51
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Du Z, de Paiva REF, Nelson K, Farrell NP. Diversity in Gold Finger Structure Elucidated by Traveling‐Wave Ion Mobility Mass Spectrometry. Angew Chem Int Ed Engl 2017; 56:4464-4467. [DOI: 10.1002/anie.201612494] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/13/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Zhifeng Du
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
| | | | - Kristina Nelson
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
| | - Nicholas P. Farrell
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
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52
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Seo J, Jang J, Warnke S, Gewinner S, Schöllkopf W, von Helden G. Stacking Geometries of Early Protoporphyrin IX Aggregates Revealed by Gas-Phase Infrared Spectroscopy. J Am Chem Soc 2016; 138:16315-16321. [DOI: 10.1021/jacs.6b08700] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jongcheol Seo
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Jinhyeong Jang
- Department
of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea
| | - Stephan Warnke
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Sandy Gewinner
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Wieland Schöllkopf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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53
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Gillig KJ. Gas-phase protein conformation/multimer ion formation by electrospray ion mobility-mass spectrometry: bovine insulin and ubiquitin. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:20150368. [PMID: 27644980 PMCID: PMC5031634 DOI: 10.1098/rsta.2015.0368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/28/2016] [Indexed: 06/06/2023]
Abstract
Ion mobility-mass spectrometry (IMMS) is a very attractive method for studies in structural biology because of the ability of rapid isolation by nearly simultaneous m/z characterization and size separation, leading to an emergence of IMMS as a complimentary biochemical tool. Earlier, we developed a method based on varying the protein concentration in solution prior to electrospray ionization (ESI) with subsequent m/z selection and dissociation of protein multimers by IMMS of cytochrome c. The focus of this work will be to correctly distinguish truly different ion conformations formed by ESI versus homomultimeric complexes with the same m/z for well-studied proteins bovine ubiquitin and insulin. These proteins were chosen due to their large difference in solution phase structures: insulin tightly bound by disulfide linkages, and ubiquitin-a protein that may adopt a range of states from compact to extended. Our preliminary results, as with cytochrome c reveal false negatives for protein oligomer formation and false positives for protein conformational states. In addition, these results will be couched in terms of the need for quantification of IMMS analysis of proteins given the total area under IMMS peaks can also distinguish conformation versus aggregation as higher order oligomers have more mass per ion.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Kent J Gillig
- Genomics Research Center, Academia Sinica, 128 Academia Road, Nangang Section 2, Taipei 115, Taiwan, Republic of China
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54
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Theisen A, Yan B, Brown JM, Morris M, Bellina B, Barran PE. Use of Ultraviolet Photodissociation Coupled with Ion Mobility Mass Spectrometry To Determine Structure and Sequence from Drift Time Selected Peptides and Proteins. Anal Chem 2016; 88:9964-9971. [DOI: 10.1021/acs.analchem.6b01705] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Alina Theisen
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Insitute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Bin Yan
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Insitute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Jeffery M. Brown
- Waters Corporation, Stamford
Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Michael Morris
- Waters Corporation, Stamford
Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Bruno Bellina
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Insitute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Insitute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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55
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Cammarata MB, Schardon CL, Mehaffey MR, Rosenberg J, Singleton J, Fast W, Brodbelt JS. Impact of G12 Mutations on the Structure of K-Ras Probed by Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2016; 138:13187-13196. [DOI: 10.1021/jacs.6b04474] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael B. Cammarata
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Christopher L. Schardon
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - M. Rachel Mehaffey
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jake Rosenberg
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jonathan Singleton
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Walter Fast
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
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56
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Seo J, Hoffmann W, Warnke S, Huang X, Gewinner S, Schöllkopf W, Bowers MT, von Helden G, Pagel K. An infrared spectroscopy approach to follow β-sheet formation in peptide amyloid assemblies. Nat Chem 2016; 9:39-44. [PMID: 27995915 DOI: 10.1038/nchem.2615] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 08/10/2016] [Indexed: 12/18/2022]
Abstract
Amyloidogenic peptides and proteins play a crucial role in a variety of neurodegenerative disorders such as Alzheimer's and Parkinson's disease. These proteins undergo a spontaneous transition from a soluble, often partially folded form, into insoluble amyloid fibrils that are rich in β-sheets. Increasing evidence suggests that highly dynamic, polydisperse folding intermediates, which occur during fibril formation, are the toxic species in the amyloid-related diseases. Traditional condensed-phase methods are of limited use for characterizing these states because they typically only provide ensemble averages rather than information about individual oligomers. Here we report the first direct secondary-structure analysis of individual amyloid intermediates using a combination of ion mobility spectrometry-mass spectrometry and gas-phase infrared spectroscopy. Our data reveal that oligomers of the fibril-forming peptide segments VEALYL and YVEALL, which consist of 4-9 peptide strands, can contain a significant amount of β-sheet. In addition, our data show that the more-extended variants of each oligomer generally exhibit increased β-sheet content.
