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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, 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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3
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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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4
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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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5
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Miller ZM, Zhang JD, Donald WA, Prell JS. Gas-Phase Protonation Thermodynamics of Biological Lipids: Experiment, Theory, and Implications. Anal Chem 2020; 92:10365-10374. [PMID: 32628014 DOI: 10.1021/acs.analchem.0c00613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Phospholipids are important to cellular function and are a vital structural component of plasma and organelle membranes. These membranes isolate the cell from its environment, allow regulation of the internal concentrations of ions and small molecules, and host diverse types of membrane proteins. It remains extremely challenging to identify specific membrane protein-lipid interactions and their relative strengths. Native mass spectrometry, an intrinsically gas-phase method, has recently been demonstrated as a promising tool for identifying endogenous protein-lipid interactions. However, to what extent the identified interactions reflect solution- versus gas-phase binding strengths is not known. Here, the "Extended" Kinetic Method and ab initio computations at three different levels of theory are used to experimentally and theoretically determine intrinsic gas-phase basicities (GB, ΔG for deprotonation of the protonated base) and proton affinities (PA, ΔH for deprotonation of the protonated base) of six lipids representing common phospholipid types. Gas-phase acidities (ΔG and ΔH for deprotonation) of neutral phospholipids are also evaluated computationally and ranked experimentally. Intriguingly, it is found that two of these phospholipids, sphingomyelin and phosphatidylcholine, have the highest GB of any small, monomeric biomolecules measured to date and are more basic than arginine. Phosphatidylethanolamine and phosphatidylserine are found to be similar in GB to basic amino acids lysine and histidine, and phosphatidic acid and phosphatidylglycerol are the least basic of the six lipid types studied, though still more basic than alanine. Kinetic Method experiments and theory show that the gas-phase acidities of these phospholipids are high but less extreme than their GB values, with phosphatidylserine and phosphatidylglycerol being the most acidic. These results indicate that sphingomyelin and phosphatidylcholine lipids can act as charge-reducing agents when dissociated from native membrane protein-lipid complexes in the gas phase and provide a straightforward model to explain the results of several recent native mass spectrometry studies of protein-lipid complexes.
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Affiliation(s)
- Zachary M Miller
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - J Diana Zhang
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia, 2052
| | - W Alexander Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia, 2052
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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6
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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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7
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Lamsabhi AM, Mó O, Yáñez M, Salpin JY. Combined Experimental and Theoretical Survey of the Gas-Phase Reactions of Serine-Ca 2+ Adducts. J Phys Chem A 2019; 123:6241-6250. [PMID: 31268328 DOI: 10.1021/acs.jpca.9b03977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The association of Ca2+ to serine and the subsequent gas-phase unimolecular reactivity of the [Ca(Ser)]2+ (Ser = Serine) adduct was investigated throughout the use of tandem mass spectrometry techniques and B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) density functional theory calculations. In a first step, the structure and relative stability of all possible conformers of serine were obtained and analyzed, as well as the most stable [serine-Ca]2+ adducts. For the analysis of the different potential energy surfaces associated with the gas-phase unimolecular reactivity of these adducts, only those that differ by less than 100 kJ·mol-1 from the global minimum were taken into account. In agreement with previous studies, the serine-Ca2+ global minimum corresponds to a charge-solvated structure in which Ca is tricoordinated to neutral serine. The major peaks observed in the nanoelectrospray-MS/MS spectrum of [Ca(Ser)]2+ adduct correspond to both Coulomb explosions, yielding either CaOH+ + [C3,H6,N,O2]+ or [C2,H4,O,N]+ + [Ca(C,H3,O2)]+, and to the loss of neutrals, namely, CH2O and H2O. Our theoretical survey of the energy profile allow us to conclude that, although all the aforementioned fragmentation processes can have their origin at the global minimum, similar fragmentations involving low-lying conformers, both zwitterionic and nonzwitterionic, compete and should be considered to account for the observed reactivity. We have also found that in some specific cases post-transition state dynamics similar to the ones described before in the literature for formamide-Ca2+ reactions, may also play a role.
