Works by Timofeev, Vladimir I.

Results: 36

Crystal structure of mutant carboxypeptidase T from Thermoactinomyces vulgaris with an implanted S1′ subsite from pancreatic carboxypeptidase B.

Published in:

Acta Crystallographica: Section F, Structural Biology Communications, 2018, v. 74, n. 10, p. 638, doi. 10.1107/S2053230X18011962

By:

Akparov, Valery Kh.;
Timofeev, Vladimir I.;
Kuranova, Inna P.;
Rakitina, Tatiana V.

Publication type:

Article

Crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with acyclovir.

Published in:

Acta Crystallographica: Section F, Structural Biology Communications, 2018, v. 74, n. 7, p. 402, doi. 10.1107/S2053230X18008087

By:

Timofeev, Vladimir I.;
Zhukhlistova, Nadezhda E.;
Abramchik, Yuliya A.;
Muravieva, Tatiana I.;
Esipov, Roman S.;
Kuranova, Inna P.

Publication type:

Article

Crystal structure of Escherichia coli purine nucleoside phosphorylase in complex with 7‐deazahypoxanthine.

Published in:

Acta Crystallographica: Section F, Structural Biology Communications, 2018, v. 74, n. 6, p. 355, doi. 10.1107/S2053230X18006337

By:

Timofeev, Vladimir I.;
Zhukhlistova, Nadezhda E.;
Abramchik, Yuliya A.;
Fateev, Ilya I.;
Kostromina, Maria A.;
Muravieva, Tatiana I.;
Esipov, Roman S.;
Kuranova, Inna P.

Publication type:

Article

14C Chronology of Archaeological Sites in European Russia and Changes in Environmental Processes: A Database Investigation

Published in:

Radiocarbon, 1998, v. 40, n. 2, p. 759

By:

Zaitseva, Ganna I.;
Dergachev, Valentin A.;
Timofeev, Vladimir I.;
Sementsov, Anatoly A.

Publication type:

Article

14c Chronology of Archaeological Sites in European Russia and Changes in Environmental Processes: A Database Investigation

Published in:

Radiocarbon, 1998, v. 40, n. 1, p. 759

By:

Zaitseva, Ganna I.;
Dergachev, Valentin A.;
Timofeev, Vladimir I.;
Sementsov, Anatoly A.

Publication type:

Article

How the Hinge Region Affects Interactions between the Catalytic and β-Propeller Domains in Oligopeptidase B.

Published in:

Crystals (2073-4352), 2023, v. 13, n. 12, p. 1642, doi. 10.3390/cryst13121642

By:

Timofeev, Vladimir I.;
Gaponov, Yury A.;
Petrenko, Dmitry E.;
Peters, Georgy S.;
Agapova, Yulia K.;
Nikolaeva, Alena Y.;
Mikhailova, Anna G.;
Rakitina, Tatiana V.

Publication type:

Article

Study of the Formation of Precursor Clusters in an Aqueous Solution of KH 2 PO 4 by Small-Angle X-ray Scattering and Molecular Dynamics.

Published in:

Crystals (2073-4352), 2023, v. 13, n. 11, p. 1577, doi. 10.3390/cryst13111577

By:

Sukhanov, Andrey E.;
Konarev, Petr V.;
Timofeev, Vladimir I.;
Garipov, Ildar F.;
Smirnova, Ekaterina S.;
Peters, Georgy S.;
Ilina, Kseniia B.;
Pisarevsky, Yury V.;
Alekseeva, Olga A.;
Kovalchuk, Mikhail V.

Publication type:

Article

An Algorithm for the Development of a Recombinant Antiherpetic Subunit Vaccine Combining the Crystal Structure Analysis, AlphaFold2-Based Modeling, and Immunoinformatics.

Published in:

Crystals (2073-4352), 2023, v. 13, n. 10, p. 1416, doi. 10.3390/cryst13101416

By:

Rakitina, Tatiana V.;
Smirnova, Evgeniya V.;
Podshivalov, David D.;
Timofeev, Vladimir I.;
Komolov, Aleksandr S.;
Vlaskina, Anna V.;
Gaeva, Tatiana N.;
Vasilov, Raif G.;
Dyakova, Yulia A.;
Kovalchuk, Mikhail V.

