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Guan S, Rabus JM, Maître P, Bythell BJ. Gas-Phase Dissociation Chemistry of Deprotonated RGD. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:55-63. [PMID: 32267154 DOI: 10.1021/jasms.0c00074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We investigate the structure and dissociation pathways of the deprotonated amphoteric peptide arginylglycylasparic acid, [RGD-H]-. We model the pertinent gas-phase structures and fragmentation chemistry of the precursor anions and predominant sequence-informative bond cleavages (b2+H2O, c2, and z1 peaks) and compare these predictions to our tandem mass spectra and infrared spectroscopy experiments. Formation of the b2+H2O anions requires rate-limiting intramolecular back biting to cleave the second amide bond and generate an anhydride structure. Facile cleavage of the newly formed ester bond with concerted expulsion of a cyclic anhydride neutral generates the product structure. IR spectroscopy supports this b2+H2O anion having structures that are essentially identical to C-terminally deprotonated arginylglycine, [RG-H]-. Formation of the c2 anion is predicted to require concerted expulsion of CO2 from the aspartyl side chain carboxylate and cleavage of the N-Calpha bond to produce a proton-bound dimer of arginylglycinamide and acrylate. Proton transfers within the dimer then enable predominant detection of a c2 anion with the negative charge nominally on the central, glycine nitrogen (amidate structure) as the proton affinity of this structure is predicted to be lower than acrylate by ∼27 kJ mol-1. Alternate means of cleaving the same N-Calpha bond produce deprotonated cis-1,4-dibut-2-enoic acid z1 anion structures. These lowest energy processes involve C-H proton mobilization from the aspartyl side chain prior to N-Calpha bond cleavage consistent with proposals from the literature.
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Affiliation(s)
- Shanshan Guan
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Jordan M Rabus
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Philippe Maître
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
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2
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Yousef EN, Angel LA. Comparison of the pH-dependent formation of His and Cys heptapeptide complexes of nickel(II), copper(II), and zinc(II) as determined by ion mobility-mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4489. [PMID: 31881105 DOI: 10.1002/jms.4489] [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] [Received: 10/28/2019] [Revised: 12/05/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
The analog methanobactin (amb) peptide with the sequence ac-His1 -Cys2 -Gly3 -Pro4 -Tyr5 -His6 -Cys7 (amb5A ) will bind the metal ions of zinc, nickel, and copper. To further understand how amb5A binds these metals, we have undertaken a series of studies of structurally related heptapeptides where one or two of the potential His or Cys binding sites have been replaced by Gly, or the C-terminus has been blocked by amidation. The studies were designed to compare how these metals bind to these sequences in different pH solutions of pH 4.2 to 10 and utilized native electrospray ionization (ESI) with ion mobility-mass spectrometry (IM-MS) which allows for the quantitative analysis of the charged species produced during the reactions. The native ESI conditions were chosen to conserve as much of the solution-phase behavior of the amb peptides as possible and an analysis of how the IM-MS results compare with the expected solution-phase behavior is discussed. The oligopeptides studied here have applications for tag-based protein purification methods, as therapeutics for diseases caused by elevated metal ion levels or as inhibitors for metal-protein enzymes such as matrix metalloproteinases.
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Affiliation(s)
- Enas N Yousef
- Department of Chemistry, Texas A&M University-Commerce, Commerce, Texas, 75428, USA
| | - Laurence A Angel
- Department of Chemistry, Texas A&M University-Commerce, Commerce, Texas, 75428, USA
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3
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Cui C, McNeill AS, Jackson WC, Raddatz MA, Stover ML, Dixon DA, Cassady CJ. Experimental and Computational Study of the Gas-Phase Acidities of Acidic Di- and Tripeptides. J Phys Chem B 2019; 123:606-613. [DOI: 10.1021/acs.jpcb.8b10924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Can Cui
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Ashley S. McNeill
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Will C. Jackson
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Michael A. Raddatz
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Michele L. Stover
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - David A. Dixon
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Carolyn J. Cassady
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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Batoon P, Ren J. Proton Affinity of Isomeric Dipeptides Containing Lysine and Non-Proteinogenic Lysine Homologues. J Phys Chem B 2016; 120:7783-94. [DOI: 10.1021/acs.jpcb.6b03776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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
| | - Jianhua Ren
- Department of Chemistry, University of the Pacific, 3601 Pacific
Avenue, Stockton, California 95211, United States
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Plummer CE, Stover ML, Bokatzian SS, Davis JTM, Dixon DA, Cassady CJ. An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides. J Phys Chem B 2015. [PMID: 26196065 DOI: 10.1021/acs.jpcb.5b04486] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.
