Группа структурных исследований макромолекулярных комплексов

Азат Габдрахманович Габдулхаков

Кандидат физико-математических наук c 2005 г.
 

Сотрудники

к.б.н. И. А. Коляденко
к.б.н. Г. К. Селиханов
м.н.с. А. С. Глухов
асп. Б. Ф. Фатхуллин
инженер О. В. Сазонова

Основные научные достижения

Группа занимается определением структур макромолекулярных комплексов с использованием методов рентгеноструктурного анализа (РСА) и криоэлектронной микроскопии (криоЭМ).

Наиболее перспективные направления касаются структур рибосом в комплексах с факторами гибернации (совместно с Institute of Genetics and Molecular and Cellular Biology, CNRS, France, лабораторией Структурного анализа биомакромолекул Казанского Научного Центра РАН и Лабораторией Структурной биологии Казанского (Поволжского) государственного университета), структурных исследований фотосинтетического центра Rhodobacter sphaeroides (совместно с институтами ФИЦ ПНЦ РАН), ряда биотехнологически значимых ферментов. Сотрудники группы активно участвовали в разработке методов применения рентгеновского лазера на свободных электронах eXFEL для исследования механизма работы фотосинтетического центра пурпурных бактерий на атомарном уровне с пикосекундным разрешением.

Перспективы исследований

Продолжаются структурно-функциональные исследования сложных макромолекулярных комплексов и биотехнологически значимых ферментов методами рентгеноструктурного анализа. Второе направление - использование криоЭМ для исследования структур полноразмерных Т5-подобных бактериофагов.

PubMed
Bacteriophage T5 dUTPase: Combination of Common Enzymatic and Novel Functions.

Anatoly Glukhov, Victor Marchenkov, Ulyana Dzhus, Antonina Krutilina, Georgii Selikhanov, Azat Gabdulkhakov.
 

Int J Mol Sci. 2024, 25 (2): 892. doi: 10.3390/ijms25020892.
2024
PubMed
PubMed
Bright and stable monomeric green fluorescent protein derived from StayGold.

Hanbin Zhang, Gleb D. Lesnov, Oksana M. Subach, Wenhao Zhang, Tatyana P. Kuzmicheva, Anna V. Vlaskina, Valeriya R. Samygina, Liangyi Chen, Xianxin Ye, Alena Yu. Nikolaeva, Azat Gabdulkhakov, Stavrini Papadaki, Wenming Qin, Valentin Borshchevskiy, Maxim M. Perfilov, Alexey S. Gavrikov, Mikhail Drobizhev, Alexander S. Mishin, Kiryl D. Piatkevich, Fedor V. Subach.
 

Nat Methods. 2024, 21(4): 657-665. doi: 10.1038/s41592-024-02203-y.
2024
PubMed
mdpi
Site-Directed Mutagenesis of Two-Domain Laccase ScaSL for Obtaining a Biocatalyst with Improved Characteristics

Liubov Trubitsina, Ivan Trubitsin, Azat Gabdulkhakov, Azat Abdullatypov, Anna Larionova, Marina Petrakova, Vladimir Trubitsyn, Konstantin Egorov, Svetlana Tishchenko, Alexey Leontievsky, Sergey Alferov and Olga Ponamoreva.
 

Catalysts. 2024, 14 (10): 69. https://doi.org/10.3390/catal14100694
2024
mdpi
patents
Кассета для системы кристаллизации мембранных белков для целей поточного рентгеноструктурного анализа.

Г.К. Селиханов, Т.Ю. Фуфина, Л.Г. Васильева, А.Г. Габдулхаков.

патент на изобретение RU2809851C1
2024
patents
Springer
The structural features of skeletal muscle titin aggregates.

L. G. Bobyleva, T. A. Uryupina, N. V. Penkov, M. A. Timchenko, A. D. Ulanova, A. G. Gabdulkhakov, I. M. Vikhlyantsev & A. G. Bobylev.
 

Mol. Biol. 2024, 58: 319-327. doi: 10.1134/S0026893324020043
2024
Springer
elibrary
Влияние возвращения cys11 на структуру и функцию s11c cys-free nt.bspd6i.

