1
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Armentrout PB. Perspective: intrinsic interactions of metal ions with biological molecules as studied by threshold collision-induced dissociation and infrared multiple photon dissociation. Phys Chem Chem Phys 2024. [PMID: 39042103 DOI: 10.1039/d4cp00897a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
In this perspective, gas-phase studies of group 1 monocations and group 12 dications with amino acids and small peptides are highlighted. Although the focus is on two experimental techniques, threshold collision-induced dissociation and infrared multiple photon dissociation action spectroscopy, these methods as well as complementary approaches are summarized. The synergistic interplay with theory, made particularly powerful by the small sizes of the systems explored and the absence of solvent and support, is also elucidated. Importantly, these gas-phase methods permit quantitative insight into the structures and thermodynamics of metal cations interacting with biological molecules. Periodic trends in how these interactions vary as the metal cations get heavier are discussed as are quantitative trends with changes in the amino acid side chain and effects of hydration. Such trends allow these results to transcend the limitations associated with the biomimetic model systems.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
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2
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Armentrout PB. Energetics and mechanisms for decomposition of cationized amino acids and peptides explored using guided ion beam tandem mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:928-953. [PMID: 34392555 DOI: 10.1002/mas.21723] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Fragmentation studies of cationized amino acids and small peptides as studied using guided ion beam tandem mass spectrometry (GIBMS) are reviewed. After a brief examination of the key attributes of the GIBMS approach, results for a variety of systems are examined, compared, and contrasted. Cationization of amino acids, diglycine, and triglycine with alkali cations generally leads to dissociations in which the intact biomolecule is lost. Exceptions include most lithiated species as well as a few examples for sodiated and one example for potassiated species. Like the lithiated species, cationization by protons leads to numerous dissociation channels. Results for protonated glycine, cysteine, asparagine, diglycine, and a series of tripeptides are reviewed, along with the thermodynamic consequences that can be gleaned. Finally, the important physiological process of the deamidation of asparagine (Asn) residues is explored by the comparison of five dipeptides in which the C-terminal partner (AsnXxx) is altered. The GIBMS thermochemistry is shown to correlate well with kinetic results from solution phase studies.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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3
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Stevenson BC, Berden G, Martens J, Oomens J, Armentrout PB. Spectroscopic Investigation of the Metal Coordination of the Aromatic Amino Acids with Zinc and Cadmium. J Phys Chem A 2023; 127:3560-3569. [PMID: 37053556 DOI: 10.1021/acs.jpca.2c08940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The aromatic amino acids (AAA), phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), were cationized with ZnCl+ and CdCl+, and the complexes were evaluated using infrared multiple photon dissociation (IRMPD) action spectroscopy. Specifically, the ZnCl+(Phe), CdCl+(Phe), ZnCl+(Tyr), CdCl+(Tyr), and ZnCl+(Trp) species were examined because the CdCl+(Trp) IRMPD spectrum is available in the literature. Several low-energy conformers for all complexes were found using quantum chemical calculations, and their simulated vibrational spectra were compared to the experimental IRMPD spectra to identify dominant isomers formed. In the case of MCl+(Phe) and MCl+(Tyr), these comparisons indicated the dominant binding motif is a tridentate structure, where the metal atom coordinates with the backbone amino nitrogen and carbonyl oxygen, as well as the aryl ring. These observations are consistent with the predicted ground states at the B3LYP, B3P86, B3LYP-GD3BJ, and MP2 levels of theory. For the ZnCl+(Trp) system, the experimental spectrum indicates a similar binding motif, with the zinc atom coordinating with the backbone nitrogen and carbonyl oxygen and either the pyrrole ring or the benzene ring of the indole side chain. These observations are consistent with the predicted low-lying conformers identified by the aforementioned levels of theory, with the B3LYP and B3P86 levels predicting the metal-pyrrole ring interaction is more favorable than the metal-benzene ring interactions and the opposite at the B3LYP-GD3BJ and MP2 levels.
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Affiliation(s)
- Brandon C Stevenson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098 XH Amsterdam, The Netherlands
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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4
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Armentrout PB, Stevenson BC, Ghiassee M, Boles GC, Berden G, Oomens J. Infrared multiple-photon dissociation spectroscopy of cationized glycine: effects of alkali metal cation size on gas-phase conformation. Phys Chem Chem Phys 2022; 24:22950-22959. [PMID: 36125205 DOI: 10.1039/d2cp03469g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The gas-phase structures of cationized glycine (Gly), including complexes with Li+, Na+, K+, Rb+, and Cs+, are examined using infrared multiple-photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, in conjunction with ab initio calculations. To identify the structures present in the experimental studies, measured IRMPD spectra are compared to spectra calculated at B3LYP/6-311+G(d,p) for the Li+, Na+, and K+ complexes and at B3LYP/def2TZVP for the Rb+ and Cs+ complexes. Single-point energy calculations were carried out at the B3LYP, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set for Li+, Na+, K+ and the def2TZVPP basis set for Rb+ and Cs+. The Li+ and Na+ complexes are identified as metal cation coordination to the amino nitrogen and carbonyl oxygen, [N,CO]-tt, although Na+(Gly) may have contributions from additional structures. The heavier metal cations coordinate to either the carbonyl oxygen, [CO]-cc, or the carbonyl oxygen and hydroxy oxygen, [CO,OH]-cc, with the former apparently preferred for Rb+ and Cs+ and the latter for K+. These two structures reside in a double-well potential and different levels of theory predict very different relative stabilities. Some experimental evidence is provided that MP2(full) theory provides the most accurate relative energies.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, USA.
| | - Brandon C Stevenson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, USA.
| | - Maryam Ghiassee
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, USA.
| | - Georgia C Boles
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, USA.
