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Schultz M, Parker SL, Fernando MT, Wellalage MM, Thomas DA. Diserinol Isophthalamide: A Novel Reagent for Complexation with Biomolecular Anions in Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:745-753. [PMID: 36975839 DOI: 10.1021/jasms.3c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Transferring biomolecules from solution to vacuum facilitates a detailed analysis of molecular structure and dynamics by isolating molecules of interest from a complex environment. However, inherent in the ion desolvation process is the loss of solvent hydrogen bonding partners, which are critical for the stability of a condensed-phase structure. Thus, transfer of ions to vacuum can favor structural rearrangement, especially near solvent-accessible charge sites, which tend to adopt intramolecular hydrogen bonding motifs in the absence of solvent. Complexation of monoalkylammonium moieties (e.g., lysine side chains) with crown ethers such as 18-crown-6 can disfavor structural rearrangement of protonated sites, but no equivalent ligand has been investigated for deprotonated groups. Herein we describe diserinol isophthalamide (DIP), a novel reagent for the gas-phase complexation of anionic moieties within biomolecules. Complexation is observed to the C-terminus or side chains of the small model peptides GD, GE, GG, DF-OMe, VYV, YGGFL, and EYMPME in electrospray ionization mass spectrometry (ESI-MS) studies. In addition, complexation is observed with the phosphate and carboxylate moieities of phosphoserine and phosphotyrosine. DIP performs favorably in comparison to an existing anion recognition reagent, 1,1'-(1,2-phenylene)bis(3-phenylurea), that exhibits moderate carboxylate binding in organic solvent. This improved performance in ESI-MS experiments is attributed to reduced steric constraints to complexation with carboxylate groups of larger molecules. Overall, diserinol isophthalamide is an effective complexation reagent that can be applied in future work to study retention of solution-phase structure, investigate intrinsic molecular properties, and examine solvation effects.
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Affiliation(s)
- Madeline Schultz
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Sarah L Parker
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Maleesha T Fernando
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Miyuru M Wellalage
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Daniel A Thomas
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
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2
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Silzel JW, Murphree TA, Paranji RK, Guttman MM, Julian RR. Probing the Stability of Proline Cis/Trans Isomers in the Gas Phase with Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1974-1980. [PMID: 32808771 DOI: 10.1021/jasms.0c00242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although most peptide bonds in proteins exist in the trans configuration, when cis peptide bonds do occur, they can have major impact on protein structure and function. The rapid identification of cis peptide bonds is therefore an important task. Peptide bonds containing proline are more likely to adopt the cis configuration because the ring connecting the side chain and backbone in proline flattens the energetic landscape relative to amino acids with free side chains. Examples of cis proline isomers have been identified in both solution and in the gas phase by a variety of structure-probing methods. Mass spectrometry is an attractive potential method for identifying cis proline due to its speed and sensitivity; however, the question remains of whether cis/trans proline isomers originating in solution are preserved during ionization and manipulation within a mass spectrometer. Herein, we investigate the gas-phase stability of isolated solution-phase cis and trans proline isomers using a synthetic peptide sequence with a Tyr-Pro-Pro motif. A variety of dissociation methods were explored to evaluate their potential to distinguish cis/trans configuration, including collision-induced dissociation, radical-directed dissociation, and photodissociation. Only photodissociation employed in conjunction with extremely gentle electrospray and charge solvation by 18-crown-6 ether was able to distinguish cis/trans isomers for our model peptide, suggesting that any thermal activation during transfer or while in the gas phase leads to isomer scrambling. Furthermore, the necessity for 18-crown-6 suggests that intramolecular charge solvation taking place during electrospray ionization can override cis/trans isomer homogeneity. Overall, the results suggest that solution-phase cis/trans proline isomers are fragile and easily lost during electrospray, requiring careful selection of instrument parameters and consideration of charge solvation to prevent cis/trans scrambling.
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Affiliation(s)
- Jacob W Silzel
- Department of Chemistry, University of California, 501 Big Springs Road, Riverside, California 92521, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Rajan K Paranji
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Miklos M Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ryan R Julian
- Department of Chemistry, University of California, 501 Big Springs Road, Riverside, California 92521, United States
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3
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Yao Y, Ye JT, Li X, Zhang Y, Zhu SN, Qiu YQ. Regulating the NLO response of anthraquinone-supported thiourea-linked crown ether macrocycle by introducing metal cations: A DFT study. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020. [DOI: 10.1142/s0219633620500170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recently, an anthraquinone-supported thiourea group linking a 1-aza-18-crown-6 macrocycle L has been the subject of extensive attention due to the perfect affinity towards metal cations. This work systematically researched the effects of different metal cations ([Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text]) on the second-order nonlinear optical (NLO) properties of macrocycle L by density functional theory (DFT). DFT calculations revealed that the values of first hyperpolarizabilities ([Formula: see text] decrease significantly when alkaline earth metal cations ([Formula: see text] and [Formula: see text]) were injected into macrocycle L due to the smaller charge transfer (CT) transition and larger transition energy. Conversely, the variations of [Formula: see text] values in alkali metal cations ([Formula: see text] and [Formula: see text] and transition metal cations ([Formula: see text] and [Formula: see text]) derivatives are not obvious compared to the [Formula: see text] value of macrocycle L. Therefore, the NLO properties of macrocycle can be effectively regulated by alkaline earth metal cations. Furthermore, we found that the [Formula: see text] value of anion-controlled complex Na(L)(ClO4) is larger than that of L*Na+ complex because the anion [Formula: see text] improves the planarity of anthraquinone-supported thiourea group leading to the enhancement of the CT ability. In addition, the influence of frequency-dependent on the first hyperpolarizabilities is weak for the current systems. Hence, we look forward to the conception of this work will offer a fundamental guideline and reference for further research for novel NLO materials.
