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Li J, Lyu W, Rossetti G, Konijnenberg A, Natalello A, Ippoliti E, Orozco M, Sobott F, Grandori R, Carloni P. Proton Dynamics in Protein Mass Spectrometry. J Phys Chem Lett 2017; 8:1105-1112. [PMID: 28207277 DOI: 10.1021/acs.jpclett.7b00127] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas phase, and its impact on protein structural determinants, have not been investigated so far. Here, we address this issue by a multistep simulation strategy on a pharmacologically relevant peptide, the N-terminal residues of amyloid-β peptide (Aβ(1-16)). Our calculations reproduce the experimental maximum charge state from ESI-MS and are also in fair agreement with collision cross section (CCS) data measured here by ESI/IM-MS. Although the main structural features are preserved, subtle conformational changes do take place in the first ∼0.1 ms of dynamics. In addition, intramolecular proton dynamics processes occur on the picosecond-time scale in the gas phase as emerging from quantum mechanics/molecular mechanics (QM/MM) simulations at the B3LYP level of theory. We conclude that proton transfer phenomena do occur frequently during fly time in ESI-MS experiments (typically on the millisecond time scale). However, the structural changes associated with the process do not significantly affect the structural determinants.
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Affiliation(s)
- Jinyu Li
- College of Chemistry, Fuzhou University , 350002 Fuzhou, China
| | - Wenping Lyu
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH-Aachen University , 52056 Aachen, Germany
- Computation-Based Science and Technology Research Center, Cyprus Institute , 2121 Aglantzia, Nicosia, Cyprus
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University , 52062 Aachen, Germany
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich , D-52425 Jülich, Germany
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp , 2000 Antwerpen, Belgium
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Emiliano Ippoliti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
| | - Modesto Orozco
- Joint BSC-IRB Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona , Avgda Diagonal 647, Barcelona 08028, Spain
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp , 2000 Antwerpen, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- JARA-HPC, 52425 Jülich, Germany
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Wang J, Song W, Hu X, Yu Z, Liu Y, Liu R. Comparative studies on the discrepant fragmentation mechanisms of the GLy-Asp-Gly-Arg and Arg-Gly-Asp-Gly: evidence for the mobile proton model. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2014; 20:317-325. [PMID: 25420344 DOI: 10.1255/ejms.1287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The fragmentation mechanisms of singly protonated Gly-Asp-Gly-Arg (GDGRI and Arg-Gly-Asp-Gly (RGDGJ were investigated by mass spectrometry and theoretical methods. Both protonated molecules are fragmented mainly at the Asp-Gly amide bond C-terminal to Asp, as supported by quantum chemical calculations. Charge distributions of C and N atoms (Qc + QN) on the amide bonds were collected when the ionizing proton was fixed at different nitrogen atoms along the backbone for each peptide. Compared with the neutral molecules, the total charges of C and N atoms (Qc + QN] for the singly charged peptides tended to be negative when the proton was located at the backbone nitrogen atoms. A relatively larger value of QC + QN corresponds to a higher trend of fragmentation, which is consistent with the experimental relative abundances data that the predominant ions are y2 for [GDGR + H]+ and b3 for [RGDG + H]+. Also, the anhydride mechanism driven by the C-terminal COOH for [RGDG + H]+ was explored by a quantum-mechanical/molecular-mechanical method. Calculations indicate that the protonated peptide can be cleaved through an unusual charge-directed pathway by forming a salt bridge at the C-termini. The formation of the anhydride linkage is much more feasible since this process needs very little energy and is exother- mic, though the subsequent nucleophilic attack on the Asp carbonyl carbon is more difficult. The combined experimental and theoretical methods substantiate the mobile proton model, which opens a way to analyze quantitatively the discrepant fragmentation of dissociated peptides in peptide/protein identification.
