation by human stefin B, which proved to be a good model system. Due to relative stability of the initial oligomers of stefin B, electrospray ionization mass spectrometry (ESI MS) could be applied in addition to size exclusion chromatography (SEC). These two techniques enabled us to separate and detect distinguished oligomers from the monomers: dimers, trimers, tetramers, up to decamers. The amyloid fibril formation process was followed at different pH and temperatures, including such conditions where the process was slow enough to detect the initial oligomeric species at the very beginning of the lag phase and those at the end of the lag phase. Taking into account the results of the lower-order oligomers transformations early in the process, we were able to propose an improved model for the stefin B fibril formation.
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56
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Webb IK, Gao Y, Londry FA, McLuckey SA. Trapping mode dipolar DC collisional activation in the RF-only ion guide of a linear ion trap/time-of-flight instrument for gaseous bio-ion declustering. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:1059-65. [PMID: 24078247 PMCID: PMC3799974 DOI: 10.1002/jms.3255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/10/2013] [Accepted: 07/12/2013] [Indexed: 05/11/2023]
Abstract
The application of dipolar direct current (DDC) to the radio frequency-only ion guide (Q0) of a hybrid quadrupole/time-of-flight mass spectrometer for collision-induced declustering of large bio-ions is described. As a broadband technique, ion trap DDC collisional activation (CA) is employed to decluster ions simultaneously over a relatively broad mass-to-charge (m/z) range. Declustering DDC CA can yield significantly narrower peaks relative to those observed in the absence of declustering methods, depending upon the extent of noncovalent adduction associated with the ions, and can also be used in conjunction with other methods, such as nozzle-skimmer CA. The key experimental variables in the DDC experiment are the DDC voltage (VDDC), VRF , and the time over which VDDC is applied. The VDDC/VRF ratio is key to the extent to which ion temperatures are elevated and also influences the upper m/z limit for ion storage. The VDDC/VRF ratio affects ion temperatures and the upper m/z limit in opposing directions. That is, as the ratio increases, the ion temperature also increases, whereas the upper m/z storage limit decreases. However, for a given VDDC /VRF ratio, the upper m/z storage limit can be increased by increasing VRF, at the expense of the lower m/z limit for ion storage. The key value of the approach is that it affords a relatively precise degree of control over ion temperatures as well as the time over which they are elevated to a higher temperature. The utility of the method is illustrated by the application of ion trap DDC CA in Q0 to oligonucleotide, protein, and multimeric protein complex analyte ions.
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Affiliation(s)
- Ian K. Webb
- Department of Chemistry Purdue University West Lafayette, Indiana, USA, 47907-2084
| | - Yang Gao
- Department of Chemistry Purdue University West Lafayette, Indiana, USA, 47907-2084
| | - Frank A. Londry
- AB Sciex 71 Four Valley Drive Concord, Ontario, Canada L4K 4V8
| | - Scott A. McLuckey
- Department of Chemistry Purdue University West Lafayette, Indiana, USA, 47907-2084
- Phone: (765) 494-5270 Fax: (765) 494-0239
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57
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Thompson NJ, Rosati S, Heck AJR. Performing native mass spectrometry analysis on therapeutic antibodies. Methods 2013; 65:11-7. [PMID: 23688935 DOI: 10.1016/j.ymeth.2013.05.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 12/11/2022] Open
Abstract
Since the introduction of "soft" ionization techniques, the role of mass spectrometry (MS) in the field of structural biology has increasingly expanded. With the incorporation of volatile buffers as electrospray ionization (ESI) solvents, non-covalent protein complexes could be efficiently transferred to the gas phase for mass analysis. While native MS has not become a technique used for standard characterization of therapeutic proteins in an industrial setting, it is increasingly used to probe the structural heterogeneity of these complex biomolecules. Here, we describe a detailed sample protocol for the analysis of monoclonal antibodies (mAbs) by native MS and highlight some recent applications of native MS in the analysis of intact mAbs and mAb-based therapeutics.
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Affiliation(s)
- Natalie J Thompson
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Sara Rosati
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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58
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Bereszczak JZ, Rose RJ, van Duijn E, Watts NR, Wingfield PT, Steven AC, Heck AJR. Epitope-distal effects accompany the binding of two distinct antibodies to hepatitis B virus capsids. J Am Chem Soc 2013; 135:6504-12. [PMID: 23597076 PMCID: PMC3658141 DOI: 10.1021/ja402023x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Infection of humans by hepatitis B virus (HBV) induces the copious production of antibodies directed against the capsid protein (Cp). A large variety of anticapsid antibodies have been identified that differ in their epitopes. These data, and the status of the capsid as a major clinical antigen, motivate studies to achieve a more detailed understanding of their interactions. In this study, we focused on the Fab fragments of two monoclonal antibodies, E1 and 3120. E1 has been shown to bind to the side of outward-protruding spikes whereas 3120 binds to the "floor" region of the capsid, between spikes. We used hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) to investigate the effects on HBV capsids of binding these antibodies. Conventionally, capsids loaded with saturating amounts of Fabs would be too massive to be readily amenable to HDX-MS. However, by focusing on the Cp protein, we were able to acquire deuterium uptake profiles covering the entire 149-residue sequence and reveal, in localized detail, changes in H/D exchange rates accompanying antibody binding. We find increased protection of the known E1 and 3120 epitopes on the capsid upon binding and show that regions distant from the epitopes are also affected. In particular, the α2a helix (residues 24-34) and the mobile C-terminus (residues 141-149) become substantially less solvent-exposed. Our data indicate that even at substoichiometric antibody binding an overall increase in the rigidity of the capsid is elicited, as well as a general dampening of its breathing motions.
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Affiliation(s)
- Jessica Z. Bereszczak
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- The Netherlands Proteomics Centre, The Netherlands
| | - Rebecca J. Rose
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- The Netherlands Proteomics Centre, The Netherlands
| | - Esther van Duijn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- The Netherlands Proteomics Centre, The Netherlands
| | - Norman R. Watts
- Protein Expression Laboratory, National Institute for Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda MD 20892, USA
| | - Paul T. Wingfield
- Protein Expression Laboratory, National Institute for Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda MD 20892, USA
| | - Alasdair C. Steven
- Laboratory of Structural Biology, National Institute for Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda MD 20892, USA
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- The Netherlands Proteomics Centre, The Netherlands
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59
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Snijder J, Uetrecht C, Rose RJ, Sanchez-Eugenia R, Marti GA, Agirre J, Guérin DMA, Wuite GJL, Heck AJR, Roos WH. Probing the biophysical interplay between a viral genome and its capsid. Nat Chem 2013; 5:502-9. [DOI: 10.1038/nchem.1627] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/15/2013] [Indexed: 11/09/2022]
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60
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Snijder J, Rose RJ, Veesler D, Johnson JE, Heck AJ. Studying 18 MDa virus assemblies with native mass spectrometry. Angew Chem Int Ed Engl 2013; 52:4020-3. [PMID: 23450509 PMCID: PMC3949431 DOI: 10.1002/anie.201210197] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Indexed: 11/05/2022]
Affiliation(s)
- Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Rebecca J. Rose
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - David Veesler
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John E. Johnson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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61
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Snijder J, Rose RJ, Veesler D, Johnson JE, Heck AJR. Untersuchung von 18 MDa großen Viruspartikeln mit nativer Massenspektrometrie. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201210197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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62
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Coupling electrospray corona discharge, charge reduction and ion mobility mass spectrometry: From peptides to large macromolecular protein complexes. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12127-013-0120-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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63
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Atmanene C, Wagner-Rousset E, Corvaïa N, Van Dorsselaer A, Beck A, Sanglier-Cianférani S. Noncovalent mass spectrometry for the characterization of antibody/antigen complexes. Methods Mol Biol 2013; 988:243-268. [PMID: 23475725 DOI: 10.1007/978-1-62703-327-5_16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Monoclonal antibodies (mAbs) have taken on an increasing importance for the treatment of various diseases including cancers, immunological disorders, and other pathologies. These large biomolecules display specific structural features, which affect their efficiency and need therefore to be extensively characterized using sensitive and orthogonal analytical techniques. Among them, mass spectrometry (MS) has become the method of choice to study mAb amino acid sequences as well as their posttranslational modifications with the aim of reducing their chemistry, manufacturing, and control liabilities. This chapter will provide the reader with a description of the general approach allowing antibody/antigen systems to be characterized by noncovalent MS. In the present chapter, we describe how recent noncovalent MS technologies are used to characterize immune complexes involving both murine and humanized mAb 6F4 directed against human JAM-A, a newly identified antigenic protein (Ag) over-expressed in tumor cells. We will detail experimental conditions (sample preparation, optimization of instrumental parameters, etc.) required for the detection of noncovalent antibody/antigen complexes by MS. We will then focus on the type and the reliability of the information that we get from noncovalent MS data, with emphasis on the determination of the stoichiometry of antibody/antigen systems. Noncovalent MS appears as an additional supporting technique for therapeutic mAbs lead characterization and development.