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Affiliation(s)
- Jongcheol Seo
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany
| | - Waldemar Hoffmann
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, Berlin 14195, Germany
| | - Stephan Warnke
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany
| | - Xing Huang
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany
| | - Sandy Gewinner
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany
| | - Wieland Schöllkopf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, Berlin 14195, Germany
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57
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Lietz CB, Chen Z, Yun Son C, Pang X, Cui Q, Li L. Multiple gas-phase conformations of proline-containing peptides: is it always cis/trans isomerization? Analyst 2016; 141:4863-9. [PMID: 27434776 PMCID: PMC4972606 DOI: 10.1039/c5an00835b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) is often employed to look at the secondary, tertiary, and quaternary structures of naked peptides and proteins in the gas-phase. Recently, it has offered a unique glimpse into proline-containing peptides and their cis/trans Xxx-Pro isomers. An experimental "signature" has been identified wherein a proline-containing peptide has its Pro residues substituted with another amino acid and the presence or absence of conformations in the IM-MS spectra is observed. Despite the high probability that one could attribute these conformations to cis/trans isomers, it is also possible that cis/trans isomers are not the cause of the additional conformations in proline-containing peptides. However, the experimental evidence of such a system has not been demonstrated or reported. Herein, we present the IM-MS analysis of Neuropeptide Y's wild-type (WT) signal sequence and Leu7Pro (L7P) mutant. Although comparison of arrival times and collision cross-sections of [M + 4H](4+) ions yields the cis/trans "signature", molecular dynamics indicates that a cis-Pro7 is not very stable and that trans-Pro7 conformations of the same cross-section arise with equal frequency. We believe that this work further underscores the importance of theoretical calculations in IM-MS structural assignments.
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Affiliation(s)
- Christopher B Lietz
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Chang Yun Son
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Xueqin Pang
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA. and School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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58
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Voronina L, Masson A, Kamrath M, Schubert F, Clemmer D, Baldauf C, Rizzo T. Conformations of Prolyl–Peptide Bonds in the Bradykinin 1–5 Fragment in Solution and in the Gas Phase. J Am Chem Soc 2016; 138:9224-33. [DOI: 10.1021/jacs.6b04550] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Liudmila Voronina
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Antoine Masson
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Michael Kamrath
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Franziska Schubert
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, D-14195 Berlin, Germany
| | - David Clemmer
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, D-14195 Berlin, Germany
| | - Thomas Rizzo
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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59
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Jeanne Dit Fouque K, Lavanant H, Zirah S, Steinmetz V, Rebuffat S, Maître P, Afonso C. IRMPD Spectroscopy: Evidence of Hydrogen Bonding in the Gas Phase Conformations of Lasso Peptides and their Branched-Cyclic Topoisomers. J Phys Chem A 2016; 120:3810-6. [DOI: 10.1021/acs.jpca.6b04496] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin Jeanne Dit Fouque
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Hélène Lavanant
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Séverine Zirah
- Muséum national d’Histoire naturelle, Sorbonne Universités, Centre national de la Recherche scientifique, Laboratoire Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex, France
| | - Sylvie Rebuffat
- Muséum national d’Histoire naturelle, Sorbonne Universités, Centre national de la Recherche scientifique, Laboratoire Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Philippe Maître
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex, France
| | - Carlos Afonso
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
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60
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Kopysov V, Makarov A, Boyarkin OV. Nonstatistical UV Fragmentation of Gas-Phase Peptides Reveals Conformers and Their Structural Features. J Phys Chem Lett 2016; 7:1067-1071. [PMID: 26950179 DOI: 10.1021/acs.jpclett.6b00292] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Solving the 3D structure of a biomolecule requires recognition of its conformers and measurements of their individual structural identities, which can be compared with calculations. We employ the phenomenon of nonstatistical photofragmentation, detected by a combination of UV cold ion spectroscopy and high-resolution mass spectrometry, to identify the main conformers of gas-phase peptides and to recover individual UV absorption and mass spectra of all of these conformers in a single laser scan. We first validate this approach with a benchmark dipeptide, Tyr-Ala, and then apply it to a decapeptide, gramicidin S. The revealed characteristic structural difference between the conformers of the latter identifies some of the previously calculated structures of gramicidin S as the most likely geometries of its remaining unsolved conformer.