Р. И. Артюх, Б. Ф. Фатхуллин, В. Н. Антипова, Т. А. Перевязова, Г. С. Качалова, А. К. Юнусова.

Кристаллография. 2023, 68 (6): 859-865. DOI: 10.31857/S0023476123600702.
2023
elibrary
PubMed
A Novel Two-Domain Laccase with Middle Redox Potential: Physicochemical and Structural Properties.

Liubov I. Trubitsina, Ivan V. Trubitsin, Alexander V. Lisov, Azat G. Gabdulkhakov, Anna G. Zavarzina, Oxana V. Belova, Anna P. Larionova, Svetlana V. Tishchenko, Alexey A. Leontievsky.
 

Biochemistry (Mosc). 2023, 88 (10): 1658-1667. doi: 10.1134/S0006297923100188.
2023
PubMed
preprints
Bacteriophage T5 dUTPase: Combination of Common Enzymatic and a Novel Function.

Anatoly Glukhov, Victor Marchenkov, Ulyana Dzhus , Antonina Krutilina, Georgii K. Selikhanov, Azat Gabdulkhakov.

Biorxiv, 2023. DOI: 10.20944/preprints202312.1157.v1
2023
preprints
PubMed
Structural Insight into the Amino Acid Environment of the Two-Domain Laccase's Trinuclear Copper Cluster.

Ilya Kolyadenko, Svetlana Tishchenko, Azat Gabdulkhakov.

Int J Mol Sci. 2023, 24 (15): 11909. doi: 10.3390/ijms241511909
2023
PubMed
PubMed
Properties and Crystal Structure of the Cereibacter sphaeroides Photosynthetic Reaction Center with Double Amino Acid Substitution I(L177)H + F(M197)H.

Tatiana Yu. Fufina, Georgii K. Selikhanov, Azat G. Gabdulkhakov, Lyudmila G. Vasilieva.

Membranes (Basel). 2023, 13 (2): 157. doi: 10.3390/membranes13020157.
2023
PubMed
PubMed
Nonspecific Amyloid Aggregation of Chicken Smooth-Muscle Titin: In Vitro Investigations.

Alexander G. Bobylev, Elmira I. Yakupova, Liya G. Bobyleva, Nikolay V. Molochkov, Alexander A. Timchenko, Maria A. Timchenko, Hiroshi Kihara, Alexey D. Nikulin, Azat G. Gabdulkhakov, Tatiana N. Melnik, Nikita V. Penkov, Michail Y. Lobanov, Alexey S. Kazakov, Miklós Kellermayer, Zsolt Mártonfalvi, Oxana V. Galzitskaya, Ivan M. Vikhlyantsev.
 

Int J Mol Sci . 2023,24 (2):1056. doi: 10.3390/ijms24021056.
2023
PubMed
PubMed
Stabilization of Cereibacter sphaeroides Photosynthetic Reaction Center by the Introduction of Disulfide Bonds.

Georgii Selikhanov, Anastasia Atamas, Diana Yukhimchuk, Tatiana Fufina, Lyudmila Vasilieva, Azat Gabdulkhakov.
 

Membranes (Basel). 2023, 13 (2): 154. doi: 10.3390/membranes13020154.
2023
PubMed
PubMed
Yet Another Similarity between Mitochondrial and Bacterial Ribosomal Small Subunit Biogenesis Obtained by Structural Characterization of RbfA from S. aureus.

Aydar G. Bikmullin, Bulat Fatkhullin, Artem Stetsenko, Azat Gabdulkhakov, Natalia Garaeva, Liliia Nurullina, Evelina Klochkova, Alexander Golubev, Iskander Khusainov, Natalie Trachtmann, Dmitriy Blokhin, Albert Guskov, Shamil Validov, Konstantin Usachev, Marat Yusupov.
 

Int J Mol Sci . 2023, 24 (3): 2118. doi: 10.3390/ijms24032118.
2023
PubMed
PubMed
Two Epitope Regions Revealed in the Complex of IL-17A and Anti-IL-17A VHH Domain.

Olga Kostareva, Arina Svoeglazova, Ilya Kolyadenko, Alexey Nikulin, Stanislav Evdokimov, Uliana Dzhus, Azat Gabdulkhakov, Svetlana Tishchenko.
 