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Affiliation(s)
- Cédric Atmanene
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, CNRS, UMR7178, Université de Strasbourg, Strasbourg, France
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64
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Blanc B, Rodgers KR, Lukat-Rodgers GS, DuBois JL. Understanding the roles of strictly conserved tryptophan residues in O2 producing chlorite dismutases. Dalton Trans 2012; 42:3156-69. [PMID: 23241559 DOI: 10.1039/c2dt32312e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chlorite dismutases (Clds) degrade ClO(2)(-) to O(2) and Cl(-) in perchlorate respiring bacteria, and they serve still poorly defined cellular roles in other diverse microbes. These proteins share 3 highly conserved Trp residues, W155, W156, and W227, on the proximal side of the heme. The Cld from Dechloromonas aromatica (DaCld) has been shown to form protein-based radicals in its reactions with ClO(2)(-) and peracetic acid. The roles of the conserved Trp residues in radical generation and in enzymatic function were assessed via spectroscopic and kinetic analysis of their Phe mutants. The W155F mutant was the most dramatically affected, appearing to lose the characteristic pentameric oligomerization state, secondary structure, and heme binding properties of the WT protein. The W156F mutant initially retains many features of the WT protein but over time acquires many of the features of W155F. Conversion to an inactive, heme-free form is accelerated by dilution, suggesting loss of the protein's pentameric state. Hence, both W155 and W156 are important for heme binding and maintenance of the protein's reactive pentameric structure. W227F by contrast retains many properties of the WT protein. Important differences are noted in the transient kinetic reactions with peracetic acid (PAA), where W227F appears to form an [Fe(IV)=O]-containing intermediate, which subsequently converts to an uncoupled [Fe(IV)=O + AA(+)˙] system in a [PAA]-dependent manner. This is in contrast to the peroxidase-like formation of [Fe(IV)=O] coupled to a porphyrin π-cation radical in the WT protein, which decays in a [PAA]-independent manner. These observations and the lack of redox protection for the heme in any of the Trp mutants suggests a tendency for protein radical formation in DaCld that is independent of any of these conserved active site residues.
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Affiliation(s)
- Beatrice Blanc
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46656, USA
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65
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Konijnenberg A, Butterer A, Sobott F. Native ion mobility-mass spectrometry and related methods in structural biology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:1239-56. [PMID: 23246828 DOI: 10.1016/j.bbapap.2012.11.013] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 11/19/2012] [Accepted: 11/29/2012] [Indexed: 12/12/2022]
Abstract
Mass spectrometry-based methods have become increasingly important in structural biology - in particular for large and dynamic, even heterogeneous assemblies of biomolecules. Native electrospray ionization coupled to ion mobility-mass spectrometry provides access to stoichiometry, size and architecture of noncovalent assemblies; while non-native approaches such as covalent labeling and H/D exchange can highlight dynamic details of protein structures and capture intermediate states. In this overview article we will describe these methods and highlight some recent applications for proteins and protein complexes, with particular emphasis on native MS analysis. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.
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66
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Kükrer B, Barbu IM, Copps J, Hogan P, Taylor SS, van Duijn E, Heck AJR. Conformational isomers of calcineurin follow distinct dissociation pathways. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1534-43. [PMID: 22811075 PMCID: PMC4120237 DOI: 10.1007/s13361-012-0441-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 06/28/2012] [Accepted: 06/28/2012] [Indexed: 05/12/2023]
Abstract
In the gas-phase, ions of protein complexes typically follow an asymmetric dissociation pathway upon collisional activation, whereby an expelled small monomer takes a disproportionately large amount of the charges from the precursor ion. This phenomenon has been rationalized by assuming that upon activation, a single monomer becomes unfolded, thereby attracting charges to its newly exposed basic residues. Here, we report on the atypical gas-phase dissociation of the therapeutically important, heterodimeric calcium/calmodulin-dependent serine/threonine phosphatase calcineurin, using a combination of tandem mass spectrometry, ion mobility mass spectrometry, and computational modeling. Therefore, a hetero-dimeric calcineurin construct (62 kDa), composed of CNa (44 kDa, a truncation mutant missing the calmodulin binding and auto-inhibitory domains), and CNb (18 kDa), was used. Upon collisional activation, this hetero-dimer follows the commonly observed dissociation behavior, whereby the smaller CNb becomes highly charged and is expelled. Surprisingly, in addition, a second atypical dissociation pathway, whereby the charge partitioning over the two entities is more symmetric is observed. The presence of two gas-phase conformational isomers of calcineurin as revealed by ion mobility mass spectrometry (IM-MS) may explain the co-occurrence of these two dissociation pathways. We reveal the direct relationship between the conformation of the calcineurin precursor ion and its concomitant dissociation pathway and provide insights into the mechanisms underlying this co-occurrence of the typical and atypical fragmentation mechanisms.