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Affiliation(s)
- Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , Station-6, 1015 Lausanne, Switzerland
| | - Alexander Makarov
- Thermo Fisher Scientific , Hanna-Kunath Str. 11, 28199 Bremen, Germany
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , Station-6, 1015 Lausanne, Switzerland
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61
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Choi C, Simon AL, Chirot F, Kulesza A, Knight G, Daly S, MacAleese L, Antoine R, Dugourd P. Charge, Color, and Conformation: Spectroscopy on Isomer-Selected Peptide Ions. J Phys Chem B 2016; 120:709-14. [PMID: 26756462 PMCID: PMC4819951 DOI: 10.1021/acs.jpcb.5b11919] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 01/10/2016] [Indexed: 11/28/2022]
Abstract
Monitoring the chromism induced by intramolecular hydrogen and charge transfers within proteins as well as the isomerization of both protein and cofactor is essential not only to understand photoactive signaling pathways but also to design targeted opto-switchable proteins. We used a dual-ion mobility drift tube coupled to a tunable picosecond laser to explore the optical and structural properties of a peptide chain bound to a chromophore-a prototype system allowing for a proton transfer coupled to conformational change. With the support of molecular dynamics and DFT calculations, we show how proton transfer between the peptide and its cofactor can dramatically modify the optical properties of the system and demonstrate that these changes can be triggered by collisional activation in the gas phase.
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Affiliation(s)
- Chang
Min Choi
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Anne-Laure Simon
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Fabien Chirot
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Alexander Kulesza
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Geoffrey Knight
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Steven Daly
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Luke MacAleese
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Rodolphe Antoine
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Philippe Dugourd
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
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62
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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63
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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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64
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Shi L, Holliday AE, Glover MS, Ewing MA, Russell DH, Clemmer DE. Ion Mobility-Mass Spectrometry Reveals the Energetics of Intermediates that Guide Polyproline Folding. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:22-30. [PMID: 26362047 PMCID: PMC4713193 DOI: 10.1007/s13361-015-1255-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 08/12/2015] [Accepted: 08/14/2015] [Indexed: 05/06/2023]
Abstract
Proline favors trans-configured peptide bonds in native proteins. Although cis/trans configurations vary for non-native and unstructured states, solvent also influences these preferences. Water induces the all-cis right-handed polyproline-I (PPI) helix of polyproline to fold into the all-trans left-handed polyproline-II (PPII) helix. Our recent work has shown that this occurs via a sequential mechanism involving six resolved intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702-12711 (2014)]. Here, we use ion mobility-mass spectrometry to make the first detailed thermodynamic measurements of the folding intermediates, which inform us about how and why this transition occurs. It appears that early intermediates are energetically favorable because of the hydration of the peptide backbone, whereas late intermediates are enthalpically unfavorable. However, folding continues, as the entropy of the system increases upon successive formation of each new structure. When PPII is immersed in 1-propanol, the PPII→PPI transition occurs, but this reaction occurs through a very different mechanism. Early on, the PPII population splits onto multiple pathways that eventually converge through a late intermediate that continues on to the folded PPI helix. Nearly every step is endothermic. Folding results from a stepwise increase in the disorder of the system, allowing a wide-scale search for a critical late intermediate. Overall, the data presented here allow us to establish the first experimentally determined energy surface for biopolymer folding as a function of solution environment.