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Affiliation(s)
- Chelsea E Plummer
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Michele L Stover
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Samantha S Bokatzian
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - John T M Davis
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - David A Dixon
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Carolyn J Cassady
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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Nguyen QNN, Lodewyk MW, Bezer S, Gagné MR, Waters ML, Tantillo DJ. Effects of Helix Macrodipole and Local Interactions on Catalysis of Acyl Transfer by α-Helical Peptides. ACS Catal 2015. [DOI: 10.1021/cs5019277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Q. Nhu N. Nguyen
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Michael W. Lodewyk
- Physical Science Department, Butte College, Oroville, California 95965, United States
| | - Silvia Bezer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Michel R. Gagné
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Dean J. Tantillo
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
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Kanchi V, Shin JW. Kinetic Method Analysis of the Effect of cis- and trans-Hydroxylation on the Proton Affinity of Proline. Aust J Chem 2015. [DOI: 10.1071/ch15047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Proton affinities of proline and hydroxyproline were measured using the Cooks’ kinetic method. The measurements show that hydroxylation increases the proton affinity, which is consistent with X3LYP computation results. This work supports findings from a previous study (S. Mezzache et al., Rapid Commun. Mass Spectrom. 2005, 19, 2279) that modification of proline increases its proton affinity, but it does not provide compelling evidence for the prediction in the same study that proton affinity of the molecule is substantially influenced by intramolecular interactions involving the proton. PBE1PBE calculations suggest that isotropic polarizability rather than intramolecular hydrogen-bonding interactions provides a more suitable diagnosis for trends in proton affinity changes associated with modifications.
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Ren J, Sawhney A, Tian Y, Padda B, Batoon P. Determination of the gas-phase acidities of oligopeptides. J Vis Exp 2013. [PMID: 23851399 DOI: 10.3791/4348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Amino acid residues located at different positions in folded proteins often exhibit different degrees of acidities. For example, a cysteine residue located at or near the N-terminus of a helix is often more acidic than that at or near the C-terminus (1-6). Although extensive experimental studies on the acid-base properties of peptides have been carried out in the condensed phase, in particular in aqueous solutions (6-8), the results are often complicated by solvent effects (7). In fact, most of the active sites in proteins are located near the interior region where solvent effects have been minimized (9,10). In order to understand intrinsic acid-base properties of peptides and proteins, it is important to perform the studies in a solvent-free environment. We present a method to measure the acidities of oligopeptides in the gas-phase. We use a cysteine-containing oligopeptide, Ala3CysNH2 (A3CH), as the model compound. The measurements are based on the well-established extended Cooks kinetic method (Figure 1) (11-16). The experiments are carried out using a triple-quadrupole mass spectrometer interfaced with an electrospray ionization (ESI) ion source (Figure 2). For each peptide sample, several reference acids are selected. The reference acids are structurally similar organic compounds with known gas-phase acidities. A solution of the mixture of the peptide and a reference acid is introduced into the mass spectrometer, and a gas-phase proton-bound anionic cluster of peptide-reference acid is formed. The proton-bound cluster is mass isolated and subsequently fragmented via collision-induced dissociation (CID) experiments. The resulting fragment ion abundances are analyzed using a relationship between the acidities and the cluster ion dissociation kinetics. The gas-phase acidity of the peptide is then obtained by linear regression of the thermo-kinetic plots (17,18). The method can be applied to a variety of molecular systems, including organic compounds, amino acids and their derivatives, oligonucleotides, and oligopeptides. By comparing the gas-phase acidities measured experimentally with those values calculated for different conformers, conformational effects on the acidities can be evaluated.
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Affiliation(s)
- Jianhua Ren
- Department of Chemistry, University of the Pacific
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Bokatzian-Johnson SS, Stover ML, Dixon DA, Cassady CJ. Gas-Phase Deprotonation of the Peptide Backbone for Tripeptides and Their Methyl Esters with Hydrogen and Methyl Side Chains. J Phys Chem B 2012. [DOI: 10.1021/jp3113528] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | - Michele L. Stover
- Department
of Chemistry, University of Alabama, Tuscaloosa, Alabama 35487, United
States
| | - David A. Dixon
- Department
of Chemistry, University of Alabama, Tuscaloosa, Alabama 35487, United
States
| | - Carolyn J. Cassady
- Department
of Chemistry, University of Alabama, Tuscaloosa, Alabama 35487, United
States
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Renaud JB, Mayer PM. The applicability of the kinetic method for measuring relative affinities of macromolecules for polyatomic substrates. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2012; 18:223-234. [PMID: 22641721 DOI: 10.1255/ejms.1173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This paper is a review of the kinetic method for the determination of thermochemical values for gas-phase molecules. In addition, we have explored the utility of the kinetic method to obtain meaningful relative binding energies of macromolecules for polyatomic substrates using a system comprising poly(methylmethacrylate) (PMMA) oligomers and doubly protonated diaminoalkanes. The major factors which determined the suitability of the kinetic method for this system were identified as (i) the structural arrangement of the parent ion complex, (ii) possible reverse activation barriers, and (iii) the evaluations of Δ(ΔS‡). Molecular mechanics/molecular dynamics (MM/MD) simulations, together with ion mobility spectrometry, suggests the parent ion complexes represent a relatively equal sharing of the substrate between two the PMMA oligomers within the complex and that the two PMMA oligomers interact almost exclusively with the substrate, and not with each other. MS/MS of the trimeric parent complexes resulted in one PMMA unit leaving as a neutral which suggests very limited coulombic repulsion (that would contribute to a reverse activation barrier). The drift times of PMMA-diaminoalkane complexes that were generated directly by ESI-MS or by dissociation of a trimeric PMMA-diaminoalkane-PMMA complex were found to be identical, and when combined with MM/MD simulations suggested that the product PMMA-diaminoalkane dication has the same conformation as it does when part of a trimeric complex. This is evidence for Δ(ΔS‡) ≃ Δ(ΔS) and using a statistical mechanics approach, Δ(ΔS) ≃ 0. The effective temperature variable in the kinetic method expression was found to decrease as a function of the size of the trimeric complex, suggesting that the population distribution of the dissociating ensemble of complexes narrows as size increases.