Publication type:

Article

Comparison of histone-like HU protein DNA-binding properties and HU/IHF protein sequence alignment.

Published in:

PLoS ONE, 2017, v. 12, n. 11, p. 1, doi. 10.1371/journal.pone.0188037

By:

Kamashev, Dmitri;
Agapova, Yulia;
Rastorguev, Sergey;
Talyzina, Anna A.;
Boyko, Konstantin M.;
Korzhenevskiy, Dmitry A.;
Vlaskina, Anna;
Vasilov, Raif;
Timofeev, Vladimir I.;
Rakitina, Tatiana V.

Publication type:

Article

Structure-based inhibitors targeting the alpha-helical domain of the Spiroplasma melliferum histone-like HU protein.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-72113-4

By:

Agapova, Yuliya K.;
Altukhov, Dmitry A.;
Timofeev, Vladimir I.;
Stroylov, Victor S.;
Mityanov, Vitaly S.;
Korzhenevskiy, Dmitry A.;
Vlaskina, Anna V.;
Smirnova, Eugenia V.;
Bocharov, Eduard V.;
Rakitina, Tatiana V.

Publication type:

Article

First Crystal Structure of Bacterial Oligopeptidase B in an Intermediate State: The Roles of the Hinge Region Modification and Spermine.

Published in:

Biology (2079-7737), 2021, v. 10, n. 10, p. 1021, doi. 10.3390/biology10101021

By:

Petrenko, Dmitry E.;
Timofeev, Vladimir I.;
Britikov, Vladimir V.;
Britikova, Elena V.;
Kleymenov, Sergey Y.;
Vlaskina, Anna V.;
Kuranova, Inna P.;
Mikhailova, Anna G.;
Rakitina, Tatiana V.

Publication type:

Article

The Role of Cations and Anions in the Formation of Crystallization Oligomers in Protein Solutions as Revealed by Combination of Small-Angle X-ray Scattering and Molecular Dynamics.

Published in:

Crystals (2073-4352), 2022, v. 12, n. 6, p. 751, doi. 10.3390/cryst12060751

By:

Marchenkova, Margarita A.;
Konarev, Petr V.;
Kordonskaya, Yuliya V.;
Ilina, Kseniia B.;
Pisarevsky, Yury V.;
Soldatov, Alexander V.;
Timofeev, Vladimir I.;
Kovalchuk, Mikhail V.

Publication type:

Article

Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation.

Published in:

Crystals (2073-4352), 2022, v. 12, n. 5, p. N.PAG, doi. 10.3390/cryst12050712

By:

Britikov, Vladimir V.;
Timofeev, Vladimir I.;
Petrenko, Dmitry E.;
Britikova, Elena V.;
Nikolaeva, Alena Y.;
Vlaskina, Anna V.;
Boyko, Konstantin M.;
Mikhailova, Anna G.;
Rakitina, Tatiana V.

Publication type:

Article

Identification of the Precursor Cluster in the Crystallization Solution of Proteinase K Protein by Molecular Dynamics Methods.

Published in:

Crystals (2073-4352), 2022, v. 12, n. 4, p. 484, doi. 10.3390/cryst12040484

By:

Kordonskaya, Yuliya V.;
Timofeev, Vladimir I.;
Marchenkova, Margarita A.;
Konarev, Petr V.

Publication type:

Article

The Role of Cations of the Precipitant in the Interaction of Protein Molecules in the Lysozyme Oligomers in Crystallization Solutions.

Published in:

Crystals (2073-4352), 2021, v. 11, n. 12, p. 1534, doi. 10.3390/cryst11121534

By:

Kordonskaya, Yuliya V.;
Timofeev, Vladimir I.;
Dyakova, Yulia A.;
Marchenkova, Margarita A.;
Pisarevsky, Yury V.;
Kovalchuk, Mikhail V.

Publication type:

Article

The Crystal Structure of Nα-p-tosyl-lysyl Chloromethylketone-Bound Oligopeptidase B from Serratia Proteamaculans Revealed a New Type of Inhibitor Binding.