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Affiliation(s)
- Liuqing Shi
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Alison E Holliday
- Department of Chemistry, Moravian College, Bethlehem, PA, 18018, USA
| | - Matthew S Glover
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Michael A Ewing
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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65
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Hendricks NG, Julian RR. Leveraging ultraviolet photodissociation and spectroscopy to investigate peptide and protein three-dimensional structure with mass spectrometry. Analyst 2016; 141:4534-40. [DOI: 10.1039/c6an01020b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent advances in mass spectrometry and lasers have facilitated the development of novel experiments combining the benefits of both technologies.
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Affiliation(s)
| | - Ryan R. Julian
- Department of Chemistry
- University of California
- Riverside
- USA
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66
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Baldauf C, Rossi M. Going clean: structure and dynamics of peptides in the gas phase and paths to solvation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:493002. [PMID: 26598600 DOI: 10.1088/0953-8984/27/49/493002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.
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Affiliation(s)
- Carsten Baldauf
- Fritz Haber Institute, Faradayweg 4-6, 14195 Berlin, Germany
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67
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Holden DD, McGee WM, Brodbelt JS. Integration of Ultraviolet Photodissociation with Proton Transfer Reactions and Ion Parking for Analysis of Intact Proteins. Anal Chem 2015; 88:1008-16. [DOI: 10.1021/acs.analchem.5b03911] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Dustin D. Holden
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - William M. McGee
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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68
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Characterization of top-down ETD in a travelling-wave ion guide. Methods 2015; 89:22-9. [DOI: 10.1016/j.ymeth.2015.05.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/30/2015] [Accepted: 05/19/2015] [Indexed: 11/20/2022] Open
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69
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Czar MF, Jockusch RA. Sensitive probes of protein structure and dynamics in well-controlled environments: combining mass spectrometry with fluorescence spectroscopy. Curr Opin Struct Biol 2015; 34:123-34. [DOI: 10.1016/j.sbi.2015.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 10/25/2022]
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70
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McAllister RG, Metwally H, Sun Y, Konermann L. Release of Native-like Gaseous Proteins from Electrospray Droplets via the Charged Residue Mechanism: Insights from Molecular Dynamics Simulations. J Am Chem Soc 2015; 137:12667-76. [DOI: 10.1021/jacs.5b07913] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Robert G. McAllister
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Haidy Metwally
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Yu Sun
- 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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71
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Simon AL, Chirot F, Choi CM, Clavier C, Barbaire M, Maurelli J, Dagany X, MacAleese L, Dugourd P. Tandem ion mobility spectrometry coupled to laser excitation. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:094101. [PMID: 26429458 DOI: 10.1063/1.4930604] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This manuscript describes a new experimental setup that allows to perform tandem ion mobility spectrometry (IMS) measurements and which is coupled to a high resolution time-of-flight mass spectrometer. It consists of two 79 cm long drift tubes connected by a dual ion funnel assembly. The setup was built to permit laser irradiation of the ions in the transfer region between the two drift tubes. This geometry allows selecting ions according to their ion mobility in the first drift tube, to irradiate selected ions, and examine the ion mobility of the product ions in the second drift tube. Activation by collision is possible in the same region (between the two tubes) and between the second tube and the time-of-flight. IMS-IMS experiments on Ubiquitin are reported. We selected a given isomer of charge state +7 and explored its structural rearrangement following collisional activation between the two drift tubes. An example of IMS-laser-IMS experiment is reported on eosin Y, where laser irradiation was used to produce radical ions by electron photodetachment starting from doubly deprotonated species. This allowed measuring the collision cross section of the radical photo-product, which cannot be directly produced with an electrospray source.