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Affiliation(s)
- Yao Yao
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Jin-Ting Ye
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Xiang Li
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Yuan Zhang
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Si-Nan Zhu
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Yong-Qing Qiu
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
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4
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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Zheng S, Yuan S, Hou Z, Li G, Chen Y, Pan Y, Liu Y, Huang G. Charge-dependent modulation of specific and nonspecific protein-metal ion interactions in nanoelectrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1502-1511. [PMID: 31151135 DOI: 10.1002/rcm.8493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Previous studies found that charge state could affect both specific and nonspecific binding of protein-metal ion interactions in nanoelectrospray ionization mass spectrometry (nESI-MS). However, the two kinds of interactions have been studied individually in spite of the problem that they often coexist in the same system. Thus, it is necessary to study the effects of charge state on specific and nonspecific protein-metal ion interactions in one system to reveal more accurate binding state. METHODS The HIV-1 nucleocapsid protein (NCp7(31-55)) which can bind specifically and nonspecifically to Zn2+ served as the model to show the charge-dependent protein-metal ion interactions. Hydrogen/deuterium exchange (HDX) and photodissociation (PD) were used to demonstrate that specific binding state was correlated with protein structure. In addition to NCp7(31-55), three other model proteins were used to investigate the reason for the charge-dependent nonspecific binding. RESULTS For specific binding, we proposed that protein ions with different charge states had different conformations. The HDX results showed that labile protons in the NCp7(31-55)-Zn complex were exchanged in a charge-state-dependent way. The PD experiments revealed differential fragment yields for different charge states. For nonspecific binding, higher charge states had more Zn2+ additions, but less SO4 2- additions. The effects of charge states on nonspecific binding levels were entirely the opposite for Zn2+ and SO4 2- . These results could reveal that the nonspecific binding was caused by electrostatic interaction. CONCLUSIONS For specific binding, NCp7(31-55) with lower charge states have folding and undenatured structures. The binding states of lower charge states can better reflect more native binding states. For nonspecific binding, when multiple metal ions adduct to proteins, the proteins have more net positive charges, which tend to generate higher charge ions during electrospray.
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Affiliation(s)
- Shihui Zheng
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Siming Yuan
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Zhuanghao Hou
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Gongyu Li
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Yuting Chen
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Yang Pan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, 230029, P. R. China
| | - Yangzhong Liu
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Guangming Huang
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, 230029, P. R. China
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6
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McNary CP, Nei YW, Maitre P, Rodgers MT, Armentrout PB. Infrared multiple photon dissociation action spectroscopy of protonated glycine, histidine, lysine, and arginine complexed with 18-crown-6 ether. Phys Chem Chem Phys 2019; 21:12625-12639. [PMID: 31155616 DOI: 10.1039/c9cp02265a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Complexes of 18-crown-6 ether (18C6) with four protonated amino acids (AAs) are examined using infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by the infrared free electron laser at the Centre Laser Infrarouge d'Orsay (CLIO). The AAs examined in this work include glycine (Gly) and the three basic AAs: histidine (His), lysine (Lys), and arginine (Arg). To identify the (AA)H+(18C6) conformations present in the experimental studies, the measured IRMPD spectra are compared to spectra calculated at the B3LYP/6-311+G(d,p) level of theory. Relative energies of various conformers and isomers are provided by single point energy calculations carried out at the B3LYP, B3P86, M06, and MP2(full) levels using the 6-311+G(2p,2d) basis set. The comparisons between the IRMPD and theoretical IR spectra indicate that 18C6 binds to Gly and His via the protonated backbone amino group, whereas protonated Lys prefers binding via the protonated side-chain amino group. Results for Arg are less definitive with strong evidence for binding to the protonated guanidino side chain (the calculated ground conformer at most levels of theory), but contributions from backbone binding to a zwitterionic structure are likely.
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Affiliation(s)
- Christopher P McNary
- Department of Chemistry, University of Utah, 315 S. 1400 E. Room 2020, Salt Lake City, Utah 84112, USA.
| | - Y-W Nei
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - Philippe Maitre
- Université Paris Sud, Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Bâtiment 350, 91405 Orsay Cedex, France
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Room 2020, Salt Lake City, Utah 84112, USA.
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7
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Aprahamian ML, Chea EE, Jones LM, Lindert S. Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data. Anal Chem 2018; 90:7721-7729. [PMID: 29874044 DOI: 10.1021/acs.analchem.8b01624] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years mass spectrometry-based covalent labeling techniques such as hydroxyl radical footprinting (HRF) have emerged as valuable structural biology techniques, yielding information on protein tertiary structure. These data, however, are not sufficient to predict protein structure unambiguously, as they provide information only on the relative solvent exposure of certain residues. Despite some recent advances, no software currently exists that can utilize covalent labeling mass spectrometry data to predict protein tertiary structure. We have developed the first such tool, which incorporates mass spectrometry derived protection factors from HRF labeling as a new centroid score term for the Rosetta scoring function to improve the prediction of protein tertiary structures. We tested our method on a set of four soluble benchmark proteins with known crystal structures and either published HRF experimental results or internally acquired data. Using the HRF labeling data, we rescored large decoy sets of structures predicted with Rosetta for each of the four benchmark proteins. As a result, the model quality improved for all benchmark proteins as compared to when scored with Rosetta alone. For two of the four proteins we were even able to identify atomic resolution models with the addition of HRF data.
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Affiliation(s)
- Melanie L Aprahamian
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
| | - Emily E Chea
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
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8
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Metwally H, Konermann L. Crown Ether Effects on the Location of Charge Carriers in Electrospray Droplets: Implications for the Mechanism of Protein Charging and Supercharging. Anal Chem 2018; 90:4126-4134. [DOI: 10.1021/acs.analchem.8b00099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Haidy Metwally
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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9
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Bonner JG, Hendricks NG, Julian RR. Structural Effects of Solvation by 18-Crown-6 on Gaseous Peptides and TrpCage after Electrospray Ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1661-1669. [PMID: 27506205 DOI: 10.1007/s13361-016-1456-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 06/06/2023]
Abstract
Significant effort is being employed to utilize the inherent speed and sensitivity of mass spectrometry for rapid structural determination of proteins; however, a thorough understanding of factors influencing the transition from solution to gas phase is critical for correct interpretation of the results from such experiments. It was previously shown that combined use of action excitation energy transfer (EET) and simulated annealing can reveal detailed structural information about gaseous peptide ions. Herein, we utilize this method to study microsolvation of charged groups by retention of 18-crown-6 (18C6) in the gas phase. In the case of GTP (CEGNVRVSRE LAGHTGY), solvation of the 2+ charge state leads to reduced EET, whereas the opposite result is obtained for the 3+ ion. For the mini-protein C-Trpcage, solvation by 18C6 leads to dramatic increase in EET for the 3+ ion. Examination of structural details probed by molecular dynamics calculations illustrate that solvation by 18C6 alleviates the tendency of charged side chains to seek intramolecular solvation, potentially preserving native-like structures in the gas phase. These results suggest that microsolvation may be an important tool for facilitating examination of native-like protein structures in gas phase experiments. Graphical Abstract ᅟ.
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Affiliation(s)
- James G Bonner
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Nathan G Hendricks
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, CA, 92521, USA.