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Affiliation(s)
- Basak Kükrer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Ioana M. Barbu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Jeffrey Copps
- The Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Patrick Hogan
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Susan S. Taylor
- The Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Esther van Duijn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
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67
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Rosati S, Thompson NJ, Barendregt A, Hendriks LJA, Bakker ABH, de Kruif J, Throsby M, van Duijn E, Heck AJR. Qualitative and Semiquantitative Analysis of Composite Mixtures of Antibodies by Native Mass Spectrometry. Anal Chem 2012; 84:7227-32. [DOI: 10.1021/ac301611d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sara Rosati
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH
Utrecht, The Netherlands
| | - Natalie J. Thompson
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH
Utrecht, The Netherlands
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH
Utrecht, The Netherlands
| | - Linda J. A. Hendriks
- Merus Biopharmaceuticals, Postvak 133,
Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | - John de Kruif
- Merus Biopharmaceuticals, Postvak 133,
Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Mark Throsby
- Merus Biopharmaceuticals, Postvak 133,
Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Esther van Duijn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH
Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH
Utrecht, The Netherlands
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68
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Atmanene C, Petiot-Bécard S, Zeyer D, Van Dorsselaer A, Vivat Hannah V, Sanglier-Cianférani S. Exploring Key Parameters to Detect Subtle Ligand-Induced Protein Conformational Changes Using Traveling Wave Ion Mobility Mass Spectrometry. Anal Chem 2012; 84:4703-10. [DOI: 10.1021/ac203223h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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69
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Moreno-Córdoba I, Diago-Navarro E, Barendregt A, Heck AJR, Alfonso C, Díaz-Orejas R, Nieto C, Espinosa M. The toxin-antitoxin proteins relBE2Spn of Streptococcus pneumoniae: characterization and association to their DNA target. Proteins 2012; 80:1834-46. [PMID: 22488579 DOI: 10.1002/prot.24081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 03/21/2012] [Accepted: 03/23/2012] [Indexed: 01/07/2023]
Abstract
The chromosome of the pathogenic Gram-positive bacterium Streptococcus pneumoniae contains between six to 10 operons encoding toxin-antitoxin systems (TAS). TAS are widespread and redundant in bacteria and archaea and their role, albeit still obscure, may be related to important aspects of bacteria lifestyle like response to stress. One of the most abundant TAS is the relBE family, being present in the chromosome of many bacteria and archaea. Because of the high rates of morbility and mortality caused by S. pneumoniae, it has been interesting to gain knowledge on the pneumococcal TAS, among them the RelBE2Spn proteins. Here, we have analyzed the DNA binding capacity of the RelB2Spn antitoxin and the RelB2Spn-RelE2Spn proteins by band-shift assays. Thus, a DNA region encompassing the operator region of the proteins was identified. In addition, we have used analytical ultracentrifugation and native mass spectrometry to measure the oligomerization state of the antitoxin alone and the RelBE2Spn complex in solution bound or unbound to its DNA substrate. Using native mass spectrometry allowed us to unambiguously determine the stoichiometry of the RelB2Spn and of the RelBE2Spn complex alone or associated to its DNA target.
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Affiliation(s)
- Inma Moreno-Córdoba
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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70
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Hilton GR, Benesch JLP. Two decades of studying non-covalent biomolecular assemblies by means of electrospray ionization mass spectrometry. J R Soc Interface 2012; 9:801-16. [PMID: 22319100 PMCID: PMC3306659 DOI: 10.1098/rsif.2011.0823] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 01/16/2012] [Indexed: 12/31/2022] Open
Abstract
Mass spectrometry (MS) is a recognized approach for characterizing proteins and the complexes they assemble into. This application of a long-established physico-chemical tool to the frontiers of structural biology has stemmed from experiments performed in the early 1990s. While initial studies focused on the elucidation of stoichiometry by means of simple mass determination, developments in MS technology and methodology now allow researchers to address questions of shape, inter-subunit connectivity and protein dynamics. Here, we chart the remarkable rise of MS and its application to biomolecular complexes over the last two decades.
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Affiliation(s)
| | - Justin L. P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX3 1QZ, UK
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71
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Brand GD, Salbo R, Jørgensen TJD, Bloch C, Boeri Erba E, Robinson CV, Tanjoni I, Moura-da-Silva AM, Roepstorff P, Domont GB, Perales J, Valente RH, Neves-Ferreira AGC. The interaction of the antitoxin DM43 with a snake venom metalloproteinase analyzed by mass spectrometry and surface plasmon resonance. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:567-73. [PMID: 22549991 DOI: 10.1002/jms.2990] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
DM43 is a circulating dimeric antitoxin isolated from Didelphis aurita, a South American marsupial naturally immune to snake envenomation. This endogenous inhibitor binds non-covalently to jararhagin, the main hemorrhagic metalloproteinase from Bothrops jararaca snake venom, and efficiently neutralizes its toxicity. The aim of this study was to apply mass spectrometry (MS) and surface plasmon resonance (SPR) to improve the molecular characterization of this heterocomplex. The stoichiometry of the interaction was confirmed by nanoelectrospray ionization-quadrupole-time-of-flight MS; from native solution conditions, the complex showed a molecular mass of ~94 kDa, indicating that one molecule of jararhagin (50 kDa) interacts with one monomer of DM43 (43 kDa). Although readily observed in solution, the dimeric structure of the inhibitor was barely preserved in the gas phase. This result suggests that, in contrast to the toxin-antitoxin complex, hydrophobic interactions are the primary driving force for the inhibitor dimerization. For the real-time interaction analysis, the toxin was captured on a sensor chip derivatized with the anti-jararhagin monoclonal antibody MAJar 2. The sensorgrams obtained after successive injections of DM43 in a concentration series were globally fitted to a simple bimolecular interaction, yielding the following kinetic rates for the DM43/jararhagin interaction: k(a) = 3.54 ± 0.03 × 10(4) M(-1) s(-1) and k(d) = 1.16 ± 0.07 × 10(-5) s(-1), resulting in an equilibrium dissociation constant (K(D) ) of 0.33 ± 0.06 nM. Taken together, MS and SPR results show that DM43 binds to its target toxin with high affinity and constitute the first accurate quantitative study on the extent of the interaction between a natural inhibitor and a metalloproteinase toxin, with unequivocal implications for the use of this kind of molecule as template for the rational development of novel antivenom therapies.
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Affiliation(s)
- Guilherme D Brand
- Laboratório de Espectrometria de Massa, Embrapa-Recursos Genéticos e Biotecnologia, Estação Parque Biológico, Final W5, Asa Norte, 70770-900, Brasília, DF, Brazil
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72
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Jaquillard L, Saab F, Schoentgen F, Cadene M. Improved accuracy of low affinity protein-ligand equilibrium dissociation constants directly determined by electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:908-922. [PMID: 22430390 DOI: 10.1007/s13361-011-0305-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/07/2011] [Accepted: 11/23/2011] [Indexed: 05/31/2023]
Abstract
There is continued interest in the determination by ESI-MS of equilibrium dissociation constants (K(D)) that accurately reflect the affinity of a protein-ligand complex in solution. Issues in the measurement of K(D) are compounded in the case of low affinity complexes. Here we present a K(D) measurement method and corresponding mathematical model dealing with both gas-phase dissociation (GPD) and aggregation. To this end, a rational mathematical correction of GPD (f(sat)) is combined with the development of an experimental protocol to deal with gas-phase aggregation. A guide to apply the method to noncovalent protein-ligand systems according to their kinetic behavior is provided. The approach is validated by comparing the K(D) values determined by this method with in-solution K(D) literature values. The influence of the type of molecular interactions and instrumental setup on f(sat) is examined as a first step towards a fine dissection of factors affecting GPD. The method can be reliably applied to a wide array of low affinity systems without the need for a reference ligand or protein.
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Affiliation(s)
- Lucie Jaquillard
- Centre de Biophysique Moléculaire, CNRS UPR 4301, affiliated with Université d'Orléans, rue Charles-Sadron, 45071 Orléans, Cedex 2, France
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73
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Tsai YCC, Mueller-Cajar O, Saschenbrecker S, Hartl FU, Hayer-Hartl M. Chaperonin cofactors, Cpn10 and Cpn20, of green algae and plants function as hetero-oligomeric ring complexes. J Biol Chem 2012; 287:20471-81. [PMID: 22518837 DOI: 10.1074/jbc.m112.365411] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The chloroplast chaperonin system of plants and green algae is a curiosity as both the chaperonin cage and its lid are encoded by multiple genes, in contrast to the single genes encoding the two components of the bacterial and mitochondrial systems. In the green alga Chlamydomonas reinhardtii (Cr), three genes encode chaperonin cofactors, with cpn10 encoding a single ∼10-kDa domain and cpn20 and cpn23 encoding tandem cpn10 domains. Here, we characterized the functional interaction of these proteins with the Escherichia coli chaperonin, GroEL, which normally cooperates with GroES, a heptamer of ∼10-kDa subunits. The C. reinhardtii cofactor proteins alone were all unable to assist GroEL-mediated refolding of bacterial ribulose-bisphosphate carboxylase/oxygenase but gained this ability when CrCpn20 and/or CrCpn23 was combined with CrCpn10. Native mass spectrometry indicated the formation of hetero-oligomeric species, consisting of seven ∼10-kDa domains. The cofactor "heptamers" interacted with GroEL and encapsulated substrate protein in a nucleotide-dependent manner. Different hetero-oligomer arrangements, generated by constructing cofactor concatamers, indicated a preferential heptamer configuration for the functional CrCpn10-CrCpn23 complex. Formation of heptamer Cpn10/Cpn20 hetero-oligomers was also observed with the Arabidopsis thaliana (At) cofactors, which functioned with the chloroplast chaperonin, AtCpn60α(7)β(7). It appears that hetero-oligomer formation occurs more generally for chloroplast chaperonin cofactors, perhaps adapting the chaperonin system for the folding of specific client proteins.