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Affiliation(s)
- Anne-Laure Simon
- Institut Lumière Matière, Université de Lyon, Université Lyon 1-CNRS, 69622 Villeurbanne cedex, France
| | - Fabien Chirot
- Institut des Sciences Analytiques, Université de Lyon, Université Lyon 1-CNRS, 69622 Villeurbanne cedex, France
| | - Chang Min Choi
- Institut Lumière Matière, Université de Lyon, Université Lyon 1-CNRS, 69622 Villeurbanne cedex, France
| | - Christian Clavier
- Institut Lumière Matière, Université de Lyon, Université Lyon 1-CNRS, 69622 Villeurbanne cedex, France
| | - Marc Barbaire
- Institut Lumière Matière, Université de Lyon, Université Lyon 1-CNRS, 69622 Villeurbanne cedex, France
| | - Jacques Maurelli
- Institut Lumière Matière, Université de Lyon, Université Lyon 1-CNRS, 69622 Villeurbanne cedex, France
| | - Xavier Dagany
- Institut Lumière Matière, Université de Lyon, Université Lyon 1-CNRS, 69622 Villeurbanne cedex, France
| | - Luke MacAleese
- Institut Lumière Matière, Université de Lyon, Université Lyon 1-CNRS, 69622 Villeurbanne cedex, France
| | - Philippe Dugourd
- Institut Lumière Matière, Université de Lyon, Université Lyon 1-CNRS, 69622 Villeurbanne cedex, France
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72
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Masson A, Kamrath MZ, Perez MAS, Glover MS, Rothlisberger U, Clemmer DE, Rizzo TR. Infrared Spectroscopy of Mobility-Selected H+-Gly-Pro-Gly-Gly (GPGG). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1444-54. [PMID: 26091889 DOI: 10.1007/s13361-015-1172-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/16/2015] [Accepted: 04/18/2015] [Indexed: 05/14/2023]
Abstract
We report the first results from a new instrument capable of acquiring infrared spectra of mobility-selected ions. This demonstration involves using ion mobility to first separate the protonated peptide Gly-Pro-Gly-Gly (GPGG) into two conformational families with collisional cross-sections of 93.8 and 96.8 Å(2). After separation, each family is independently analyzed by acquiring the infrared predissociation spectrum of the H(2)-tagged molecules. The ion mobility and spectroscopic data combined with density functional theory (DFT) based molecular dynamics simulations confirm the presence of one major conformer per family, which arises from cis/trans isomerization about the proline residue. We induce isomerization between the two conformers by using collisional activation in the drift tube and monitor the evolution of the ion distribution with ion mobility and infrared spectroscopy. While the cis-proline species is the preferred gas-phase structure, its relative population is smaller than that of the trans-proline species in the initial ion mobility drift distribution. This suggests that a portion of the trans-proline ion population is kinetically trapped as a higher energy conformer and may retain structural elements from solution.
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Affiliation(s)
- Antoine Masson
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland
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73
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Abstract
A recent ion mobility spectrometry-mass spectrometry (IMS-MS) study revealed that tryptic peptide ions containing a proline residue at the second position from the N-terminus (i.e., penultimate proline) frequently adopt multiple conformations, owing to the cis-trans isomerization of Xaa(1)-Pro(2) peptide bonds [J. Am. Soc. Mass Spectrom. 2015, 26, 444]. Here, we present a statistical analysis of a neuropeptide database that illustrates penultimate proline residues are frequently found in neuropeptides. In order to probe the effect of penultimate proline on neuropeptide conformations, IMS-MS experiments were performed on two model peptides in which penultimate proline residues were known to be important for biological activity: the N-terminal region of human neuropeptide Y (NPY1-9, Tyr(1)-Pro(2)-Ser(3)-Lys(4)-Pro(5)-Asp(6)-Asn(7)-Pro(8)-Gly(9)-NH2) and a tachykinin-related peptide (CabTRP Ia, Ala(1)-Pro(2)-Ser(3)-Gly(4)-Phe(5)-Leu(6)-Gly(7)-Met(8)-Arg(9)-NH2). From these studies, it appears that penultimate prolines allow neuropeptides to populate multiple conformations arising from the cis-trans isomerization of Xaa(1)-Pro(2) peptide bonds. Although it is commonly proposed that the role of penultimate proline residues is to protect peptides from enzymatic degradation, the present results indicate that penultimate proline residues also are an important means of increasing the conformational heterogeneity of neuropeptides.