Int J Mol Sci. 2022 Nov 28;23(23):14904. doi: 10.3390/ijms232314904.
2022
PubMed
PubMed
Y98 Mutation Leads to the Loss of RsfS Anti-Association Activity in Staphylococcus aureus.

Bulat Fatkhullin, Alexander Golubev, Natalia Garaeva, Shamil Validov, Azat Gabdulkhakov, Marat Yusupov.
 

Int J Mol Sci. 2022, 23 (18):10931. doi: 10.3390/ijms231810931.
2022
PubMed
PubMed
Some useful ideas for multistate protein design: Effect of amino acid substitutions on the multistate proteins stability and the rate of protein structure formation.

M. A. Majorina, T. N. Melnik, A. S. Glukhov, B. S. Melnik.

Front Mol Biosci. 2022, 9: 983009. doi: 10.3389/fmolb.2022.983009.
2022
PubMed
PubMed
Is RsfS a Hibernation Factor or a Ribosome Biogenesis Factor?

Bulat F. Fatkhullin, Azat G. Gabdulkhakov, Marat M. Yusupov.

Biochemistry (Mosc). 2022, 87(6): 500-510. doi: 10.1134/S0006297922060025.
2022
PubMed
PubMed
X-ray structure of the Rhodobacter sphaeroides reaction center with an M197 Phe→His substitution clarifies the properties of the mutant complex.

Georgii Selikhanov, Tatiana Fufina, Sebastian Guenther, Alke Meents, Azat Gabdulkhakov, Lyudmila Vasilieva.

IUCrJ. 2022, 9 (2): 261-271. doi: 10.1107/S2052252521013178.
2022
PubMed
PubMed
Structural analysis of cysteine-free Nt.BspD6 nicking endonuclease and its functional features.

Rimma I. Artyukh, Bulat F. Fatkhullin, Galina S. Kachalova, Valeriya N. Antipova, Tatyana A. Perevyazova, Alfiya K. Yunusova.

Biochim Biophys Acta Proteins Proteom. 2022, 1870 (3): 140756. doi: 10.1016/j.bbapap.2022.140756.
2022
PubMed
PubMed
Carbonic anhydrase amyloid fibrils composed of laterally associated protofilaments show reduced cytotoxicity.

Natalya Ryabova, Liliia Fakhranurova, Vitaly Balobanov, Victor Marchenkov, Anatoly Glukhov, Nelly Ilyina, Alexey Kochetov, Mariya Suvorina, Alexey Surin, Natalya Katina.

Biochem Biophys Res Commun. 2022, 19; 593:46-51. doi: 10.1016/j.bbrc.2022.01.040.
2022
PubMed
PubMed
Backbone and side chain NMR assignments for the ribosome maturation factor P (RimP) from Staphylococcus aureus.

Natalia S. Garaeva, Aydar G. Bikmullin, Bulat F. Fatkhullin, Shamil Z. Validov, Bruno Keiffer, Marat M. Yusupov, Konstantin S. Usachev.

Biomol NMR Assign. 2022, 16(2): 373-377. doi: 10.1007/s12104-022-10106-2.
2022
PubMed
PubMed
Engineering the Catalytic Properties of Two-Domain Laccase from Streptomyces griseoflavus Ac-993.

Ilya Kolyadenko, Anastasia Scherbakova, Kirill Kovalev, Azat Gabdulkhakov, Svetlana Tishchenko.

Int. J. Mol. Sci. 2022, 23 (1), 65. doi:10.3390/ijms23010065
2022
PubMed
PubMed
The role of positive charged residue in the proton-transfer mechanism of two-domain laccase from Streptomyces griseoflavus Ac-993.

Azat Gabdulkhakov, Ilya Kolyadenko, Paulo Oliveira, Paula Tamagnini, Alisa Mikhaylina, Svetlana Tishchenko.

J Biomol Struct Dyn., 2021; 1-8. doi: 10.1080/07391102.2021.1911852.
2021
PubMed
PubMed
Identification of amyloidogenic regions in pseudomonas aeruginosa ribosomal s1 protein.

S.Y. Grishin, U.F. Dzhus, A.S. Glukhov, O.M. Selivanova, A.K. Surin, O.V. Galzitskaya.