| | - Giel Berden
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands.,van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098 XH Amsterdam, The Netherlands
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5
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Jones RM, Nilsson T, Walker S, Armentrout PB. Potassium Binding Interactions with Aliphatic Amino Acids: Thermodynamic and Entropic Effects Analyzed via a Guided Ion Beam and Computational Study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1427-1442. [PMID: 35535863 DOI: 10.1021/jasms.2c00079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Noncovalent interactions between alkali metals and amino acids are critical for many biological processes, especially for proper function of protein ion channels; however, many precise binding affinities between alkali metals and amino acids still need to be measured. This study addresses this need by using threshold collision-induced dissociation with a guided ion beam tandem mass spectrometer to measure binding affinities between potassium cations and the aliphatic amino acids: Gly, Ala, hAla, Val, Leu, and Ile. These measurements are supplemented by theoretical calculations and include commentary on effects of enthalpy, entropy, and structural preference. Notably, all levels of theory indicate that the lowest-lying isomers at 298 K have K+ binding to the carbonyl oxygen in either a monodentate ([CO]) or bidentate ([CO,OH]) fashion, isomers that are linked in a double-well potential. This complicates the analysis of the data, although does not greatly influence the final results. Analysis of the resulting cross sections includes accounting for multiple ion-molecule collisions, internal energy of reactant ions, and unimolecular decay rates. The resulting experimental bond dissociation energies generally increase as the polarizability of the amino acid increases, results that agree well with quantum chemical calculations done at the B3LYP, B3P86, and MP2(full) levels of theory, with B3LYP-GD3BJ predicting systematically larger values.
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Affiliation(s)
- Roland M Jones
- Department of Chemistry, University of Utah, 315 South 1400 East Rm 2020, Salt Lake City, Utah 84112, United States
| | - Taylor Nilsson
- Department of Chemistry, University of Utah, 315 South 1400 East Rm 2020, Salt Lake City, Utah 84112, United States
| | - Samantha Walker
- Department of Chemistry, University of Utah, 315 South 1400 East Rm 2020, Salt Lake City, Utah 84112, United States
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East Rm 2020, Salt Lake City, Utah 84112, United States
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6
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Armentrout PB, Boles GC, Ghiassee M, Berden G, Oomens J. Infrared Multiple-Photon Dissociation Spectra of Sodiated Complexes of the Aliphatic Amino Acids. J Phys Chem A 2021; 125:6348-6355. [PMID: 34270243 DOI: 10.1021/acs.jpca.1c04708] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sodiated complexes of the aliphatic amino acids, Gly, Ala, Val, Leu, and Ile, were examined with infrared multiple-photon dissociation action spectroscopy utilizing light from a free-electron laser. To identify structures, the experimental spectra were compared to linear spectra calculated at the B3LYP/6-311+G(d,p) level of theory. Relative energetics of all complexes were calculated at B3LYP, B3P86, MP2(full), B3LYP-GD3BJ, and M06-2X levels using a 6-311+G(2d,2p) basis set. Spectral comparison for all complexes indicates that the dominant conformation, [N, CO], binds to the amino nitrogen and carbonyl oxygen. For all complexes except Gly, contributions are observed from [CO2-] structures, where the sodium cation binds to both oxygens of the carboxylate group in the zwitterionic form of the amino acid. The semiquantitative distribution between these two structures appears to be best-predicted by the B3LYP and MP2(full) levels of theory, with predictions from the other three levels inconsistent with the experiment.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Georgia C Boles
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Maryam Ghiassee
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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7
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Stevenson BC, Martens J, Berden G, Oomens J, Schäfer M, Armentrout PB. IRMPD Spectroscopic and Theoretical Structural Investigations of Zinc and Cadmium Dications Bound to Histidine Dimers. J Phys Chem A 2020; 124:10266-10276. [PMID: 33241937 DOI: 10.1021/acs.jpca.0c08861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallated gas-phase structures consisting of a deprotonated and an intact histidine (His) ligand, yielding M(His-H)(His)+, where M = Zn and Cd, were examined with infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light from a free-electron laser (FEL). In parallel, quantum chemical calculations identified several low-energy isomers for each complex. Experimental action spectra were compared to linear spectra calculated at the B3LYP level of theory using the 6-311+G(d,p) and def2-TZVP basis sets for the zinc and cadmium complexes, respectively. For both Zn and Cd species, the definitive assignment is complicated by conflicting relative energetics, which were calculated at B3LYP, B3LYP-GD3BJ, B3P86, and MP2(full) levels. Spectral comparison for both species indicates that the dominant conformation, [Nα,Nπ,CO-][CO2-](NπH+), has the deprotonated His chelating the metal at the amine nitrogen, π nitrogen of the imidazole ring, and the deprotonated carbonyl oxygen and that the intact His ligand adopts a salt-bridge bidentate binding motif, coordinating the metal with both carboxylate oxygens. There is also evidence for a conformation where the deprotonated His coordination is maintained, but the intact His ligand adopts a more canonical structure, coordinating with the metal atom at the amine nitrogen and π nitrogen, [Nα,Nπ,CO-][Nα,Nπ]gtgg. For both metallated species, B3LYP, B3P86, and B3LYP-GD3BJ levels of theory appear to describe the relative stability of the dominant zwitterionic species more accurately than the MP2(full) level.
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Affiliation(s)
- Brandon C Stevenson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.,van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL, 1098 XH Amsterdam, The Netherlands
| | - Mathias Schäfer
- Department of Chemistry, University of Cologne, 50939 Cologne, Germany
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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8
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Acharya B, Kaushalya WKDN, Martens J, Berden G, Oomens J, Patrick AL. A Combined Infrared Ion Spectroscopy and Computational Chemistry Study of Hydroxyproline Isomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1205-1211. [PMID: 32383378 DOI: 10.1021/jasms.0c00061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hydroxyproline is a common variation of proline, with diverse biological roles. The hydroxylation of proline gives rise to several (natural and/or synthetic) isomeric forms, including both positional isomers and stereoisomers. While mass spectrometry is widely touted as a very selective analytical technique, the identification of closely related isomers often poses a challenge. In these cases, allied technologies become helpful in providing full characterization. Here, infrared multiple photon dissociation (IRMPD) spectroscopy is used to differentiate between three isomers, namely cis-3-hydroxyproline, cis-4-hydroxyproline, and trans-4-hydroxyproline. In contrast to the protonated species which show only minor variations in their IRMPD spectra, lithiated species were found to display significant spectral differences, making their differentiation more straightforward. The conformational origin of these spectral differences was investigated by complementary quantum-chemical calculations.