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Affiliation(s)
- Jinhu Wang
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
- College of Chemistry Chemical Engineering and Material Science, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Wei Song
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Xinxin Hu
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Zehua Yu
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Yongjun Liu
- Key Lab of Theoretical and Computational Chemistry in University of Shandong, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
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Sun F, Zong W, Liu R, Wang M, Zhang P, Xu Q. The relative charge ratio between C and N atoms in amide bond acts as a key factor to determine peptide fragment efficiency in different charge states. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1857-1862. [PMID: 20688527 DOI: 10.1016/j.jasms.2010.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Revised: 06/24/2010] [Accepted: 06/30/2010] [Indexed: 05/29/2023]
Abstract
The influence of charge state on the peptide dissociation behavior in tandem mass spectrometry (MS/MS) is worthy of discussion. Comparative studies of singly- and doubly-protonated peptide molecules are performed to explore the effect and mechanism of charge state on peptide fragmentation. In view of the charge-directed cleavage of protonated peptides described in the mobile proton model, radiolytic oxidation was applied to change the charge distribution of peptides but retain the sequence. Experimental studies of collision energy-dependent fragmentation efficiencies coupled with quantum chemical calculations indicated that the cleavage of ARRA and its side-chain oxidation products with oxygen atoms added followed a trend that doubly-protonated peptides fragment more easily than singly-protonated forms, while the oxidation product with the guanidine group deleted showed the opposite trend. By analyzing the charge distribution around the amide bonds, we found that the relative charge ratios between C and N atoms (Q(C)/Q(N)) in the amide bonds provided a reasonable explanation for peptide fragmentation efficiencies. An increase of the Q(C)/Q(N) value of the amide bond means that a peptide fragments more easily, and vice versa. The results described in this paper provide an experimental and calculation strategy for predicting peptide fragmentation efficiency.
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Affiliation(s)
- Feng Sun
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment and Health, Jinan, PR China
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Tureček F, Panja S, Wyer JA, Ehlerding A, Zettergren H, Nielsen SB, Hvelplund P, Bythell B, Paizs B. Carboxyl-Catalyzed Prototropic Rearrangements in Histidine Peptide Radicals upon Electron Transfer: Effects of Peptide Sequence and Conformation. J Am Chem Soc 2009; 131:16472-87. [DOI: 10.1021/ja9050229] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Subhasis Panja
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Jean A. Wyer
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Anneli Ehlerding
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Henning Zettergren
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Steen Brøndsted Nielsen
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Preben Hvelplund
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Benjamin Bythell
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Béla Paizs
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
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Pfeifer N, Leinenbach A, Huber CG, Kohlbacher O. Improving Peptide Identification in Proteome Analysis by a Two-Dimensional Retention Time Filtering Approach. J Proteome Res 2009; 8:4109-15. [PMID: 19492844 DOI: 10.1021/pr900064b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nico Pfeifer
- Division for Simulation of Biological Systems, Eberhard Karls University Tübingen, 72076 Tübingen, Germany, Department of Chemistry, Instrumental Analysis and Bioanalysis, Saarland University, 66123 Saarbrücken, Germany, and Department of Molecular Biology, Division of Chemistry, University of Salzburg, 5020 Salzburg, Austria
| | - Andreas Leinenbach
- Division for Simulation of Biological Systems, Eberhard Karls University Tübingen, 72076 Tübingen, Germany, Department of Chemistry, Instrumental Analysis and Bioanalysis, Saarland University, 66123 Saarbrücken, Germany, and Department of Molecular Biology, Division of Chemistry, University of Salzburg, 5020 Salzburg, Austria
| | - Christian G. Huber
- Division for Simulation of Biological Systems, Eberhard Karls University Tübingen, 72076 Tübingen, Germany, Department of Chemistry, Instrumental Analysis and Bioanalysis, Saarland University, 66123 Saarbrücken, Germany, and Department of Molecular Biology, Division of Chemistry, University of Salzburg, 5020 Salzburg, Austria
| | - Oliver Kohlbacher
- Division for Simulation of Biological Systems, Eberhard Karls University Tübingen, 72076 Tübingen, Germany, Department of Chemistry, Instrumental Analysis and Bioanalysis, Saarland University, 66123 Saarbrücken, Germany, and Department of Molecular Biology, Division of Chemistry, University of Salzburg, 5020 Salzburg, Austria
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