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Blevins MS, Walker JN, Schaub JM, Finkelstein IJ, Brodbelt JS. Characterization of the T4 gp32-ssDNA complex by native, cross-linking, and ultraviolet photodissociation mass spectrometry. Chem Sci 2021; 12:13764-13776. [PMID: 34760161 PMCID: PMC8549804 DOI: 10.1039/d1sc02861h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/23/2021] [Indexed: 12/28/2022] Open
Abstract
Protein-DNA interactions play crucial roles in DNA replication across all living organisms. Here, we apply a suite of mass spectrometry (MS) tools to characterize a protein-ssDNA complex, T4 gp32·ssDNA, with results that both support previous studies and simultaneously uncover novel insight into this non-covalent biological complex. Native mass spectrometry of the protein reveals the co-occurrence of Zn-bound monomers and homodimers, while addition of differing lengths of ssDNA generates a variety of protein:ssDNA complex stoichiometries (1 : 1, 2 : 1, 3 : 1), indicating sequential association of gp32 monomers with ssDNA. Ultraviolet photodissociation (UVPD) mass spectrometry allows characterization of the binding site of the ssDNA within the protein monomer via analysis of holo ions, i.e. ssDNA-containing protein fragments, enabling interrogation of disordered regions of the protein which are inaccessible via traditional crystallographic techniques. Finally, two complementary cross-linking (XL) approaches, bottom-up analysis of the crosslinked complexes as well as MS1 analysis of the intact complexes, are used to showcase the absence of ssDNA binding with the intact cross-linked homodimer and to generate two homodimer gp32 model structures which highlight that the homodimer interface overlaps with the monomer ssDNA-binding site. These models suggest that the homodimer may function in a regulatory capacity by controlling the extent of ssDNA binding of the protein monomer. In sum, this work underscores the utility of a multi-faceted mass spectrometry approach for detailed investigation of non-covalent protein-DNA complexes.
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Affiliation(s)
- Molly S Blevins
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Jada N Walker
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
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Sasiene ZJ, Mendis PM, Jackson GP. Quantitative Assessment of Six Different Reagent Gases for Charge Transfer Dissociation (CTD) of Biological Ions. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 462:116532. [PMID: 33679212 PMCID: PMC7928426 DOI: 10.1016/j.ijms.2021.116532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Charge transfer dissociation mass spectrometry (CTD-MS) has been shown to induce high energy fragmentation of biological ions in the gas phase and provide fragmentation spectra similar to extreme ultraviolet photodissociation (XUVPD). To date, CTD has typically employed helium cations with kinetic energies between 4-10 keV to initiate radical-directed fragmentation of analytes. However, as a reagent, helium has recently been listed as a critical mineral that is becoming scarcer and more expensive, so this study explored the potential for using cheaper and more readily available reagent gases. A model peptide, bradykinin, and a model oligosaccharide, κ-carrageenan with a degree of polymerization of 4, were fragmented using a variety of CTD reagent gases, which included helium, hydrogen, oxygen, nitrogen, argon and lab air. The CTD results were also contrasted with low-energy collision-induced dissociation (LE-CID), which were collected on the same 3D ion trap. Using constant reagent ion fluxes and kinetic energies, all five alterative reagent gases generated remarkably consistent sequence coverage and fragmentation efficiencies relative to He-CTD, which suggests that the ionization energy of the reagent gas has a negligible effect on the activation of the biological ions. The CTD efficiencies of all the gases ranged from 11-13% for bradykinin and 7-8% for κ-carrageenan. Within these tight ranges, the abundance of the CTnoD peak of bradykinin and the efficiency of CTD fragmentation of bradykinin both correlated with the ionization energy of the CTD reagent gas, which suggests that resonant charge transfer plays a small role in the activation of this peptide. The majority of the excitation energy for bradykinin and for κ-carrageenan comes from an electron stopping mechanism, which is described by long-range interactions between the reagent cations and electrons in the highest occupied molecular orbitals (HOMOs) of the biological ions. The CTD spectra do not provide any evidence for covalently bound products between the biological ions and the more-reactive gases like hydrogen, oxygen and nitrogen, which implies that the high kinetic energies of the reagent ions make them unavailable for covalent reactions. This work demonstrates that any of the substitute reagent gases tested are viable options for future CTD-MS experiments.
