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Structural Diversity of Di-Metalized Arginine Evidenced by Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy in the Gas Phase. Molecules 2021; 26:molecules26216546. [PMID: 34770955 PMCID: PMC8587954 DOI: 10.3390/molecules26216546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 12/18/2022] Open
Abstract
Although metal cations are prevalent in biological media, the species of multi-metal cationized biomolecules have received little attention so far. Studying these complexes in isolated state is important, since it provides intrinsic information about the interaction among them on the molecular level. Our investigation here demonstrates the unexpected structural diversity of such species generated by a matrix-assisted laser desorption ionization (MALDI) source in the gas phase. The photodissociation spectroscopic and theoretical study reflects that the co-existing isomers of [Arg+Rb+K−H]+ can have energies ≥95 kJ/mol higher than that of the most stable one. While the result can be rationalized by the great isomerization energy barrier due to the coordination, it strongly reminds us to pay more attention to their structural diversities for multi-metalized fundamental biological molecules, especially for the ones with the ubiquitous alkali metal ions.
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2
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Chemical labeling – Assisted mass spectrometry analysis for sensitive detection of cytidine dual modifications in RNA of mammals. Anal Chim Acta 2020; 1098:56-65. [DOI: 10.1016/j.aca.2019.11.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/13/2019] [Accepted: 11/10/2019] [Indexed: 12/15/2022]
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3
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Janek T, Rodrigues LR, Czyżnikowska Ż. Study of metal-lipopeptide complexes and their self-assembly behavior, micelle formation, interaction with bovine serum albumin and biological properties. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.07.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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4
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Zenaidee MA, Leeming MG, Zhang F, Funston TT, Donald WA. Highly Charged Protein Ions: The Strongest Organic Acids to Date. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Michael G. Leeming
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology University of Melbourne Parkville Victoria 3010 Australia
| | - Fangtong Zhang
- School of Chemistry University of New South Wales Sydney NSW 2052 Australia
| | - Toby T. Funston
- School of Chemistry University of New South Wales Sydney NSW 2052 Australia
| | - William A. Donald
- School of Chemistry University of New South Wales Sydney NSW 2052 Australia
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5
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Zenaidee MA, Leeming MG, Zhang F, Funston TT, Donald WA. Highly Charged Protein Ions: The Strongest Organic Acids to Date. Angew Chem Int Ed Engl 2017; 56:8522-8526. [DOI: 10.1002/anie.201702781] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/19/2017] [Indexed: 11/09/2022]
Affiliation(s)
| | - Michael G. Leeming
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology University of Melbourne Parkville Victoria 3010 Australia
| | - Fangtong Zhang
- School of Chemistry University of New South Wales Sydney NSW 2052 Australia
| | - Toby T. Funston
- School of Chemistry University of New South Wales Sydney NSW 2052 Australia
| | - William A. Donald
- School of Chemistry University of New South Wales Sydney NSW 2052 Australia
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6
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Tang F, Cen SY, He H, Liu Y, Yuan BF, Feng YQ. Peptidylation for the determination of low-molecular-weight compounds by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Analyst 2016; 141:3259-65. [DOI: 10.1039/c6an00604c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A universal peptide-based derivatization (peptidylation) strategy for the sensitive detection of low-molecular-weight compounds by MALDI-TOF-MS was developed.
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Affiliation(s)
- Feng Tang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- P.R. China
| | - Si-Ying Cen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- P.R. China
| | - Huan He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- P.R. China
| | - Yi Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- P.R. China
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7
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Nonose S, Yamashita K, Okamura T, Fukase S, Kawashima M, Sudo A, Isono H. Conformations of disulfide-intact and -reduced lysozyme ions probed by proton-transfer reactions at various temperatures. J Phys Chem B 2014; 118:9651-61. [PMID: 25046209 DOI: 10.1021/jp505621f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton-transfer reactions of disulfide-intact and -reduced lysozyme ions (7+ through 14+) to 2,6-dimethylpyridine were examined in the gas phase using tandem mass spectrometry with electrospray ionization. By changing temperature of a collision cell from 280 to 460 K, temperature dependence of reaction rate constants and branching fractions was measured. Absolute reaction rate constants for the protein ions of specific charge states were determined from intensities of parent and product ions in the mass spectra. Remarkable change was observed for the rate constants and distribution of product ions. The rate constants for disulfide-intact ions changed more drastically with change of charge states and temperature than those for disulfide-reduced ions. Observed branching fractions for parent and product ions were represented by calculated reaction rate constants with a scheme of sequential process. The reaction rate constants are closely related to conformation changes with change of temperature, which are profoundly influenced by amputation of disulfide bonds.
