1
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Oomens J, Kempkes LJM, Geurts TPJ, van Dijk L, Martens J, Berden G, Armentrout PB. Water Loss from Protonated XxxSer and XxxThr Dipeptides Gives Oxazoline-Not Oxazolone-Product Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2111-2123. [PMID: 32876444 PMCID: PMC7552115 DOI: 10.1021/jasms.0c00239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Neutral loss of water and ammonia are often significant fragmentation channels upon collisional activation of protonated peptides. Here, we deploy infrared ion spectroscopy to investigate the dehydration reactions of protonated AlaSer, AlaThr, GlySer, GlyThr, PheSer, PheThr, ProSer, ProThr, AsnSer, and AsnThr, focusing on the question of the structure of the resulting [M + H - H2O]+ fragment ion and the site from which H2O is expelled. In all cases, the second residue of the selected peptides contains a hydroxyl moiety, so that H2O loss can potentially occur from this side-chain, as an alternative to loss from the C-terminal free acid of the dipeptide. Infrared action spectra of the product ions along with quantum-chemical calculations unambiguously show that dehydration consistently produces fragment ions containing an oxazoline moiety. This contrasts with the common oxazolone structure that would result from dehydration at the C-terminus analogous to the common b/y dissociation forming regular b2-type sequence ions. The oxazoline product structure suggests a reaction mechanism involving water loss from the Ser/Thr side-chain with concomitant nucleophilic attack of the amide carbonyl oxygen at its β-carbon, forming an oxazoline ring. However, an extensive quantum-chemical investigation comparing the potential energy surfaces for three entirely different dehydration reaction pathways indicates that it is actually the backbone amide oxygen atom that leaves as the water molecule.
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Affiliation(s)
- Jos Oomens
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
- Van’t Hoff Institute for Molecular Sciences,
University of Amsterdam, Science Park 904, 1098 XH Amsterdam,
The Netherlands
| | - Lisanne J. M. Kempkes
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - Thijs P. J. Geurts
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - Luuk van Dijk
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - Jonathan Martens
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - Giel Berden
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, 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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2
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Thermal dissociation of the singly protonated Arginine: Competition between side-chain and backbone fragmentation. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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3
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Gu M, Zhang J, Hase WL, Yang L. Direct Dynamics Simulations of the Thermal Fragmentation of a Protonated Peptide Containing Arginine. ACS OMEGA 2020; 5:1463-1471. [PMID: 32010819 PMCID: PMC6990424 DOI: 10.1021/acsomega.9b03091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/25/2019] [Indexed: 05/31/2023]
Abstract
Arginine has significant effects on fragmentation patterns of the protonated peptide due to its high basicity guanidine tail. In this article, thermal dissociation of the singly protonated glycine-arginine dipeptide (GR-H+) was investigated by performing direct dynamics simulations at different vibrational temperatures of 2000-3500 K. Fourteen principal fragmentation mechanisms containing side-chain and backbone fragmentation were found and discussed in detail. The mechanism involving partial or complete loss of a guanidino group dominates side-chain fragmentation, while backbone fragmentation mainly involves the three cleavage sites of a1-x1+, a2+-x0, and b1-y1+. Fragmentation patterns for primary dissociation have been compared with experimental results, and the peak that was not identified by the experiment has been assigned by our simulation. Kinetic parameters for GR-H+ unimolecular dissociation may be determined by direct dynamics simulations, which are helpful in exploring the complex biomolecules.
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Affiliation(s)
- Meng Gu
- MIIT
Key Laboratory of Critical Materials Technology for New Energy Conversion
and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Jiaxu Zhang
- MIIT
Key Laboratory of Critical Materials Technology for New Energy Conversion
and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79401, United States
| | - Li Yang
- MIIT
Key Laboratory of Critical Materials Technology for New Energy Conversion
and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
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4
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Martin Somer A, Macaluso V, Barnes GL, Yang L, Pratihar S, Song K, Hase WL, Spezia R. Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2-24. [PMID: 32881516 DOI: 10.1021/jasms.9b00062] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.