Published in:

Crystals (2073-4352), 2021, v. 11, n. 11, p. 1438, doi. 10.3390/cryst11111438

By:

Timofeev, Vladimir I.;
Petrenko, Dmitry E.;
Agapova, Yulia K.;
Vlaskina, Anna V.;
Karlinsky, David M.;
Mikhailova, Anna G.;
Kuranova, Inna P.;
Rakitina, Tatiana V.

Publication type:

Article

Free Energy Change during the Formation of Crystalline Contact between Lysozyme Monomers under Different Physical and Chemical Conditions.

Published in:

Crystals (2073-4352), 2021, v. 11, n. 9, p. 1121, doi. 10.3390/cryst11091121

By:

Kordonskaya, Yuliya V.;
Timofeev, Vladimir I.;
Dyakova, Yulia A.;
Marchenkova, Margarita A.;
Pisarevsky, Yury V.;
Kovalchuk, Mikhail V.

Publication type:

Article

Structural insights into the broad substrate specificity of carboxypeptidase T from Thermoactinomyces vulgaris.

Published in:

FEBS Journal, 2015, v. 282, n. 7, p. 1214, doi. 10.1111/febs.13210

By:

Akparov, Valery Kh.;
Timofeev, Vladimir I.;
Khaliullin, Ilyas G.;
Švedas, Vytas;
Chestukhina, Galina G.;
Kuranova, Inna P.

Publication type:

Article

The nature of the ligand's side chain interacting with the S1'-subsite of metallocarboxypeptidase T (from Thermoactinomyces vulgaris) determines the geometry of the tetrahedral transition complex.

Published in:

PLoS ONE, 2019, v. 14, n. 12, p. N.PAG, doi. 10.1371/journal.pone.0226636

By:

Akparov, Valery Kh.;
Timofeev, Vladimir I.;
Konstantinova, Galina E.;
Khaliullin, Ilyas G.;
Kuranova, Inna P.;
Rakitina, Tatiana V.;
Švedas, Vytas

Publication type:

Article

Myelin Basic Protein Attenuates Furin-Mediated Bri2 Cleavage and Postpones Its Membrane Trafficking.

Published in:

International Journal of Molecular Sciences, 2024, v. 25, n. 5, p. 2608, doi. 10.3390/ijms25052608

By:

Smirnova, Evgeniya V.;
Timofeev, Vladimir I.;
Rakitina, Tatiana V.;
Petrenko, Dmitry E.;
Elmeeva, Olga S.;
Saratov, George A.;
Kudriaeva, Anna A.;
Bocharov, Eduard V.;
Belogurov Jr., Alexey A.

Publication type:

Article

Crystal Structure of Inhibitor-Bound Bacterial Oligopeptidase B in the Closed State: Similarity and Difference between Protozoan and Bacterial Enzymes.

Published in:

International Journal of Molecular Sciences, 2023, v. 24, n. 3, p. 2286, doi. 10.3390/ijms24032286

By:

Petrenko, Dmitry E.;
Karlinsky, David M.;
Gordeeva, Veronika D.;
Arapidi, Georgij P.;
Britikova, Elena V.;
Britikov, Vladimir V.;
Nikolaeva, Alena Y.;
Boyko, Konstantin M.;
Timofeev, Vladimir I.;
Kuranova, Inna P.;
Mikhailova, Anna G.;
Bocharov, Eduard V.;
Rakitina, Tatiana V.

Publication type:

Article

Rational Mutagenesis in the Lid Domain of Ribokinase from E. coli Results in an Order of Magnitude Increase in Activity towards D-arabinose.

Published in:

International Journal of Molecular Sciences, 2022, v. 23, n. 20, p. 12540, doi. 10.3390/ijms232012540

By:

Zayats, Evgeniy A.;
Fateev, Ilya V.;
Kostromina, Maria A.;
Abramchik, Yulia A.;
Lykoshin, Dmitry D.;
Yurovskaya, Daria O.;
Timofeev, Vladimir I.;
Berzina, Maria Ya.;
Eletskaya, Barbara Z.;
Konstantinova, Irina D.;
Esipov, Roman S.

Publication type:

Article

Unusual Cytochrome c 552 from Thioalkalivibrio paradoxus : Solution NMR Structure and Interaction with Thiocyanate Dehydrogenase.