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Affiliation(s)
- Yi-Chin C Tsai
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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74
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Ruigrok VJB, van Duijn E, Barendregt A, Dyer K, Tainer JA, Stoltenburg R, Strehlitz B, Levisson M, Smidt H, van der Oost J. Kinetic and stoichiometric characterisation of streptavidin-binding aptamers. Chembiochem 2012; 13:829-36. [PMID: 22416028 DOI: 10.1002/cbic.201100774] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Indexed: 01/06/2023]
Abstract
Aptamers are oligonucleotide ligands that are selected for high-affinity binding to molecular targets. Only limited knowledge relating to relations between structural and kinetic properties that define aptamer-target interactions is available. To this end, streptavidin-binding aptamers were isolated and characterised by distinct analytical techniques. Binding kinetics of five broadly similar aptamers were determined by surface plasmon resonance (SPR); affinities ranged from 35-375 nM with large differences in association and dissociation rates. Native mass spectrometry showed that streptavidin can accommodate up to two aptamer units. In a 3D model of one aptamer, conserved regions are exposed, strongly suggesting that they directly interact with the biotin-binding pockets of streptavidin. Mutational studies confirmed both conserved regions to be crucial for binding. An important result is the observation that the most abundant aptamer in our selections is not the tightest binder, emphasising the importance of having insight into the kinetics of complex formation. To find the tightest binder it might be better to perform fewer selection rounds and to focus on post-selection characterisation, through the use of complementary approaches as described in this study.
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Affiliation(s)
- Vincent J B Ruigrok
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
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75
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Morgner N, Robinson CV. Massign: an assignment strategy for maximizing information from the mass spectra of heterogeneous protein assemblies. Anal Chem 2012; 84:2939-48. [PMID: 22409725 DOI: 10.1021/ac300056a] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has evolved into a powerful adjunct for structural biology, helping to unravel the quaternary structure of protein complexes. Increasing interest has led to the study of ever larger multicomponent systems. Investigating these large complexes with ESI has meant that progressively more complicated mass spectra have been recorded. Correct assignment of these spectra is essential to maximize the information content available. Here we present a new assignment strategy and a supporting software package that allows the investigation of large heterogeneous systems, previously beyond the scope of full spectral assignment due to their complexity. The strategy involves two parts. The first includes a peak fitting routine to determine charge state distributions and consequently the masses of the various subcomplexes. The second module distinguishes between solution and gas phase products depending on their mass to charge ratio and assigns these charge states to different subunit combinations. These fitting and assignment routines contain many internal checks for consistency and reveal mass shifts, dependent upon desolvation conditions and small molecule binding. Using a rotary ATPase as a working example, we show how this assignment strategy is capable of determining the stoichiometry and interactions of the 8 different subunits within this 29-subunit assembly.
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Affiliation(s)
- Nina Morgner
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.
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76
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Bereszczak JZ, Barbu IM, Tan M, Xia M, Jiang X, van Duijn E, Heck AJR. Structure, stability and dynamics of norovirus P domain derived protein complexes studied by native mass spectrometry. J Struct Biol 2012; 177:273-82. [PMID: 22266117 DOI: 10.1016/j.jsb.2012.01.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 11/24/2011] [Accepted: 01/04/2012] [Indexed: 02/05/2023]
Abstract
Expression of the protruding (P) domain of the norovirus capsid protein, in vitro, results in the formation of P dimers and larger oligomers, 12-mer and 24-mer P particles. All these P complexes retain the authentic antigenicity and carbohydrate-binding function of the norovirus capsid. They have been used as tools to study norovirus-host interactions, and the 24-mer P particle has been proposed as a vaccine and vaccine platform against norovirus and other pathogens. In view of their pharmaceutical interest it is important to characterise the structure, stability and dynamics of these protein complexes. Here we use a native mass spectrometric approach. We analyse the P particles under both non-reducing and reducing conditions, as it is known that the macromolecular assemblies are stabilised by inter-subunit disulphide bonding. A novel 18-mer complex is identified, and we show that under reducing conditions the 24-mer dissociates into P dimers that reassemble into the 12-mer small P particle and another novel 36-mer complex. The collisional cross-sections of the 12-mer and 24-mer P particles determined by ion mobility MS are in good agreement with theoretical predictions and electron microscopy data. We propose a model structure for the 18-mer based on ion mobility experiments. Our results demonstrate the interchangeable nature and dynamic relationship of all P domain complexes and confirm their binding activity to the host receptors - human histo blood group antigens (HBGAs). These findings, together with the identification of the 18-mer and 36-mer P complexes add new information to the intriguing interactions of the norovirus P domain.
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Affiliation(s)
- Jessica Z Bereszczak
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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77
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Maple HJ, Garlish RA, Rigau-Roca L, Porter J, Whitcombe I, Prosser CE, Kennedy J, Henry AJ, Taylor RJ, Crump MP, Crosby J. Automated Protein–Ligand Interaction Screening by Mass Spectrometry. J Med Chem 2012; 55:837-51. [DOI: 10.1021/jm201347k] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hannah J. Maple
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| | - Rachel A. Garlish
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Laura Rigau-Roca
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| | - John Porter
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Ian Whitcombe
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | | | - Jeff Kennedy
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Alistair J. Henry
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Richard J. Taylor
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Matthew P. Crump
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| | - John Crosby
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
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78
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Stengel F, Aebersold R, Robinson CV. Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Mol Cell Proteomics 2011; 11:R111.014027. [PMID: 22180098 PMCID: PMC3316738 DOI: 10.1074/mcp.r111.014027] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein assemblies are critical for cellular function and understanding their physical organization is the key aim of structural biology. However, applying conventional structural biology approaches is challenging for transient, dynamic, or polydisperse assemblies. There is therefore a growing demand for hybrid technologies that are able to complement classical structural biology methods and thereby broaden our arsenal for the study of these important complexes. Exciting new developments in the field of mass spectrometry and proteomics have added a new dimension to the study of protein-protein interactions and protein complex architecture. In this review, we focus on how complementary mass spectrometry-based techniques can greatly facilitate structural understanding of protein assemblies.
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Affiliation(s)
- Florian Stengel
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA United Kingdom
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79
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Chen LC, Mandal MK, Hiraoka K. Super-atmospheric pressure electrospray ion source: applied to aqueous solution. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:2108-2114. [PMID: 21989705 DOI: 10.1007/s13361-011-0253-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 09/04/2011] [Accepted: 09/13/2011] [Indexed: 05/31/2023]
Abstract
This is a follow-up paper of our previous report on an ion source, which was operated at an operating pressure higher than the atmospheric pressure. Besides having more working gas for desolvation, the reduction of mean free path of electrons in a higher pressure environment increases the threshold voltage for gaseous breakdown, thus enabling a stable electrospray for the sample solution with high surface tension without the occurrence of electric discharge. In our previous work, the ion source was not coupled directly to the mass spectrometer and significant amount of ions were lost before entering the vacuum of the mass spectrometer. In this paper, we report the new design of our second prototype in which, by using a modified ion transport capillary, the pressurized ESI ion source was coupled directly to the first pumping stage of the mass spectrometer without additional modification on the vacuum pumping system. Demonstrations of the new ion source on the sensitive detection of native proteins from aqueous solution in both positive and negative ion modes are presented.