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Affiliation(s)
- Baku Acharya
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, United States
| | - W K D N Kaushalya
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, United States
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Amanda L Patrick
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, United States
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9
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Boles GC, Stevenson BC, Hightower RL, Berden G, Oomens J, Armentrout PB. Zinc and cadmium complexation of L-methionine: An infrared multiple photon dissociation spectroscopy and theoretical study. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 56:e4580. [PMID: 32677757 DOI: 10.1002/jms.4580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Methionine (Met) cationized with Zn2+ , forming Zn (Met-H)+ (ACN) where ACN = acetonitrile, Zn (Met-H)+ , and ZnCl+ (Met), as well as Cd2+ , forming CdCl+ (Met), were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from the FELIX free electron laser. A series of low-energy conformers for each complex was found using quantum-chemical calculations in order to identify the structures formed experimentally. For all four complexes, spectral comparison indicated that the main binding motif observed is a charge solvated, tridentate structure where the metal center binds to the backbone amino group nitrogen, backbone carbonyl oxygen (where the carboxylic acid is deprotonated in two of the Zn2+ complexes), and side-chain sulfur. For all species, the predicted ground structures reproduce the experimental spectra well, although low-lying conformers characterized by similar binding motifs may also contribute in each system. The current work provides valuable information regarding the binding interaction between Met and biologically relevant metals. Further, the comparison between the current work and previous analyses involving alkali metal cationized Met as well as cysteine (the other sulfur containing amino acid) cationized with Zn2+ and Cd2+ allows for the elucidation of important metal dependent trends associated with physiologically important metal-sulfur binding.
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Affiliation(s)
- Georgia C Boles
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | | | - Randy L Hightower
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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10
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Owen CJ, Boles GC, Berden G, Oomens J, Armentrout PB. Experimental and theoretical investigations of infrared multiple photon dissociation spectra of lysine complexes with Zn 2+ and Cd 2. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:97-111. [PMID: 30526028 DOI: 10.1177/1469066718792902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The gas-phase structures of zinc and cadmium complexes of lysine (Lys) are investigated via a combination of infrared multiple photon dissociation action spectroscopy and ab initio quantum chemical calculations. In order to unambiguously identify the experimentally observed species, [Zn(Lys-H)]+ and CdCl+(Lys), the action spectra were compared to linear absorption spectra calculated at the B3LYP level of theory, using 6-311+G(d,p) and def2-TVZP basis sets for the zinc and cadmium systems, respectively. Single point energies were also calculated at the B3LYP, B3P86, MP2, and B3LYP-GD3BJ (accounting for empirical dispersion) levels of theory using larger basis sets. Identification of the experimentally formed isomers is possible through good agreement between infrared multiple photon dissociation action spectra and the theoretically predicted spectra. The [Zn(Lys-H)]+ complex adopts a tridentate orientation involving the amino acid backbone amine and deprotonated carboxylic acid groups as well as the side-chain amine group, [Nα,CO-,Nɛ]. The CdCl+(Lys) complex similarly adopts a tridentate chelation involving the amino acid backbone amine and carbonyl groups, as well as the side-chain amine group, [Nα,CO,Nɛ]. In both cases, the identified complexes are the lowest energy gas-phase structures at all levels of theory.
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Affiliation(s)
- Cameron J Owen
- 1 Department of Chemistry, University of Utah, Salt Lake City, USA
| | - Georgia C Boles
- 1 Department of Chemistry, University of Utah, Salt Lake City, USA
| | - Giel Berden
- 2 FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Jos Oomens
- 2 FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- 3 Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P B Armentrout
- 1 Department of Chemistry, University of Utah, Salt Lake City, USA
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11
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Clark AA, Yang B, Rodgers MT, Armentrout PB. Experimental and Computational Study of the Group 1 Metal Cation Chelates with Lysine: Bond Dissociation Energies, Structures, and Structural Trends. J Phys Chem B 2019; 123:1983-1997. [DOI: 10.1021/acs.jpcb.8b11967] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Amy A. Clark
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Bo Yang
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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12
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Patel U, Shin J. Experimental and Computational Studies of Dissociation Behavior and Structures of [M·pSer]
+
(M = Li, Na, Ag, Rb, and Cs) Complexes. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Urmi Patel
- Division of Science, Mathematics, and TechnologyGovernors State University University Park, Illinois 60484‐0975 USA
| | - Joong‐Won Shin
- Division of Science, Mathematics, and TechnologyGovernors State University University Park, Illinois 60484‐0975 USA
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13
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Dunbar RC, Martens J, Berden G, Oomens J. Binding of Divalent Metal Ions with Deprotonated Peptides: Do Gas-Phase Anions Parallel the Condensed Phase? J Phys Chem A 2018; 122:5589-5596. [PMID: 29847124 PMCID: PMC6026845 DOI: 10.1021/acs.jpca.8b02926] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Chelation complexes
of the histidine-containing tripeptides HisAlaAla,
AlaHisAla, and AlaAlaHis with Ni(II) and Cu(II) having a −1
net charge are characterized in the gas phase by infrared multiple-photon
dissociation (IRMPD) spectroscopy and density functional theory calculations.
