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He M, Jiang Y, Wang X, Zhao Y, Ye S, Ma J, Fang X, Xu W. Rapid characterization of structure-dependency gas-phase ion/ion reaction via accumulative tandem MS. Talanta 2018; 195:17-22. [PMID: 30625528 DOI: 10.1016/j.talanta.2018.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/24/2018] [Accepted: 11/05/2018] [Indexed: 12/25/2022]
Abstract
To enable the rapid detection of biomolecule reactivity and reaction sites, we developed a method based on gas-phase ion/ion reaction and accumulative tandem mass spectrometry (MS). Structure-dependency reactions in gas-phase were performed between biomolecule ions and their reaction partner ions with opposite polarities in a quadrupole ion trap. Gas-phase peptide bioconjugation with pyridoxal-5-phosphate (PLP) was chosen as a proof-of-principle example. It is found that the Coulomb attraction force holds reaction partners close together, which increasing the reaction probability. Post reaction, reaction sites were identified by the consequent accumulative tandem MS method, in which informative product ions in low abundance were enriched by more than 100 times in another quadrupole ion trap. With enough product ions, tandem MS was performed, and reaction sites could be identified unambiguously. Since those reactions are normally biomolecular structure dependent, density functional theory (DFT) calculations were also carried out to understand the reaction mechanism. The method allows for rapid characterization of structure dependent reactivity of a biomolecule, and opens a new avenue for drug development and biomolecule structure analyses.
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Affiliation(s)
- Muyi He
- College of Information Science, Shenzhen University, Shenzhen 518060, China; School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian Dist, Beijing 100081, PR China
| | - You Jiang
- National Institute of Metrology, No.18, Bei San Huan Dong Lu, Chaoyang Dist, Beijing 100013, PR China
| | - Xiaofeng Wang
- Institute of High Energy Physics, Chinese Academy of Science, Beijing, PR China
| | - Yue Zhao
- School of Chemistry, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian Dist, Beijing, PR China
| | - Sijian Ye
- Department of Chemistry & Environmental Engineering, Changchun University of Science and Technology, Changchun, Jilin, PR China
| | - Jiabi Ma
- School of Chemistry, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian Dist, Beijing, PR China
| | - Xiang Fang
- National Institute of Metrology, No.18, Bei San Huan Dong Lu, Chaoyang Dist, Beijing 100013, PR China.
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian Dist, Beijing 100081, PR China.
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Baldassarre M, Li C, Eremina N, Goormaghtigh E, Barth A. Simultaneous Fitting of Absorption Spectra and Their Second Derivatives for an Improved Analysis of Protein Infrared Spectra. Molecules 2015; 20:12599-622. [PMID: 26184143 PMCID: PMC6331840 DOI: 10.3390/molecules200712599] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 02/06/2023] Open
Abstract
Infrared spectroscopy is a powerful tool in protein science due to its sensitivity to changes in secondary structure or conformation. In order to take advantage of the full power of infrared spectroscopy in structural studies of proteins, complex band contours, such as the amide I band, have to be decomposed into their main component bands, a process referred to as curve fitting. In this paper, we report on an improved curve fitting approach in which absorption spectra and second derivative spectra are fitted simultaneously. Our approach, which we name co-fitting, leads to a more reliable modelling of the experimental data because it uses more spectral information than the standard approach of fitting only the absorption spectrum. It also avoids that the fitting routine becomes trapped in local minima. We have tested the proposed approach using infrared absorption spectra of three mixed α/β proteins with different degrees of spectral overlap in the amide I region: ribonuclease A, pyruvate kinase, and aconitase.
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Affiliation(s)
- Maurizio Baldassarre
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
| | - Chenge Li
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
| | - Nadejda Eremina
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
| | - Erik Goormaghtigh
- Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium.
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
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