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Affiliation(s)
- Zachary J. Sasiene
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506-6121, USA
| | - Praneeth M. Mendis
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506-6121, USA
| | - Glen P. Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506-6121, USA
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV 26506-6121, USA
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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Kaczorowska MA, Jędrzejewska B. Electrospray ionization collision induced dissociation of thiocarbocyanine and selenocarbocyanine dyes. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:592-599. [PMID: 31066154 DOI: 10.1002/jms.4368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
The effect of the properties of sulphur and selenium atoms, the composition and location of substituents (-CH3 , -OCH3 , -C2 H5 , and -C3 H6 -((N+ Br- )C5 H5 )), and the charge state on the collision induced dissociation (CID) behaviour of ions generated by electrospray ionization (ESI) of thiocarbocyanine and selenocarbocyanine dyes have been investigated. The results show that, for of all the examined singly charged ions, the main dissociation channel was related to the formation of distonic ions, generated as a result of cleavages within the dimethine bridge. In the case of doubly charged ions (with propyl-pyridinium substituents), competition between fragmentation processes related to charges located at different nitrogen atoms has been observed. The S/Se replacement also has an impact on the CID behaviour of the examined carbocyanine dyes. On the basis of the performed CID MS/MS experiments, general rules for the CID of thiocarbocyanine and selenocarbocyanine dyes have been proposed.
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Affiliation(s)
- Małgorzata A Kaczorowska
- Faculty of Chemical Technology and Engineering, UTP University of Science and Technology, Seminaryjna 3, PL-85-326, Bydgoszcz, Poland
| | - Beata Jędrzejewska
- Faculty of Chemical Technology and Engineering, UTP University of Science and Technology, Seminaryjna 3, PL-85-326, Bydgoszcz, Poland
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Herburger A, van der Linde C, Beyer MK. Photodissociation spectroscopy of protonated leucine enkephalin. Phys Chem Chem Phys 2018; 19:10786-10795. [PMID: 28233882 DOI: 10.1039/c6cp08436b] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protonated leucine enkephalin (YGGFL) was studied by ultraviolet photodissociation (UVPD) from 225 to 300 nm utilizing an optical parametric oscillator tunable wavelength laser system (OPO). Fragments were identified by absolute mass measurement in a 9.4 T Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). Bond cleavage was preferred in the vicinity of the two aromatic residues, resulting in high ion abundances for a4, a1, b3, y2 and y1 fragments. a, b and y ions dominated the mass spectrum, and full sequence coverage was achieved for those types. Photodissociation was most effective at the short wavelength end of the studied range, which is assigned to the onset of the La π-π* transition of the tyrosine chromophore, but worked well also at the Lb π-π* chromophore absorption maxima in the 35 000-39 000 cm-1 region. Several side-chain and internal fragments were observed. H atom loss is observed only above 41 000 cm-1, consistent with the requirement of a curve crossing to a repulsive 1πσ* state. It is suggested that the photochemically generated mobile H atom plays a role in further backbone cleavages, similar to the mechanism for electron capture dissociation. The b4 fragment is most intense at the Lb chromophore absorptions, undergoing additional fragmentation at higher photon energies. The high resolution of the FT-ICR MS revealed that out of all x and z-type fragments only x3 and x4 were formed, with low intensity. Other previously reported x- and z-fragments were re-assigned to internal fragments, based on exact mass measurement.
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Affiliation(s)
- Andreas Herburger
- Institut für Ionenphysik und Angewandte Physik, Leopold-Franzens-Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria.
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Morrison LJ, Chai W, Rosenberg JA, Henkelman G, Brodbelt JS. Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry. Phys Chem Chem Phys 2018; 19:20057-20074. [PMID: 28722742 DOI: 10.1039/c7cp04073c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.
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Quick MM, Mehaffey MR, Johns RW, Parker WR, Brodbelt JS. SITS Derivatization of Peptides to Enhance 266 nm Ultraviolet Photodissociation (UVPD). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1462-1472. [PMID: 28315237 DOI: 10.1007/s13361-017-1650-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 06/06/2023]
Abstract
N-terminal derivatization of peptides with the chromogenic reagent 4-acetamido-4-isothiocyanatostilbene-2,2-disulfonic acid (SITS) is demonstrated to enhance the efficiency of 266 nm ultraviolet photodissociation (UVPD). Attachment of the chromophore results in a mass shift of 454 Da and provides significant gains in the number and abundances of diagnostic fragment ions upon UVPD. Activation of SITS-tagged peptides with 266 nm UVPD leads to many fragment ions akin to the a/b/y ions commonly produced by CID, along with other sequence ions (c, x, and z) typically accessed through higher energy pathways. Extreme bias towards C-terminal fragment ions is observed upon activation of SITS-tagged peptides using multiple 266 nm laser pulses. Due to the high reaction efficiency of the isothiocyanate coupling to the N-terminus of peptides, we demonstrate the ability to adapt this strategy to a high-throughput LC-MS/MS workflow with 266 nm UVPD. Graphical Abstract ᅟ.