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Affiliation(s)
- Ana Martin Somer
- Departamento de Química, Facultad de Ciencias, Módulo 13 Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049 Madrid, Spain
| | - Veronica Macaluso
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Evry, France
| | - George L Barnes
- Department of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United States
| | - Li Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P.R. China
| | - Subha Pratihar
- Department of Chemistry and Biochemistry Texas Tech University, Lubbock, Texas 79409, United States
| | - Kihyung Song
- Department of Chemistry, Korea National University of Education, Chungbuk 28644, Republic of Korea
| | - William L Hase
- Department of Chemistry and Biochemistry Texas Tech University, Lubbock, Texas 79409, United States
| | - Riccardo Spezia
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, LCT, 4, Place Jussieu, Paris, 75252 Cedex 05, France
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5
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Malik A, Angel LA, Spezia R, Hase WL. Collisional dynamics simulations revealing fragmentation properties of Zn(ii)-bound poly-peptide. Phys Chem Chem Phys 2020; 22:14551-14559. [DOI: 10.1039/d0cp02463e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Collisional simulations show how peptide fragmentation is modified by the presence of Zn(ii).
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Affiliation(s)
- Abdul Malik
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
| | | | - Riccardo Spezia
- Laboratoire de Chimie Théorique
- Sorbonne Université
- UMR 7616 CNRS
- 75005 Paris
- France
| | - William L. Hase
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
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6
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Smith ZM, Wang X, Scheerer JR, Martens J, Berden G, Oomens J, Steinmetz V, Somogyi A, Wysocki V, Poutsma JC. Spectroscopic Evidence for Lactam Formation in Terminal Ornithine b 2+ and b 3+ Fragment Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1565-1577. [PMID: 31183839 PMCID: PMC6697629 DOI: 10.1007/s13361-019-02244-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Infrared multiple photon dissociation action spectroscopy was performed on the AlaOrn b2+ and AlaAlaOrn b3+ fragment ions from ornithine-containing tetrapeptides. Infrared spectra were obtained in the fingerprint region (1000-2000 cm-1) using the infrared free electron lasers at the Centre Laser Infrarouge d'Orsay (CLIO) facility in Orsay, France, and the free electron lasers for infrared experiments (FELIX) facility in Nijmegen, the Netherlands. A novel terminal ornithine lactam AO+ b2+ structure was synthesized for experimental comparison and spectroscopy confirms that the b2+ fragment ion from AOAA forms a lactam structure. Comparison of experimental spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory shows that AO+ b2+ forms a terminal lactam protonated either on the lactam carbonyl oxygen or the N-terminal nitrogen atom. Several low-lying conformers of these isomers are likely populated following IRMPD dissociation. Similarly, a comparison of the experimental IRMPD spectrum with calculated spectra shows that AAO+ b3+-ions also adopt a lactam structure, again with multiple different protonation sites, during fragmentation. This study provides spectroscopic confirmation for the lactam cyclization proposed for the "ornithine effect" and represents an alternative bn+ structure to the oxazolone and diketopiperazine/macrocycle structures most often formed.
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Affiliation(s)
- Zachary M Smith
- Department of Chemistry, The College of William & Mary, Williamsburg, VA, 23187-8795, USA
| | - Xiye Wang
- Department of Chemistry, The College of William & Mary, Williamsburg, VA, 23187-8795, USA
| | - Jonathan R Scheerer
- Department of Chemistry, The College of William & Mary, Williamsburg, VA, 23187-8795, USA
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Vincent Steinmetz
- Laboratorie de Chimie Physique, CNRS UMR 8000, Université Paris, 91405, Orsay, France
| | - Arpad Somogyi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210-1173, USA
| | - Vicki Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210-1173, USA
| | - John C Poutsma
- Department of Chemistry, The College of William & Mary, Williamsburg, VA, 23187-8795, USA.