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Affiliation(s)
- Al Mokhtar Lamsabhi
- Departamento de Química, Módulo 13, Facultad de Ciencias and Institute of Advanced Chemical Sciences (IadChem) , Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid , Spain
| | - Otilia Mó
- Departamento de Química, Módulo 13, Facultad de Ciencias and Institute of Advanced Chemical Sciences (IadChem) , Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid , Spain
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Facultad de Ciencias and Institute of Advanced Chemical Sciences (IadChem) , Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid , Spain
| | - Jean-Yves Salpin
- LAMBE, Univ Evry, CNRS, CEA , Université Paris-Saclay , F-91025 Evry-Courcouronnes , France.,LAMBE, UCP , Université Paris-Seine , F-91025 Evry-Courcouronnes , France
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8
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Habka S, Very T, Donon J, Vaquero-Vara V, Tardivel B, Charnay-Pouget F, Mons M, Aitken DJ, Brenner V, Gloaguen E. Identification of ion pairs in solution by IR spectroscopy: crucial contributions of gas phase data and simulations. Phys Chem Chem Phys 2019; 21:12798-12805. [PMID: 30977483 DOI: 10.1039/c9cp00700h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In a context where structure elucidation of ion pairs in solution remains a contemporary challenge, this work explores an original approach where accurate gas phase spectroscopic data are used to refine high level quantum chemistry calculations of ion pairs in solution, resulting in an unprecedented level of accuracy in vibrational frequency prediction. First, gas phase studies focus on a series of isolated contact ion pairs (M+, Ph-CH2-COO-, with M = Li, Na, K, Rb, Cs) for which conformer-selective IR spectra in the CO2- stretch region are recorded. These experiments reveal the interactions at play in isolated contact ion pairs, and provide vibrational frequencies enabling us to assess the accuracy of the theoretical approach used, i.e., mode-dependent scaled harmonic frequency calculations at the RI-B97-D3/dhf-TZVPP level. This level of calculation is then employed on large water clusters embedding either a free acetate ion or its contact or solvent-shared pairs with a sodium cation in order to simulate the individual vibrational spectra of these species in solution. This study shows that the stretching modes of carboxylate are sensitive to both solvent-shared and contact ion pair formation. FTIR spectra of solutions of increasing concentrations indeed reveal several spectral changes consistent with the presence of specific types of solvent-shared and contact ion pairs. By providing relevant guidelines for the interpretation of solution phase IR spectra, this work illustrates the potential of the approach for the elucidation of supramolecular structures in electrolyte solutions.
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Affiliation(s)
- Sana Habka
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Thibaut Very
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Jeremy Donon
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Vanesa Vaquero-Vara
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Benjamin Tardivel
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Florence Charnay-Pouget
- ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, UMR 8182, Bât. 420, 15 rue Georges Clémenceau, 91405 Orsay cedex, France
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - David J Aitken
- ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, UMR 8182, Bât. 420, 15 rue Georges Clémenceau, 91405 Orsay cedex, France
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
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9
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Oomens J, Polfer NC, Berden G, Eyler JR. Gas-phase metal ion chelation investigated with IRMPD spectroscopy: A brief review of Robert Dunbar's contributions. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:86-96. [PMID: 30205710 DOI: 10.1177/1469066718799175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
With the passing of Prof. Robert C. Dunbar on 31 October 2017, the field of ion chemistry lost one of its modern heroes. Throughout his career in mass spectrometry, two of his main research interests involved the interaction of trapped ions with electromagnetic radiation and the chelation motifs of metal ions with organic ligands. The focus of his early career was on the fundamental processes that take place in molecules upon ultraviolet and infrared excitation. From 2003 to 2017, his scientific interests shifted to more structural questions, notably to resolving the structures and binding motifs of metal ion chelation complexes by application of infrared photodissociation spectroscopy. These experiments were carried out during numerous visits to the (Free Electron Laser for Infrared eXperiments) (FELIX) facility in the Netherlands and were complemented by extensive theoretical investigations by Rob. As a tribute to our friend, we present in this contribution a brief review of this work.
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Affiliation(s)
- Jos Oomens
- 1 FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- 2 Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Nicolas C Polfer
- 3 Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Giel Berden
- 1 FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - John R Eyler
- 3 Department of Chemistry, University of Florida, Gainesville, Florida, USA
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10
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Heller J, Ončák M, Bersenkowitsch NK, van der Linde C, Beyer MK. Infrared multiple photon dissociation of cesium iodide clusters doped with mono-, di- and triglycine. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:122-132. [PMID: 30284923 PMCID: PMC7100558 DOI: 10.1177/1469066718803307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Charged cesium iodide clusters doped with mono-, di- and triglycine serve as a model system for sea salt aerosols containing biological molecules. Here, we investigate reactions of these complexes under infrared irradiation, with spectra obtained by infrared multiple photon dissociation. The cluster ions are generated via electrospray ionization and analyzed in the cell of a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Depending on the cluster size and peptide length, loss of HI or loss of a glycine unit is observed. The experimental measurements are supported by quantum chemical calculations. We show that N-H and O-H stretching modes dominate the spectrum, with large shifts depending on local interactions, namely due to interaction with iodide anions or intramolecular hydrogen bonding. Both experiment and theory indicate that several isomers are present in the experimental mixture, with different infrared fingerprints as well as dissociation pathways.
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Affiliation(s)
- Jakob Heller
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | - Milan Ončák
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | - Nina K Bersenkowitsch
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | | | - Martin K Beyer
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
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11
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An ab iniio study on the micro-solvation of amino acids: On the number of water molecules necessary to stabilize the zwitter ion. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.12.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Devereaux ZJ, Zhu Y, Rodgers MT. Relative glycosidic bond stabilities of naturally occurring methylguanosines: 7-methylation is intrinsically activating. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:16-29. [PMID: 30189754 DOI: 10.1177/1469066718798097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The frequency and diversity of posttranscriptional modifications add an additional layer of chemical complexity beyond canonical nucleic acid sequence. Methylations are particularly frequently occurring and often highly conserved throughout the kingdoms of life. However, the intricate functions of these modified nucleic acid constituents are often not fully understood. Systematic foundational research that reduces systems to their minimum constituents may aid in unraveling the complexities of nucleic acid biochemistry. Here, we examine the relative intrinsic N-glycosidic bond stabilities of guanosine and five naturally occurring methylguanosines (O2'-, 1-, 7-, N2,N2-di-, and N2,N2,O2'-trimethylguanosine) probed by energy-resolved collision-induced dissociation tandem mass spectrometry and complemented with quantum chemical calculations. Apparent glycosidic bond stability is generally found to increase with increasing methyl substitution (canonical < mono- < di- < trimethylated). Many biochemical transformations, including base excision repair mechanisms, involve protonation and/or noncovalent interactions to increase nucleobase leaving-group ability. The protonated gas-phase methylguanosines require less activation energy for glycosidic bond cleavage than their sodium cationized forms. However, methylation at the N7 position intrinsically weakens the glycosidic bond of 7-methylguanosine more significantly than subsequent cationization, and thus 7-methylguanosine is suggested to be under perpetually activated conditions. N7 methylation also alters the nucleoside geometric preferences relative to the other systems, including the nucleobase orientation in the neutral form, sugar puckering in the protonated form, and the preferred protonation and sodium cation binding sites. All of the methylated guanosines examined here are predicted to have proton affinities and gas-phase basicities that exceed that of canonical guanosine. Additionally, the proton affinity and gas-phase basicity trends exhibit a roughly inverse correlation with the apparent glycosidic bond stabilities.