We address the question of whether the gas-phase complexes carry over
characteristics from the corresponding condensed-phase species. We
focus particularly on three aspects of their structure: (i) square-planar
chelation by the deprotonated amide nitrogens around the metal ion
(low-spin for the Ni case), (ii) metal-ion coordination of the imidazole
side chain nitrogen, and (iii) the exceptional preference for metal-ion
chelation by peptides with His in the third position from the N-terminus,
as in the amino terminal Cu and Ni (ATCUN) motif. We find that square-planar
binding around the metal ion, involving bonds to both deprotonated
backbone nitrogens, one of the carboxylate oxygens and the N-terminal
nitrogen, is the dominant binding motif for all three isomers. In
contrast to the condensed-phase behavior, the dominant mode of binding
for all three isomers does not involve the imidazole side chain, which
is instead placed outside the coordination zone. Only for the AlaAlaHis
isomer, the imidazole-bound structure is also detected as a minority
population, as identified from a distinctive short-wavelength IR absorption.
The observation that this conformation exists only for AlaAlaHis correlates
with condensed-phase behavior at neutral-to-basic pH, in the sense
that the isomer with His in the third position is exceptionally disposed
to metal ion chelation by four nitrogen atoms (4N) when compared with
the other isomers. These results also emphasize the divergence between
the conformational stabilities in the gas phase and in solution or
crystalline environments: in the gas phase, direct metal binding of
the imidazole is overall less favorable than the alternative of a
remote imidazole that can act as an intramolecular H-bond donor enhancing
the gas-phase stability.
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Affiliation(s)
- Robert C Dunbar
- Chemistry Department , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials , FELIX Laboratory , Toernooiveld 7c , 6525ED Nijmegen , The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials , FELIX Laboratory , Toernooiveld 7c , 6525ED Nijmegen , The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials , FELIX Laboratory , Toernooiveld 7c , 6525ED Nijmegen , The Netherlands.,University of Amsterdam , Science Park 904 , 1098XH Amsterdam , The Netherlands
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14
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Smith ZM, Steinmetz V, Martens J, Oomens J, Poutsma JC. Infrared Multiple Photon Dissociation Spectroscopy of Cationized Canavanine: Side-Chain Substitution Influences Gas-Phase Zwitterion Formation †. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 429:158-173. [PMID: 29962900 PMCID: PMC6020040 DOI: 10.1016/j.ijms.2017.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Infrared multiple photon dissociation spectroscopy was performed on protonated and cationized canavanine (Cav), a non-protein amino acid oxy-analog of arginine. Infrared spectra in the XH stretching region (3000 - 4000 cm-1) were obtained at the Centre Laser Infrarouge d'Orsay (CLIO) facility. Comparison of the experimental infrared spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory indicates that canavanine is in a canonical neutral form in CavH+, CavLi+, and CavNa+; therefore, these cations are charge-solvated structures. The infrared spectrum of CavK+ is consistent with a mixture of Cav in canonical and zwitterionic forms leading to both charge-solvated and salt-bridged cationic structures. The Cav moiety in CavCs+ is shown to be zwitterionic, forming a salt-bridged structure for the cation. Infrared spectra in the fingerprint region (1000 - 2000 cm-1) obtained at the FELIX Laboratory in Nijmegen, Netherlands support these assignments. These results show that that a single oxygen atom substitution in the side chain reduces the stability of the zwitterion compared to that of the protein amino acid arginine (Arg), which has been shown previously to adopt a zwitterionic structure in ArgNa+ and ArgK+. This difference can be explained in part due to the decreased basicity of Cav (PA = 1001 kJ/mol) as compared to arginine (PA = 1051 kJ/mol), but not entirely, as lysine, which has nearly the same proton affinity as Cav, (~993 kJ/mol) forms only canonical structures with Na+, K+, and Cs+. A major difference between the zwitterionic forms of ArgM+ and CavM+ is that the protonation site is on the side chain for Arg and on the N-terminus for Cav. This results in systematically weaker salt bridges in the Cav zwitterions. In addition, the presence of another hydrogen-bonding acceptor atom in the side chain contributes to the stability of the canonical structures for the smaller alkali cations.
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Affiliation(s)
- Zachary M Smith
- Department of Chemistry, The College of William and Mary, Williamsburg, VA 23187-8795
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris Sud, Université Paris Saclay, CNRS, Orsay France
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Nijmegen, The Netherlands
- Van't Hoff Institute for Molecular Sciences University of Amsterdam, Amsterdam, The Netherlands
| | - John C Poutsma
- Department of Chemistry, The College of William and Mary, Williamsburg, VA 23187-8795
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15
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Boles GC, Hightower RL, Coates RA, McNary CP, Berden G, Oomens J, Armentrout PB. Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Aspartic Acid Complexes with Zn2+ and Cd2+. J Phys Chem B 2018; 122:3836-3853. [DOI: 10.1021/acs.jpcb.8b00801] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Georgia C. Boles
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Randy L. Hightower
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Rebecca A. Coates
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Christopher P. McNary
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098 XH Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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16
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Chalifoux AM, Boles GC, Berden G, Oomens J, Armentrout PB. Experimental and theoretical investigations of infrared multiple photon dissociation spectra of arginine complexes with Zn2+ and Cd2+. Phys Chem Chem Phys 2018; 20:20712-20725. [DOI: 10.1039/c8cp03484b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Arginine (Arg) complexes with Zn2+ and Cd2+ were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light from a free electron laser.
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Affiliation(s)
| | | | - Giel Berden
- Radboud University
- FELIX Laboratory
- Institute for Molecules and Materials
- NL-6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- FELIX Laboratory
- Institute for Molecules and Materials
- NL-6525 ED Nijmegen
- The Netherlands
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17
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Heiles S, Berden G, Oomens J, Williams ER. Competition between salt bridge and non-zwitterionic structures in deprotonated amino acid dimers. Phys Chem Chem Phys 2018; 20:15641-15652. [DOI: 10.1039/c8cp01458b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The effect of side chain functional groups on salt bridge structures in deprotonated amino acid homodimers is investigated using both infrared multiple photon dissociation spectroscopy between 650 and 1850 cm−1 and theory.