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7
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Homayoon Z, Macaluso V, Martin-Somer A, Muniz MCNB, Borges I, Hase WL, Spezia R. Chemical dynamics simulations of CID of peptide ions: comparisons between TIK(H +) 2 and TLK(H +) 2 fragmentation dynamics, and with thermal simulations. Phys Chem Chem Phys 2018; 20:3614-3629. [PMID: 29340378 DOI: 10.1039/c7cp06818b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gas phase unimolecular fragmentation of the two model doubly protonated tripeptides threonine-isoleucine-lysine (TIK) and threonine-leucine-lysine (TLK) is studied using chemical dynamics simulations. Attention is focused on different aspects of collision induced dissociation (CID): fragmentation pathways, energy transfer, theoretical mass spectra, fragmentation mechanisms, and the possibility of distinguishing isoleucine (I) and leucine (L). Furthermore, discussion is given regarding the differences between single collision CID activation, which results from a localized impact between the ions and a colliding molecule N2, and previous thermal activation simulation results; Z. Homayoon, S. Pratihar, E. Dratz, R. Snider, R. Spezia, G. L. Barnes, V. Macaluso, A. Martin-Somer and W. L. Hase, J. Phys. Chem. A, 2016, 120, 8211-8227. Upon thermal activation unimolecular fragmentation is statistical and in accord with RRKM unimolecular rate theory. Simulations show that in collisional activation some non-statistical fragmentation occurs, including shattering, which is not present when the ions dissociate statistically. Products formed by non-statistical shattering mechanisms may be related to characteristic mass spectrometry peaks which distinguish the two isomers I and L.
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Affiliation(s)
- Zahra Homayoon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 USA.
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8
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Batoon P, Oomens J, Berden G, Ren J. Conformations of Protonated AlaDap and DapAla Characterized by IRMPD Spectroscopy and Molecular Modeling. J Phys Chem B 2018; 122:2191-2202. [DOI: 10.1021/acs.jpcb.7b10435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick Batoon
- Department
of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, California 95211, United States
| | - Jos Oomens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jianhua Ren
- Department
of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, California 95211, United States
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9
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Guan X, Wang B, Wang H, Liu J, Li Y, Guo X. Characteristic NH 3 and CO losses from sodiated peptides C-terminated by glutamine residues. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:649-657. [PMID: 28158936 DOI: 10.1002/rcm.7831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/18/2017] [Accepted: 01/31/2017] [Indexed: 06/06/2023]
Abstract
RATIONALE Under certain conditions some amino acid (AA) residues undergo special reactions in the gas phase, generating characteristic neutral losses and product ions. Taking these special fragments into account and understanding the effect of AA residues on peptide cleavages will consummate database search algorithms and manual data interpretation in peptide sequencing by mass spectrometry (MS). In this study, the details of the characteristic NH3 and CO losses of glutamine (Gln) residues located at the C-terminus of peptides are presented. METHODS A number of selected peptides were fragmented under collision-induced dissociation (CID) in electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-QTOF-MS). Density functional theory (DFT) quantum mechanical calculations at the B3LYP/6-31+G(d,p) level were carried out to optimize the geometry of peptide ions and provide energy barriers of ions in each step during fragmentations. RESULTS Two characteristic peaks appear near the precursor ions of sodiated Gln C-terminated peptides, suggesting the loss of neutral NH3 and CO via a two-step process. The proposed mechanism of their formation is as follows: after losing NH3 , a non-classical bn * ion is formed with a glutaric anhydride structure that further dissociates to lose CO. The sodiated peptides show more intensive peaks corresponding to the loss of neutral molecules than the protonated ones. This type of neutral loss can also occur at the Gln residue that is rearranged to the C-terminus of sodiated peptides. CONCLUSIONS The experiments and calculations suggest that the two-step characteristic NH3 and CO loss of sodiated peptides is energetically favored, and can be applied to identify C-terminated Gln residues. This study provides a mechanistic insight into the role of sodium ion during peptide fragmentation. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Xinshu Guan
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Bing Wang
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Huixin Wang
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Jinrong Liu
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Ying Li
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Xinhua Guo
- College of Chemistry, Jilin University, Changchun, 130012, China
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10
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Kempkes LJM, Martens J, Grzetic J, Berden G, Oomens J. Deamidation Reactions of Asparagine- and Glutamine-Containing Dipeptides Investigated by Ion Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1855-1869. [PMID: 27624159 PMCID: PMC5059420 DOI: 10.1007/s13361-016-1462-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 05/27/2023]