Published in:

International Journal of Molecular Sciences, 2022, v. 23, n. 17, p. 9969, doi. 10.3390/ijms23179969

By:

Britikov, Vladimir V.;
Bocharov, Eduard V.;
Britikova, Elena V.;
Dergousova, Natalia I.;
Kulikova, Olga G.;
Solovieva, Anastasia Y.;
Shipkov, Nikolai S.;
Varfolomeeva, Larisa A.;
Tikhonova, Tamara V.;
Timofeev, Vladimir I.;
Shtykova, Eleonora V.;
Altukhov, Dmitry A.;
Usanov, Sergey A.;
Arseniev, Alexander S.;
Rakitina, Tatiana V.;
Popov, Vladimir O.

Publication type:

Article

Computational designing of a novel subunit vaccine for human cytomegalovirus by employing the immunoinformatics framework.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 3, p. 833, doi. 10.1080/07391102.2021.2014969

By:

Moin, Abu Tayab;
Singh, Gagandeep;
Ahmed, Nafisa;
Saiara, Syeda Afra;
Timofeev, Vladimir I.;
Ahsan Faruqui, Nairita;
Sharika Ahsan, Shama;
Tabassum, Afrida;
Nebir, Sadman Sakib;
Andalib, K. M. Salim;
Araf, Yusha;
Ullah, Md. Asad;
Sarkar, Bishajit;
Islam, Nafisa Nawal;
Zohora, Umme Salma

Publication type:

Article

Immunoinformatics analysis to design novel epitope based vaccine candidate targeting the glycoprotein and nucleoprotein of Lassa mammarenavirus (LASMV) using strains from Nigeria.

Published in:

Journal of Biomolecular Structure & Dynamics, 2022, v. 40, n. 16, p. 7283, doi. 10.1080/07391102.2021.1896387

By:

Abass, Ohilebo Abdulateef;
Timofeev, Vladimir I.;
Sarkar, Bishajit;
Onobun, Desmond Odiamehi;
Ogunsola, Samuel Olarewaju;
Aiyenuro, Ademola Emmanuel;
Aborode, Abdullahi Tunde;
Aigboje, Adebayo Emmanuel;
Omobolanle, Basheer Nabilat;
Imolele, Anthony Goodwill;
Abiodun, Alade Adebowale

Publication type:

Article

The comparative analysis of the properties and structures of purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27.

Published in:

Journal of Biomolecular Structure & Dynamics, 2022, v. 40, n. 8, p. 3626, doi. 10.1080/07391102.2020.1848628

By:

Timofeev, Vladimir I.;
Fateev, Ilya V.;
Kostromina, Maria A.;
Abramchik, Yuliya A.;
Konstantinova, Irina D.;
Volkov, Vladimir V.;
Lykoshin, Dmitry D.;
Mikheeva, Olga O.;
Muravieva, Tatiana I.;
Esipov, Roman S.;
Kuranova, Inna P.

Publication type:

Article

Precipitant ions influence on lysozyme oligomers stability investigated by molecular dynamics simulation at different temperatures.

Published in:

2021

By:

Kordonskaya, Yuliya V.;
Marchenkova, Margarita A.;
Timofeev, Vladimir I.;
Dyakova, Yulia A.;
Pisarevsky, Yurii V.;
Kovalchuk, Michael V.

Publication type:

Letter

The binding of precipitant ions in the tetragonal crystals of hen egg white lysozyme.

Published in:

Journal of Biomolecular Structure & Dynamics, 2020, v. 38, n. 17, p. 5159, doi. 10.1080/07391102.2019.1696706

By:

Marchenkova, Margarita A.;
Kuranova, Inna P.;
Timofeev, Vladimir I.;
Boikova, Anastasiia S.;
Dorovatovskii, Pavel V.;
Dyakova, Yulia A.;
Ilina, Kseniia B.;
Pisarevskiy, Yury V.;
Kovalchuk, Mikhail V.

Publication type:

Article

Molecular dynamics complemented by site-directed mutagenesis reveals significant difference between the interdomain salt bridge networks stabilizing oligopeptidases B from bacteria and protozoa in their active conformations.