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Affiliation(s)
- M Montana Quick
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - M Rachel Mehaffey
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - Robert W Johns
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, 78712, USA
| | - W Ryan Parker
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
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Holden DD, Brodbelt JS. Improving Performance Metrics of Ultraviolet Photodissociation Mass Spectrometry by Selective Precursor Ejection. Anal Chem 2016; 89:837-846. [PMID: 28105830 DOI: 10.1021/acs.analchem.6b03777] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Confident protein identifications derived from high-throughput bottom-up and top-down proteomics workflows depend on acquisition of thousands of tandem mass spectrometry (MS/MS) spectra with adequate signal-to-noise and accurate mass assignments of the fragment ions. Ultraviolet photodissociation (UVPD) using 193 nm photons has proven to be well-suited for activation and fragmentation of peptides and proteins in ion trap mass spectrometers, but the spectral signal-to-noise ratio (S/N) is typically lower than that obtained from collisional activation methods. The lower S/N is attributed to the dispersion of ion current among numerous fragment ion channels (a,b,c,x,y,z ions). In addition, frequently UVPD is performed such that a relatively large population of precursor ions remains undissociated after the UV photoactivation period in order to prevent overdissociation into small uninformative or internal fragment ions. Here we report a method to improve spectral S/N and increase the accuracy of mass assignments of UVPD mass spectra via resonance ejection of undissociated precursor ions after photoactivation. This strategy, termed precursor ejection UVPD or PE-UVPD, allows the ion trap to be filled with more ions prior to UVPD while at the same time alleviating the space charge problems that would otherwise contribute to the skewing of mass assignments and reduction of S/N. Here we report the performance gains by implementation of PE-UVPD for peptide analysis in an ion trap mass spectrometer.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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Holden DD, Makarov A, Schwartz JC, Sanders JD, Zhuk E, Brodbelt JS. Ultraviolet Photodissociation Induced by Light‐Emitting Diodes in a Planar Ion Trap. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Dustin D. Holden
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen) GmbH Hanna-Kunath-Strasse 11 28199 Bremen Germany
| | - Jae C. Schwartz
- Thermo Fisher Scientific Inc. 355 River Oaks Pkwy San Jose CA 95134 USA
| | - James D. Sanders
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
| | - Eugene Zhuk
- Thermo Fisher Scientific Inc. 355 River Oaks Pkwy San Jose CA 95134 USA
| | - Jennifer S. Brodbelt
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
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Holden DD, Makarov A, Schwartz JC, Sanders JD, Zhuk E, Brodbelt JS. Ultraviolet Photodissociation Induced by Light-Emitting Diodes in a Planar Ion Trap. Angew Chem Int Ed Engl 2016; 55:12417-21. [PMID: 27605434 DOI: 10.1002/anie.201605850] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/02/2016] [Indexed: 11/09/2022]
Abstract
The first application of light-emitting diodes (LEDs) for ultraviolet photodissociation (UVPD) mass spectrometry is reported. LEDs provide a compact, low cost light source and have been incorporated directly into the trapping cell of an Orbitrap mass spectrometer. MS/MS efficiencies of over 50 % were obtained using an extended irradiation period, and UVPD was optimized by modulating the ion trapping parameters to maximize the overlap between the ion cloud and the irradiation volume.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen) GmbH, Hanna-Kunath-Strasse 11, 28199, Bremen, Germany
| | - Jae C Schwartz
- Thermo Fisher Scientific Inc., 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA
| | - Eugene Zhuk
- Thermo Fisher Scientific Inc., 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA.
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Morrison LJ, Rosenberg JA, Singleton JP, Brodbelt JS. Statistical Examination of the a and a + 1 Fragment Ions from 193 nm Ultraviolet Photodissociation Reveals Local Hydrogen Bonding Interactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1443-53. [PMID: 27206509 PMCID: PMC4974117 DOI: 10.1007/s13361-016-1418-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/01/2016] [Accepted: 05/06/2016] [Indexed: 05/11/2023]
Abstract
Dissociation of proteins and peptides by 193 nm ultraviolet photodissociation (UVPD) has gained momentum in proteomic studies because of the diversity of backbone fragments that are produced and subsequent unrivaled sequence coverage obtained by the approach. The pathways that form the basis for the production of particular ion types are not completely understood. In this study, a statistical approach is used to probe hydrogen atom elimination from a + 1 radical ions, and different extents of elimination are found to vary as a function of the identity of the C-terminal residue of the a product ions and the presence or absence of hydrogen bonds to the cleaved residue. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Jake A Rosenberg
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
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