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Affiliation(s)
- Lee Chuin Chen
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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80
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Sciuto SV, Liu J, Konermann L. An electrostatic charge partitioning model for the dissociation of protein complexes in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1679-1689. [PMID: 21952881 DOI: 10.1007/s13361-011-0205-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 06/27/2011] [Accepted: 06/28/2011] [Indexed: 05/31/2023]
Abstract
Electrosprayed multi-protein complexes can be dissociated by collisional activation in the gas phase. Typically, these processes follow a mechanism whereby a single subunit gets ejected with a disproportionately high amount of charge relative to its mass. This asymmetric behavior suggests that the departing subunit undergoes some degree of unfolding prior to being separated from the residual complex. These structural changes occur concomitantly with charge (proton) transfer towards the subunit that is being unraveled. Charge accumulation takes place up to the point where the subunit loses physical contact with the residual complex. This work develops a simple electrostatic model for studying the relationship between conformational changes and charge enrichment during collisional activation. Folded subunits are described as spheres that carry continuum surface charge. The unfolded chain is envisioned as random coil bead string. Simulations are guided by the principle that the system will adopt the charge configuration with the lowest potential energy for any backbone conformation. A finite-difference gradient algorithm is used to determine the charge on each subunit throughout the dissociation process. Both dimeric and tetrameric protein complexes are investigated. The model reproduces the occurrence of asymmetric charge partitioning for dissociation events that are preceded by subunit unfolding. Quantitative comparisons of experimental MS/MS data with model predictions yield estimates of the structural changes that occur during collisional activation. Our findings suggest that subunit separation can occur over a wide range of scission point structures that correspond to different degrees of unfolding.
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Affiliation(s)
- Stephen V Sciuto
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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81
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Downard KM, Kokabu Y, Ikeguchi M, Akashi S. Homology-modelled structure of the βB2B3-crystallin heterodimer studied by ion mobility and radical probe MS. FEBS J 2011; 278:4044-54. [PMID: 21848669 DOI: 10.1111/j.1742-4658.2011.08309.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Ion mobility MS was employed to study the structure of the βB2B3-crystallin heterodimer following its detection by ESI-TOF MS. The results demonstrate that the heterodimer has a similar cross-section (3 165 Å(2)) and structure to the βB2B2-crystallin homodimer. Several homology-modelled structures for the βB2B3 heterodimer were constructed and assessed in terms of their calculated collision cross-sections and whether the solvent accessibilities of reactive amino acid side chains throughout the βB3 subunit are in accord with measured oxidation levels in radical probe MS protein footprinting experiments. The βB2B3 heterodimer AD model provides the best representation of the heterodimer's structure overall following a consideration of both the ion mobility and radical probe MS data.
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Affiliation(s)
- Kevin M Downard
- School of Molecular Bioscience, University of Sydney, Sydney, Australia.
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82
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Monti MC, Cohen SX, Fish A, Winterwerp HHK, Barendregt A, Friedhoff P, Perrakis A, Heck AJR, Sixma TK, van den Heuvel RHH, Lebbink JHG. Native mass spectrometry provides direct evidence for DNA mismatch-induced regulation of asymmetric nucleotide binding in mismatch repair protein MutS. Nucleic Acids Res 2011; 39:8052-64. [PMID: 21737427 PMCID: PMC3185415 DOI: 10.1093/nar/gkr498] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The DNA mismatch repair protein MutS recognizes mispaired bases in DNA and initiates repair in an ATP-dependent manner. Understanding of the allosteric coupling between DNA mismatch recognition and two asymmetric nucleotide binding sites at opposing sides of the MutS dimer requires identification of the relevant MutS.mmDNA.nucleotide species. Here, we use native mass spectrometry to detect simultaneous DNA mismatch binding and asymmetric nucleotide binding to Escherichia coli MutS. To resolve the small differences between macromolecular species bound to different nucleotides, we developed a likelihood based algorithm capable to deconvolute the observed spectra into individual peaks. The obtained mass resolution resolves simultaneous binding of ADP and AMP.PNP to this ABC ATPase in the absence of DNA. Mismatched DNA regulates the asymmetry in the ATPase sites; we observe a stable DNA-bound state containing a single AMP.PNP cofactor. This is the first direct evidence for such a postulated mismatch repair intermediate, and showcases the potential of native MS analysis in detecting mechanistically relevant reaction intermediates.
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Affiliation(s)
- Maria Chiara Monti
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Serge X. Cohen
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alexander Fish
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Herrie H. K. Winterwerp
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Peter Friedhoff
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Anastassis Perrakis
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
- *To whom correspondence should be addressed. Tel: +31 10 7043604; Fax +31 10 7044747;
| | - Titia K. Sixma
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert H. H. van den Heuvel
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Joyce H. G. Lebbink
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
- *To whom correspondence should be addressed. Tel: +31 10 7043604; Fax +31 10 7044747;
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Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders APL, Dickman MJ, Doudna JA, Boekema EJ, Heck AJR, van der Oost J, Brouns SJJ. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol 2011; 18:529-36. [PMID: 21460843 DOI: 10.1038/nsmb.2019] [Citation(s) in RCA: 421] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 01/24/2011] [Indexed: 12/17/2022]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats) immune system in prokaryotes uses small guide RNAs to neutralize invading viruses and plasmids. In Escherichia coli, immunity depends on a ribonucleoprotein complex called Cascade. Here we present the composition and low-resolution structure of Cascade and show how it recognizes double-stranded DNA (dsDNA) targets in a sequence-specific manner. Cascade is a 405-kDa complex comprising five functionally essential CRISPR-associated (Cas) proteins (CasA(1)B(2)C(6)D(1)E(1)) and a 61-nucleotide CRISPR RNA (crRNA) with 5'-hydroxyl and 2',3'-cyclic phosphate termini. The crRNA guides Cascade to dsDNA target sequences by forming base pairs with the complementary DNA strand while displacing the noncomplementary strand to form an R-loop. Cascade recognizes target DNA without consuming ATP, which suggests that continuous invader DNA surveillance takes place without energy investment. The structure of Cascade shows an unusual seahorse shape that undergoes conformational changes when it binds target DNA.
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Affiliation(s)
- Matthijs M Jore
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
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84
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Snijder J, Rose RJ, Raijmakers R, Heck AJ. Site-specific methionine oxidation in calmodulin affects structural integrity and interaction with Ca2+/calmodulin-dependent protein kinase II. J Struct Biol 2011; 174:187-95. [DOI: 10.1016/j.jsb.2010.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 12/02/2010] [Accepted: 12/08/2010] [Indexed: 10/18/2022]
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85
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Chen LC, Mandal MK, Hiraoka K. High pressure (>1 atm) electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:539-544. [PMID: 21472572 DOI: 10.1007/s13361-010-0058-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Revised: 11/20/2010] [Accepted: 11/25/2010] [Indexed: 05/30/2023]
Abstract
High pressure electrospray ionization mass spectrometry has been performed by pressurizing a custom made ion source chamber with compressed air to a pressure higher than the atmospheric pressure. The ion source was coupled to a commercial time-of-flight mass spectrometer using a nozzle-skimmer arrangement. The onset voltage for the electrospray of aqueous solution was found to be independent on the operating pressure. The onset voltage for the corona discharge, however, increased with the rise of pressure following the Paschen's law. Thus, besides having more working gas for the desolvation process, gaseous breakdown could also be avoided by pressurizing the ESI ion source with air to an appropriate level. Stable electrospray ionization has been achieved for the sample solution with high surface tension such as pure water in both positive and negative ion modes. Fragmentation of labile compounds during the ionization process could also be reduced by optimizing the operating pressure of the ion source.