Int. J. Mol. Sci. 2021; 22 (14): 7291. doi: 10.3390/ijms22147291
2021
PubMed
PubMed
Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach.

Khusainov I, Fatkhullin B, Pellegrino S, Bikmullin A, Liu WT, Gabdulkhakov A, Shebel AA, Golubev A, Zeyer D, Trachtmann N, Sprenger GA, Validov S, Usachev K, Yusupova G, Yusupov M.

Nat Commun. 2020 Apr 3;11(1):1656. doi: 10.1038/s41467-020-15517-0. PMID: 32245971; PMCID: PMC7125091.
2020
PubMed
PubMed
Cryo-EM structure of the ribosome functional complex of the human pathogen Staphylococcus aureus at 3.2 Å resolution.

Golubev A, Fatkhullin B, Khusainov I, Jenner L, Gabdulkhakov A, Validov S, Yusupova G, Yusupov M, Usachev K.

FEBS Lett. 2020 Nov;594(21):3551-3567. doi: 10.1002/1873-3468.13915. Epub 2020 Sep 10. PMID: 32852796
2020
PubMed
full text
Structure of the ribosomal P stalk base in archaean Methanococcus jannaschii.

Gabdulkhakov A, Mitroshin I, Garber M.

J Struct Biol. 2020 Sep 1;211(3):107559. doi: 10.1016/j.jsb.2020.107559. Epub 2020 Jul 10. PMID: 32653645
2020
full text
PubMed
In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors.

Nass, K; Redecke, L; Perbandt, M; Yefanov, O; Klinge, M; Koopmann, R; Stellato, F; Gabdulkhakov, A; Schonherr, R; Rehders, D; Lahey-Rudolph, JM; Aquila, A; Barty, A; Basu, S; Doak, RB; Duden, R; Frank, M; Fromme, R; Kassemeyer, S; Katona, G; Kirian, R; Liu, H; Majoul, I; Martin-Garcia, JM; Messerschmidt, M; Shoeman, RL; Weierstall, U; Westenhoff, S; White, TA; Williams, GJ; Yoon, CH; Zatsepin, N; Fromme, P; Duszenko, M; Chapman, HN; Betzel, C

Nat Commun. 2020 Jan 30;11(1):620. doi: 10.1038/s41467-020-14484-w.
2020
PubMed
PubMed
NMR and crystallographic structural studies of the Elongation factor P from Staphylococcus aureus.

Golubev, A; Fatkhullin, B; Gabdulkhakov, A; Bikmullin, A; Nurullina, L; Garaeva, N; Islamov, D; Klochkova, E; Klochkov, V; Aganov, A; Khusainov, I; Validov, S; Yusupova, G; Yusupov, M; Usachev, K.

Eur Biophys J. 2020 May;49(3-4):223-230. doi: 10.1007/s00249-020-01428-x. Epub 2020 Mar 9.
2020
PubMed
PubMed
The key role of E418 carboxyl group in the formation of Nt.BspD6I nickase active site: Structural and functional properties of Nt.BspD6I E418A mutant.

Artyukh, RI; Kachalova, GS; Yunusova, AK; Fatkhullin, BF; Atanasov, BP; Perevyazova, TA; Popov, AN; Gabdulkhakov, AG; Zheleznaya, LA

JOURNAL OF STRUCTURAL BIOLOGY 2020 Jun 1;210(3):107508. doi: 10.1016/j.jsb.2020.107508. Epub 2020 Apr 13.
2020
PubMed
PubMed
Dimerization of long hibernation promoting factor from Staphylococcus aureus: Structural analysis and biochemical characterization.

Usachev K.S., Fatkhullin B.F., Klochkova E.A., Miftakhov A.K., Golubev A.A., Bikmullin A.G., Nurullina L.I., Garaeva N.S., Islamov D.R., Gabdulkhakov A.G., Lekontseva N.V., Tishchenko S.V., Balobanov V.A., Khusainov I.S., Yusupov M.M., Validov S.Z.

J. Struct. Biol. 2019, 25:107408. doi: 10.1016/j.jsb.2019.107408.
2020
PubMed
Идентификация каналов т2/t3 центра двухдоменных лакказ.