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Affiliation(s)
| | - Y Zhu
- Department of Chemistry, Wayne State University, Detroit, USA
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, USA
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13
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Rodgers MT. Robert C. Dunbar: CURRICULUM VITAE: June 26, 1943, Boston, Massachusetts-October 31, 2017, Cleveland, Ohio. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:8-15. [PMID: 30773921 DOI: 10.1177/1469066718817618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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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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Dilger JM, Glover MS, Clemmer DE. A Database of Transition-Metal-Coordinated Peptide Cross-Sections: Selective Interaction with Specific Amino Acid Residues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1293-1303. [PMID: 28357817 DOI: 10.1007/s13361-016-1592-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/17/2016] [Accepted: 12/18/2016] [Indexed: 05/18/2023]
Abstract
Ion mobility mass spectrometry (IMS-MS) techniques were used to generate a database of 2288 collision cross sections of transition-metal-coordinated tryptic peptide ions. This database consists of cross sections for 1253 [Pep + X]2+ and 1035 [Pep + X + H]3+, where X2+ corresponds to Mn2+, Co2+, Ni2+, Cu2+, or Zn2+. This number of measurements enables the extraction of structural trends for transition-metal-coordinated peptide ions. The range of structures and changes in collision cross sections for X2+-coordinated species (compared with protonated species of the same charge state) is similar to Mg2+-coordinated species. This suggests that the structures are largely determined by similarities in cation size with differences among the cross section distributions presumably caused by X2+ interactions with specific functional groups offered by the residue R-groups or the peptide backbone. Cross section contributions for individual residues upon X2+ solvation are assessed with the derivation of intrinsic size parameters (ISPs). The comparison of the [Pep + X]2+ ISPs with those previously reported for [Pep + Mg]2+ ions displays a lower contribution to the cross section for His, carboxyamidomethylated Cys, and Met, and is consistent with specific metal-residue interactions identified within protein X-ray crystallography databases. Graphical Abstract ᅟ.
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Affiliation(s)
- Jonathan M Dilger
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
- Spectrum Warfare Systems Department, Naval Surface Warfare Center, Crane Division, Crane, IN, 47522, USA.
| | - Matthew S Glover
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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16
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Cismesia AP, Nicholls GR, Polfer NC. Amine vs. carboxylic acid protonation in ortho-, meta-, and para-aminobenzoic acid: An IRMPD spectroscopy study. JOURNAL OF MOLECULAR SPECTROSCOPY 2017; 332:79-85. [PMID: 28439142 PMCID: PMC5400370 DOI: 10.1016/j.jms.2016.10.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy and computational chemistry are applied to the ortho-, meta-, and para- positional isomers of aminobenzoic acid to investigate whether the amine or the carboxylic acid are the favored sites of proton attachment in the gas phase. The NH and OH stretching modes yield distinct patterns that establish the carboxylic acid as the site of protonation in para-aminobenzoic acid, as opposed to the amine group in ortho- and meta-aminobenzoic acid, in agreement with computed thermochemistries. The trends for para- and meta-substitutions can be rationalized simplistically by inductive effects and resonant stabilization, and will be discussed in light of computed charge distributions based from electrostatic potentials. In ortho-aminobenzoic acid, the close proximity of the amine and acid groups allow a simultaneous interaction of the proton with both groups, thus stabilizing and delocalizing the charge more effectively, and compensating for some of the resonance stabilization effects.