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Affiliation(s)
- Shinji Nonose
- Graduate School of Nanobioscience, Yokohama City University , Yokohama, Japan
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8
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Nonose S, Yamashita K, Sudo A, Kawashima M. Proton transfer and complex formation of angiotensin I ions with gaseous molecules at various temperature. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Dilger JM, Valentine SJ, Glover MS, Clemmer DE. A database of alkaline-earth-coordinated peptide cross sections: insight into general aspects of structure. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:768-79. [PMID: 23512423 DOI: 10.1007/s13361-013-0579-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 12/14/2012] [Accepted: 12/20/2012] [Indexed: 05/18/2023]
Abstract
A database of 1470 collision cross sections (666 doubly- and 804 triply-charged) of alkaline-earth-coordinated tryptic peptide ions [where the cation (M(2+)) correspond to Mg(2+), Ca(2+), or Ba(2+)] is presented. The utility of such an extensive set of measurements is illustrated by extraction of general properties of M(2+)-coordinated peptide structures. Specifically, we derive sets of intrinsic size parameters (ISPs) for individual amino acid residues for M(2+)-coordinated peptides. Comparison of these parameters with existing ISPs for protonated peptides suggests that M(2+) binding occurs primarily through interactions with specific polar aliphatic residues (Asp, Ser, and Thr) and the peptide backbone. A comparison of binding interactions for these alkaline-earth metals with interactions reported previously for alkali metals is provided. Finally, we describe a new analysis in which ISPs are used as probes for assessing peptide structure based on amino acid composition.
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Affiliation(s)
- Jonathan M Dilger
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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10
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Ai H, Zhang C, He W, Chan K, Li Q. Solvation counteracts coulombic repulsion in the binding of two cations to a model hexapeptide. J Mol Model 2011; 18:53-64. [DOI: 10.1007/s00894-011-1026-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 02/14/2011] [Indexed: 10/18/2022]
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11
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Kupser P, Pagel K, Oomens J, Polfer N, Koksch B, Meijer G, von Helden G. Amide-I and -II Vibrations of the Cyclic β-Sheet Model Peptide Gramicidin S in the Gas Phase. J Am Chem Soc 2010; 132:2085-93. [DOI: 10.1021/ja909842j] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Kupser
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Jos Oomens
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Nick Polfer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Beate Koksch
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
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12
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Schnier PD, Price WD, Jockusch RA, Williams ER. Blackbody infrared radiative dissociation of bradykinin and its analogues: energetics, dynamics, and evidence for salt-bridge structures in the gas phase. J Am Chem Soc 2009; 118:7178-89. [PMID: 16525512 PMCID: PMC1393282 DOI: 10.1021/ja9609157] [Citation(s) in RCA: 296] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Blackbody infrared radiative dissociation (BIRD) spectra of singly and doubly protonated bradykinin and its analogues are measured in a Fourier-transform mass spectrometer. Rate constants for dissociation are measured as a function of temperature with reaction delays up to 600 s. From these data, Arrhenius activation parameters in the zero-pressure limit are obtained. The activation parameters and dissociation products for the singly protonated ions are highly sensitive to small changes in ion structure. The Arrhenius activation energy (E(a)) and pre-exponential (or frequency factor, A) of the singly protonated ions investigated here range from 0.6 to 1.4 eV and 10(5) to 10(12) s(-1), respectively. For bradykinin and its analogues differing by modification of the residues between the two arginine groups on either end of the molecule, the singly and doubly protonated ions have average activation energies of 1.2 and 0.8 eV, respectively, and average A values of 10(8) and 10(12) s(-1), respectively, i.e., the presence of a second charge reduces the activation energy by 0.4 eV and decreases the A value by a factor of 10(4). This demonstrates that the presence of a second charge can dramatically influence the dissociation dynamics of these ions. The doubly protonated methyl ester of bradykinin has an E(a) of 0.82 eV, comparable to the value of 0.84 eV for bradykinin itself. However, this value is 0.21 +/- 0.08 eV greater than that of singly protonated methyl ester of bradykinin, indicating that the Coulomb repulsion is not the most significant factor in the activation energy of this ion. Both singly and doubly protonated Lys-bradykinin ions have higher activation energies than the corresponding bradykinin ions indicating that the addition of a basic residue stabilizes these ions with respect to dissociation. Methylation of the carboxylic acid group of the C-terminus reduces the E(a) of bradykinin from 1.3 to 0.6 eV and the A factor from 1012 to 105 s(-1). This modification also dramatically changes the dissociation products. Similar results are observed for [Ala(6)]-bradykinin and its methyl ester. These results, in combination with others presented here, provide experimental evidence that the most stable form of singly protonated bradykinin is a salt-bridge structure.