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Affiliation(s)
- Sven Heiles
- Department of Chemistry
- University of California
- Berkeley
- USA
- Institute of Inorganic and Analytical Chemistry
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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18
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Boles GC, Owen CJ, Berden G, Oomens J, Armentrout PB. Experimental and theoretical investigations of infrared multiple photon dissociation spectra of glutamic acid complexes with Zn2+and Cd2+. Phys Chem Chem Phys 2017; 19:12394-12406. [DOI: 10.1039/c7cp01786c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IRMPD of [Zn(Glu-H)ACN]+was particularly interesting because fragmentation of the amino acid was favored, rather than dissociation of the ACN ligand.
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Affiliation(s)
| | | | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525 ED Nijmegen
- The Netherlands
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19
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Peckelsen K, Martens J, Czympiel L, Oomens J, Berden G, Gründemann D, Meijer AJHM, Schäfer M. Ergothioneine and related histidine derivatives in the gas phase: tautomer structures determined by IRMPD spectroscopy and theory. Phys Chem Chem Phys 2017; 19:23362-23372. [DOI: 10.1039/c7cp03843g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gas-phase analysis of ergothioneine molecular ions allows differentiating thiol from thione tautomer structures.
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Affiliation(s)
- Katrin Peckelsen
- Department für Chemie
- Institut für Organische Chemie
- Universität zu Köln
- Greinstrasse 4
- Köln
| | - Jonathan Martens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Toernooiveld 7c
- Nijmegen
| | - Lisa Czympiel
- Department für Chemie
- Institut für Organische Chemie
- Universität zu Köln
- Greinstrasse 4
- Köln
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Toernooiveld 7c
- Nijmegen
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Toernooiveld 7c
- Nijmegen
| | - Dirk Gründemann
- Department of Pharmacology
- University of Cologne
- Gleueler Straße 24
- Cologne
- Germany
| | | | - Mathias Schäfer
- Department für Chemie
- Institut für Organische Chemie
- Universität zu Köln
- Greinstrasse 4
- Köln
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20
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Corinti D, De Petris A, Coletti C, Re N, Chiavarino B, Crestoni ME, Fornarini S. Cisplatin Primary Complex with l-Histidine Target Revealed by IR Multiple Photon Dissociation (IRMPD) Spectroscopy. Chemphyschem 2016; 18:318-325. [PMID: 27935248 DOI: 10.1002/cphc.201601172] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/07/2016] [Indexed: 11/08/2022]
Abstract
The primary complex obtained from cisplatin and l-histidine in water has been detected and isolated by electrospray ionization. The so-obtained cis-[PtCl(NH3 )2 (histidine)]+ complex has been characterized in detail by high-resolution mass spectrometry (MS), tandem MS, IR multiple photon dissociation (IRMPD) spectroscopy, and by quantum chemical calculations. The structural features revealed by IRMPD spectroscopy indicate that platinum binds to the imidazole group, which presents tautomeric forms. Thus, depending on the position of the amino acid pendant on the imidazole ring, isomeric complexes are formed that are remarkably different with respect to the ease with which they undergo fragmentation when activated either by energetic collisions or by multiple IR photon absorption. It is shown here how IRMPD kinetics can allow their relative proportions to be estimated.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Alberto De Petris
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Cecilia Coletti
- Dipartimento di Farmacia, Università G. D'Annunzio, Via dei Vestini 31, 66100, Chieti, Italy
| | - Nazzareno Re
- Dipartimento di Farmacia, Università G. D'Annunzio, Via dei Vestini 31, 66100, Chieti, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Maria E Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
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21
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Boles GC, Coates RA, Berden G, Oomens J, Armentrout PB. Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Asparagine Complexes with Zn2+ and Cd2+ and Their Deamidation Processes. J Phys Chem B 2016; 120:12486-12500. [DOI: 10.1021/acs.jpcb.6b10326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Georgia C. Boles
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Rebecca A. Coates
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
- van‘t
Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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22
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Lesslie M, Lau JKC, Lawler JT, Siu KWM, Steinmetz V, Maître P, Hopkinson AC, Ryzhov V. Cysteine Radical/Metal Ion Adducts: A Gas-Phase Structural Elucidation and Reactivity Study. Chempluschem 2016; 81:444-452. [DOI: 10.1002/cplu.201500558] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Michael Lesslie
- Department of Chemistry and Biochemistry; Northern Illinois University; DeKalb IL 60115 USA
| | - Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry; York University; Toronto ON M3J 1P3 Canada
- Department of Chemistry and Biochemistry; University of Windsor; Windsor ON N9B 3P4 Canada
| | - John T. Lawler
- Department of Chemistry and Biochemistry; Northern Illinois University; DeKalb IL 60115 USA
| | - K. W. Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry; York University; Toronto ON M3J 1P3 Canada
- Department of Chemistry and Biochemistry; University of Windsor; Windsor ON N9B 3P4 Canada
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique; Université Paris-Sud; UMR8000 CNRS; 91405 Orsay France
| | - Philippe Maître
- Laboratoire de Chimie Physique; Université Paris-Sud; UMR8000 CNRS; 91405 Orsay France
| | - Alan C. Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry; York University; Toronto ON M3J 1P3 Canada
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry; Northern Illinois University; DeKalb IL 60115 USA
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23
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Jami-Alahmadi Y, Fridgen TD. Structures and unimolecular chemistry of M(Pro2-H)+(M = Mg, Ca, Sr, Ba, Mn, Fe, Co, Ni, Cu, Zn) by IRMPD spectroscopy, SORI-CID, and theoretical studies. Phys Chem Chem Phys 2016; 18:2023-33. [DOI: 10.1039/c5cp05188f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
M(Pro2-H)+complexes were electrosprayed and isolated in an FTICR cell where their unimolecular chemistries and structures were explored using SORI-CID and IRMPD spectroscopy.
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24
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Coates RA, Boles GC, McNary CP, Berden G, Oomens J, Armentrout PB. Zn2+ and Cd2+ cationized serine complexes: infrared multiple photon dissociation spectroscopy and density functional theory investigations. Phys Chem Chem Phys 2016; 18:22434-45. [DOI: 10.1039/c6cp03805k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zinc and cadmium dications bind serine in tridentate structures at the amine and carbonyl groups and side-chain hydroxyl group.