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Affiliation(s)
- Matthew S Glover
- †Department of Chemistry, ‡Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States
| | - Earl P Bellinger
- †Department of Chemistry, ‡Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States
| | - Predrag Radivojac
- †Department of Chemistry, ‡Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States
| | - David E Clemmer
- †Department of Chemistry, ‡Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States
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74
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Lermyte F, Sobott F. Electron transfer dissociation provides higher-order structural information of native and partially unfolded protein complexes. Proteomics 2015; 15:2813-22. [DOI: 10.1002/pmic.201400516] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 03/13/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Frederik Lermyte
- UA-VITO Center for Proteomics; University of Antwerp; Antwerp Belgium
- Biomolecular & Analytical Mass Spectrometry group; Department of Chemistry; University of Antwerp; Antwerp Belgium
| | - Frank Sobott
- UA-VITO Center for Proteomics; University of Antwerp; Antwerp Belgium
- Biomolecular & Analytical Mass Spectrometry group; Department of Chemistry; University of Antwerp; Antwerp Belgium
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75
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Cammarata MB, Thyer R, Rosenberg J, Ellington A, Brodbelt JS. Structural Characterization of Dihydrofolate Reductase Complexes by Top-Down Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2015; 137:9128-35. [PMID: 26125523 DOI: 10.1021/jacs.5b04628] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The stepwise reduction of dihydrofolate to tetrahydrofolate entails significant conformational changes of dihydrofolate reductase (DHFR). Binary and ternary complexes of DHFR containing cofactor NADPH, inhibitor methotrexate (MTX), or both NADPH and MTX were characterized by 193 nm ultraviolet photodissociation (UVPD) mass spectrometry. UVPD yielded over 80% sequence coverage of DHFR and resulted in production of fragment ions that revealed the interactions between DHFR and each ligand. UVPD of the binary DHFR·NADPH and DHFR·MTX complexes led to an unprecedented number of fragment ions containing either an N- or C-terminal protein fragment still bound to the ligand via retention of noncovalent interactions. In addition, holo-fragments retaining both ligands were observed upon UVPD of the ternary DHFR·NADPH·MTX complex. The combination of extensive holo and apo fragment ions allowed the locations of the NADPH and MTX ligands to be mapped, with NADPH associated with the adenosine binding domain of DHFR and MTX interacting with the loop domain. These findings are consistent with previous crystallographic evidence. Comparison of the backbone cleavage propensities for apo DHFR and its holo counterparts revealed significant variations in UVPD fragmentation in the regions expected to experience conformational changes upon binding NADPH, MTX, or both ligands. In particular, the subdomain rotation and loop movements, which are believed to occur upon formation of the transition state of the ternary complex, are reflected in the UVPD mass spectra. The UVPD spectra indicate enhanced backbone cleavages in regions that become more flexible or show suppressed backbone cleavages for those regions either shielded by the ligand or involved in new intramolecular interactions. This study corroborates the versatility of 193 nm UVPD mass spectrometry as a sensitive technique to track enzymatic cycles that involve conformational rearrangements.
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Affiliation(s)
- Michael B Cammarata
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ross Thyer
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jake Rosenberg
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew Ellington
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
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76
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Hanozin E, Morsa D, De Pauw E. Energetics and structural characterization of isomers using ion mobility and gas-phase H/D exchange: Learning from lasso peptides. Proteomics 2015; 15:2823-34. [DOI: 10.1002/pmic.201400534] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 03/03/2015] [Accepted: 03/17/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Emeline Hanozin
- Mass Spectrometry Laboratory, Department of Chemistry; University of Liege; Liege Belgium
| | - Denis Morsa
- Mass Spectrometry Laboratory, Department of Chemistry; University of Liege; Liege Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, Department of Chemistry; University of Liege; Liege Belgium
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77
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Warnke S, von Helden G, Pagel K. Analyzing the higher order structure of proteins with conformer-selective ultraviolet photodissociation. Proteomics 2015; 15:2804-12. [PMID: 25644066 DOI: 10.1002/pmic.201400480] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/19/2014] [Accepted: 01/28/2015] [Indexed: 11/09/2022]
Abstract
The top-down approach in protein sequencing requires simple methods in which the analyte can be readily dissociated at every position along the backbone. In this context, ultraviolet photodissociation (UVPD) recently emerged as a promising tool because, in contrast to slow heating techniques such as CID, the absorption of UV light is followed by a rather statistically distributed cleavage of backbone bonds. As a result, nearly complete sequence coverage can be obtained. It is well known, however, that gas-phase proteins can adopt a variety of different, sometimes coexisting conformations and the influence of this structural diversity on the UVPD fragmentation behavior is not clear. Using ion mobility-UVPD-MS, we recently showed that UVPD is sensitive to the higher order structure of gas-phase proteins. In particular, the cis/trans isomerization of certain proline peptide bonds was shown to significantly influence the UVPD fragmentation pattern of two extended conformers of 11(+) ubiquitin. Building on these results, we here provide conformer-selective UVPD data for 7(+) ubiquitin ions, which are known to be present in a much more diverse and wider ensemble of different structures, ranging from very compact to highly extended species. Our data show that certain conformers fall into groups with similar UVPD fragmentation pattern. Surprisingly, however, the conformers within each group can differ tremendously in their collision cross-section. This indicates that the multiple coexisting conformations typically observed for 7(+) ubiquitin are caused by a few, not easily interconvertible, subpopulations.