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Affiliation(s)
- P D Schnier
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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13
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Prell JS, Demireva M, Oomens J, Williams ER. Role of Sequence in Salt-Bridge Formation for Alkali Metal Cationized GlyArg and ArgGly Investigated with IRMPD Spectroscopy and Theory. J Am Chem Soc 2008; 131:1232-42. [DOI: 10.1021/ja808177z] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Maria Demireva
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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14
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15
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Raczyńska ED, Gal JF, Maria PC, Zientara K, Szelag M. Application of FT-ICR-MS for the study of proton-transfer reactions involving biomolecules. Anal Bioanal Chem 2007; 389:1365-80. [PMID: 17786415 DOI: 10.1007/s00216-007-1508-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 07/06/2007] [Accepted: 07/12/2007] [Indexed: 10/22/2022]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry, combined with modern ionization (fast atom bombardment , electrospray ionization, matrix-assisted laser desorption-ionization), fragmentation (collision-induced dissociation, surface-induced dissociation, one-photon ultraviolet photodissociation, infrared multiphoton dissociation, blackbody infrared radiative dissociation, electron-capture dissociation), and separation (high-performance liquid chromatography, liquid chromatography, capillary electrophoresis) techniques is now becoming one of the most attractive and frequently used instrumental platforms for gas-phase studies of biomolecules such as amino acids, bioamines, peptides, polypeptides, proteins, nucleobases, nucleosides, nucleotides, polynucleotides, nucleic acids, saccharides, polysaccharides, etc. Since it gives the possibilities to trap the ions from a few seconds up to thousands of seconds, it is often applied to study ion/molecule reactions in the gas phase, particularly proton-transfer reactions which provide important information on acid-base properties. These properties determine in part the three-dimensional structure of biomolecules, most of their intramolecular and intermolecular interactions, and consequently their biological activity. They also indicate the form (unionized, zwitterionic, protonated, or deprotonated) which the biomolecule may take in a nonpolar environment.
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Affiliation(s)
- E D Raczyńska
- Department of Chemistry, Warsaw University of Agriculture (SGGW), 02-726 Warsaw, Poland.
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16
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Abstract
Matrix Assisted Laser Desorption/Ionization (MALDI) is a very widely used analytical method, but has been developed in a highly empirical manner. Deeper understanding of ionization mechanisms could help to design better methods and improve interpretation of mass spectra. This review summarizes current mechanistic thinking, with emphasis on the most common MALDI variant using ultraviolet laser excitation. A two-step framework is gaining acceptance as a useful model for many MALDI experiments. The steps are primary ionization during or shortly after the laser pulse, followed by secondary reactions in the expanding plume of desorbed material. Primary ionization in UV-MALDI remains somewhat controversial, the two main approaches are the cluster and pooling/photoionization models. Secondary events are less contentious, ion-molecule reaction thermodynamics and kinetics are often invoked, but details differ. To the extent that local thermal equilibrium is approached in the plume, the mass spectra may be straightforwardly interpreted in terms of charge transfer thermodynamics.
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17
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Benzakour M, Mcharfi M, Cartier A, Daoudi A. Interactions of peptides with metallic cations. I. Complexes glycylglycine–M+ (M=Li, Na). ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.09.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Ruotolo BT, Tate CC, Russell DH. Ion mobility-mass spectrometry applied to cyclic peptide analysis: conformational preferences of gramicidin S and linear analogs in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:870-878. [PMID: 15144976 DOI: 10.1016/j.jasms.2004.02.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Revised: 02/17/2004] [Accepted: 02/19/2004] [Indexed: 05/24/2023]
Abstract
In this paper, we present an investigation of the gas-phase structural differences between cyclic and linear peptide ions by matrix-assisted laser desorption ionization-ion mobility-mass spectrometry. Specifically, data is shown for gramicidin S (cyclo-VOLFPVOLFP where phenylalanines are D rather than L-type amino acids and the O designates the non-standard amino acid ornithine) and five linear gramicidin S analogues. Results are interpreted as evidence for a beta-sheet (or beta-hairpin) conformational preference in both linear-protonated and sodiated-cyclic gramicidin S gas-phase peptides, and a preference for the protonated-cyclic peptide to adopt a collapsed, random coil-type conformation. A comparison with solution-phase circular dichroism measurements is performed, and structures similar to those observed in the gas phase appear to be favored in low-dielectric solvents such as 2,2,2-triflouroethanol. The utility of ion mobility-mass spectrometry (IM-MS) as a means of rapidly distinguishing between linear and cyclic peptide forms in also discussed.