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10
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Shaffer CJ, Martens J, Marek A, Oomens J, Tureček F. Photoleucine Survives Backbone Cleavage by Electron Transfer Dissociation. A Near-UV Photodissociation and Infrared Multiphoton Dissociation Action Spectroscopy Study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1176-1185. [PMID: 27059977 DOI: 10.1007/s13361-016-1390-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 06/05/2023]
Abstract
We report a combined experimental and computational study aimed at elucidating the structure of N-terminal fragment ions of the c type produced by electron transfer dissociation of photo-leucine (L*) peptide ions GL*GGKX. The c 4 ion from GL*GGK is found to retain an intact diazirine ring that undergoes selective photodissociation at 355 nm, followed by backbone cleavage. Infrared multiphoton dissociation action spectra point to the absence in the c 4 ion of a diazoalkane group that could be produced by thermal isomerization of vibrationally hot ions. The c 4 ion from ETD of GL*GGK is assigned an amide structure by a close match of the IRMPD action spectrum and calculated IR absorption. The energetics and kinetics of c 4 ion dissociations are discussed. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Jonathan Martens
- FELIX Laboratory, Radboud University Nijmegen, Institute for Molecules and Materials, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - Aleš Marek
- Department of Chemistry, University of Washington, Seattle, WA, 98195-1700, USA
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jos Oomens
- FELIX Laboratory, Radboud University Nijmegen, Institute for Molecules and Materials, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098XH, Amsterdam, Science Park 908, The Netherlands
| | - František Tureček
- Department of Chemistry, University of Washington, Seattle, WA, 98195-1700, USA.
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11
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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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12
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Yu HL, Wang WY, Hong B, Zong Y, Si YL, Hu ZQ. Variational first hyperpolarizabilities of 2,3-naphtho-15-crown-5 ether derivatives with cation-complexing: a potential and selective cation detector. Phys Chem Chem Phys 2016; 18:26487-26494. [DOI: 10.1039/c6cp04577d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
When the crown ether and its cation derivatives display obvious contrasts in NLO properties, the NLO-based detection of cations is achieved.
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Affiliation(s)
- Hai-Ling Yu
- College of Resources and Environmental Science
- Jilin Agricultural University
- Changchun 130118
- People's Republic of China
| | - Wen-Yong Wang
- JiangSu XinHai Senior High School
- Jangsu
- People's Republic of China
| | - Bo Hong
- College of Resources and Environmental Science
- Jilin Agricultural University
- Changchun 130118
- People's Republic of China
| | - Ying Zong
- College of Resources and Environmental Science
- Jilin Agricultural University
- Changchun 130118
- People's Republic of China
| | - Yan-Ling Si
- College of Resources and Environmental Science
- Jilin Agricultural University
- Changchun 130118
- People's Republic of China
| | - Zhong-Qiang Hu
- College of Resources and Environmental Science
- Jilin Agricultural University
- Changchun 130118
- People's Republic of China
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13
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Göth M, Lermyte F, Schmitt XJ, Warnke S, von Helden G, Sobott F, Pagel K. Gas-phase microsolvation of ubiquitin: investigation of crown ether complexation sites using ion mobility-mass spectrometry. Analyst 2016; 141:5502-10. [DOI: 10.1039/c6an01377e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The influence of side chain to backbone interactions on the gas-phase structure of ubiquitin and ubiquitin lysine-to-arginine mutants was analysed.
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Affiliation(s)
- Melanie Göth
- Department of Biology
- Chemistry
- Pharmacy
- Freie Universität Berlin
- 14195 Berlin
| | - Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry
- Chemistry Department
- University of Antwerp
- 2020 Antwerp
- Belgium
| | - Xiao Jakob Schmitt
- Department of Molecular Physics
- Fritz Haber Institute of the Max Planck Society
- 14195 Berlin
- Germany
| | - Stephan Warnke
- Department of Molecular Physics
- Fritz Haber Institute of the Max Planck Society
- 14195 Berlin
- Germany
| | - Gert von Helden
- Department of Molecular Physics
- Fritz Haber Institute of the Max Planck Society
- 14195 Berlin
- Germany
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry
- Chemistry Department
- University of Antwerp
- 2020 Antwerp
- Belgium
| | - Kevin Pagel
- Department of Biology
- Chemistry
- Pharmacy
- Freie Universität Berlin
- 14195 Berlin
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14
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Pham HT, Julian RR. Characterization of glycosphingolipid epimers by radical-directed dissociation mass spectrometry. Analyst 2016; 141:1273-8. [DOI: 10.1039/c5an02383a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Radical chemistry can efficiently distinguish isomers varying in position at a single alcohol.
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15
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Qi Y, Volmer DA. Electron-capture dissociation for investigating host/guest complexes of 18-crown-6-ether and peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:2316-2318. [PMID: 26522326 DOI: 10.1002/rcm.7399] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 09/18/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Yulin Qi
- Institute of Bioanalytical Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Dietrich A Volmer
- Institute of Bioanalytical Chemistry, Saarland University, 66123, Saarbrücken, Germany
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16
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Gutowska N, Pasternak B, Seliger P, Andrijewski G. Studies of the complexation behavior of tetramorpholinylo-PNP-lariat ether with Ag(i), Ca(ii), Cd(ii), Cu(ii) and Pb(ii) using Electrospray Ionization Mass Spectrometry. NEW J CHEM 2015. [DOI: 10.1039/c4nj01904k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The identification of complexes containing PNP-lariat ether with Ag(i), Ca(ii), Cu(ii), Cd(ii) and Pb(ii) by ESI-MS technique is presented. The tandem mass spectra of these complexes were done in order to evaluate the stability of the different types of the complexes formed.
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Affiliation(s)
- Natalia Gutowska
- Department of Inorganic and Analytical Chemistry
- Faculty of Chemistry
- University of Lodz
- 91-403 Łódź
- Poland
| | - Beata Pasternak
- Laboratory of Molecular Spectroscopy
- Faculty of Chemistry
- University of Lodz
- 91-403 Łódź
- Poland
| | - Piotr Seliger
- Department of Inorganic and Analytical Chemistry
- Faculty of Chemistry
- University of Lodz
- 91-403 Łódź
- Poland
| | - Grzegorz Andrijewski
- Department of Inorganic and Analytical Chemistry
- Faculty of Chemistry
- University of Lodz
- 91-403 Łódź
- Poland
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17
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Yue X, Vahidi S, Konermann L. Insights into the mechanism of protein electrospray ionization from salt adduction measurements. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1322-1331. [PMID: 24839193 DOI: 10.1007/s13361-014-0905-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/03/2014] [Indexed: 06/03/2023]
Abstract
The mechanisms whereby protein ions are liberated from charged droplets during electrospray ionization (ESI) remain under investigation. Compact conformers electrosprayed from aqueous solution in positive ion mode likely follow the charged residue model (CRM), which envisions analyte release after solvent evaporation to dryness. The concentration of nonvolatile salts such as NaCl increases sharply within vanishing CRM droplets, promoting nonspecific pairing of Cl(-) and Na(+) with charged groups on the protein surface. For unfolded proteins, it has been proposed that ion formation occurs via the chain ejection model (CEM). During the CEM proteins are expelled from the droplet long before complete solvent evaporation has taken place. Here we examine whether salt adduction levels support the view that folded and unfolded proteins follow different ESI mechanisms. Solvent evaporation during the CEM is expected to be less extensive and, hence, the salt concentration at the point of protein release should be substantially lower than for the CRM. CEM ions should therefore exhibit lower adduction levels than CRM species. We explore the adduction behavior of several proteins that were chosen to allow comparative studies on folded and unfolded structures in the same solution. In-source activation eliminates chloride adducts via HCl release, generating protein ions that are heterogeneously charged because of sodiation and protonation. Sodiation levels measured under such conditions provide estimates of the salt adduction behavior experienced by the "nascent" analyte ions. Sodiation levels are significantly reduced for unfolded proteins, supporting the view that these species are indeed formed via the CEM.
