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Smirnova EV, Timofeev VI, Rakitina TV, Petrenko DE, Elmeeva OS, Saratov GA, Kudriaeva AA, Bocharov EV, Belogurov AA. Myelin Basic Protein Attenuates Furin-Mediated Bri2 Cleavage and Postpones Its Membrane Trafficking. Int J Mol Sci 2024; 25:2608. [PMID: 38473856 DOI: 10.3390/ijms25052608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Myelin basic protein (MBP) is the second most abundant protein in the central nervous system and is responsible for structural maintenance of the myelin sheath covering axons. Previously, we showed that MBP has a more proactive role in the oligodendrocyte homeostasis, interacting with membrane-associated proteins, including integral membrane protein 2B (ITM2B or Bri2) that is associated with familial dementias. Here, we report that the molecular dynamics of the in silico-generated MBP-Bri2 complex revealed that MBP covers a significant portion of the Bri2 ectodomain, assumingly trapping the furin cleavage site, while the surface of the BRICHOS domain, which is responsible for the multimerization and activation of the Bri2 high-molecular-weight oligomer chaperone function, remains unmasked. These observations were supported by the co-expression of MBP with Bri2, its mature form, and disease-associated mutants, which showed that in mammalian cells, MBP indeed modulates the post-translational processing of Bri2 by restriction of the furin-catalyzed release of its C-terminal peptide. Moreover, we showed that the co-expression of MBP and Bri2 also leads to an altered cellular localization of Bri2, restricting its membrane trafficking independently of the MBP-mediated suppression of the Bri2 C-terminal peptide release. Further investigations should elucidate if these observations have physiological meaning in terms of Bri2 as a MBP chaperone activated by the MBP-dependent postponement of Bri2 membrane trafficking.
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Affiliation(s)
- Evgeniya V Smirnova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Tatiana V Rakitina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitry E Petrenko
- National Research Centre "Kurchatov Institute", 123182 Moscow, Russia
| | - Olga S Elmeeva
- Department of Chemistry and Technology of Biologically Active Compounds, Medical and Organic Chemistry Named after N.A. Preobrazhensky, Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russia
| | - George A Saratov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia
| | - Anna A Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Eduard V Bocharov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia
| | - Alexey A Belogurov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Department of Biological Chemistry, Federal State Budgetary Educational Institution of Higher Education "Russian University of Medicine" of the Ministry of Health of the Russian Federation, 127473 Moscow, Russia
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Shilova SA, Matyuta IO, Petrova ES, Nikolaeva AY, Rakitina TV, Minyaev ME, Boyko KM, Popov VO, Bezsudnova EY. Expanded Substrate Specificity in D-Amino Acid Transaminases: A Case Study of Transaminase from Blastococcus saxobsidens. Int J Mol Sci 2023; 24:16194. [PMID: 38003383 PMCID: PMC10671532 DOI: 10.3390/ijms242216194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Enzymes with expanded substrate specificity are good starting points for the design of biocatalysts for target reactions. However, the structural basis of the expanded substrate specificity is still elusive, especially in the superfamily of pyridoxal-5'-phosphate-dependent transaminases, which are characterized by a conserved organization of both the active site and functional dimer. Here, we analyze the structure-function relationships in a non-canonical D-amino acid transaminase from Blastococcus saxobsidens, which is active towards D-amino acids and primary (R)-amines. A detailed study of the enzyme includes a kinetic analysis of its substrate scope and a structural analysis of the holoenzyme and its complex with phenylhydrazine-a reversible inhibitor and analogue of (R)-1-phenylethylamine-a benchmark substrate of (R)-selective amine transaminases. We suggest that the features of the active site of transaminase from B. saxobsidens, such as the flexibility of the R34 and R96 residues, the lack of bulky residues in the β-turn at the entrance to the active site, and the short O-pocket loop, facilitate the binding of substrates with and without α-carboxylate groups. The proposed structural determinants of the expanded substrate specificity can be used for the design of transaminases for the stereoselective amination of keto compounds.