С.В. Тищенко, И.А. Коляденко, А.Г. Габдулхаков

Acta Naturae. 2019; спецвыпуск том 2: 86.
2019
abstract
Crystallization in lipid mesophases affects pigment composition of photosynthetic reaction center

Selikhanov, G (Selikhanov, G.); Fufina, T (Fufina, T.); Vasilieva, L (Vasilieva, L.); Gabdulkhakov, A

FEBS OPEN BIO P-27-027, 9: 255-256 WOS:000486972403185
2019
abstract
PubMed
Controlling Photosynthetic Excitons by Selective Pigment Photooxidation

Leiger, K (Leiger, Kristjan); Linnanto, JM (Linnanto, Juha Matti); Ratsep, M (Ratsep, Margus); Timpmann, K (Timpmann, Kou); Ashikhmin, AA (Ashikhmin, Aleksandr A.); Moskalenko, AA (Moskalenko, Andrey A.); Fufina, TY (Fufina, Tatiana Y.); Gabdulkhakov, AG (Gabdulkhakov, Azat G.); Freiberg, A (Freiberg, Arvi)

JOURNAL OF PHYSICAL CHEMISTRY B Том: 123 Выпуск: 1 Стр.: 29-38 DOI: 10.1021/acs.jpcb.8b08083 WOS:000455560800009 PubMed: 30543422
2019
PubMed
abstract
Serine bacteriolytic protease L1 of Lysobacter sp. XL1 complexed with protease inhibitor AEBSF: features of interaction

Kudryakova, IV (Kudryakova, Irina V.); Gabdulkhakov, AG (Gabdulkhakov, Azat G.); Tishchenko, SV (Tishchenko, Svetlana V.); Afoshin, AS (Afoshin, Alexey S.); Vasilyeva, NV (Vasilyeva, Natalia V.)

PROCESS BIOCHEMISTRY Том: 80 Стр.: 89-94 DOI: 10.1016/j.procbio.2019.02.013 WOS:000466616800012
2019
abstract
abstract
Fab Fragment of VHH-Based Antibody Netakimab: Crystal Structure and Modeling Interaction with Cytokine IL-17A

Kostareva, O (Kostareva, Olga); Kolyadenko, I (Kolyadenko, Ilya); Ulitin, A (Ulitin, Andrey); Ekimova, V (Ekimova, Victoria); Evdokimov, S (Evdokimov, Stanislav); Garber, M (Garber, Maria); Tishchenko, S (Tishchenko, Svetlana); Gabdulkhakov, A (Gabdulkhakov, Azat)

CRYSTALS Том: 9 Выпуск: 3 Номер статьи: 177 DOI: 10.3390/cryst9030177 WOS:000464478100002
2019
abstract
PubMed
Interleukin-17: Functional and Structural Features, Application as a Therapeutic Target

Kostareva, OS (Kostareva, O. S.); Gabdulkhakov, AG (Gabdulkhakov, A. G.); Kolyadenko, IA (Kolyadenko, I. A.); Garber, MB (Garber, M. B.); Tishchenko, SV (Tishchenko, S. V.)

BIOCHEMISTRY-MOSCOW Том: 84 Стр.: 193-205 DOI: 10.1134/S0006297919140116 WOS:000468501300011 PubMed: 31213202
2019
PubMed
PubMed
Investigations of Accessibility of T2/T3 Copper Center of Two-Domain Laccase from Streptomyces griseoflavus Ac-993

Gabdulkhakov, A (Gabdulkhakov, Azat); Kolyadenko, I (Kolyadenko, Ilya); Kostareva, O (Kostareva, Olga); Mikhaylina, A (Mikhaylina, Alisa); Oliveira, P (Oliveira, Paulo); Tamagnini, P (Tamagnini, Paula); Lisov, A (Lisov, Alexander); Tishchenko, S

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Том: 20 Выпуск: 13 Номер статьи: 3184 DOI: 10.3390/ijms20133184 WOS:000477041100072 PubMed: 31261802
2019
PubMed
PubMed
Properties of Rhodobacter sphaeroides Reaction Centers with the Ile -> Tyr Substitution at Positions L177 and M206

Fufina, TY (Fufina, T. Yu); Selikhanov, K (Selikhanov, K.); Proskuryakov, II (Proskuryakov, I. I.); Shuvalov, VA (Shuvalov, V. A.); Vasilieva, LG (Vasilieva, L. G.)