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17
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Pepin R, Laszlo KJ, Marek A, Peng B, Bush MF, Lavanant H, Afonso C, Tureček F. Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1647-60. [PMID: 27400696 PMCID: PMC5031493 DOI: 10.1007/s13361-016-1437-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 05/27/2016] [Accepted: 06/16/2016] [Indexed: 05/18/2023]
Abstract
Heptapeptide ions containing combinations of polar Lys, Arg, and Asp residues with non-polar Leu, Pro, Ala, and Gly residues were designed to study polar effects on gas-phase ion conformations. Doubly and triply charged ions were studied by ion mobility mass spectrometry and electron structure theory using correlated ab initio and density functional theory methods and found to exhibit tightly folded 3D structures in the gas phase. Manipulation of the basic residue positions in LKGPADR, LRGPADK, KLGPADR, and RLGPADK resulted in only minor changes in the ion collision cross sections in helium. Replacement of the Pro residue with Leu resulted in only marginally larger collision cross sections for the doubly and triply charged ions. Disruption of zwitterionic interactions in doubly charged ions was performed by converting the C-terminal and Asp carboxyl groups to methyl esters. This resulted in very minor changes in the collision cross sections of doubly charged ions and even slightly diminished collision cross sections in most triply charged ions. The experimental collision cross sections were related to those calculated for structures of lowest free energy ion conformers that were obtained by extensive search of the conformational space and fully optimized by density functional theory calculations. The predominant factors that affected ion structures and collision cross sections were due to attractive hydrogen bonding interactions and internal solvation of the charged groups that overcompensated their Coulomb repulsion. Structure features typically assigned to the Pro residue and zwitterionic COO-charged group interactions were only secondary in affecting the structures and collision cross sections of these gas-phase peptide ions. Graphical Abstract ᅟ.
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Affiliation(s)
- Robert Pepin
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, USA
| | - Kenneth J Laszlo
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, USA
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Bo Peng
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, USA
| | - Matthew F Bush
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, USA
| | - Helène Lavanant
- Laboratoire COBRA CNRS UMR 6014 & FR 3038, Université de Rouen, INSA de Rouen, Mont St Aignan Cedex, France
| | - Carlos Afonso
- Laboratoire COBRA CNRS UMR 6014 & FR 3038, Université de Rouen, INSA de Rouen, Mont St Aignan Cedex, France
| | - František Tureček
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, USA.
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18
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Khalili B, Rimaz M. Interaction of l-proline with group IIB (Zn2+, Cd2+, Hg2+) metal cations in the gas and aqueous phases: a quantum computational study. CAN J CHEM 2016. [DOI: 10.1139/cjc-2015-0616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The gas and aqueous phase complexation geometries, electronic interactions, and metal ion affinities of Zn2+, Cd2+, and Hg2+ metal cations with the two most stable conformations of l-proline complexes were studied. The complexes were optimized by density functional theory (B3LYP) using the 6-311++G(d,p) orbital basis set and relativistic pseudopotentials for the metal cations. The interactions of the metal cations at different nucleophilic sites of l-proline were considered as were three modes of interactions including salt bridged, charge solvated 1, and charge solvated 2, which are indicative of binding in a bidentate manner through the carboxylate group, carbonyl and hydroxyl oxygen, and carbonyl oxygen and the nitrogen atom of l-proline. All of the coordination patterns were characterized by both charge transfer and ionic interactions between l-proline and the metal cation. The metal ion affinity (MIA) and interaction energy were also computed for all of the complexes at both the gas and aqueous phases. Results showed that the order of MIA at the gas and aqueous phases are different. MIA order at the gas phase was in the order of Zn2+ > Hg2+ > Cd2+ whereas at the aqueous phase, the order of Zn2+ > Cd2+ > Hg2+ was obtained for MIA. The infrared stretching vibrational modes of the N–H and O–H groups of free l-proline were compared with l-proline–M2+ in both CS1 and CS2 coordination patterns at the gas phase and results showed a considerable shift to lower frequency during complexation process.
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Affiliation(s)
- Behzad Khalili
- Department of Chemistry, Faculty of Sciences, University of Guilan, P.O. Box 41335-1914 Rasht, Iran
| | - Mehdi Rimaz
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran, Iran
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19
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Habka S, Brenner V, Mons M, Gloaguen E. Gas-Phase Spectroscopic Signatures of Carboxylate-Li(+) Contact Ion Pairs: New Benchmarks For Characterizing Ion Pairing in Solution. J Phys Chem Lett 2016; 7:1192-1197. [PMID: 26978595 DOI: 10.1021/acs.jpclett.6b00454] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The coexistence of several types of ion pairs in solution together with their elusive nature hampers their experimental characterization, which relies in practice on theoretical models resorting to numerous approximations. In this context, a series of isolated contact ion pairs between a lithium cation and phenyl-tagged carboxylate anions of various lengths (Ph-(CH2)n-COO(-), n = 1-3) has been investigated in a conformer-selective manner by IR and UV laser spectroscopy, in conjunction with quantum chemistry calculations. The typical gas-phase IR signature of the bidentate structure formed between the carboxylate moiety and Li(+) has thus been obtained in the CO2(-) stretch region. In addition to the cation-anion interaction, a cation-π interaction occurs simultaneously in the largest system investigated (n = 3). The resulting distorted ion pair structure has been evidenced from both the IR signature of the CO2(-) stretches and the unique vibrationally resolved UV spectroscopy of a phenyl ring interacting with a cation. Such specific spectroscopic signatures of contact ion pairs provide experimental benchmarks, alternative to theoretical predictions, that can assist the assignment of vibrational spectra in solution.