Published in:

Journal of Biomolecular Structure & Dynamics, 2020, v. 38, n. 16, p. 4868, doi. 10.1080/07391102.2019.1692694

By:

Petrenko, Dmitry E.;
Mikhailova, Anna G.;
Timofeev, Vladimir I.;
Agapova, Yulia К.;
Karlinsky, David M.;
Komolov, Aleksandr S.;
Korzhenevskiy, Dmitry A.;
Vlaskina, Anna V.;
Rumsh, Lev D.;
Rakitina, Tatiana V.

Publication type:

Article

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.

Published in:

Journal of Biomolecular Structure & Dynamics, 2020, v. 38, n. 10, p. 2939, doi. 10.1080/07391102.2019.1649195

By:

Marchenkova, Margarita A.;
Konarev, Petr V.;
Rakitina, Tatiana V.;
Timofeev, Vladimir I.;
Boikova, Anastasiia S.;
Dyakova, Yulia A.;
Ilina, Kseniia B.;
Korzhenevskiy, Dmitry A.;
Yu Nikolaeva, Alena;
Pisarevsky, Yurii V.;
Kovalchuk, Mikhail V.

Publication type:

Article

An explanation for the narrow carbohydrate substrate specificity of adenine phosphoribosyltransferase from Thermus thermophilus from the model of the enzyme, substrate, and magnesium cation cofactor complex.

Published in:

2019

By:

Zayats, Evgeniy A.;
Timofeev, Vladimir I.;
Kostromina, Maria A.;
Esipov, Roman S.

Publication type:

Letter

Pre-crystallization phase formation of thermolysin hexamers in solution close to crystallization conditions.

Published in:

2019

By:

Kovalchuk, Mikhail V.;
Boikova, Anastasiia S.;
Dyakova, Yulia A.;
Ilina, Kseniia B.;
Konarev, Petr V.;
Kryukova, Alyona E.;
Marchenkova, Margarita A.;
Pisarevsky, Yurii V.;
Timofeev, Vladimir I.

Publication type:

Letter

Structural plasticity and thermal stability of the histone-like protein from Spiroplasma melliferum are due to phenylalanine insertions into the conservative scaffold.

Published in:

Journal of Biomolecular Structure & Dynamics, 2018, v. 36, n. 16, p. 4392, doi. 10.1080/07391102.2017.1417162

By:

Timofeev, Vladimir I.;
Altukhov, Dmitry A.;
Talyzina, Anna A.;
Agapova, Yulia K.;
Vlaskina, Anna V.;
Korzhenevskiy, Dmitry A.;
Kleymenov, Sergey Yu.;
Bocharov, Eduard V.;
Rakitina, Tatiana V.

Publication type:

Article

Crystal structures of carboxypeptidase T complexes with transition-state analogs.

Published in:

Journal of Biomolecular Structure & Dynamics, 2018, v. 36, n. 15, p. 3958, doi. 10.1080/07391102.2017.1404932

By:

Akparov, Valery Kh.;
Timofeev, Vladimir I.;
Khaliullin, Ilyas G.;
Švedas, Vytas;
Kuranova, Inna P.;
Rakitina, Tatiana V.

Publication type:

Article

Enhanced conformational flexibility of the histone-like (HU) protein from Mycoplasma gallisepticum.

Published in:

Journal of Biomolecular Structure & Dynamics, 2018, v. 36, n. 1, p. 45, doi. 10.1080/07391102.2016.1264893

By:

Altukhov, Dmitry A.;
Talyzina, Anna A.;
Agapova, Yulia K.;
Vlaskina, Anna V.;
Korzhenevskiy, Dmitry A.;
Bocharov, Eduard V.;
Rakitina, Tatiana V.;
Timofeev, Vladimir I.;
Popov, Vladimir O.

Publication type:

Article

Crystal structure of recombinant phosphoribosylpyrophosphate synthetase 2 from Thermus thermophilus HB27 complexed with ADP and sulfate ions.

Published in:

Acta Crystallographica: Section F, Structural Biology Communications, 2017, v. 73, n. 6, p. 369, doi. 10.1107/S2053230X17007488

By:

Timofeev, Vladimir I.;
Sinitsyna, Ekaterina V.;
Kostromina, Maria A.;
Muravieva, Tatiana I.;
Makarov, Dmitry A.;
Mikheeva, Olga O.;
Kuranova, Inna P.;
Esipov, Roman S.

Publication type:

Article