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Affiliation(s)
- Brandon T Ruotolo
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
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19
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Affiliation(s)
- Michelle M. Kish
- Department of Chemistry, The University of Akron, Akron, Ohio 44325-3601
| | - Chrys Wesdemiotis
- Department of Chemistry, The University of Akron, Akron, Ohio 44325-3601
| | - Gilles Ohanessian
- Laboratoire des Mecanismes Reactionnels, UMR 7651 du CNRS, Ecole Polytechnique, F-91128 Palaiseau Cedex, France
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20
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Jurchen JC, Cooper RE, Williams ER. The role of acidic residues and of sodium ion adduction on the gas-phase H/D exchange of peptides and peptide dimers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:1477-87. [PMID: 14652194 PMCID: PMC1343451 DOI: 10.1016/j.jasms.2003.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Gas-phase H/D exchange is widely used for characterizing the structure of ions. However, many structural parameters that affect the rate of H/D exchange are poorly understood, which complicates the interpretation of experimental data. Here, the effects of sodium ion adduction on the rate of H/D exchange with D2O for a series of peptides and peptide dimers with varying numbers of acidic residues are described. The maximum number of sodium ion adducts that can be accommodated by the peptides and peptide dimers in this study is N + 1, where N is the number of free carboxylic acid groups. The formation of methyl-esters at all carboxylic acid groups, or the replacement of all the acidic hydrogens with sodium ions, effectively shuts down H/D exchange with D2O. In contrast, both the rate and the extent of H/D exchange with D2O are increased for most of the peptides and peptide dimers by the adduction of an intermediate number of sodium ions. These results are consistent with the H/D exchange occurring via a salt-bridge mechanism and show that the presence of two carboxylic acid groups is much better than one. The results with peptide dimers also indicate that surface accessibility may not be a dominant factor in the extent of H/D exchange for these ions.
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Affiliation(s)
| | | | - Evan R. Williams
- Address reprint requests to Dr. E. R. Williams, Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA. E-mail:
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Leymarie N, Costello CE, O'Connor PB. Electron capture dissociation initiates a free radical reaction cascade. J Am Chem Soc 2003; 125:8949-58. [PMID: 12862492 DOI: 10.1021/ja028831n] [Citation(s) in RCA: 176] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For small cyclic peptides, one electron capture by the [M + 2H](2+) ion generates numerous fragments corresponding to amino acid losses, side-chain losses, and losses of some low molecular weight species such as H(2)O, CH(3)(*), C(3)H(6), and (*)CONH(2). As predicted, the side-chain cleavages are amplified relative to linear peptides of similar size, but the amino acid losses were unexpected because they require that one electron capture cause more than one backbone cleavage, a phenomenon which necessitates further refinement or reinterpretation of current ECD mechanisms. A modified mechanism is postulated in which nonergodic electron capture fragmentation generates an alpha-carbon radical species that then propagates along the protein backbone. This radical migration initiates multiple free radical rearrangements, which cause both multiple backbone cleavages and additional side-chain cleavages.
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Affiliation(s)
- Nancy Leymarie
- Department of Biochemistry, Boston University School of Medicine, 715 Albany Street, R806, Boston, Massachusetts 02118, USA
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22
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Knochenmuss R. A quantitative model of ultraviolet matrix-assisted laser desorption/ionization including analyte ion generation. Anal Chem 2003; 75:2199-207. [PMID: 12918956 DOI: 10.1021/ac034032r] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A quantitative model of ionization in ultraviolet matrix-assisted laser desorption/ionization (Knochenmuss, R. J. Mass Spectrom. 2002, 37, 867) is extended to include secondary ion-molecule reactions. Matrix-to-analyte charge-transfer reaction kinetics are described by a hard-sphere Arrhenius expression. The activation energy is derived from the reaction exoergicity using a nonlinear free energy relationship. The approach is applied to the specific case of proton-transfer reactions. With no adjustable parameters, the model correctly predicts the existence and characteristics of the matrix and analyte suppression effects, the shapes of the two-pulse time-delayed yield curves, and the dependence of analyte yields on laser fluence, molecular weight, relative concentrations, and reaction exoergicity.