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Affiliation(s)
- Sana Habka
- LIDYL, CEA, CNRS, Université Paris-Saclay , CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay , CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris-Saclay , CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris-Saclay , CEA Saclay, 91191 Gif-sur-Yvette, France
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20
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Rodgers MT, Armentrout PB. Cationic Noncovalent Interactions: Energetics and Periodic Trends. Chem Rev 2016; 116:5642-87. [PMID: 26953819 DOI: 10.1021/acs.chemrev.5b00688] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In this review, noncovalent interactions of ions with neutral molecules are discussed. After defining the scope of the article, which excludes anionic and most protonated systems, methods associated with measuring thermodynamic information for such systems are briefly recounted. An extensive set of tables detailing available thermodynamic information for the noncovalent interactions of metal cations with a host of ligands is provided. Ligands include small molecules (H2, NH3, CO, CS, H2O, CH3CN, and others), organic ligands (O- and N-donors, crown ethers and related molecules, MALDI matrix molecules), π-ligands (alkenes, alkynes, benzene, and substituted benzenes), miscellaneous inorganic ligands, and biological systems (amino acids, peptides, sugars, nucleobases, nucleosides, and nucleotides). Hydration of metalated biological systems is also included along with selected proton-based systems: 18-crown-6 polyether with protonated peptides and base-pairing energies of nucleobases. In all cases, the literature thermochemistry is evaluated and, in many cases, reanchored or adjusted to 0 K bond dissociation energies. Trends in these values are discussed and related to a variety of simple molecular concepts.
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Affiliation(s)
- M T Rodgers
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - P B Armentrout
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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21
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Sharma B, Neela YI, Narahari Sastry G. Structures and energetics of complexation of metal ions with ammonia, water, and benzene: A computational study. J Comput Chem 2016; 37:992-1004. [PMID: 26833683 DOI: 10.1002/jcc.24288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/26/2015] [Accepted: 12/01/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Bhaskar Sharma
- Center for Molecular Modelling; CSIR-Indian Institute of Chemical Technology; Tarnaka, Hyderabad Telangana 500 607 India
| | - Y. Indra Neela
- Center for Molecular Modelling; CSIR-Indian Institute of Chemical Technology; Tarnaka, Hyderabad Telangana 500 607 India
| | - G. Narahari Sastry
- Center for Molecular Modelling; CSIR-Indian Institute of Chemical Technology; Tarnaka, Hyderabad Telangana 500 607 India
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22
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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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23
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An insight into the interaction of L-proline with the transition metal cations Fe(2+), Co(2+), Ni(2+): a gas phase theoretical study. J Mol Model 2015; 22:11. [PMID: 26676722 DOI: 10.1007/s00894-015-2865-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 11/15/2015] [Indexed: 10/22/2022]
Abstract
The interaction of Fe(2+), Co(2+), and Ni(2+) with L-proline has been studied. Three modes of interaction have been considered: salt bridged (SB), involving binding in a bi-dentate manner through the carboxylate group of L-proline, charge solvated 1 (CS1) involving carbonyl and hydroxyl oxygen, and charge solvated 2 (CS2) involving carbonyl oxygen and the lone pair of the nitrogen atom. All calculations including geometry optimization, metal ion affinities (MIAs), and frequency calculations of the binding structures of Fe(2+), Co(2+), and Ni(2+) to L-proline were calculated using the hybrid density functional theory (DFT-B3LYP) method. All three cations were found to bind preferentially in a zwitterionic (SB) coordination pattern with the metal ion affinity in the order Ni(2+) ˃ Co(2+) ˃ Fe(2+) in all binding forms. The nature of the binding interaction between metal cations and L-proline was found to be mainly electrostatic. Comparison of the infrared vibrations of the C=O, the N-H and the O-H groups of free L-proline with L-proline-M(2+) in both CS1 and CS2 complex structures indicated a considerable shift to lower frequency during complexation. In order to gain more insight into the nature of the interaction of L-proline with group VIIIB metal ions, comparison of the interaction of L-proline with other cations such as (Li(+), Na(+), K(+), Be(2+), Mg(2+), and Ca(2+)) was made. Graphical Abstract L-proline with the transition metal cations Fe(2+), Co(2+), Ni(2.)
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24
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Dunbar RC, Berden G, Martens JK, Oomens J. Divalent Metal-Ion Complexes with Dipeptide Ligands Having Phe and His Side-Chain Anchors: Effects of Sequence, Metal Ion, and Anchor. J Phys Chem A 2015; 119:9901-9. [PMID: 26325483 DOI: 10.1021/acs.jpca.5b06315] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational preferences have been surveyed for divalent metal cation complexes with the dipeptide ligands AlaPhe, PheAla, GlyHis, and HisGly. Density functional theory results for a full set of complexes are presented, and previous experimental infrared spectra, supplemented by a number of newly recorded spectra obtained with infrared multiple photon dissociation spectroscopy, provide experimental verification of the preferred conformations in most cases. The overall structural features of these complexes are shown, and attention is given to comparisons involving peptide sequence, nature of the metal ion, and nature of the side-chain anchor. A regular progression is observed as a function of binding strength, whereby the weakly binding metal ions (Ba(2+) to Ca(2+)) transition from carboxylate zwitterion (ZW) binding to charge-solvated (CS) binding, while the stronger binding metal ions (Ca(2+) to Mg(2+) to Ni(2+)) transition from CS binding to metal-ion-backbone binding (Iminol) by direct metal-nitrogen bonds to the deprotonated amide nitrogens. Two new sequence-dependent reversals are found between ZW and CS binding modes, such that Ba(2+) and Ca(2+) prefer ZW binding in the GlyHis case but prefer CS binding in the HisGly case. The overall binding strength for a given metal ion is not strongly dependent on the sequence, but the histidine peptides are significantly more strongly bound (by 50-100 kJ mol(-1)) than the phenylalanine peptides.