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Affiliation(s)
- Xuanfeng Yue
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
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18
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Sowole MA, Konermann L. Effects of Protein–Ligand Interactions on Hydrogen/Deuterium Exchange Kinetics: Canonical and Noncanonical Scenarios. Anal Chem 2014; 86:6715-22. [DOI: 10.1021/ac501849n] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Modupeola A. Sowole
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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19
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Pham HT, Julian RR. Mass Shifting and Radical Delivery with Crown Ether Attachment for Separation and Analysis of Phosphatidylethanolamine Lipids. Anal Chem 2014; 86:3020-7. [DOI: 10.1021/ac403754j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Huong T. Pham
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department
of Chemistry, University of California, Riverside, California 92521, United States
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20
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Konermann L, Rodriguez AD, Sowole MA. Type 1 and Type 2 scenarios in hydrogen exchange mass spectrometry studies on protein–ligand complexes. Analyst 2014; 139:6078-87. [DOI: 10.1039/c4an01307g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ligand binding to a protein can elicit a wide range of responses when studied by HDX mass spectrometry.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry
- The University of Western Ontario
- London, Canada
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21
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O'Brien JP, Mayberry LK, Murphy PA, Browning KS, Brodbelt JS. Evaluating the conformation and binding interface of cap-binding proteins and complexes via ultraviolet photodissociation mass spectrometry. J Proteome Res 2013; 12:5867-77. [PMID: 24200290 DOI: 10.1021/pr400869u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report the structural analysis of cap-binding proteins using a chemical probe/ultraviolet photodissociation (UVPD) mass spectrometry strategy for evaluating solvent accessibility of proteins. Our methodology utilized a chromogenic probe (NN) to probe the exposed amine residues of wheat eukaryotic translation initiation factor 4E (eIF4E), eIF4E in complex with a fragment of eIF4G ("mini-eIF4F"), eIF4E in complex with full length eIF4G, and the plant specific cap-binding protein, eIFiso4E. Structural changes of eIF4E in the absence and presence of excess dithiothreitol and in complex with a fragment of eIF4G or full-length eIF4G are mapped. The results indicate that there are particular lysine residues whose environment changes in the presence of dithiothreitol or eIF4G, suggesting that changes in the structure of eIF4E are occurring. On the basis of the crystal structure of wheat eIF4E and a constructed homology model of the structure for eIFiso4E, the reactivities of lysines in each protein are rationalized. Our results suggest that chemical probe/UVPD mass spectrometry can successfully predict dynamic structural changes in solution that are consistent with known crystal structures. Our findings reveal that the binding of m(7)GTP to eIF4E and eIFiso4E appears to be dependent on the redox state of a pair of cysteines near the m(7)GTP binding site. In addition, tertiary structural changes of eIF4E initiated by the formation of a complex containing a fragment of eIF4G and eIF4E were observed.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry and Biochemistry and ‡Institute for Cell and Molecular Biology, The University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712, United States
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22
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Tao Y, Julian RR. Factors that influence competitive intermolecular solvation of protonated groups in peptides and proteins in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1634-40. [PMID: 23836378 PMCID: PMC3806280 DOI: 10.1007/s13361-013-0684-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/17/2013] [Accepted: 05/19/2013] [Indexed: 05/13/2023]
Abstract
The ability of 18-crown-6 (18C6) to form noncovalent complexes with cationic groups in the gas phase has been leveraged in numerous, largely orthogonal mass spectrometry-based applications. Although the fundamental interaction between 18C6 and a charged group in the gas phase is quite strong, the strength of attachment of 18C6 to large molecules is more difficult to predict because intramolecular binding of the cation can be competitive. Herein, we demonstrate in experiments with model peptides that 18C6 adducts are not strongly attached to flexible molecules with numerous potential hydrogen bonding sites. 18C6 adduct stability is increased if intramolecular charge complexation is inhibited by sterics or competitive binding. It is demonstrated with molecular mechanics that significant structural changes occur upon loss of 18C6 in model peptides. Examination of the loss of 18C6 adducts from proteins following collisional activation reveals that lower charge states lose the most 18C6. The degree of 18C6 adduct stability may reflect the degree of structural reorganization that occurs following collisional activation, suggesting that lower charge states represent structures that are not similar to gas phase idealized states. In this regard, 18C6 may serve the function of protecting solution phase protein structure. Collisional activation of holomyoglobin with 18C6 adducts attached reveals that heme loss occurs primarily after 18C6 loss, further supporting the notion that 18C6 protects native structure by solvating charged sites.
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Affiliation(s)
- Yuanqi Tao
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
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23
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Zhou Y, Vachet RW. Covalent labeling with isotopically encoded reagents for faster structural analysis of proteins by mass spectrometry. Anal Chem 2013; 85:9664-70. [PMID: 24010814 DOI: 10.1021/ac401978w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covalent labeling and mass spectrometry (MS) are increasingly being used to obtain higher-order structure of proteins and protein complexes. Because most covalent labels are relatively large, steps must be taken to ensure the structural integrity of the modified protein during the labeling reactions so that correct structural information can be obtained. Measuring labeling kinetics is a reliable way to ensure that a given labeling reagent does not perturb a protein's structure, but obtaining such kinetic information is time and sample intensive because it requires multiple liquid chromatography (LC)-MS experiments. Here we present a new strategy that uses isotopically encoded labeling reagents to measure labeling kinetics in a single LC-MS experiment. We illustrate this new strategy by labeling solvent-exposed lysine residues with commercially available tandem mass tags. After tandem MS experiments, these tags allow the simultaneous identification of modified sites and determination of the reaction rates at each site in a way that is just as reliable as experiments that involve multiple LC-MS measurements.