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Affiliation(s)
| | | | | | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525ED Nijmegen
- The Netherlands
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25
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Discriminating Properties of Alkali Metal Ions Towards the Constituents of Proteins and Nucleic Acids. Conclusions from Gas-Phase and Theoretical Studies. Met Ions Life Sci 2016; 16:103-31. [DOI: 10.1007/978-3-319-21756-7_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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26
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Boles GC, Coates RA, Berden G, Oomens J, Armentrout PB. Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Glutamine Complexes with Zn2+ and Cd2+. J Phys Chem B 2015; 119:11607-17. [DOI: 10.1021/acs.jpcb.5b06528] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Georgia C. Boles
- Department
of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| | - Rebecca A. Coates
- Department
of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
- Van‘t
Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department
of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
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27
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Wang H, Wang B, Wei Z, Zhang H, Guo X. Structure and further fragmentation of significant [a3 + Na - H]+ ions from sodium-cationized peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:212-219. [PMID: 25601695 DOI: 10.1002/jms.3520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 09/21/2014] [Accepted: 10/02/2014] [Indexed: 06/04/2023]
Abstract
A good understanding of gas-phase fragmentation chemistry of peptides is important for accurate protein identification. Additional product ions obtained by sodiated peptides can provide useful sequence information supplementary to protonated peptides and improve protein identification. In this work, we first demonstrate that the sodiated a3 ions are abundant in the tandem mass spectra of sodium-cationized peptides although observations of a3 ions have rarely been reported in protonated peptides. Quantum chemical calculations combined with tandem mass spectrometry are used to investigate this phenomenon by using a model tetrapeptide GGAG. Our results reveal that the most stable [a3 + Na - H](+) ion is present as a bidentate linear structure in which the sodium cation coordinates to the two backbone carbonyl oxygen atoms. Due to structural inflexibility, further fragmentation of the [a3 + Na - H](+) ion needs to overcome several relatively high energetic barriers to form [b2 + Na - H](+) ion with a diketopiperazine structure. As a result, low abundance of [b2 + Na - H](+) ion is detected at relatively high collision energy. In addition, our computational data also indicate that the common oxazolone pathway to generate [b2 + Na - H](+) from the [a3 + Na - H](+) ion is unlikely. The present work provides a mechanistic insight into how a sodium ion affects the fragmentation behaviors of peptides.
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Affiliation(s)
- Huixin Wang
- College of Chemistry, Jilin University, Changchun, 130012, China
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28
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Coates RA, McNary CP, Boles GC, Berden G, Oomens J, Armentrout PB. Structural characterization of gas-phase cysteine and cysteine methyl ester complexes with zinc and cadmium dications by infrared multiple photon dissociation spectroscopy. Phys Chem Chem Phys 2015; 17:25799-808. [DOI: 10.1039/c5cp01500f] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zinc and cadmium dications bind cysteine in tridentate structures at the amine and carbonyl groups and deprotonated sulfur atom.
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Affiliation(s)
| | | | | | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525ED Nijmegen
- The Netherlands
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29
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Salpin JY, Haldys V, Guillaumont S, Tortajada J, Hurtado M, Lamsabhi AM. Gas-Phase Interactions between Lead(II) Ions and Cytosine: Tandem Mass Spectrometry and Infrared Multiple-Photon Dissociation Spectroscopy Study. Chemphyschem 2014; 15:2959-71. [DOI: 10.1002/cphc.201402369] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Indexed: 12/07/2022]
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30
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van Stipdonk MJ, Basu P, Dille SA, Gibson JK, Berden G, Oomens J. Infrared multiple photon dissociation spectroscopy of a gas-phase oxo-molybdenum complex with 1,2-dithiolene ligands. J Phys Chem A 2014; 118:5407-18. [PMID: 24988369 PMCID: PMC4338922 DOI: 10.1021/jp503222v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Electrospray
ionization (ESI) in the negative ion mode was used
to create anionic, gas-phase oxo-molybdenum complexes with dithiolene
ligands. By varying ESI and ion transfer conditions, both doubly and
singly charged forms of the complex, with identical formulas, could
be observed. Collision-induced dissociation (CID) of the dianion generated
exclusively the monoanion, while fragmentation of the monoanion involved
decomposition of the dithiolene ligands. The intrinsic structure of
the monoanion and the dianion were determined by using wavelength-selective
infrared multiple-photon dissociation (IRMPD) spectroscopy and density
functional theory calculations. The IRMPD spectrum for the dianion
exhibits absorptions that can be assigned to (ligand) C=C,
C–S, C—C≡N, and Mo=O stretches. Comparison
of the IRMPD spectrum to spectra predicted for various possible conformations
allows assignment of a pseudo square pyramidal structure with C2v symmetry, equatorial coordination
of MoO2+ by the S atoms of the dithiolene ligands, and
a singlet spin state. A single absorption was observed for the oxidized
complex. When the same scaling factor employed for the dianion is
used for the oxidized version, theoretical spectra suggest that the
absorption is the Mo=O stretch for a distorted square pyramidal
structure and doublet spin state. A predicted change in conformation
upon oxidation of the dianion is consistent with a proposed bonding
scheme for the bent-metallocene dithiolene compounds [Lauher, J. W.; Hoffmann, R. J. Am.
Chem. Soc.1976, 98, 1729−1742], where a large
folding of the dithiolene moiety along the S···S vector
is dependent on the occupancy of the in-plane metal d-orbital.