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Affiliation(s)
- Robert C Dunbar
- Chemistry Department, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jonathan K Martens
- 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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25
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Kowalska-Baron A. Theoretical study of the complexes of tyrosine and tryptophan with biologically important metal cations in aqueous solutions. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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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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27
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Eldridge K, Wu R, Martens JK, McMahon TB. Gas-Phase Solvation of Protonated Amino Acids by Methanol. J Phys Chem A 2014; 118:11629-40. [DOI: 10.1021/jp5086729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kris Eldridge
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Ronghu Wu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Jonathan K. Martens
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Terry B. McMahon
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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28
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Pathak AK. Stabilizing the zwitter-ionic form of amino acids in the gas phase: An ab initio study on the minimum number of solvents and ions. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.07.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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29
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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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30
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31
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Qin P, Lü W, Qin W, Zhang W, Xie H. Theoretical studies on complexes of calcium ion with amino acids. Chem Res Chin Univ 2014. [DOI: 10.1007/s40242-014-3303-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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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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33
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Theoretical study of hydrated Ca2+-amino acids (glycine, threonine and phenylalanine) clusters. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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34
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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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35
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Gholami A, Fridgen TD. Structures and unimolecular reactivity of gas-phase [Zn(proline-H)]+ and [Zn(proline-H)(H2O)]+. J Phys Chem B 2013; 117:8447-56. [PMID: 23786341 DOI: 10.1021/jp404697g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A combination of IRMPD spectroscopy, collision-induced dissociation, deuterium isotopic substitution, and computational chemistry was used to determine the structure and unimolecular chemistry of [Zn(Pro-H)](+) and the singly hydrated complex in the gas phase. Five competing dissociation channels were observed: loss of H2O, CO, CO2, and HCOOH and the main fragmentation pathway, loss of neutral Zn. By comparing the IRMPD spectrum with the predicted IR spectra of the lowest energy structures, it was confirmed that [Zn(Pro-H)](+) complex is deprotonated at the amine moiety, and a hydrogen from either C2 or C5 migrated to Zn(2+). In this H-type complex, ZnH(+) was chelated between the amine nitrogen and the carbonyl oxygen. Calculations of the potential energy surface revealed that the loss of neutral zinc is energetically more favorable than the loss of dehydrogenated proline leading to ZnH(+) product. Furthermore, calculations on all five primary decomposition routes, all beginning with the lowest energy structure, revealed that loss of Zn has the lowest energy requirement, consistent with it being the most abundant product of unimolecular dissociation following collisional or IR multiphoton activation. For the singly hydrated complex, [Zn(Pro-H)(H2O)](+), IRMPD spectroscopy confirms a structure with water added to the H-type structure and intramolecularly hydrogen bonded to the deprotonated amine site. This structure is not the lowest-energy [Zn(Pro-H)(H2O)](+) isomer, but it is the one where water is added to the lowest energy [Zn(Pro-H)](+) isomer.
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Affiliation(s)
- Ameneh Gholami
- Department of Chemistry, Memorial University, St. John's, Newfoundland and Labrador, Canada A1B 3X7
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36
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Luxford TF, Milner EM, Yoshikawa N, Bullivant C, Dessent CE. Complexation of carboxylate anions with the arginine gas-phase amino acid: Effects of chain length on the geometry of extended ion binding. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.05.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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37
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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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38
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Moghaddam MB, Fridgen TD. IRMPD Spectroscopic Study of Microsolvated [Na(GlyAla)]+ and [Ca(GlyAla–H)]+ and the Blue Shifting of the Hydrogen-Bonded Amide Stretch with Each Water Addition. J Phys Chem B 2013; 117:6157-64. [DOI: 10.1021/jp402217g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maryam B. Moghaddam
- Department
of Chemistry, Memorial University, St. John’s, Newfoundland
and Labrador, Canada A1B 3X7 Canada
| | - Travis D. Fridgen
- Department
of Chemistry, Memorial University, St. John’s, Newfoundland
and Labrador, Canada A1B 3X7 Canada
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39
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Chiavarino B, Crestoni ME, Fornarini S, Scuderi D, Salpin JY. Interaction of Cisplatin with Adenine and Guanine: A Combined IRMPD, MS/MS, and Theoretical Study. J Am Chem Soc 2013; 135:1445-55. [DOI: 10.1021/ja309857d] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie
del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie
del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie
del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Roma, Italy
| | - Debora Scuderi
- Laboratoire de Chimie-Physique, Université Paris Sud Orsay, Avenue Georges Clémenceau,
91405 Orsay Cedex, France
- CNRS-UMR 8000
| | - 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
- CNRS-UMR 8587
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40
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Piccirillo S, Ciavardini A, Bodo E, Rondino F, Scuderi D, Steinmetz V, Paladini A. Probing the competition among different coordination motifs in metal-ciprofloxacin complexes through IRMPD spectroscopy and DFT calculations. Inorg Chem 2013; 52:103-12. [PMID: 23252622 DOI: 10.1021/ic301299e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The vibrational spectra of ciprofloxacin complexes with monovalent (Li(+), Na(+), K(+), Ag(+)) and polyvalent (Mg(2+), Al(3+)) metal ions are recorded in the range 1000-1900 cm(-1) by means of infrared multiple-photon dissociation (IRMPD) spectroscopy. The IRMPD spectra are analyzed and interpreted in the light of density functional theory (DFT)-based quantum chemical calculations in order to identify the possible structures present under our experimental conditions. For each metal-ciprofloxacin complex, four isomers are predicted, considering different chelation patterns. A good agreement is found between the measured IRMPD spectrum and the calculated absorption spectrum of the most stable isomer for each complex. Metal ion size and charge are found to drive the competition among the different coordination motifs: small size and high charge density metal ions prefer to coordinate the quinolone between the two carbonyl oxygen atoms, whereas large-size metal ions prefer the carboxylate group as a coordination site. In the latter case, an intramolecular hydrogen bond compensates the weaker interaction established by these cations. The role of the metal cation on the stabilization of ionic and nonionic structures of ciprofloxacin is also investigated. It is found that large-size metal ions preferentially stabilize charge separated motifs and that the increase of metal ion charge has a stabilizing effect on the zwitterionic form of ciprofloxacin.