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Affiliation(s)
- Stephan Warnke
- Fritz Haber Institute of the Max Planck Society, Berlin, Germany
| | - Gert von Helden
- Fritz Haber Institute of the Max Planck Society, Berlin, Germany
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society, Berlin, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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78
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Warnke S, Seo J, Boschmans J, Sobott F, Scrivens JH, Bleiholder C, Bowers MT, Gewinner S, Schöllkopf W, Pagel K, von Helden G. Protomers of Benzocaine: Solvent and Permittivity Dependence. J Am Chem Soc 2015; 137:4236-42. [DOI: 10.1021/jacs.5b01338] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Stephan Warnke
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany
| | - Jongcheol Seo
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany
| | - Jasper Boschmans
- Biomolecular
and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Frank Sobott
- Biomolecular
and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - James H. Scrivens
- School
of Life Sciences, University of Warwick, Coventry CV47AL, United Kingdom
| | - Christian Bleiholder
- Department
of Chemistry and Biochemistry, University of California Santa Barbara, Santa
Barbara, California 93106, United States
| | - Michael T. Bowers
- Department
of Chemistry and Biochemistry, University of California Santa Barbara, Santa
Barbara, California 93106, United States
| | - Sandy Gewinner
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany
| | - Wieland Schöllkopf
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Freie Universität Berlin, Institute of
Chemistry and Biochemistry − Organic Chemistry, Takustrasse 3, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany
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79
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Glover MS, Shi L, Fuller DR, Arnold RJ, Radivojac P, Clemmer DE. On the split personality of penultimate proline. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:444-52. [PMID: 25503299 PMCID: PMC4336576 DOI: 10.1007/s13361-014-1049-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/03/2014] [Accepted: 11/10/2014] [Indexed: 05/12/2023]
Abstract
The influence of the position of the amino acid proline in polypeptide sequences is examined by a combination of ion mobility spectrometry-mass spectrometry (IMS-MS), amino acid substitutions, and molecular modeling. The results suggest that when proline exists as the second residue from the N-terminus (i.e., penultimate proline), two families of conformers are formed. We demonstrate the existence of these families by a study of a series of truncated and mutated peptides derived from the 11-residue peptide Ser(1)-Pro(2)-Glu(3)-Leu(4)-Pro(5)-Ser(6)-Pro(7)-Gln(8)-Ala(9)-Glu(10)-Lys(11). We find that every peptide from this sequence with a penultimate proline residue has multiple conformations. Substitution of Ala for Pro residues indicates that multiple conformers arise from the cis-trans isomerization of Xaa(1)-Pro(2) peptide bonds as Xaa-Ala peptide bonds are unlikely to adopt the cis isomer, and examination of spectra from a library of 58 peptides indicates that ~80% of sequences show this effect. A simple mechanism suggesting that the barrier between the cis- and trans-proline forms is lowered because of low steric impedance is proposed. This observation may have interesting biological implications as well, and we note that a number of biologically active peptides have penultimate proline residues.