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Affiliation(s)
- Michael J van Stipdonk
- Department of Chemistry and Biochemistry, Duquesne University , 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
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31
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Sun S, Liu J, Liu ZF. Structural stabilities and transformations in cationized asparagine at finite temperatures: An ab initio molecular dynamics study. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The cationic complexes of Asparagine (Asn), M +( Asn ), with M + = Li +, Na +, K +, Cs +, and H +, are models for studying the interaction between cations and Asn. Ab initio molecular dynamics (AIMD) method is employed to simulate their behavior at finite temperatures. Structural transformation between conformers is observed, which becomes progressively easier as the cation varies from Li +, to Na +, K +, Cs +, and H +. The fluctuation of the M +– N and M +– O distances and rotation of torsional angles are significant even at room temperature for K +, Cs + and H +. Vibrational profiles based on AIMD trajectories provide insights into the broadening and shifts in relative intensities observed in the vibrational spectra measured by infrared multi-photon dissociation (IRMPD) experiments.
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Affiliation(s)
- Shoutian Sun
- Department of Chemistry and Centre for Scientific Modeling and Computation, Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Jianwen Liu
- National Supercomputing Center in Shenzhen, Shenzhen, P. R. China
| | - Zhi-Feng Liu
- Department of Chemistry and Centre for Scientific Modeling and Computation, Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
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32
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Meng L, Lin Z. Complexations of alkali/alkaline earth metal cations with gaseous glutamic acid. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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Salpin JY, MacAleese L, Chirot F, Dugourd P. Structure of the Pb²⁺-deprotonated dGMP complex in the gas phase: a combined MS-MS/IRMPD spectroscopy/ion mobility study. Phys Chem Chem Phys 2014; 16:14127-38. [PMID: 24901754 DOI: 10.1039/c4cp00163j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure of the Pb(2+)-deprotonated 2'-deoxyguanosine-5'-monophosphate (dGMP) complex, generated in the gas phase by electrospray ionization, was examined by combining tandem mass spectrometry, mid-infrared multiple-photon dissociation (IRMPD) spectroscopy and ion mobility. In the gas phase, the main binding site of Pb(2+) onto deprotonated dGMP is the deprotonated phosphate group, but the question is whether an additional stabilization of the metallic complex can occur via participation of the carbonyl group of guanine. Such macrochelates indeed correspond to the most stable structures according to theoretical calculations. A multiplexed experimental approach was used to characterize the gas-phase conformation of the metallic complex and hence determine the binding mode of Pb(2+) with [dGMP](-). MS/MS analysis, observation of characteristic bands by IRMPD spectroscopy, and measurement of the ion mobility collision cross section suggest that gaseous [Pb(dGMP)-H](+) complexes adopt a macrochelate folded structure, which consequently differs strongly from the zwitterionic forms postulated in solution from potentiometric studies.
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Affiliation(s)
- Jean-Yves Salpin
- Université d'Evry Val d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Boulevard François Mitterrand, 91025 Evry, France.
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34
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Carron JD, Shin JW. Tandem mass spectrometric analysis of alkali metal cation–tripeptide clusters. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Armentrout PB, Yang B, Rodgers MT. Metal Cation Dependence of Interactions with Amino Acids: Bond Dissociation Energies of Rb+ and Cs+ to the Acidic Amino Acids and Their Amide Derivatives. J Phys Chem B 2014; 118:4300-14. [DOI: 10.1021/jp5001754] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- P. B. Armentrout
- Department
of Chemistry, University of Utah, 315 South 1400 E, Room 2020, Salt Lake City, Utah 84112, United States
| | - Bo Yang
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M. T. Rodgers
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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36
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Dunbar RC. Spectroscopy of Metal-Ion Complexes with Peptide-Related Ligands. Top Curr Chem (Cham) 2014; 364:183-223. [DOI: 10.1007/128_2014_578] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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37
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Sanader Ž, Mitrić R, Bonačić-Koutecký V, Bellina B, Antoine R, Dugourd P. The nature of electronic excitations at the metal–bioorganic interface illustrated on histidine–silver hybrids. Phys Chem Chem Phys 2014; 16:1257-61. [DOI: 10.1039/c3cp52712c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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38
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Kim JY, Ahn DS, Park SW, Lee S. Gas phase hydration of amino acids and dipeptides: effects on the relative stability of zwitterion vs. canonical conformers. RSC Adv 2014. [DOI: 10.1039/c4ra01217h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
This review highlights the effects of explicit water molecules on the structures of amino acids and dipeptides, focusing on the relative stability of canonical vs. zwitterionic conformers.
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Affiliation(s)
- Ju-Young Kim
- Department of Applied Chemistry
- College of Applied Sciences
- Kyung Hee University
- Kyungki 446-701, S. Korea
| | - Doo-Sik Ahn
- Department of Applied Chemistry
- College of Applied Sciences
- Kyung Hee University
- Kyungki 446-701, S. Korea
| | - Sung-Woo Park
- Department of Applied Chemistry
- College of Applied Sciences
- Kyung Hee University
- Kyungki 446-701, S. Korea
| | - Sungyul Lee
- Department of Applied Chemistry
- College of Applied Sciences
- Kyung Hee University
- Kyungki 446-701, S. Korea
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Jaeqx S, Oomens J, Rijs AM. Gas-phase salt bridge interactions between glutamic acid and arginine. Phys Chem Chem Phys 2013; 15:16341-52. [PMID: 23999680 DOI: 10.1039/c3cp52508b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The gas-phase side chain-side chain (SC-SC) interaction and possible proton transfer between glutamic acid (Glu) and arginine (Arg) residues are studied under low-temperature conditions in an overall neutral peptide. Conformation-specific IR spectra, obtained with the free electron laser FELIX, in combination with density functional theory (DFT) calculations, provide insight into the occurrence of intramolecular proton transfer and detailed information on the conformational preferences of the peptides Z-Glu-Alan-Arg-NHMe (n = 0,1,3). Low-energy structures are obtained using molecular dynamics simulations via the simulated annealing approach, resulting in three types of SC-SC interactions, in particular two types of pair-wise interactions and one bifurcated interaction. These low-energy structures are optimized and frequency calculations are performed using the B3LYP functional, for structural analysis, and the M05-2x functional, for relative energies, employing the 6-311+G(d,p) basis set. Comparison of experimental and computed spectra suggests that only a single conformation was present for each of the three peptides. Despite the increasing spacing between the Glu and Arg residues, the peptides have several types of interactions in common, in particular specific SC-SC and dispersion interactions between the Arg side chain and the phenyl ring of the Z-cap. Comparison with previous experiments on Ac-Glu-Ala-Phe-Ala-Arg-NHMe as well as molecular dynamics simulations further suggest that the pairwise interaction observed here is indeed energetically most favorable for short peptide sequences.