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Affiliation(s)
- R Knochenmuss
- Novartis Pharma AG, Postfach, 4002 Basel, Switzerland.
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Slocik JM, Somayajula KV, Shepherd RE. Electrospray mass spectrometry of trans-[Ru(NO)Cl(dpaH)2]2+ (dpaH=2,2′-dipyridylamine) and ‘caged NO’, [RuCl3(NO)(H2O)2]: loss of HCl and NO from positive ions versus NO and Cl from negative ions. Inorganica Chim Acta 2001. [DOI: 10.1016/s0020-1693(01)00487-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Knochenmuss R, Stortelder A, Breuker K, Zenobi R. Secondary ion-molecule reactions in matrix-assisted laser desorption/ionization. JOURNAL OF MASS SPECTROMETRY : JMS 2000; 35:1237-1245. [PMID: 11114080 DOI: 10.1002/1096-9888(200011)35:11<1237::aid-jms74>3.0.co;2-o] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Ion-molecule charge- and proton-transfer reactions in the desorption plume are considered for the case of matrix-assisted laser desorption/ionization (MALDI) with ultraviolet laser excitation, and it is proposed that they are major determinants of the observed mass spectrum. Specific MALDI phenomena which are discussed include the dominance of singly charged ions and analyte-matrix or analyte-analyte signal suppression. Should any be formed, highly charged products can be reduced by reaction with neutral matrix, yet singly charged ions cannot generally be neutralized in the same manner. Ion suppression effects can also be explained by similar reactions, which in some cases involve interconversion of dissimilar ion types. The plume is proposed often to be more under thermodynamic rather than kinetic control owing to these secondary reactions. UV/MALDI mass spectra should therefore be largely predictable, given sufficient thermodynamic information, and appropriate experimental conditions of sufficient analyte and plume density. Copyright 2000 John Wiley & Sons, Ltd.
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Affiliation(s)
- R Knochenmuss
- Laboratory for Organic Chemistry, Swiss Federal Institute of Technology, Universitatsstrasse 16, 8092 Zurich, Switzerland
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Knochenmuss R, Stortelder A, Breuker K, Zenobi R. Secondary ion-molecule reactions in matrix-assisted laser desorption/ionization. JOURNAL OF MASS SPECTROMETRY : JMS 2000; 35:1237-1245. [PMID: 11114080 DOI: 10.1002/1096-9888(200011)35:11%3c1237::aid-jms74%3e3.0.co;2-o] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Ion-molecule charge- and proton-transfer reactions in the desorption plume are considered for the case of matrix-assisted laser desorption/ionization (MALDI) with ultraviolet laser excitation, and it is proposed that they are major determinants of the observed mass spectrum. Specific MALDI phenomena which are discussed include the dominance of singly charged ions and analyte-matrix or analyte-analyte signal suppression. Should any be formed, highly charged products can be reduced by reaction with neutral matrix, yet singly charged ions cannot generally be neutralized in the same manner. Ion suppression effects can also be explained by similar reactions, which in some cases involve interconversion of dissimilar ion types. The plume is proposed often to be more under thermodynamic rather than kinetic control owing to these secondary reactions. UV/MALDI mass spectra should therefore be largely predictable, given sufficient thermodynamic information, and appropriate experimental conditions of sufficient analyte and plume density. Copyright 2000 John Wiley & Sons, Ltd.