Abstract
Deamidation is a major fragmentation channel upon activation by collision induced dissociation (CID) for protonated peptides containing glutamine (Gln) and asparagine (Asn) residues. Here, we investigate these NH3-loss reactions for four Asn- and Gln-containing protonated peptides in terms of the resulting product ion structures using infrared ion spectroscopy with the free electron laser FELIX. The influence of the side chain length (Asn versus Gln) and of the amino acid sequence on the deamidation reaction has been examined. Molecular structures for the product ions are determined by comparison of experimental IR spectra with spectra predicted by density functional theory (DFT). The reaction mechanisms identified for the four dipeptides AlaAsn, AsnAla, AlaGln, and GlnAla are not the same. For all four dipeptides, primary deamidation takes place from the amide side chain (and not from the N-terminus) and, in most cases, resembles the mechanisms previously identified for the protonated amino acids asparagine and glutamine. Secondary fragmentation reactions of the deamidation products have also been characterized and provide further insight in - and confirmation of - the identified mechanisms. Overall, this study provides a comprehensive molecular structure map of the deamidation chemistry of this series of dipeptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Lisanne J M Kempkes
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Jonathan Martens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Josipa Grzetic
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 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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11
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Homayoon Z, Pratihar S, Dratz E, Snider R, Spezia R, Barnes GL, Macaluso V, Martin Somer A, Hase WL. Model Simulations of the Thermal Dissociation of the TIK(H+)2 Tripeptide: Mechanisms and Kinetic Parameters. J Phys Chem A 2016; 120:8211-8227. [DOI: 10.1021/acs.jpca.6b05884] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zahra Homayoon
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Subha Pratihar
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | | | | | - Riccardo Spezia
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne UMR 8587 CNRS-CEA-UEVE, Bd. F. Mitterrand, 91025 Evry Cedex, France
| | - George L. Barnes
- Department
of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United States
| | - Veronica Macaluso
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne UMR 8587 CNRS-CEA-UEVE, Bd. F. Mitterrand, 91025 Evry Cedex, France
| | - Ana Martin Somer
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne UMR 8587 CNRS-CEA-UEVE, Bd. F. Mitterrand, 91025 Evry Cedex, France
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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12
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Synthesis, crystal structure, spectroscopic properties and potential anti-cancerous activities of four unsaturated bis-norcantharimides. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.02.093] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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13
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Kempkes LJM, Martens JK, Grzetic J, Berden G, Oomens J. Deamidation reactions of protonated asparagine and glutamine investigated by ion spectroscopy. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:483-490. [PMID: 26777678 DOI: 10.1002/rcm.7464] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/14/2015] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Deamidation of Asn and Gln residues is a primary route for spontaneous post-translational protein modification. Several structures have been proposed for the deamidation products of the protonated amino acids. Here we verify these structures by ion spectroscopy, as well as the structures of parallel and sequential fragmentation products. METHODS Infrared ion spectroscopy using the free electron laser FELIX has been applied to the reaction products from deamidation of protonated glutamine and asparagine in a tandem mass spectrometer. IR spectra were recorded over the 800-1900 cm(-1) spectral range by infrared multiple-photon dissociation (IRMPD) spectroscopy. Molecular structures of the fragment ions are derived from comparison of the experimental spectra with spectra predicted for different candidate structures by density functional theory (DFT) calculations. RESULTS [AsnH(+) -NH3](+) is found to possess a 3-aminosuccinic anhydride structure protonated on the amino group. The dissociation reaction involving loss of H2O and CO forms a linear immonium ion. For [GlnH(+)-NH3](+), the N-terminal nitrogen acts as the nucleophile leading to an oxo-proline product ion structure. For [GlnH(+)-NH3](+), a sequential loss of [CO + H2O] is found, leading to a pyrolidone-like structure. We also confirm by IR spectroscopy that dehydration of protonated aspartic acid (AspH(+)) and glutamic acid (GluH(+)) leads to identical structures as to those found for the loss of NH3 from AsnH(+) and GlnH(+). CONCLUSIONS The structure determined for AsnH(+) is in agreement with the suggested structure derived from measured and computed activation energies. IR ion spectra for the NH3 -loss product from GlnH(+) establish that a different reaction mechanism occurs for this species as compared to AsnH(+). For both amino acids, loss of NH3 occurs from the side chain.