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Affiliation(s)
- Sander Jaeqx
- Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
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40
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Dunbar RC, Oomens J, Berden G, Lau JKC, Verkerk UH, Hopkinson AC, Siu KWM. Metal Ion Complexes with HisGly: Comparison with PhePhe and PheGly. J Phys Chem A 2013; 117:5335-43. [DOI: 10.1021/jp4021917] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Robert C. Dunbar
- Chemistry
Department, Case Western Reserve University, Cleveland, Ohio 44106,
United States
| | - Jos Oomens
- Radboud University Nijmegen, Institute
for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525
ED Nijmegen, The Netherlands
- University of Amsterdam, Science Park
904, 1098XH Amsterdam, The Netherlands
| | - Giel Berden
- Radboud University Nijmegen, Institute
for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525
ED Nijmegen, The Netherlands
| | - Justin Kai-Chi Lau
- Department of Chemistry and
Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, M3J 1P3, Canada
| | - Udo H. Verkerk
- Department of Chemistry and
Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, M3J 1P3, Canada
| | - Alan C. Hopkinson
- Department of Chemistry and
Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, M3J 1P3, Canada
| | - K. W. Michael Siu
- Department of Chemistry and
Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, M3J 1P3, Canada
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Schmidt J, Kass SR. Zwitterion vs Neutral Structures of Amino Acids Stabilized by a Negatively Charged Site: Infrared Photodissociation and Computations of Proline–Chloride Anion. J Phys Chem A 2013; 117:4863-9. [DOI: 10.1021/jp402267c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Jacob Schmidt
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Steven R. Kass
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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42
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Armentrout PB, Yang B, Rodgers MT. Metal Cation Dependence of Interactions with Amino Acids: Bond Energies of Rb+ and Cs+ to Met, Phe, Tyr, and Trp. J Phys Chem B 2013; 117:3771-81. [DOI: 10.1021/jp401366g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. B. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake
City, Utah 84112, United States
| | - Bo Yang
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United
States
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United
States
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Shoeib T, Zhao J, Ei Aribi H, Hopkinson AC, Siu KWM. Dissociations of complexes between monovalent metal ions and aromatic amino acid or histidine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:38-48. [PMID: 23238948 DOI: 10.1007/s13361-012-0511-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 10/02/2012] [Accepted: 10/02/2012] [Indexed: 06/01/2023]
Abstract
The fragmentations of [AA + M](+) complexes, where AA = Phe, Tyr, Trp, or His, and M is a monovalent metal (Li, Na, or Ag), have been exhaustively studied through collision-induced dissociation (CID) and through deuterium labeling. Dissociations of the Li- and Ag-containing complexes gave a large number of fragment ions; by contrast, the sodium/amino acid complexes have lower binding energies, and dissociation resulted in much simpler spectra, with loss of the entire ligand dominating. Unambiguous assignments of these fragment ions were made and formation mechanisms are proposed. Of particular interest are fragmentations in which the charge was retained on the organic fragment and the metal was lost, either as a metal hydride (AgH) or hydroxide (LiOH) or as the silver atom (Ag(•)).
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Affiliation(s)
- Tamer Shoeib
- Department of Chemistry, The American University in Cairo, New Cairo, Egypt
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44
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Riffet V, Bouchoux G. Gas-phase structures and thermochemistry of neutral histidine and its conjugated acid and base. Phys Chem Chem Phys 2013; 15:6097-106. [DOI: 10.1039/c3cp00043e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Armentrout PB, Citir M, Chen Y, Rodgers MT. Thermochemistry of Alkali Metal Cation Interactions with Histidine: Influence of the Side Chain. J Phys Chem A 2012; 116:11823-32. [DOI: 10.1021/jp310179c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- P. B. Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East,
Room 2020, Salt Lake City, Utah 84112, United States
| | - Murat Citir
- Department of Chemistry, University of Utah, 315 South 1400 East,
Room 2020, Salt Lake City, Utah 84112, United States
| | - Yu Chen
- Department of Chemistry, Wayne State University, Detroit, Michigan
48202, United States
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan
48202, United States
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46
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Osburn S, Burgie T, Berden G, Oomens J, O’Hair RAJ, Ryzhov V. Structure and Reactivity of Homocysteine Radical Cation in the Gas Phase Studied by Ion–Molecule Reactions and Infrared Multiple Photon Dissociation. J Phys Chem A 2012; 117:1144-50. [DOI: 10.1021/jp304769y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sandra Osburn
- Department of Chemistry and
Biochemistry, and Center for Biochemical and Biophysical Studies, Northern Illinois University, Dekalb, Illinois 60115,
United States
| | - Ticia Burgie
- Department of Chemistry and
Biochemistry, and Center for Biochemical and Biophysical Studies, Northern Illinois University, Dekalb, Illinois 60115,
United States
| | - Giel Berden
- FOM Institute for Plasma Physics Rijnhuizen, Nieuwegein, The Netherlands
| | - Jos Oomens
- FOM Institute for Plasma Physics Rijnhuizen, Nieuwegein, The Netherlands
- University of Amsterdam, Amsterdam, The Netherlands
| | - Richard A. J. O’Hair
- School of Chemistry, The University of Melbourne, Melbourne, Victoria 3010,
Australia
- Bio21 Institute
of Molecular
Science and Biotechnology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, Melbourne,
Victoria 3010, Australia
| | - Victor Ryzhov
- Department of Chemistry and
Biochemistry, and Center for Biochemical and Biophysical Studies, Northern Illinois University, Dekalb, Illinois 60115,
United States
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