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Affiliation(s)
- R Knochenmuss
- Laboratory for Organic Chemistry, Swiss Federal Institute of Technology, Universitatsstrasse 16, 8092 Zurich, Switzerland
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Rautenbach M, Swart P, van der Merwe MJ. The interaction of analogues of the antimicrobial lipopeptide, iturin A2, with alkali metal ions. Bioorg Med Chem 2000; 8:2539-48. [PMID: 11092539 DOI: 10.1016/s0968-0896(00)00186-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Electrospray mass spectrometry was employed as a tool in this first study on the molecular interaction between the alkali metal ions and antifungal lipopeptide iturin A, and some analogues. Cationisation by sodium and signal intensity of lipopeptide species depended on sodium concentration, but was independent of sample solvent, carrier solvent polarity and sample pH between 4 and 11. 8-Beta, a linear analogue of iturin A2 (8-Beta; beta-aminotetradecanoyl-NYNQPNS), and its shorter linear lipopeptide analogues, associated either one or two alkali metal cations, while the N-->C cyclic peptides associated with only one cation. The chirality of the beta-NC14 residue had a limited influence on the cationisation. It was observed that 8-Beta contained at least four interaction sites for a cation of which two, the C-terminal carboxylate and the side-chain of tyrosine, can take part in ionic interaction with a cation. It is proposed that the remaining two interaction centres of alkali metal ions are within the two type II beta-turns found in conformation of natural iturin A. This was corroborated by the diminished capacity of the shorter peptides, in which one of the beta-turns was eliminated to bind a second larger cation. All the lipopeptides showed the same order of alkali metal ion selectivity: Na+ > K+ > Rb+. These results indicated a size limitation in the interaction cavity or cavities. The absence of, or observation of only low abundance, di-cationised complexes of cyclic peptides the indicated association of the cation in the interior of the peptide ring. It is thus hypothesised that alkali metal ions can bind in one of the two beta-turns in the natural iturin A molecule.
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Affiliation(s)
- M Rautenbach
- Departmnent of Biochemistry, University of Stellenbosch, Matieland, South Africa.
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Bouchard M, Benjamin DR, Tito P, Robinson CV, Dobson CM. Solvent effects on the conformation of the transmembrane peptide gramicidin A: insights from electrospray ionization mass spectrometry. Biophys J 2000; 78:1010-7. [PMID: 10653814 PMCID: PMC1300704 DOI: 10.1016/s0006-3495(00)76659-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The binding of sodium ions to the transmembrane channel peptide gramicidin A has permitted the use of electrospray ionization mass spectrometry to study its conformation in different solvent environments. The mass spectra of the peptide in the various solvents suggest that different conformations of gramicidin A differ in their ability to bind metal ions. The data are consistent with monomeric behavior of gramicidin A in trifluoroethanol and dimethyl sulfoxide solutions, but reveal the presence of noncovalent intermolecular interactions in ethanol solution through the observation of heterodimers formed between the naturally occurring variants of the peptide. The addition of 50% v/v of water to the ethanolic solution causes changes in the circular dichroism spectrum of the peptide, suggestive of a shift in the equilibrium mixture of conformers present toward monomeric species, a result supported by its mass spectrum. The structure of gramicidin A in trifluoroethanol has also been investigated by hydrogen exchange measurements monitored by mass spectrometry. The observation of significant protection against exchange suggests that the monomeric peptide is highly structured in trifluoroethanol. The results indicate that mass spectrometry has the potential to probe the conformational behavior of neutral hydrophobic peptides in environments that mimic their functional states.
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Affiliation(s)
- M Bouchard
- Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, Oxford OX1 3QT, United Kingdom
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Reimann CT, Velázquez I, Bittner M, Tapia O. Proteins in vacuo: a molecular dynamics study of the unfolding behavior of highly charged disulfide-bond-intact lysozyme subjected to a temperature pulse. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1999; 60:7277-84. [PMID: 11970672 DOI: 10.1103/physreve.60.7277] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/1999] [Revised: 08/11/1999] [Indexed: 04/18/2023]
Abstract
Molecular dynamics simulations were used to interpret a variety of experimental data on highly charged disulfide-bond-intact lysozyme in vacuo. The simulation approach involved submitting a model of the protein [Reimann, Velázquez, and Tapia, J. Phys. Chem. B 102, 9344 (1998)] in a given charge state to a 3-ns-long heat pulse (usually at 500 K) followed by cooling or relaxation for 1 ns back to room temperature (293 K). This treatment yielded a charge threshold around Q(0)=8+ for obtaining significant unfolding, as indicated by an enhancement in collision cross section and conformer length. The collision cross sections and lengths theoretically obtained, along with the threshold charge state for initiating unfolding, were compatible with experimental results on lysozyme in vacuo. The unfolded, highly elongated conformations obtained for Q> or = 9+ displayed a significant level of non-native beta-sheet content which appeared to be additionally stabilized by charge self-solvation.