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Affiliation(s)
- Lee Chuin Chen
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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86
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Lorenzen K, van Duijn E. Native mass spectrometry as a tool in structural biology. ACTA ACUST UNITED AC 2011; Chapter 17:Unit17.12. [PMID: 21104986 DOI: 10.1002/0471140864.ps1712s62] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Native mass spectrometry (native MS) gives information about the composition, topological arrangements, dynamics, and structural properties of protein complexes. The mass range is principally unlimited and highly dynamic, allowing the detection of small subunits and large complexes within the same measurement. The amount of protein needed for an analysis is, compared to most other structural biology methods, very low. This unit provides an introduction to native MS. It starts with an explanation of the basic method and details on how to measure intact proteins and protein complexes, and continues with the study of dynamics and complex stability in the gas phase. The final section discusses the most recent extension to the native MS field, ion mobility, which allows the direct assessment of the structural properties of the complexes of interest.
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87
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Pukala TL. Mass Spectrometry for Structural Biology: Determining the Composition and Architecture of Protein Complexes. Aust J Chem 2011. [DOI: 10.1071/ch11025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Knowledge of protein structure and protein–protein interactions is vital for appreciating the elaborate biochemical pathways that underlie cellular function. While many techniques exist to probe the structure and complex interplay between functional proteins, none currently offer a complete picture. Mass spectrometry and associated methods provide complementary information to established structural biology tools, and with rapidly evolving technological advances, can in some cases even exceed other techniques by its diversity in application and information content. This is primarily because of the ability of mass spectrometry to precisely identify protein complex stoichiometry, detect individual species present in a mixture, and concomitantly offer conformational information. This review describes the attributes of mass spectrometry for the structural investigation of multiprotein assemblies in the context of recent developments and highlights in the field.
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88
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Abstract
The introduction of electrospray ionization (ESI) and in particular nano-electrospray (nESI) has enabled the routine mass spectrometric (MS) analysis of large protein complexes in native aqueous buffers. Time-of-flight (ToF) mass spectrometers, in particular the hybrid quadrupole time-of-flight (Q-ToF) instruments, are well suited to the analysis of large protein complexes. When ionized under native-MS conditions, protein complexes routinely exhibit multiple charge states in excess of m/z 6,000, well above the standard mass range of many quadrupole or ion cyclotron-based instruments. The research area of native MS has expanded considerably in the last decade and has shown particular relevance in the area of protein structure determination. Researchers are now able to routinely measure intact MS spectra of protein complexes above 1 MDa in mass. The advent of ion mobility mass spectrometry (IM-MS), in combination with molecular dynamics (MD) studies, is now allowing researchers to infer the shape of the protein complex being analyzed. Herein, we describe how to acquire IM-MS data that ranges from inorganic salt clusters of caesium iodide (CsI) to large biomolecular complexes such as the chaperone protein GroEL.
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89
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Interrogating viral capsid assembly with ion mobility-mass spectrometry. Nat Chem 2010; 3:126-32. [PMID: 21258385 DOI: 10.1038/nchem.947] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 11/11/2010] [Indexed: 12/22/2022]
Abstract
Most proteins fulfil their function as part of large protein complexes. Surprisingly, little is known about the pathways and regulation of protein assembly. Several viral coat proteins can spontaneously assemble into capsids in vitro with morphologies identical to the native virion and thus resemble ideal model systems for studying protein complex formation. Even for these systems, the mechanism for self-assembly is still poorly understood, although it is generally thought that smaller oligomeric structures form key intermediates. This assembly nucleus and larger viral assembly intermediates are typically low abundant and difficult to monitor. Here, we characterised small oligomers of Hepatitis B virus (HBV) and norovirus under equilibrium conditions using native ion mobility mass spectrometry. This data in conjunction with computational modelling enabled us to elucidate structural features of these oligomers. Instead of more globular shapes, the intermediates exhibit sheet-like structures suggesting that they are assembly competent. We propose pathways for the formation of both capsids.
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90
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Knapman TW, Morton VL, Stonehouse NJ, Stockley PG, Ashcroft AE. Determining the topology of virus assembly intermediates using ion mobility spectrometry-mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:3033-3042. [PMID: 20872636 PMCID: PMC4789508 DOI: 10.1002/rcm.4732] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We have combined ion mobility spectrometry-mass spectrometry with tandem mass spectrometry to characterise large, non-covalently bound macromolecular complexes in terms of mass, shape (cross-sectional area) and stability (dissociation) in a single experiment. The results indicate that the quaternary architecture of a complex influences its residual shape following removal of a single subunit by collision-induced dissociation tandem mass spectrometry. Complexes whose subunits are bound to several neighbouring subunits to create a ring-like three-dimensional (3D) architecture undergo significant collapse upon dissociation. In contrast, subunits which have only a single neighbouring subunit within a complex retain much of their original shape upon complex dissociation. Specifically, we have determined the architecture of two transient, on-pathway intermediates observed during in vitro viral capsid assembly. Knowledge of the mass, stoichiometry and cross-sectional area of each viral assembly intermediate allowed us to model a range of potential structures based on the known X-ray structure of the coat protein building blocks. Comparing the cross-sectional areas of these potential architectures before and after dissociation provided tangible evidence for the assignment of the topologies of the complexes, which have been found to encompass both the 3-fold and the 5-fold symmetry axes of the final icosahedral viral shell. Such insights provide unique information about virus assembly pathways that could allow the design of anti-viral therapeutics directed at the assembly step. This methodology can be readily applied to the structural characterisation of many other non-covalently bound macromolecular complexes and their assembly pathways.
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Affiliation(s)
- Tom W. Knapman
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Victoria L. Morton
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nicola J. Stonehouse
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Peter G. Stockley
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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91
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Wu H, Sun L, Blombach F, Brouns SJJ, Snijders APL, Lorenzen K, van den Heuvel RHH, Heck AJR, Fu S, Li X, Zhang XC, Rao Z, van der Oost J. Structure of the ribosome associating GTPase HflX. Proteins 2010; 78:705-13. [PMID: 19787775 DOI: 10.1002/prot.22599] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The HflX-family is a widely distributed but poorly characterized family of translation factor-related guanosine triphosphatases (GTPases) that interact with the large ribosomal subunit. This study describes the crystal structure of HflX from Sulfolobus solfataricus solved to 2.0-A resolution in apo- and GDP-bound forms. The enzyme displays a two-domain architecture with a novel "HflX domain" at the N-terminus, and a classical G-domain at the C-terminus. The HflX domain is composed of a four-stranded parallel beta-sheet flanked by two alpha-helices on either side, and an anti-parallel coiled coil of two long alpha-helices that lead to the G-domain. The cleft between the two domains accommodates the nucleotide binding site as well as the switch II region, which mediates interactions between the two domains. Conformational changes of the switch regions are therefore anticipated to reposition the HflX-domain upon GTP-binding. Slow GTPase activity has been confirmed, with an HflX domain deletion mutant exhibiting a 24-fold enhanced turnover rate, suggesting a regulatory role for the HflX domain. The conserved positively charged surface patches of the HflX-domain may mediate interaction with the large ribosomal subunit. The present study provides a structural basis to uncover the functional role of this GTPases family whose function is largely unknown.