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Affiliation(s)
- Susanna Piccirillo
- Dip. di Scienze e Tecnologie Chimiche, Università di Roma 'Tor Vergata', via della Ricerca Scientifica, 00133 Rome, Italy
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41
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Han L, Hyung SJ, Ruotolo BT. Dramatically stabilizing multiprotein complex structure in the absence of bulk water using tuned Hofmeister salts. Faraday Discuss 2013; 160:371-88; discussion 389-403. [PMID: 23795511 PMCID: PMC3695445 DOI: 10.1039/c2fd20099f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The role that water plays in the salt-based stabilization of proteins is central to our understanding of protein biophysics. Ion hydration and the ability of ions to alter water surface tension are typically invoked, along with direct ion-protein binding, to describe Hofmeister stabilization phenomena observed for proteins experimentally, but the relative influence of these forces has been extraordinarily difficult to measure directly. Recently, we have used gas-phase measurements of proteins and large multiprotein complexes, using a combination of innovative ion mobility (IM) and mass spectrometry (MS) techniques, to assess the ability of bound cations and anions to stabilize protein ions in the absence of the solvation forces described above. Our previous work has studied a broad set of 12 anions bound to a range of proteins and protein complexes, and while primarily motivated by the analytical challenges surrounding the gas-phase measurement of solution-phase relevant protein structures, our work has also lead to a detailed physical mechanism of anion-protein complex stabilization in the absence of bulk solvent. Our more-recent work has screened a similarly-broad set of cations for their ability to stabilize gas-phase protein structure, and we have discovered surprising differences between the operative mechanisms for cations and anions in gas-phase protein stabilization. In both cases, cations and anions affect protein stabilization in the absence of solvent in a manner that is generally reversed relative to their ability to stabilize the same proteins in solution. In addition, our evidence suggests that the relative solution-phase binding affinity of the anions and cations studied here is preserved in our gas-phase measurements, allowing us to study the influence of such interactions in detail. In this report, we collect and summarize such gas-phase measurements to distill a generalized picture of salt-based protein stabilization in the absence of bulk water. Further, we communicate our most recent efforts to study the combined effects of stabilizing cations and anions on gas-phase proteins, and identify those salts that bear anion/cation pairs having the strongest stabilizing influence on protein structures
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Affiliation(s)
- Linjie Han
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109
| | - Suk-Joon Hyung
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109
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42
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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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43
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Yang G, Zhu R, Zhou L, Liu C. Interactions of Zn(II) with single and multiple amino acids. Insights from density functional and ab initio calculations. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1372-1383. [PMID: 23019170 DOI: 10.1002/jms.3075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Calculations were performed to study the interactions of metal ions (M) with (multiple) amino acids (AA) and fill the gap between single AA and proteins. A complete conformational search results in nine and eleven ZnGly isomers at B3P86 and MP2 levels, respectively, and four populated conformers of glycine are responsible for production of these isomers. For all M, the isomers via the OO and NO binding modes are the main constituents, and the OO mode is favored by stronger electrostatic interactions. Binding with more glycines causes larger structural distortions, improves relative stabilities of monodentate binding isomers and generates new binding modes (e.g. ZnB(III) via only the hydroxyl group). The scaling factor of Zn(Gly)(n) structures, the ratio of its binding affinity versus the sum of comprising ZnGly isomers, is linear with glycine number (n), and the linear relationship may not be altered by mutations of glycines and M. It thus allows to estimate M(AA)(n) binding affinities (n ≥ 2) from the comprising MAA structures and analyze their structures with kinetic methods. The DFT and MP2 results become comparable by increasing metal coordination, e.g. the ZnB(III) versus ZnA(I) (zwitterionic) relative energy differs by 41.9 kcal mol(-1) at B3P86 and MP2 levels and is close by addition of three water molecules (4.1 kcal mol(-1)). The presence of water solvent improves the relative stabilities of monodentate binding isomers and results in a broader conformational distribution.
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Affiliation(s)
- Gang Yang
- Institute of Theoretical Chemistry, Shandong University, Jinan, P R China.