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Affiliation(s)
- Justin B Renaud
- Chemistry Department, University of Ottawa, 10 Marie Curie, Ottawa, ON Canada K1N 6N5
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Couto N, Barber J, Gaskell SJ. Matrix-assisted laser desorption/ionisation mass spectrometric response factors of peptides generated using different proteolytic enzymes. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:1233-1240. [PMID: 22223413 DOI: 10.1002/jms.2009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Matrix-assisted laser desorption/ionisation (MALDI) mechanisms and the factors that influence the intensity of the ion signal in the mass spectrum remain imperfectly understood. In proteomics, it is often necessary to maximise the peptide response in the mass spectrum, especially for low abundant proteins or for proteolytic peptides of particular significance. We set out to determine which of the common proteolytic enzymes give rise to peptides with the best response factors under MALDI conditions. Standard proteins were enzymatically digested using four common proteases. We assessed relative response factors by coanalyzing the resulting digests. Thus, when tryptic peptides were added in equimolar quantities to their corresponding Asp-N, chymotrypsin and Glu-C digests, tryptic peptide signals were always predominant in the resulting MALDI mass spectra. Observable peaks attributable to non-tryptic peptides generally contained a terminal basic residue. It was proposed that a terminal basic residue has a disproportionate influence upon gas-phase basicity, and this hypothesis was supported by experiments with model isotopically labelled peptides. Experiments applying Cook's kinetic method showed that the peptide with a C-terminal arginine residue was more basic than the equivalent peptide with an N-terminal arginine, which was more basic than the peptide in which the arginine was mid-chain. Thus, the observation of the higher MALDI mass spectrometry response factors of tryptic peptides in comparison with peptides derived using other proteolytic enzymes corresponds with higher gas-phase basicities and may, along with other factors such as the complexity of the digest, influence the choice of enzyme in "bottom-up" proteomic experiments.
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Affiliation(s)
- Narciso Couto
- Michael Barber Centre for Mass Spectrometry, Manchester Interdisciplinary Biocentre, Princess Road, University of Manchester, Manchester, M1 7DN, UK
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Byun BJ, Kang YK. Conformational preferences and pK(a) value of selenocysteine residue. Biopolymers 2011; 95:345-53. [PMID: 21213257 DOI: 10.1002/bip.21581] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 12/20/2010] [Accepted: 12/22/2010] [Indexed: 12/25/2022]
Abstract
The conformational preferences of the L-selenocysteine (Sec) dipeptides with selenol and selenolate groups (Ac-Sec-NHMe and Ac-Sec(-) -NHMe, respectively) and the apparent (i.e., macroscopic) pK(a) value of the Sec residue have been studied using the dispersion-corrected density functionals M06-2X and B2PLYP-D with the implicit solvation method in the gas phase and in water. In the gas phase, the backbone-to-backbone and/or side chain-to-backbone hydrogen bonds are found to contribute in stabilizing the most preferred conformations for the Sec and Sec(-) residues, as seen for the Cys and Cys(-) residues. However, the polyproline II-like conformations prevail over the conformations with the backbone-to-backbone hydrogen bonds in water because of the weakened hydrogen bonds by the favorable direct interactions between the backbone CO and HN groups and water molecules. The Sec and Sec(-) residues are found to adopt more various conformations than the Cys and Cys(-) residues in water, although the most preferred conformations of the neutral and/or anionic forms of the two residues are similar each other in the gas phase and in water. Using the statistically weighted free energies of the Sec and Sec(-) dipeptides in the gas phase and their solvation free energies, the pK(a) value of the Sec residue is estimated to be 5.47 at 25°C, which is in good agreement with the experimental value of 5.43 ± 0.02. It is found that the lower pK(a) value of the selenol side chain for the Sec residue by ∼3 units than the thiol side chain for the Cys residue is ascribed to the higher gas-phase acidity of the Sec residue.
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Affiliation(s)
- Byung Jin Byun
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
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