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Affiliation(s)
- Hao Wu
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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92
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Bich C, Baer S, Jecklin MC, Zenobi R. Probing the hydrophobic effect of noncovalent complexes by mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:286-289. [PMID: 19931466 DOI: 10.1016/j.jasms.2009.10.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Revised: 10/15/2009] [Accepted: 10/15/2009] [Indexed: 05/28/2023]
Abstract
The study of noncovalent interactions by mass spectrometry has become an active field of research in recent years. The role of the different noncovalent intermolecular forces is not yet fully understood since they tend to be modulated upon transfer into the gas phase. The hydrophobic effect, which plays a major role in protein folding, adhesion of lipid bilayers, etc., is absent in the gas phase. Here, noncovalent complexes with different types of interaction forces were investigated by mass spectrometry and compared with the complex present in solution. Creatine kinase (CK), glutathione S-transferase (GST), ribonuclease S (RNase S), and leucine zipper (LZ), which have dissociation constants in the nM range, were studied by native nanoelectrospray mass spectrometry (nanoESI-MS) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) combined with chemical cross-linking (XL). Complexes interacting with hydrogen bonds survived the transfer into gas phase intact and were observed by nanoESI-MS. Complexes that are bound largely by the hydrophobic effect in solution were not detected or only at very low intensity. Complexes with mixed polar and hydrophobic interactions were detected by nanoESI-MS, most likely due to the contribution from polar interactions. All noncovalent complexes could easily be studied by XL MALDI-MS, which demonstrates that the noncovalently bound complexes are conserved, and a real "snap-shot" of the situation in solution can be obtained.
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Affiliation(s)
- Claudia Bich
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
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93
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Native MS: an ’ESI‚ way to support structure- and fragment-based drug discovery. Future Med Chem 2010; 2:35-50. [DOI: 10.4155/fmc.09.141] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The success of early drug-discovery programs depends on the adequate combination of complementary and orthogonal technologies allowing hit/lead compounds to be optimized and improve therapeutic activity. Among the available biophysical methods, native MS recently emerged as an efficient method for compound-binding screening. Native MS is a highly sensitive and accurate screening technique. This review provides a description of the general approach and an overview of the possible characterization of ligand-binding properties. How native MS supports structure- and fragment-based drug research will also be discussed, with examples from the literature and internal developments. Native MS shows strong potential for in-depth characterization of ligand-binding properties. It is also a reliable screening technique in drug-discovery processes.
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94
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Schenauer MR, Leary JA. An Ion Mobility-Mass Spectrometry Investigation of Monocyte Chemoattractant Protein-1. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2009; 287:70-76. [PMID: 20160907 PMCID: PMC2769070 DOI: 10.1016/j.ijms.2009.02.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In the present article we describe the gas-phase dissociation behavior of the dimeric form of monocyte chemoattractant protein-1 (MCP-1) using quadrupole-traveling wave ion mobility-time of flight mass spectrometry (q-TWIMS-TOF MS) (Waters Synapt™). Through investigation of the 9(+) charge state of the dimer, we were able to monitor dissociation product ion (monomer) formation as a function of activation energy. Using ion mobility, we were able to observe precursor ion structural changes occurring throughout the activation process. Arrival time distributions (ATDs) for the 5(+) monomeric MCP-1 product ions, derived from the gas-phase dissociation of the 9(+) dimer, were then compared with ATDs obtained for the 5(+) MCP-1 monomer isolated directly from solution. The results show that the dissociated monomer is as compact as the monomer arising from solution, regardless of the trap collision energy (CE) used in the dissociation. The solution-derived monomer, when collisionally activated, also resists significant unfolding within measure. Finally, we compared the collisional activation data for the MCP-1 dimer with an MCP-1 dimer non-covalently bound to a single molecule of the semi-synthetic glycosaminoglycan (GAG) analog Arixtra™; the latter a therapeutic anti-thrombin III-activating pentasaccharide. We observed that while dimeric MCP-1 dissociated at relatively low trap CEs, the Arixtra-bound dimer required much higher energies, which also induced covalent bond cleavage in the bound Arixtra molecule. Both the free and Arixtra-bound dimers became less compact and exhibited longer arrival times with increasing trap CEs, albeit the Arixtra-bound complex at slightly higher energies. That both dimers shifted to longer arrival times with increasing activation energy, while the dissociated MCP-1 monomers remained compact, suggests that the longer arrival times of the Arixtra-free and Arixtra-bound dimers may represent a partial breach of non-covalent interactions between the associated MCP-1 monomers, rather than extensive unfolding of individual subunits. The fact that Arixtra preferentially binds MCP-1 dimers and prevents dimer dissociation at comparable activation energies to the Arixtra-free dimer, may suggest that the drug interacts across the two monomers, thereby inhibiting their dissociation.
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Affiliation(s)
- Matthew R Schenauer
- Departments of Chemistry and Molecular and Cellular Biology, University of California, Davis, California 95616
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95
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Bagal D, Kitova EN, Liu L, El-Hawiet A, Schnier PD, Klassen JS. Gas Phase Stabilization of Noncovalent Protein Complexes Formed by Electrospray Ionization. Anal Chem 2009; 81:7801-6. [DOI: 10.1021/ac900611a] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dhanashri Bagal
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Alberta Ingenuity Center for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Elena N. Kitova
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Alberta Ingenuity Center for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Lan Liu
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Alberta Ingenuity Center for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Amr El-Hawiet
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Alberta Ingenuity Center for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Paul D. Schnier
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Alberta Ingenuity Center for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - John S. Klassen
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Alberta Ingenuity Center for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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96
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Pan J, Xu K, Yang X, Choy WY, Konermann L. Solution-Phase Chelators for Suppressing Nonspecific Protein−Metal Interactions in Electrospray Mass Spectrometry. Anal Chem 2009; 81:5008-15. [DOI: 10.1021/ac900423x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Jingxi Pan
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, People’s Republic of China, and School of Pharmaceutical Sciences and National Research Laboratories of Natural and Biomimetic Drugs, Peking University, Beijing 100083, People’s Republic of China
| | - Kun Xu
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, People’s Republic of China, and School of Pharmaceutical Sciences and National Research Laboratories of Natural and Biomimetic Drugs, Peking University, Beijing 100083, People’s Republic of China
| | - Xiaoda Yang
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, People’s Republic of China, and School of Pharmaceutical Sciences and National Research Laboratories of Natural and Biomimetic Drugs, Peking University, Beijing 100083, People’s Republic of China
| | - Wing-Yiu Choy
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, People’s Republic of China, and School of Pharmaceutical Sciences and National Research Laboratories of Natural and Biomimetic Drugs, Peking University, Beijing 100083, People’s Republic of China
| | - Lars Konermann
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, People’s Republic of China, and School of Pharmaceutical Sciences and National Research Laboratories of Natural and Biomimetic Drugs, Peking University, Beijing 100083, People’s Republic of China
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97
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Guo N, Zhang R, Song F, He J, Xia B, Abliz Z. Characterization of acid-induced protein conformational changes and noncovalent complexes in solution by using coldspray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:845-851. [PMID: 19211263 DOI: 10.1016/j.jasms.2008.12.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 12/23/2008] [Accepted: 12/24/2008] [Indexed: 05/27/2023]
Abstract
Coldspray ionization (CSI) mass spectrometry, a variant of electrospray ionization (ESI) operating at low temperature (20 to -80 degrees C), has been used to characterize protein conformation and noncovalent complexes. A comparison of CSI and ESI was presented for the investigation of the equilibrium acid-induced unfolding of cytochrome c, ubiquitin, myoglobin, and cyclophilin A (CypA) over a wide range of pH values in aqueous solutions. CSI and nanoelectrospray ionization (nanoESI) were also compared in their performance to characterize the conformational changes of cytochrome c and myoglobin. Significant differences were observed, with narrower charged-state distribution and a shift to lower charge state in the CSI mass spectra compared with those in ESI and nanoESI mass spectra. The results suggest that CSI is more prone to preserving folded protein conformations in solution than the ESI and nanoESI methods. Moreover, the CSI-MS data are comparable with those obtained by other established biophysical methods, which are generally acknowledged to be the suitable techniques for monitoring protein conformation in solution. Noncovalent complexes of holomyoglobin and the protein-ligand complex between CypA and cyclosporin A (CsA) were also investigated at a neutral pH using the CSI-MS method. The results of this study suggest the ability of CSI-MS in retaining of protein conformation and noncovalent interactions in solution and probing subtle protein conformational changes. Additionally, the CSI-MS method is capable of analyzing quantitatively equilibrium unfolding transitions of proteins. CSI-MS may become one of the promising techniques for investigating protein conformation and noncovalent protein-ligand interactions in solution.