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Affiliation(s)
- Lisanne J M Kempkes
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Jonathan K Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Josipa Grzetic
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 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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14
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Aseev O, Perez MAS, Rothlisberger U, Rizzo TR. Cryogenic Spectroscopy and Quantum Molecular Dynamics Determine the Structure of Cyclic Intermediates Involved in Peptide Sequence Scrambling. J Phys Chem Lett 2015; 6:2524-2529. [PMID: 26266729 DOI: 10.1021/acs.jpclett.5b01088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Collision-induced dissociation (CID) is a key technique used in mass spectrometry-based peptide sequencing. Collisionally activated peptides undergo statistical dissociation, forming a series of backbone fragment ions that reflect their amino acid (AA) sequence. Some of these fragments may experience a "head-to-tail" cyclization, which after proton migration, can lead to the cyclic structure opening in a different place than the initially formed bond. This process leads to AA sequence scrambling that may hinder sequencing of the initial peptide. Here we combine cryogenic ion spectroscopy and ab initio molecular dynamics simulations to isolate and characterize the precise structures of key intermediates in the scrambling process. The most stable peptide fragments show intriguing symmetric cyclic structures in which the proton is situated on a C2 symmetry axis and forms exceptionally short H-bonds (1.20 Å) with two backbone oxygens. Other nonsymmetric cyclic structures also exist, one of which is protonated on the amide nitrogen, where ring opening is likely to occur.
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Affiliation(s)
- Oleg Aseev
- †Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Marta A S Perez
- ‡Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCBC, Station 6, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- ‡Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCBC, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R Rizzo
- †Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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15
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Liu P, Cooks RG, Chen H. Nuclear Magnetic Resonance Structure Elucidation of Peptideb2Ions. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Liu P, Cooks RG, Chen H. Nuclear magnetic resonance structure elucidation of peptide b2 ions. Angew Chem Int Ed Engl 2014; 54:1547-50. [PMID: 25504444 DOI: 10.1002/anie.201410250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Indexed: 11/06/2022]
Abstract
Tandem mass spectrometry (MS/MS) is powerful for chemical identification but it is still insufficient for explicit ion structure determination. A strategy is introduced to elucidate MS fragment ion structures using NMR spectroscopy for the first time. In our experiments, precursor ions are dissociated at atmospheric pressure and the resulting fragment ions are identified by mass spectrometry but collected outside the mass spectrometer, making the subsequent NMR measurements possible. This new strategy has been applied to determine the chemical structure of the characteristic b2 fragment ion, a subject of longstanding debate in MS-based proteomics.
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Affiliation(s)
- Pengyuan Liu
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry & Edison Biotechnology Institute, Ohio University, Athens, OH 45701 (USA)
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17
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Morrison LJ, Chamot-Rooke J, Wysocki VH. IR action spectroscopy shows competitive oxazolone and diketopiperazine formation in peptides depends on peptide length and identity of terminal residue in the departing fragment. Analyst 2014; 139:2137-43. [PMID: 24618890 PMCID: PMC6467643 DOI: 10.1039/c4an00064a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The interplay between the entropically and enthalpically favored products of peptide fragmentation is probed using a combined experimental and theoretical approach. These b2 ion products can take either an oxazolone or diketopiperazine structure. Cleavage after the second amide bond is often a favorable process because the products are small ring structures that are particularly stable. These structures are structurally characterized by action IRMPD spectroscopy and semi-quantified using gas-phase hydrogen-deuterium exchange. The formation of the oxazolone and diketopiperazine has been thought to be largely governed by the identity of the first two residues at the N-terminus of the peptide. We show here that the length of the precursor peptide and identity of the third residue play a significant role in the formation of the diketopiperazine structure in peptides containing an N-terminal asparagine residue. This is additionally the first instance showing an N-terminal residue with an amide side chain can promote formation of the diketopiperazine b2 ion structure.
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Affiliation(s)
- L J Morrison
- Department of Chemistry and Biochemistry, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, USA.
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