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Affiliation(s)
- Yuping Zhou
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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24
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Stedwell CN, Galindo JF, Roitberg AE, Polfer NC. Structures of biomolecular ions in the gas phase probed by infrared light sources. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2013; 6:267-285. [PMID: 23560933 DOI: 10.1146/annurev-anchem-062012-092700] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Infrared (IR) spectroscopy of biomolecular ions combines mass spectrometry's high sensitivity and ability to analyze complex mixtures with the enhanced structural information available from vibrational spectroscopy. IR spectroscopy is in principle well placed to distinguish isomers and allow chemical classification of unknown molecules. This review gives an outline of current instrumentation, spectroscopic approaches, and potential bottlenecks. We discuss the most promising applications in bioanalytical mass spectrometry in view of recent experimental results, as well as future applications based on bioinformatics.
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Affiliation(s)
- Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA.
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25
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Warnke S, von Helden G, Pagel K. Protein Structure in the Gas Phase: The Influence of Side-Chain Microsolvation. J Am Chem Soc 2013; 135:1177-80. [DOI: 10.1021/ja308528d] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Stephan Warnke
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
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26
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Lee JW, Heo SW, Lee SJC, Ko JY, Kim H, Kim HI. Probing conformational changes of ubiquitin by host-guest chemistry using electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:21-29. [PMID: 23247966 DOI: 10.1007/s13361-012-0496-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 09/04/2012] [Accepted: 09/08/2012] [Indexed: 06/01/2023]
Abstract
We report mechanistic studies of structural changes of ubiquitin (Ub) by host-guest chemistry with cucurbit[6]uril (CB[6]) using electrospray ionization mass spectrometry (ESI-MS) combined with circular dichroism spectroscopy and molecular dynamics (MD) simulation. CB[6] binds selectively to lysine (Lys) residues of proteins. Low energy collision-induced dissociation (CID) of the protein-CB[6] complex reveals CB[6] binding sites. We previously reported (Anal. Chem. 2011, 83, 7916-7923) shifts in major charge states along with Ub-CB[6] complexes in the ESI-MS spectrum with addition of CB[6] to Ub from water. We also reported that CB[6] is present only at Lys(6) or Lys(11) in high charge state (+13) complex. In this study, we provide additional information to explain unique conformational change mechanisms of Ub by host-guest chemistry with CB[6] compared with solvent-driven conformational change of Ub. Additional CID study reveals that CB[6] is bound only to Lys(48) and Lys(63) in low charge state (+7) complex. MD simulation studies reveal that the high charge state complexes are attributed to the CB[6] bound to Lys(11). The complexation prohibits salt bridge formation between Lys(11) and Glu(34) and induces conformational change of Ub. This results in formation of high charge state complexes in the gas phase. Then, by utilizing stronger host-guest chemistry of CB[6] with pentamethylenediamine, refolding of Ub via detaching CB[6] from the protein is performed. Overall, this study gives an insight into the mechanism of denatured Ub ion formation via host-guest interactions with CB[6]. Furthermore, this provides a direction for designing function-controllable supramolecular system comprising proteins and synthetic host molecules.
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Affiliation(s)
- Jong Wha Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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27
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Moore BN, Hamdy O, Julian RR. Protein structure evolution in liquid DESI as revealed by selective noncovalent adduct protein probing. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2012; 330-332:220-225. [PMID: 23526115 PMCID: PMC3601934 DOI: 10.1016/j.ijms.2012.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Previous experiments based on charge state distributions have suggested that liquid desorption electrospray ionization (DESI) is capable of preserving solution phase protein structure during transfer to the gas phase (Journal of the American Society for Mass Spectrometry 21 (2010) 1730-1736). In order to examine this possibility more carefully, we have utilized selective non-covalent adduct protein probing (SNAPP) to evaluate protein structural evolution in both liquid DESI and standard ESI under a variety of conditions. Experiments with cytochrome c (Cytc) demonstrated that methanol induced conformational shifts previously observed with ESI are also easily observed with liquid DESI. However, undesirable acid-induced unfolding becomes apparent at very high concentrations of methanol in liquid DESI due to acetic acid in the spray solvent, suggesting that there are conditions under which liquid DESI will not preserve solution phase structure. The effects of ammonium acetate buffer on liquid DESI SNAPP experiments were examined by monitoring structural changes in myoglobin. Heme retention and SNAPP distributions were both preserved better in liquid DESI than traditional ESI, suggesting superior performance for liquid DESI in buffered conditions. Finally, liquid DESI SNAPP was used to study the natively disordered proteins α, β, and γ synuclein with SNAPP. α-Synuclein, the main component of fibrils found in patients with Parkinson's disease, yielded a significantly different SNAPP distribution compared to β and γ synuclein. This difference is indicative of highly accessible protonated basic side chains, a property known to promote fibril formation in proteins.
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Affiliation(s)
| | | | - Ryan R. Julian
- Corresponding author. Tel.: +1 951 827 3958. (R.R. Julian)
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28
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Stedwell CN, Patrick AL, Gulyuz K, Polfer NC. Screening for Phosphorylated and Nonphosphorylated Peptides by Infrared Photodissociation Spectroscopy. Anal Chem 2012; 84:9907-12. [DOI: 10.1021/ac3023058] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Corey N. Stedwell
- Department of Chemistry, University of Florida, Post Office Box 117200, Gainesville, Florida
32611, United States
| | - Amanda L. Patrick
- Department of Chemistry, University of Florida, Post Office Box 117200, Gainesville, Florida
32611, United States
| | - Kerim Gulyuz
- Department of Chemistry, University of Florida, Post Office Box 117200, Gainesville, Florida
32611, United States
| | - Nicolas C. Polfer
- Department of Chemistry, University of Florida, Post Office Box 117200, Gainesville, Florida
32611, United States
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29
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Chen Y, Rodgers MT. Structural and energetic effects in the molecular recognition of acetylated amino acids by 18-crown-6. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2020-2030. [PMID: 22926972 DOI: 10.1007/s13361-012-0466-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 07/25/2012] [Accepted: 07/31/2012] [Indexed: 06/01/2023]
Abstract
Absolute 18-crown-6 (18C6) binding affinities of four protonated acetylated amino acids (AcAAs) are determined using guided ion beam tandem mass spectrometry techniques. The AcAAs examined in this work include: N-terminal acetylated lysine (N(α)-AcLys), histidine (N(α)-AcHis), and arginine (N(α)-AcArg) as well as side chain acetylated lysine (N(ε)-AcLys). The kinetic-energy-dependent cross sections for collision-induced dissociation (CID) of the (AcAA)H(+)(18C6) complexes are analyzed using an empirical threshold law to extract absolute 0 and 298 K (AcAA)H(+)-18C6 bond dissociation energies (BDEs) after accounting for the effects of multiple collisions, kinetic and internal energy distributions of the reactants, and unimolecular dissociation lifetimes. Theoretical electronic structure calculations are performed to determine stable geometries and energetics for neutral and protonated 18C6 and the AcAAs as well as the proton bound complexes of these species, (AcAA)H(+)(18C6), at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31 G* and M06/6-311+G(2d,2p)//B3LYP/6-31G* levels of theory. For all four (AcAA)H(+)(18C6) complexes, loss of neutral 18C6 corresponds to the most favorable dissociation pathway. At elevated energies, products arising from sequential dissociation of the primary CID product, H(+)(AcAA), are also observed. Protonated N(α)-AcLys exhibits a greater 18C6 binding affinity than other protonated N(α)-AcAAs, suggesting that the side chains of Lys residues are the preferred binding sites for 18C6 complexation to peptides and proteins. N(α)-AcLys exhibits a greater 18C6 binding affinity than N(ε)-AcLys, suggesting that binding of 18C6 to the side chain of Lys residues is more favorable than to the N-terminal amino group of Lys.