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Affiliation(s)
- Na Guo
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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98
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Diemer H, Atmanene C, Sanglier S, Morrissey B, Van Dorsselaer A, Downard KM. Detection and structural features of the betaB2-B3-crystallin heterodimer by radical probe mass spectrometry (RP-MS). JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:803-812. [PMID: 19206113 DOI: 10.1002/jms.1560] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The predilection of the beta-crystallin B2 subunit to interact with the betaB3 subunit rather than self associate is evident by the detection of the betaB2-B3-crystallin heterodimer by native gel electrophoresis and electrospray ionisation time-of-flight (ESI-TOF) mass spectrometry under non denaturing conditions. The complex has been detected for the first time and its molecular mass is measured to be 47,450 +/- 1 Da. Radical probe mass spectrometry (RP-MS) was subsequently applied to investigate the nature of the heterodimer through the limited oxidation of the subunits in the complex. Two peptide segments of the betaB2 subunit and six of the betaB3 subunit were found to oxidise, with far greater oxidation observed within the betaB3 versus the betaB2 subunit. This, and the observation that the oxidation data of betaB2 subunit is inconsistent with the structure of the betaB2 monomer, demonstrates that the protection of betaB2 is conferred by its association with betaB3 subunit within the heterodimer where only the residues of, and towards, its N-terminal domain remain exposed to solvent. The results suggest that the betaB2 subunit adopts a more compacted form than in its monomeric form in order for much of its structure to be enveloped by the betaB3 subunit within the heterodimer.
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Affiliation(s)
- Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC-DSA, Université Louis Pasteur, Centre National de la Recherche Scientifique UMR7178, Strasbourg, France
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99
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Pinkse MWH, Rijkers DTS, Dostmann WR, Heck AJR. Mode of action of cGMP-dependent protein kinase-specific inhibitors probed by photoaffinity cross-linking mass spectrometry. J Biol Chem 2009; 284:16354-16368. [PMID: 19369251 DOI: 10.1074/jbc.m808521200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The inhibitor peptide DT-2 (YGRKKRRQRRRPPLRKKKKKH) is the most potent and selective inhibitor of the cGMP-dependent protein kinase (PKG) known today. DT-2 is a construct of a PKG tight binding sequence (W45, LRKKKKKH, KI=0.8 microM) and a membrane translocating sequence (DT-6, YGRKKRRQRRRPP, KI=1.1 microM), that combined strongly inhibits PKG catalyzed phosphorylation (KI=12.5 nM) with approximately 1000-fold selectivity toward PKG over protein kinase A, the closest relative of PKG. However, the molecular mechanism behind this inhibition is not entirely understood. Using a combination of photoaffinity labeling, stable isotope labeling, and mass spectrometry, we have located the binding sites of PKG-specific substrate and inhibitor peptides. Covalent linkage of a PKG-specific substrate analogue was localized in the catalytic core on residues 356-372, also known as the glycine-rich loop, essential for ATP binding. By analogy, the individual inhibitor peptides W45 and DT-6 were also found to cross-link near the glycine-rich loop, suggesting these are both substrate competitive inhibitors. A bifunctional photoreactive analogue of DT-2 was found to generate dimers of PKG. This cross-linking induced covalent PKG dimerization was not observed for an N-terminal deletion mutant of PKG, which lacks the dimerization domain. In addition, non-covalent mass spectrometry was used to determine binding stoichiometry and binding order of the inhibitor peptides. Dimeric PKG binds two W45 and DT-6 peptides, whereas only one DT-2 molecule was observed to bind to the dimeric PKG. Taken together, these findings imply that (i) the two individual components making up DT-2 are both targeted against the substrate-binding site and (ii) binding of a single DT-2 molecule inactivates both PKG monomers simultaneously, which is an indication that (iii) in cGMP-activated PKG the catalytic centers of both subunits may be in each other's proximity.
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Affiliation(s)
- Martijn W H Pinkse
- From the Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnnelaan 16, Utrecht 3584 CA, The Netherlands; Department of Biotechnology, Delft, University of Technology, Delft 2628 BC, The Netherlands
| | - Dirk T S Rijkers
- Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht 3584 CA, The Netherlands
| | - Wolfgang R Dostmann
- Department of Pharmacology, College of Medicine, University of Vermont, Burlington, Vermont 05405
| | - Albert J R Heck
- From the Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnnelaan 16, Utrecht 3584 CA, The Netherlands.
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100
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Scarff CA, Patel VJ, Thalassinos K, Scrivens JH. Probing hemoglobin structure by means of traveling-wave ion mobility mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:625-31. [PMID: 19110442 DOI: 10.1016/j.jasms.2008.11.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 11/26/2008] [Accepted: 11/26/2008] [Indexed: 05/11/2023]
Abstract
Hemoglobin (Hb) is a tetrameric noncovalent complex consisting of two alpha- and two beta-globin chains each associated with a heme group. Its exact assembly pathway is a matter of debate. Disorders of hemoglobin are the most common inherited disorders and subsequently the molecule has been extensively studied. This work attempts to further elucidate the structural properties of the hemoglobin tetramer and its components. Gas-phase conformations of hemoglobin tetramers and their constituents were investigated by means of traveling-wave ion mobility mass spectrometry. Sickle (HbS) and normal (HbA) hemoglobin molecules were analyzed to determine whether conformational differences in their quaternary structure could be observed. Rotationally averaged collision cross sections were estimated for tetramer, dimer, apo-, and holo-monomers with reference to a protein standard with known cross sections. Estimates of cross section obtained for the tetramers were compared to values calculated from X-ray crystallographic structures. HbS was consistently estimated to have a larger cross section than that of HbA, comparable with values obtained from X-ray crystallographic structures. Nontetrameric species observed included apo- and holo- forms of alpha- and beta-monomers and heterodimers; alpha- and beta-monomers in both apo- and holo- forms were found to have similar cross sections, suggesting they maintain a similar fold in the gas phase in both the presence and the absence of heme. Heme-deficient dimer, observed in the spectrum when analyzing commercially prepared Hb, was not observed when analyzing fresh blood. This implies that holo-alpha-apo-beta is not an essential intermediate within the Hb assembly pathway, as previously proposed.
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Affiliation(s)
- Charlotte A Scarff
- Department of Biological Sciences, University of Warwick, Coventry, United Kingdom
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