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44
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Burt MB, Fridgen TD. Gas-Phase Structures of Pb2+-Cationized Phenylalanine and Glutamic Acid Determined by Infrared Multiple Photon Dissociation Spectroscopy and Computational Chemistry. J Phys Chem A 2012; 117:1283-90. [DOI: 10.1021/jp306420e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael B. Burt
- Department of Chemistry, Memorial University of Newfoundland,
St. John’s,
Newfoundland and Labrador, Canada, A1B 3X7
| | - Travis D. Fridgen
- Department of Chemistry, Memorial University of Newfoundland,
St. John’s,
Newfoundland and Labrador, Canada, A1B 3X7
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45
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Chang TM, Prell JS, Warrick ER, Williams ER. Where’s the Charge? Protonation Sites in Gaseous Ions Change with Hydration. J Am Chem Soc 2012; 134:15805-13. [DOI: 10.1021/ja304929h] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Terrence M. Chang
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United
States
| | - James S. Prell
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United
States
| | - Erika R. Warrick
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United
States
| | - Evan R. Williams
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United
States
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46
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Meng L, Hu A, Pang R, Lin Z. Extensive computational study on coordination of transition metal cations and water molecules to glutamic acid. J Phys Chem A 2012; 116:7177-88. [PMID: 22671921 DOI: 10.1021/jp303289p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of the conformations of glutamic acid (Glu) and analysis of possible metal cation coordination and hydration modes, conformations of Glu metalated with transition metal cations (TMCs), Cu(+/2+), Zn(+/2+), and Fe(+/2+/3+) and hydrations of Glu-Cu(+/2+) and Glu-Zn(+/2+) complexes by up to three water molecules are determined by extensive computational searches. The BHandHLYP functional is chosen as the main computational method as its overall performance for treating the spin multiplicity of TMCs is similar to that of CCSD(T) and better than that of MP2 and B3LYP. All mono- and divalent TMCs prefer tridentate coordination to canonical Glu, while Fe(3+) favors a bidentate coordination to zwitterionic Glu. The ground state of Glu-Fe(+) is found to be a spin sextet. Metal ion affinities of Glu for the TMCs are determined, and an excellent agreement with the experiment for Cu(+) may be obtained if the entropic effect is properly accounted for. Effects of hydration on the stabilities of different Glu-Cu(+/2+)/Zn(+/2+) structures are discussed, and the hydration energies for up to three water molecules are obtained. For the global minimum to take the zwitterionic form, Glu-Zn(+) requires only monohydration, Glu-Zn(2+) needs to be trihydrated, while Glu-Cu(+/2) should be hydrated with four or more water molecules.
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Affiliation(s)
- Lingbiao Meng
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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47
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Duan X, Luo G, Chen Y, Kong X. Effects of alkali metal ion cationization on fragmentation pathways of triazole-epothilone. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1126-1134. [PMID: 22467338 DOI: 10.1007/s13361-012-0376-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 03/12/2012] [Accepted: 03/12/2012] [Indexed: 05/31/2023]
Abstract
The collisionally activated dissociation mass spectra of the protonated and alkali metal cationized ions of a triazole-epothilone analogue were studied in a Fourier transform ion cyclotron resonance mass spectrometer. The fragmentation pathway of the protonated ion was characterized by the loss of the unit of C(3)H(4)O(3). However, another fragmentation pathway with the loss of C(3)H(2)O(2) was identified for the complex ions with Na(+), K(+), Rb(+), and Cs(+). The branching ratio of the second pathway increases with the increment of the size of alkali metal ions. Theoretical calculations based on density functional theory (DFT) method show the difference in the binding position of the proton and the metal ions. With the increase of the radii of the metal ions, progressive changes in the macrocycle of the compound are induced, which cause the corresponding change in their fragmentation pathways. It has also been found that the interaction energy between the compound and the metal ion decreases with increase in the size of the latter. This is consistent with the experimental results, which show that cesiated complexes readily eject Cs(+) when subject to collisions.
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Affiliation(s)
- Xiyan Duan
- College of Pharmacy, Nankai University, 300071, Tianjin, China
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48
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Brückmann L, Tyrra W, Mathur S, Berden G, Oomens J, Meijer AJHM, Schäfer M. Examination of the Coordination Sphere of AlIII in Trifluoromethyl-Heteroarylalkenolato Complex Ions by Gas-Phase IRMPD Spectroscopy and Computational Modelling. Chemphyschem 2012; 13:2037-45. [DOI: 10.1002/cphc.201200132] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Indexed: 11/05/2022]
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49
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Citir M, Hinton CS, Oomens J, Steill JD, Armentrout PB. Infrared Multiple Photon Dissociation Spectroscopy of Cationized Histidine: Effects of Metal Cation Size on Gas-Phase Conformation. J Phys Chem A 2012; 116:1532-41. [DOI: 10.1021/jp209636a] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Murat Citir
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Christopher S. Hinton
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Jos Oomens
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan
14, 3439 MN Nieuwegein, The Netherlands
- Van’t Hoff Institute for
Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeffrey D. Steill
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan
14, 3439 MN Nieuwegein, The Netherlands
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United
States
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50
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Milner EM, Nix MGD, Dessent CEH. Collision-Induced Dissociation of Halide Ion–Arginine Complexes: Evidence for Anion-Induced Zwitterion Formation in Gas-Phase Arginine. J Phys Chem A 2012; 116:801-9. [DOI: 10.1021/jp208183p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Edward M. Milner
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Michael G. D. Nix
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
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