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Kostyukevich YI, Kononikhin AS, Indeykina MI, Popov IA, Bocharov KV, Spassky AI, Kozin SA, Makarov AA, Nikolaev EN. Secondary structure of Aβ(1–16) complexes with zinc: A study in the gas phase using deuterium/hydrogen exchange and ultra-high-resolution mass spectrometry. Mol Biol 2017. [DOI: 10.1134/s0026893317030104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kostyukevich Y, Shulga AA, Kononikhin A, Popov I, Nikolaev E, Deyev S. CID fragmentation, H/D exchange and supermetallization of Barnase-Barstar complex. Sci Rep 2017; 7:6176. [PMID: 28733680 PMCID: PMC5522418 DOI: 10.1038/s41598-017-06507-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 06/13/2017] [Indexed: 01/02/2023] Open
Abstract
The barnase-barstar complex is one of the most stable protein-protein complexes and has a very wide range of possible applications. Here we report the use of top-down mass spectrometry for the investigation of the structure of this complex, its ionization via ESI, isolation and fragmentation. It was found that the asymmetry of the resulting charge state distributions of the protein monomer product ions increased as the charge state of the precursor ions increased. For the investigation of the 3D structure of the complex, the gas phase H/D exchange reaction was used. In addition, supermetallized ions of the complex with Zn were produced and investigated. It was observed that an increase in the number of metals bound to the complex results in a change in complex stability and the charge distribution between protein fragment. Analysis of the fragmentation pattern of the supermetallized complex [bn-b* + 5Zn]10+ indicated that this ion is present in different conformations with different charges and Zn distributions. Since Zn cannot migrate, such structures must be formed during ionization.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo, 143025, Russian Federation.,Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38, k.2, 119334, Moscow, Russia.,Emanuel Institute for Biochemical Physics, Russian Academy of Sciences Kosygina st. 4, 119334, Moscow, Russia.,Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Aleksej A Shulga
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya str., Moscow, 117997, Russian Federation
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38, k.2, 119334, Moscow, Russia.,Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Igor Popov
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences Kosygina st. 4, 119334, Moscow, Russia.,Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo, 143025, Russian Federation. .,Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38, k.2, 119334, Moscow, Russia. .,Emanuel Institute for Biochemical Physics, Russian Academy of Sciences Kosygina st. 4, 119334, Moscow, Russia. .,Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia.
| | - Sergey Deyev
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya str., Moscow, 117997, Russian Federation.,National Research Tomsk Polytechnic University, 30, av. Lenina, Tomsk, 634050, Russia
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Kostyukevich Y, Kononikhin A, Popov I, Nikolaev E. Thermal dissociation of ions limits the degree of the gas-phase H/D exchange at the atmospheric pressure. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:204-209. [PMID: 28152260 DOI: 10.1002/jms.3917] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/18/2017] [Accepted: 01/27/2017] [Indexed: 06/06/2023]
Abstract
We present the application of the extended desolvating capillaries for increasing the degree of the gas-phase hydrogen/deuterium exchange reaction at atmospheric pressure. The use of the extended capillaries results in the increase of the time that ions spend in the high pressure region, what leads to the significant improvement of the efficiency of the reaction. For the small protein ubiquitin, it was observed that for the same temperature, the number of exchanges increases with the decrease of the charge state so that the lowest charge state can exchange twice the number of hydrogen than the highest one. With the increase of the temperature, the difference decreases, and eventually, the number of exchanges equalizes for all charge states. The value of this temperature and the corresponding number of exchanges depend on the geometric parameters of the capillary. Further increase of the temperature leads to the thermal dissociation of the protein ion. The observed b/y fragments are identical to those produced by collision-induced dissociation performed in the ion trap. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Y Kostyukevich
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - A Kononikhin
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - I Popov
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - E Nikolaev
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
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Evaporation of the charged droplets in the heating flow tube under atmospheric pressure: observation of the H/D exchange and supermetallization. MENDELEEV COMMUNICATIONS 2016. [DOI: 10.1016/j.mencom.2016.09.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kostyukevich Y, Borisova L, Kononikhin A, Popov I, Kukaev E, Nikolaev E. Thermal desorption combined with atmospheric pressure photo ionization for the analysis of volatile compounds and its possible applications. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2016; 22:313-317. [PMID: 27900861 DOI: 10.1255/ejms.1442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report an approach to study volatile organic compounds based on thermal desorption combined with atmospheric pressure photo ionization. The approach allows the sequential evaporation of different fractions of the sample, which simplifies the mass spectrum. We have applied the developed method for the detection of petroleum in vegetable oil. We have shown that in the negative mode, ions of fatty acids corresponding to vegetable oil dominates, while in the positive mode under relatively low temperature the light fraction of petroleum rapidly evaporates making it easy detectable.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation and Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia and Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia and Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia.