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Affiliation(s)
- Yu Chen
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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30
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Stedwell CN, Galindo JF, Gulyuz K, Roitberg AE, Polfer NC. Crown Complexation of Protonated Amino Acids: Influence on IRMPD Spectra. J Phys Chem A 2012; 117:1181-8. [DOI: 10.1021/jp305263b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Corey N. Stedwell
- Department of Chemistry
and Center for Chemical Physics, University of Florida, Gainesville, P.O. Box 117200, Florida 32611-7200,
United States
| | - Johan F. Galindo
- Department of Chemistry
and Quantum Theory Project, University of Florida, Gainesville, P.O. Box 118435, Florida 32611-8435,
United States
| | - Kerim Gulyuz
- Department of Chemistry
and Center for Chemical Physics, University of Florida, Gainesville, P.O. Box 117200, Florida 32611-7200,
United States
| | - Adrian E. Roitberg
- Department of Chemistry
and Quantum Theory Project, University of Florida, Gainesville, P.O. Box 118435, Florida 32611-8435,
United States
| | - Nicolas C. Polfer
- Department of Chemistry
and Center for Chemical Physics, University of Florida, Gainesville, P.O. Box 117200, Florida 32611-7200,
United States
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31
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Zhou Y, Vachet RW. Diethylpyrocarbonate labeling for the structural analysis of proteins: label scrambling in solution and how to avoid it. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:899-907. [PMID: 22351293 PMCID: PMC3324597 DOI: 10.1007/s13361-012-0349-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/20/2012] [Accepted: 01/23/2012] [Indexed: 05/11/2023]
Abstract
Covalent labeling along with mass spectrometry is a method that is increasingly used to study protein structure. Recently, it has been shown that diethylpyrocarbonate (DEPC) is a powerful labeling reagent because it can modify up to 30% of the residues in the average protein, including the N-terminus, His, Lys, Tyr, Ser, Thr, and Cys residues. We recently discovered, however, that Cys residues that form disulfide bonds appear to be modified by DEPC as well. In this work, we demonstrate that disulfide linked Cys residues are not actually reactive with DEPC but, instead, once reduced, free Cys residues can capture a carbethoxy group from other modified amino acids via a solution-phase reaction that can occur during the protein digestion step. This "scrambling" of carbethoxy groups decreases the amount of modification observed at other residues and can potentially provide incorrect protein structural information. Fortunately, label scrambling can be completely avoided by alkylating the free thiols after disulfide reduction.
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Affiliation(s)
| | - Richard W. Vachet
- Corresponding Author, Department of Chemistry, LGRT 104, 710 N. Pleasant St., University of Massachusetts, Amherst, MA 01003,
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32
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Zhou Y, Vachet RW. Increased protein structural resolution from diethylpyrocarbonate-based covalent labeling and mass spectrometric detection. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:708-17. [PMID: 22298289 PMCID: PMC3334416 DOI: 10.1007/s13361-011-0332-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/21/2011] [Accepted: 12/28/2011] [Indexed: 05/03/2023]
Abstract
Covalent labeling and mass spectrometry are seeing increased use together as a way to obtain insight into the 3-dimensional structure of proteins and protein complexes. Several amino acid specific (e.g., diethylpyrocarbonate) and non-specific (e.g., hydroxyl radicals) labeling reagents are available for this purpose. Diethylpyrocarbonate (DEPC) is a promising labeling reagent because it can potentially probe up to 30% of the residues in the average protein and gives only one reaction product, thereby facilitating mass spectrometric analysis. It was recently reported, though, that DEPC modifications are labile for some amino acids. Here, we show that label loss is more significant and widespread than previously thought, especially for Ser, Thr, Tyr, and His residues, when relatively long protein digestion times are used. Such label loss ultimately decreases the amount of protein structural information that is obtainable with this reagent. We find, however, that the number of DEPC modified residues and, thus, protein structural information, can be significantly increased by decreasing the time between the covalent labeling reaction and the mass spectrometric analysis. This is most effectively accomplished using short (e.g., 2 h) proteolytic digestions with enzymes such as immobilized chymotrypsin or Glu-C rather than using methods (e.g., microwave or ultrasonic irradiation) that accelerate proteolysis in other ways. Using short digestion times, we show that the percentage of solvent accessible residues that can be modified by DEPC increases from 44% to 67% for cytochrome c, 35% to 81% for myoglobin, and 76% to 95% for β-2-microglobulin. In effect, these increased numbers of modified residues improve the protein structural resolution available from this covalent labeling method. Compared with typical overnight digestion conditions, the short digestion times decrease the average distance between modified residues from 11 to 7 Å for myoglobin, 13 to 10 Å for cytochrome c, and 9 to 8 Å for β-2-microglobulin.
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Affiliation(s)
| | - Richard W. Vachet
- Corresponding Author: Department of Chemistry, LGRT 104, 710 N. Pleasant St., University of Massachusetts, Amherst, MA 01003,
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33
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Chen Y, Rodgers MT. Structural and Energetic Effects in the Molecular Recognition of Amino Acids by 18-Crown-6. J Am Chem Soc 2012; 134:5863-75. [DOI: 10.1021/ja211021h] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Yu Chen
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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34
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Tao Y, Julian RR. Examining protein surface structure in highly conserved sequence variants with mass spectrometry. Biochemistry 2012; 51:1796-802. [PMID: 22320248 DOI: 10.1021/bi2018199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A simple mass spectrometry-based method capable of examining protein structure called SNAPP (selective noncovalent adduct protein probing) is used to evaluate the structural consequences of point mutations in naturally occurring sequence variants from different species. SNAPP monitors changes in the attachment of noncovalent adducts to proteins as a function of structural state. Mutations that lead to perturbations to the electrostatic surface structure of a protein affect noncovalent attachment and are easily observed with SNAPP. Mutations that do not alter the tertiary structure or electrostatic surface structure yield similar results by SNAPP. For example, bovine, porcine, and human insulin all have very similar backbone structures and no basic or acidic residue mutations, and the SNAPP distributions for all three proteins are very similar. In contrast, four variants of cytochrome c (cytc) have varying degrees of sequence homology, which are reflected in the observed SNAPP distributions. Bovine and pigeon cytc have several basic or acidic residue substitutions relative to horse cytc, but the SNAPP distributions for all three proteins are similar. This suggests that these mutations do not significantly influence the protein surface structure. On the other hand, yeast cytc has the least sequence homology and exhibits a unique, though related, SNAPP distribution. Even greater differences are observed for lysozyme. Hen and human lysozyme have identical tertiary structures but significant variations in the locations of numerous basic and acidic residues. The SNAPP distributions are quite distinct for the two forms of lysozyme, suggesting significant differences in the surface structures. In summary, SNAPP experiments are relatively easy to perform, require minimal sample consumption, and provide a facile route for comparison of protein surface structure between highly homologous proteins.