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Affiliation(s)
- C T Reimann
- Division of Ion Physics, Department of Materials Science, Uppsala University, Box 534, S-751 21 Uppsala, Sweden.
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Schnier PD, Klassen JS, Strittmatter EF, Williams ER. Activation energies for dissociation of double strand oligonucleotide anions: evidence for watson-crick base pairing in vacuo. J Am Chem Soc 1998; 120:9605-13. [PMID: 16498487 PMCID: PMC1380309 DOI: 10.1021/ja973534h] [Citation(s) in RCA: 143] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)(2) (3-), (CCGG)(2) (3-), (AATTAAT)(2) (3-), (CCGGCCG)(2) (3-), A(7)*T(7) (3-), A(7)*A(7) (3-), T(7)*T(7) (3-), and A(7)*C(7) (3-) were investigated using blackbody infrared radiative dissociation in a Fourier transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Activation energies range from 1.2 to 1.7 eV, and preexponential factors range from 10(13) to 10(19) s(-1). Dissociation of the duplexes results in cleavage of the noncovalent bonds and/or cleavage of covalent bonds leading to loss of a neutral nucleobase followed by backbone cleavage producing sequence-specific (a - base) and w ions. Four pieces of evidence are presented which indicate that Watson-Crick (WC) base pairing is preserved in complementary DNA duplexes in the gas phase: i. the activation energy for dissociation of the complementary dimer, A(7)*T(7) (3-), to the single strands is significantly higher than that for the related noncomplementary A(7)*A(7) (3-) and T(7)*T(7) (3-) dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A(7)*A(7) (3-) and A(7)*C(7) (3-) but not for A(7)*T(7) (3-) consistent with this process being shut down by WC hydrogen bonding, iii. a correlation is observed between the measured activation energy for dissociation to single strands and the dimerization enthalpy (-DeltaH(d)) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A(7)*T(7) (3-) duplex, although the helical structure is essentially lost. In combination, these results provide strong evidence that WC base pairing can exist in the complete absence of solvent.
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Affiliation(s)
- P D Schnier
- Contribution from the Department of Chemistry, University of California, Berkeley, California 94720, USA
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Berg C, Achatz U, Beyer M, Joos S, Albert G, Schindler T, Niedner-Schatteburg G, Bondybey VE. Chemistry and charge transfer phenomena in water cluster cations. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0168-1176(97)00133-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Green MK, Lebrilla CB. Ion-molecule reactions as probes of gas-phase structures of peptides and proteins. MASS SPECTROMETRY REVIEWS 1997; 16:53-71. [PMID: 9414490 DOI: 10.1002/(sici)1098-2787(1997)16:2<53::aid-mas1>3.0.co;2-8] [Citation(s) in RCA: 123] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A review with over 100 references describes the recent applications of ion-molecule reactions to the study of gas-phase protonated peptides and proteins. The topic is focused specifically on the proton transfer and hydrogen-deuterium exchange reactions of amino acids, peptides, and proteins. A brief background is given of the various methods used for assigning proton affinities and gas-phase basicities. The methods used for measuring the kinetics of deuterium incorporation of charged ion in the presence of a background pressure of deuterating reagents are also described. Ion-molecule reactions are used to determine, among other things, the gas-phase basicities and proton affinities of amino acids, peptides, and proteins, the sites of protonation, intra- and intermolecular interactions, and conformational differences and changes in gas-phase ionic species. Singly charged and multiply charged ions are both covered.
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Affiliation(s)
- M K Green
- Department of Chemistry, University of California, Davis 95616, USA
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Schnier PD, Price WD, Williams ER. Modeling the maximum charge state of arginine-containing Peptide ions formed by electrospray ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 1996; 7:972-6. [PMID: 16467911 PMCID: PMC1350975 DOI: 10.1016/1044-0305(96)00071-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
A model for the gas-phase proton transfer reactivity of multiply protonated molecules is used to quantitatively account for the maximum charge states of a series of arginine-containing peptide ions measured by Downard and Biemann (Int. J. Mass Spectrom. Ion Processes 1995, 148, 191-202). We find that our calculations account exactly for the maximum charge state for 7 of the 10 peptides and are off by one charge for the remaining 3. These calculations clearly predict the trend in maximum charge states for these peptides and provide further evidence that the maximum charge state of ions formed by electrospray ionization is determined by their gas-phase proton transfer reactivity.
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Affiliation(s)
- P D Schnier
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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