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Dyakova YA, Kovalchuk MV. Protein Self-Assembly in Crystals and Films. CRYSTALLOGR REP+ 2022. [DOI: 10.1134/s1063774522050030] [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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Folomeshkin MS, Boikova AS, Volkovsky YA, Marchenkova MA, Prosekov PA, Seregin AY. Refined Structure of Langmuir Lysozyme Films on Single-Crystal Silicon Wafers According to X-Ray Reflectivity Data. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520060152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Marchenkova MA, Kuranova IP, Timofeev VI, Boikova AS, Dorovatovskii PV, Dyakova YA, Ilina KB, Pisarevskiy YV, Kovalchuk MV. The binding of precipitant ions in the tetragonal crystals of hen egg white lysozyme. J Biomol Struct Dyn 2019; 38:5159-5172. [PMID: 31760865 DOI: 10.1080/07391102.2019.1696706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The bonds between lysozyme molecules and precipitant ions in single crystals grown with chlorides of several metals are analysed on the basis of crystal structure data. Crystals of tetragonal hen egg lysozyme (HEWL) were grown with chlorides of several alkali and transition metals (LiCl, NaCl, KCl, NiCl2 and CuCl2) as precipitants and the three-dimensional structures were determined at 1.35 Å resolution by X-ray diffraction method. The positions of metal and chloride ions attached to the protein were located, divided into three groups and analysed. Some of them, in accordance with the recently proposed and experimentally confirmed crystal growth model, provide connections in protein dimers and octamers that are precursor clusters in the crystallization lysozyme solution. The first group, including Cu+2, Ni+2 and Na+1 cations, binds specifically to the protein molecule. The second group consists of metal and chloride ions bound inside the dimers and octamers. The third group of ions can participate in connections between the octamers that are suggested as building units during the crystal growth. The arrangement of chloride and metal ions associated with lysozyme molecule at all stages of the crystallization solution formation and crystal growth is discussed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Margarita A Marchenkova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Inna P Kuranova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Anastasiia S Boikova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | | | - Yulia A Dyakova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Kseniia B Ilina
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Yury V Pisarevskiy
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Mikhail V Kovalchuk
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation.,The Faculty of Physics, St. Petersburg State University, St. Petersburg, Russian Federation
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Marchenkova MA, Konarev PV, Rakitina TV, Timofeev VI, Boikova AS, Dyakova YA, Ilina KB, Korzhenevskiy DA, Yu Nikolaeva A, Pisarevsky YV, Kovalchuk MV. Dodecamers derived from the crystal structure were found in the pre-crystallization solution of the transaminase from the thermophilic bacterium Thermobaculum terrenum by small-angle X-ray scattering. J Biomol Struct Dyn 2019; 38:2939-2944. [PMID: 31347457 DOI: 10.1080/07391102.2019.1649195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The pre-crystallization solution of the transaminase from Thermobaculum terrenum (TaTT) has been studied by small-angle X-ray scattering (SAXS). Regular changes in the oligomeric composition of the protein were observed after the addition of the precipitant. Comparison of the observed oligomers with the crystal structure of TaTT (PDB ID 6GKR) shows that dodecamers may act as building blocks in the growth of transaminase single crystals. Correlating of these results to the similar X-ray studies of other proteins suggests that SAXS may be a valuable tool for searching optimum crystallization conditions. AbbreviationSAXSsmall-angle X-ray scatteringTatransaminaseTaTTtransaminase from Thermobaculum terrenumPLPpyridoxal-5'-phosphateR-PEAR-(þ)-1-phenylethylamineBCATbranched-chain amino acid aminotransferaseDAATD-aminoacid aminotransferaseR-TAR-amine:pyruvate transaminaseCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Margarita A Marchenkova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Petr V Konarev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Tatiana V Rakitina