BIOCHEMISTRY-MOSCOW Том: 84 Выпуск: 5 Стр.: 570-574 DOI: 10.1134/S0006297919050110 WOS:000468032800011 PubMed: 31234771
2019
PubMed
abstract
Crystal structure of the complex ribosomal silencing factor S and ribosomal protein L14 from Staphylococcus aureus

Fatkhullin, B (Fatkhullin, B.); Gabdulkhakov, A (Gabdulkhakov, A.); Validov, S (Validov, S.); Khusainov, I (Khusainov, I.); Bikmullin, A (Bikmullin, A.); Usachev, K (Usachev, K.); Yusupov, M

FEBS OPEN BIO Аннотация к встрече: P-34-010 Том: 9 Стр.: 316-316 WOS:000486972405001
2019
abstract
In vivo incorporation of photoproteins into GroEL tetradecameric quaternary structure.

Marchenkov V., Marchenko N., Ivashina T., Ryabova N., Timchenko A., Kashparov I., Ksenzenko V., Semisotnov. G.

FEBS Open Bio., 2018; 8(Suppl.1): 400-401
2018
PubMed
High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid.

Vernhes E, Renouard M, Gilquin B, Cuniasse P, Durand D, England P, Hoos S, Huet A, Conway JF, Glukhov A, Ksenzenko V, Jacquet E, Nhiri N, Zinn-Justin S, Boulanger P.

Sci Rep., 2017, 7: 41662. doi: 10.1038/srep41662
2017
PubMed
PDF
SAXS study of capsid assembly of bacteriophage T5.

Alexander Timchenko, Vladimir Ksenzenko, Anatoly Glukhov, Antonina Krutilina, Alexander Kaliman, Yoshitaka Matsumura, Hiroshi Kihara.

Photon Factory Activity Report 2016 №34 (2017)
2017
PDF
PubMed
sw ApoMb amyloid aggregation under nondenaturing conditions: the role of native structure stability.

N.S. Katina, V.A. Balobanov, N.B. Ilyina, V.D. Vasiliev, V.V. Marchenkov, A.S. Glukhov, A.D. Nikulin, V.E. Bychkova.

Biophys. J., 113(5): 991-1001.
2017
PubMed
PubMed
SS-Stabilizing Proteins Rationally: Intrinsic Disorder-Based Design of Stabilizing Disulphide Bridges in GFP.

Melnik BS, Povarnitsyna TV, Glukhov AS, Melnik TN, Uversky VN, Sarma RH.

J Biomol Struct Dyn., 29(4):815-24.
2012
PubMed
PLOSone
Multi-state proteins: approach allowing experimental determination of the formation order of structure elements in the green fluorescent protein.

Melnik TN, Povarnitsyna TV, Glukhov AS, Melnik BS.

PLoS One.,7(11):e48604.
2012
PLOSone
PLOSone
Genomic analysis of Pseudomonas putida phage tf with localized single-strand DNA interruptions.

Glukhov AS, Krutilina AI, Shlyapnikov MG, Severinov K, Lavysh D, Kochetkov VV, McGrath JW, de Leeuwe C, Shaburova OV, Krylov VN, Akulenko NV, Kulakov LA.

PLoS One;7(12): e51163
2012
PLOSone
PubMed
Sequential melting of two hydrophobic clusters within the green fluorescent protein GFP-cycle3.

Melnik TN, Povarnitsyna TV, Glukhov AS, Uversky VN, Melnik BS.

Biochemistry, Sep 13; 50(36) 7735-44.
2011
PubMed
PubMed
Identification and characterization of EctR1, a new transcriptional regulator of the ectoine biosynthesis genes in the halotolerant methanotroph Methylomicrobium alcaliphilum 20Z.

Mustakhimov II, Reshetnikov AS, Glukhov AS, Khmelenina VN, Kalyuzhnaya MG, Trotsenko YA.

J Bacteriol. Jan; 192(2):410-7.
2010
PubMed