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Affiliation(s)
- Yuanqi Tao
- Department of Chemistry, University of California, Riverside, California 92521, United States
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Chen Y, Rodgers MT. Structural and Energetic Effects in the Molecular Recognition of Protonated Peptidomimetic Bases by 18-Crown-6. J Am Chem Soc 2012; 134:2313-24. [DOI: 10.1021/ja2102345] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu Chen
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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Oshima T, Baba Y. Recognition of exterior protein surfaces using artificial ligands based on calixarenes, crown ethers, and tetraphenylporphyrins. J INCL PHENOM MACRO 2011. [DOI: 10.1007/s10847-011-0088-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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37
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Heo SW, Choi TS, Park KM, Ko YH, Kim SB, Kim K, Kim HI. Host–Guest Chemistry in the Gas Phase: Selected Fragmentations of CB[6]–Peptide Complexes at Lysine Residues and Its Utility to Probe the Structures of Small Proteins. Anal Chem 2011; 83:7916-23. [DOI: 10.1021/ac201854a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sung Woo Heo
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Tae Su Choi
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Kyung Man Park
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Young Ho Ko
- Center for Smart Supramolecules and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Seung Bin Kim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Kimoon Kim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 790-784, Republic of Korea
- Center for Smart Supramolecules and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Hugh I. Kim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 790-784, Republic of Korea
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38
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Bohrer BC, Atlasevich N, Clemmer DE. Transitions between elongated conformations of ubiquitin [M+11H]11+ enhance hydrogen/deuterium exchange. J Phys Chem B 2011; 115:4509-15. [PMID: 21449553 PMCID: PMC3091505 DOI: 10.1021/jp2008495] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hydrogen/deuterium (H/D) exchange reactions between different elongated conformations of [M + 11H](11+) ions of ubiquitin and D(2)O are studied by a combination of ion mobility spectrometry (IMS) and mass spectrometry techniques. Three conformers (B, C, and D), resolved in the IMS separation, each exchange ∼27 hydrogens upon exposure to 0.06 Torr of D(2)O vapor for ∼35 to 40 ms. However, a region of the IMS spectrum that appears between the C and D states (corresponding to ions that undergo a structural transition during the mobility separation) undergoes substantially more exchanges (∼39 total sites, 44% more than the B, C, and D states). Selection and activation of the individual B, C, and D states reveals that the increased H/D exchange occurs during the transition between structures. Overall, these studies suggest a key process in establishing the maximum exchange levels involves structural transitions, which allow protected sites to be exposed for some fraction of the reaction time. Analysis of changes in exchange levels upon structural transitions can provide insight about common regions of structure that exist in the B, C, and D conformations.
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Affiliation(s)
- Brian C. Bohrer
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405
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40
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Sun Q, Tyler RC, Volkman BF, Julian RR. Dynamic interchanging native states of lymphotactin examined by SNAPP-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:399-407. [PMID: 21472559 PMCID: PMC3061006 DOI: 10.1007/s13361-010-0042-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 11/15/2010] [Accepted: 11/15/2010] [Indexed: 05/30/2023]
Abstract
The human chemokine lymphotactin (Ltn) is a remarkable protein that interconverts between two unrelated native state structures in the condensed phase. It is possible to shift the equilibrium toward either conformation with selected sequence substitutions. Previous results have shown that a disulfide-stabilized variant preferentially adopts the canonical chemokine fold (Ltn10), while a single amino acid change (W55D) favors the novel Ltn40 dimeric structure. Selective noncovalent adduct protein probing (SNAPP) is a recently developed method for examining solution phase protein structure. Herein, it is demonstrated that SNAPP can easily recognize and distinguish between the Ltn10 and Ltn40 states of lymphotactin in aqueous solution. The effects of organic denaturants, acid, and disulfide bond reduction and blocking were also examined using SNAPP for the CC3, W55D, and wild type proteins. Only disulfide reduction was shown to significantly perturb the protein, and resulted in considerably decreased adduct formation consistent with loss of tertiary/secondary structure. Cold denaturation experiments demonstrated that wild-type Ltn is the most temperature sensitive of the three proteins. Examination of the higher charge states in all experiments, which are presumed to represent transition state structures between Ltn-10 and Ltn-40, reveals increased 18C6 attachment relative to the more folded structures. This observation is consistent with increased competitive intramolecular hydrogen bonding, which may guide the transition. Experiments examining the gas phase structures revealed that all three proteins can be structurally distinguished in the gas phase. In addition, the gas phase experiments enabled identification of preferred adduct binding sites.
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Affiliation(s)
- Qingyu Sun
- Department of Chemistry, University of California, Riverside, CA 92521 USA
| | - Robert C. Tyler
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Brian F. Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, CA 92521 USA
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Flick TG, Merenbloom SI, Williams ER. A simple and robust method for determining the number of basic sites in peptides and proteins using electrospray ionization mass spectrometry. Anal Chem 2011; 83:2210-4. [PMID: 21338067 DOI: 10.1021/ac1031012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A solution additive has been discovered that can be used to measure the number of basic sites in a peptide or protein using electrospray ionization (ESI) mass spectrometry. Addition of millimolar amounts of perchloric acid (HClO(4)) to aqueous solutions that contain peptides or proteins results in the noncovalent adduction of HClO(4) molecules to the multiply charged ions formed by ESI. For 18 oligopeptides and proteins, ranging in molecular weight from 0.5 to 18.3 kDa, the sum of the number of protons plus maximum number of HClO(4) molecules adducted to the lower charge state ions is equal to the number of basic sites in the molecule. This method provides a rapid means of obtaining information about the composition of a peptide or protein and does not require high-resolution measurements or any instrumental or experimental modifications.