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Affiliation(s)
- Matthew S. Glover
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Liuqing Shi
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Daniel R. Fuller
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Randy J. Arnold
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Predrag Radivojac
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN 47405, USA
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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80
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Markworth PB, Adamson BD, Coughlan NJA, Goerigk L, Bieske EJ. Photoisomerization action spectroscopy: flicking the protonated merocyanine–spiropyran switch in the gas phase. Phys Chem Chem Phys 2015; 17:25676-88. [DOI: 10.1039/c5cp01567g] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular ions drifting through buffer gas are exposed to tunable laser light causing a detectable change in their collision cross section and arrival time at the ion detector. The effect can be exploited to obtain action electronic spectra for selected molecular isomers in the gas phase.
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Affiliation(s)
| | - Brian D. Adamson
- School of Chemistry
- The University of Melbourne
- Melbourne
- Australia
| | | | - Lars Goerigk
- School of Chemistry
- The University of Melbourne
- Melbourne
- Australia
| | - Evan J. Bieske
- School of Chemistry
- The University of Melbourne
- Melbourne
- Australia
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81
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Ridgeway ME, Silveira JA, Meier JE, Park MA. Microheterogeneity within conformational states of ubiquitin revealed by high resolution trapped ion mobility spectrometry. Analyst 2015; 140:6964-72. [DOI: 10.1039/c5an00841g] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The present work employs trapped ion mobility spectrometry (TIMS) for the analysis of ubiquitin ions known to display a multitude of previously unresolved interchangeable conformations upon electrospray ionization.
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82
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Urner LH, Thota BNS, Nachtigall O, Warnke S, von Helden G, Haag R, Pagel K. Online monitoring the isomerization of an azobenzene-based dendritic bolaamphiphile using ion mobility-mass spectrometry. Chem Commun (Camb) 2015; 51:8801-4. [DOI: 10.1039/c5cc01488c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The isomerization process of a new azobenzene-based bolaamphiphile was monitored online using ion mobility-mass spectrometry.
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Affiliation(s)
- Leonhard H. Urner
- Freie Universität Berlin
- Department of Biology
- Chemistry and Pharmacy
- Berlin
- Germany
| | - Bala N. S. Thota
- Freie Universität Berlin
- Department of Biology
- Chemistry and Pharmacy
- Berlin
- Germany
| | - Olaf Nachtigall
- Freie Universität Berlin
- Department of Biology
- Chemistry and Pharmacy
- Berlin
- Germany
| | | | - Gert von Helden
- Fritz Haber Institute of the Max Planck Society
- Department of Molecular Physics
- Berlin
- Germany
| | - Rainer Haag
- Freie Universität Berlin
- Department of Biology
- Chemistry and Pharmacy
- Berlin
- Germany
| | - Kevin Pagel
- Freie Universität Berlin
- Department of Biology
- Chemistry and Pharmacy
- Berlin
- Germany
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83
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O'Brien JP, Li W, Zhang Y, Brodbelt JS. Characterization of native protein complexes using ultraviolet photodissociation mass spectrometry. J Am Chem Soc 2014; 136:12920-8. [PMID: 25148649 DOI: 10.1021/ja505217w] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ultraviolet photodissociation (UVPD) mass spectrometry (MS) was used to characterize the sequences of proteins in native protein-ligand and protein-protein complexes and to provide auxiliary information about the binding sites of the ligands and protein-protein interfaces. UVPD outperformed collisional induced dissociation (CID), higher-energy collisional dissociation (HCD), and electron transfer dissociation (ETD) in terms of yielding the most comprehensive diagnostic primary sequence information about the proteins in the complexes. UVPD also generated noncovalent fragment ions containing a portion of the protein still bound to the ligand which revealed some insight into the nature of the binding sites of myoglobin/heme, eIF4E/m(7)GTP, and human peptidyl-prolyl cis-trans isomerase 1 (Pin1) in complex with the peptide derived from the C-terminal domain of RNA polymerase II (CTD). Noncovalently bound protein-protein fragment ions from oligomeric β-lactoglobulin dimers and hexameric insulin complexes were also produced upon UVPD, providing some illumination of tertiary and quaternary protein structural features.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry, ‡Department of Molecular Biosciences, and §Institute for Cellular and Molecular Biology, The University of Texas at Austin , 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
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