- National Research Centre 'Kurchatov Institute', Moscow, Russian Federation.,Shemyakin - Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Hormonal Regulation Proteins, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Anastasiia S Boikova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Yulia A Dyakova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Kseniia B Ilina
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | | | - Alena Yu Nikolaeva
- National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Yurii V Pisarevsky
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Mikhail V Kovalchuk
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation.,St. Petersburg State University, St. Petersburg, Russian Federation
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Kovalchuk MV, Alekseeva OA, Blagov AE, Ilyushin GD, Il’ina KB, Konarev PV, Lomonov VA, Pisarevsky YV, Peters GS. Investigation of the Structure of Crystal-Forming Solutions of Potassium Dihydrogen Phosphate K(H2PO4) (KDP type) on the Basis of Modeling Precursor Clusters and According to Small-Angle X-Ray Scattering Data. CRYSTALLOGR REP+ 2019. [DOI: 10.1134/s1063774519010140] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Dyakova YA, Boikova AS, Ilina KB, Konarev PV, Marchenkova MA, Pisarevsky YV, Timofeev VI, Kovalchuk MV. Study of the Influence of a Precipitant Cation on the Formation of Oligomers in Crystallization Solutions of Lysozyme Protein. CRYSTALLOGR REP+ 2019. [DOI: 10.1134/s1063774519010061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kovalchuk MV, Boikova AS, Dyakova YA, Ilina KB, Konarev PV, Kryukova AE, Marchenkova MA, Pisarevsky YV, Timofeev VI. Pre-crystallization phase formation of thermolysin hexamers in solution close to crystallization conditions. J Biomol Struct Dyn 2018; 37:3058-3064. [DOI: 10.1080/07391102.2018.1507839] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Mikhail V. Kovalchuk
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
- St. Petersburg State University, St. Petersburg, Russian Federation
| | - Anastasiia S. Boikova
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Yulia A. Dyakova
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Kseniia B. Ilina
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Petr V. Konarev
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Alyona E. Kryukova
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Margarita A. Marchenkova
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Yurii V. Pisarevsky
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir I. Timofeev
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
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Kordonskaya YV, Timofeev VI, Dyakova YA, Marchenkova MA, Pisarevsky YV, Podshivalov DD, Kovalchuk MV. Study of the Behavior of Lysozyme Oligomers in Solutions by the Molecular Dynamics Method. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518060196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Boikova AS, D’yakova YA, Il’ina KB, Konarev PV, Kryukova AE, Marchenkova MA, Pisarevskii YV, Koval’chuk MV. Investigation of the Pre-crystallization Stage of Proteinase K in Solution (Influence of Temperature and Precipitant Type) by Small-Angle X-Ray Scattering. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518060068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Popov AM, Boikova AS, Volkov VV, D’yakova YA, Il’ina KB, Konarev PV, Marchenkova MA, Peters GS, Pisarevskii YV, Koval’chuk MV. Microfluidic Cell for Studying the Precrystallization Stage Structure of Protein Solutions by Small-Angle X-Ray Scattering. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518050231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Boikova AS, D’yakova YA, Il’ina KB, Marchenkova MA, Seregin AY, Prosekov PA, Volkovsky YA, Pisarevsky YV, Koval’chuk MV. Fabrication of Multilayer Films on the Basis of Lysozyme Protein and Precipitant (Iodide and Potassium) Ions on a Silicon Substrate by the Modified Langmuir–Schaefer Method. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518050061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Boikova AS, D’yakova YA, Il’ina KB, Konarev PV, Kryukova AE, Marchenkova MA, Blagov AE, Pisarevskii YV, Koval’chuk MV. Small-angle X-ray scattering study of the influence of solvent replacement (from H2O to D2O) on the initial crystallization stage of tetragonal lysozyme. CRYSTALLOGR REP+ 2017. [DOI: 10.1134/s1063774517060074] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kovalchuk MV, Boikova AS, Dyakova YA, Marchenkova MA, Opolchentsev AM, Pisarevsky YV, Prosekov PA, Seregin AY. Modification of the Langmuir–Schaefer method for fabrication of ordered protein films. CRYSTALLOGR REP+ 2017. [DOI: 10.1134/s1063774517040125] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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