| | - Ludmila Borisova
- National Research University Higher School of Economics, 20 Miasnitskaya Ulitsa, Moscow 101000, Russia
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia and Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Igor Popov
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia and Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Eugene Kukaev
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia and Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation and Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia and Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia and Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
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Kostyukevich Y, Zherebker A, Kononikhin A, Indeykina M, Popov I, Nikolaev E. Letter: Electron-capture dissociation and collision-induced dissociation fragmentation of the supermetallized complexes of Substance P with potassium, cesium and silver. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2016; 22:91-95. [PMID: 27419902 DOI: 10.1255/ejms.1411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report the investigation of the collision-induced dissociation (CID) and electron-capture dissociation (ECD) product fragmentations of the supermetallized complexes of Substance P and several monovalent metals. The supermetallization is the phenomenon of the formation of the complex ion peptide-metals in the gas phase when the peptide accepts an unexpectedly large number of metals. We have obtained and investigated complexes with the incorporation of up to four cesium (Cs), up to five potassium (K) and up to six silver (Ag) atoms. The current research reveals crucial changes in the complex behavior in the cases of different metals. It was observed that in CID spectra of complexes with Cs and K is dominated by the peak corresponding to the loss of metal cation while ECD gives a rich fragmentation. In the case of complexes with Ag, the loss of Ag(+) occurs in ECD while the CID shows a good fragmentation.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation. Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation..
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation. Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Lomonosov Moscow State University, Department of Chemistry, Leninskie Gory 1-3, 119991 Moscow, Russian Federation..
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation.
| | - Maria Indeykina
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation.
| | - Igor Popov
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation.
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation. Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation..
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Kukaev EN, Kononikhin AS, Starodubtseva NL, Kostyukevich YI, Popova IA, Chagovets V, Nagornov KO, Nikolaev EN. Atmospheric pressure thermal ionization ion source for peptide analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2016; 22:307-311. [PMID: 27900860 DOI: 10.1255/ejms.1443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel atmospheric pressure thermal ionization (APTI) ion source was developed for the analysis of liquid samples. The feasibility of the ion source was demonstrated on peptides using two configurations-assisted by hot wire or hot surface. Microalloyed molybdenum, used as a thermal ion- emitter, notably facilitated the formation of multiply-charged ions, but fragmentation products were still observed. Peptide fragmentation accompanying thermal ionization can be used for peptide identification. The described method is promising for studies of biological samples with minimal pre-treatment.
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Affiliation(s)
- Eugenii N Kukaev
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russian Federation and Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Alexey S Kononikhin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russian Federation and V.I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Natalia L Starodubtseva
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation and V.I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Yury I Kostyukevich
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russian Federation and Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation and Skolkovo Institute of Science and Technology, 143025 Skolkovo, Moscow region, Russian Federation
| | - Igor A Popova
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russian Federation and Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation and V.I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Vitaliy Chagovets
- V.I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Konstantin O Nagornov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Eugene N Nikolaev
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russian Federation and Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation and Skolkovo Institute of Science and Technology, 143025 Skolkovo, Moscow region, Russian Federation
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