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Affiliation(s)
- Tawnya G Flick
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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42
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Rounaghi GH, Mohajeri M, Tarahomi S, Rahmanian R. Study of Complex Formation of Dibenzo-18-Crown-6 with Ce3+, Y3+, $\mathrm{UO}_{2}^{2 +}$ and Sr2+ Cations in Acetonitrile–Dioxane Binary Solvent Mixtures. J SOLUTION CHEM 2011. [DOI: 10.1007/s10953-011-9651-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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43
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Extraction and separation of a lysine-rich protein by formation of supramolecule between crown ether and protein in aqueous two-phase system. Anal Chim Acta 2010; 674:211-9. [DOI: 10.1016/j.aca.2010.06.039] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 05/12/2010] [Accepted: 06/27/2010] [Indexed: 11/15/2022]
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44
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Pagel K, Hyung SJ, Ruotolo BT, Robinson CV. Alternate Dissociation Pathways Identified in Charge-Reduced Protein Complex Ions. Anal Chem 2010; 82:5363-72. [DOI: 10.1021/ac101121r] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin Pagel
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Suk-Joon Hyung
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Brandon T. Ruotolo
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Carol V. Robinson
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, U.K
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Ly T, Julian R. Ultraviolet Photodissociation: Developments towards Applications for Mass-Spectrometry-Based Proteomics. Angew Chem Int Ed Engl 2009; 48:7130-7. [DOI: 10.1002/anie.200900613] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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46
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Ly T, Julian R. Photodissoziation durch UV-Licht: Anwendungen in der massenspektrometrischen Proteomforschung. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Mendoza VL, Vachet RW. Probing protein structure by amino acid-specific covalent labeling and mass spectrometry. MASS SPECTROMETRY REVIEWS 2009; 28:785-815. [PMID: 19016300 PMCID: PMC2768138 DOI: 10.1002/mas.20203] [Citation(s) in RCA: 270] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies.
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Affiliation(s)
- Vanessa Leah Mendoza
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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Choi CM, Kim HJ, Lee JH, Shin WJ, Yoon TO, Kim NJ, Heo J. Ultraviolet Photodepletion Spectroscopy of Dibenzo-18-Crown-6-Ether Complexes with Alkali Metal Cations. J Phys Chem A 2009; 113:8343-50. [DOI: 10.1021/jp903832w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chang Min Choi
- Department of Chemistry, Chungbuk National University, Chungbuk 361-763, Korea
| | - Hwan Jin Kim
- Department of Chemistry, Chungbuk National University, Chungbuk 361-763, Korea
| | - Jun Ho Lee
- Department of Chemistry, Chungbuk National University, Chungbuk 361-763, Korea
| | - Won Jik Shin
- Department of Chemistry, Chungbuk National University, Chungbuk 361-763, Korea
| | - Tae Oh Yoon
- Department of Chemistry, Chungbuk National University, Chungbuk 361-763, Korea
| | - Nam Joon Kim
- Department of Chemistry, Chungbuk National University, Chungbuk 361-763, Korea
| | - Jiyoung Heo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
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49
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Yeh GK, Sun Q, Meneses C, Julian RR. Rapid peptide fragmentation without electrons, collisions, infrared radiation, or native chromophores. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:385-93. [PMID: 19036607 DOI: 10.1016/j.jasms.2008.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 10/28/2008] [Accepted: 10/28/2008] [Indexed: 05/16/2023]
Abstract
Ultraviolet photodissociation of peptides followed by mass analysis has several desirable advantages relative to other methods, yet it has not found widespread use due to several limitations. One shortcoming is the inefficiency with which peptides absorb in the ultraviolet. This issue has a simple solution and can be circumvented by the attachment of noncovalent adducts that contain appropriate chromophores. Subsequent photoactivation of the chromophore leads to vibrational excitation of the complex and eventually to fragmentation of the peptide. Herein, the energetics that control the efficiency of this process are examined as a function of the characteristics of both the peptide and the noncovalently attached chromophore. Fragmentation efficiency decreases with increasing peptide size and is also constrained by the binding energy of the noncovalent adduct. The optimum chromophore should have excellent absorption at the excitation wavelength and a low luminescence quantum yield. It is demonstrated that a naphthyl based 18-crown-6 adduct is ideally suited for attaching to a variety peptides and fragmenting them following absorption of 266 nm light. Potential applications and limitations of this methodology are discussed.
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Affiliation(s)
- Geoffrey K Yeh
- Department of Chemistry, University of California at Riverside, Riverside, California 92508, USA
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50
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Zhang H, Grabenauer M, Bowers MT, Dearden DV. Supramolecular modification of ion chemistry: modulation of peptide charge state and dissociation behavior through complexation with cucurbit[n]uril (n = 5, 6) or alpha-cyclodextrin. J Phys Chem A 2009; 113:1508-17. [PMID: 19191519 DOI: 10.1021/jp808625v] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electrospray Fourier transform ion cyclotron resonance mass spectrometry, ion mobility spectrometry, and computational methods were utilized to characterize the complexes between lysine or pentalysine with three prototypical host molecules: alpha-cyclodextrin (alpha-CD), cucurbit[5]uril (CB[5]), and cucurbit[6]uril (CB[6]). Ion mobility measurements show lysine forms externally bound, singly charged complexes with either alpha-CD or CB[5], but a doubly charged complex with the lysine side chain threaded through the host cavity of CB[6]. These structural differences result in distinct dissociation behaviors in collision-induced dissociation (CID) experiments: the alpha-CD complex dissociates via the simple loss of intact lysine, whereas the CB[5] complex dissociates to yield [CB[5] + H(3)O](+), and the CB[6] complex loses neutral NH(3) and CO, the product ion remaining a doubly charged complex. These results are consistent with B3LYP/6-31G* binding energies (kJ mol(-1)) of D(Lys + H(+)-alpha-CD) = 281, D(Lys + H(+)-CB[5]) = 327, and D(Lys + 2H(2+)-CB[6]) = 600. B3LYP/6-31G* geometry optimizations show complexation with alpha-CD stabilizes the salt bridge form of protonated lysine, whereas complexation with CB[6] stabilizes doubly protonated lysine. Complexation of the larger polypeptide pentalysine with alpha-CD forms a nonspecific adduct: no modification of the pentalysine charge state distribution is observed, and dissociation occurs via the simple loss of alpha-CD. Complexation of pentalysine with the cucurbiturils is more specific: the observed charge state distribution shifts higher on complexation, and fragmentation patterns are significantly altered relative to uncomplexed pentalysine: C-terminal fragment ions appear that are consistent with charge stabilization by the cucurbiturils, and the cucurbiturils are retained on the fragment ions. Molecular mechanics calculations suggest CB[5] binds to two protonated sites on pentalysine without threading onto the peptide and that CB[6] binds two adjacent protonated sites via threading onto the peptide.
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Affiliation(s)
- Haizhen Zhang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-5700, USA
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