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Affiliation(s)
- Sofia A. Shilova
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (S.A.S.); (I.O.M.); (E.S.P.); (A.Y.N.); (T.V.R.); (K.M.B.); (V.O.P.)
| | - Ilya O. Matyuta
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (S.A.S.); (I.O.M.); (E.S.P.); (A.Y.N.); (T.V.R.); (K.M.B.); (V.O.P.)
| | - Elizaveta S. Petrova
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (S.A.S.); (I.O.M.); (E.S.P.); (A.Y.N.); (T.V.R.); (K.M.B.); (V.O.P.)
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alena Y. Nikolaeva
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (S.A.S.); (I.O.M.); (E.S.P.); (A.Y.N.); (T.V.R.); (K.M.B.); (V.O.P.)
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Tatiana V. Rakitina
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (S.A.S.); (I.O.M.); (E.S.P.); (A.Y.N.); (T.V.R.); (K.M.B.); (V.O.P.)
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Mikhail E. Minyaev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119334, Russia;
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (S.A.S.); (I.O.M.); (E.S.P.); (A.Y.N.); (T.V.R.); (K.M.B.); (V.O.P.)
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (S.A.S.); (I.O.M.); (E.S.P.); (A.Y.N.); (T.V.R.); (K.M.B.); (V.O.P.)
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Ekaterina Yu. Bezsudnova
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (S.A.S.); (I.O.M.); (E.S.P.); (A.Y.N.); (T.V.R.); (K.M.B.); (V.O.P.)
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Dadinova LA, Petoukhov MV, Gordienko AM, Manuvera VA, Lazarev VN, Rakitina TV, Mozhaev AA, Peters GS, Shtykova EV. Nucleoid-Associated Proteins HU and IHF: Oligomerization in Solution and Hydrodynamic Properties. Biochemistry (Mosc) 2023; 88:640-654. [PMID: 37331710 DOI: 10.1134/s0006297923050073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 06/20/2023]
Abstract
Structure and function of bacterial nucleoid is controlled by the nucleoid-associated proteins (NAP). In any phase of growth, various NAPs, acting sequentially, condense nucleoid and facilitate formation of its transcriptionally active structure. However, in the late stationary phase, only one of the NAPs, Dps protein, is strongly expressed, and DNA-protein crystals are formed that transform nucleoid into a static, transcriptionally inactive structure, effectively protected from the external influences. Discovery of crystal structures in living cells and association of this phenomenon with the bacterial resistance to antibiotics has aroused great interest in studying this phenomenon. The aim of this work is to obtain and compare structures of two related NAPs (HU and IHF), since they are the ones that accumulate in the cell at the late stationary stage of growth, which precedes formation of the protective DNA-Dps crystalline complex. For structural studies, two complementary methods were used in the work: small-angle X-ray scattering (SAXS) as the main method for studying structure of proteins in solution, and dynamic light scattering as a complementary one. To interpret the SAXS data, various approaches and computer programs were used (in particular, the evaluation of structural invariants, rigid body modeling and equilibrium mixture analysis in terms of the volume fractions of its components were applied), which made it possible to determine macromolecular characteristics and obtain reliable 3D structural models of various oligomeric forms of HU and IHF proteins with ~2 nm resolution typical for SAXS. It was shown that these proteins oligomerize in solution to varying degrees, and IHF is characterized by the presence of large oligomers consisting of initial dimers arranged in a chain. An analysis of the experimental and published data made it possible to hypothesize that just before the Dps expression, it is IHF that forms toroidal structures previously observed in vivo and prepares the platform for formation of DNA-Dps crystals. The results obtained are necessary for further investigation of the phenomenon of biocrystal formation in bacterial cells and finding ways to overcome resistance of various pathogens to external conditions.
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Affiliation(s)
- Liubov A Dadinova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia
| | - Maxim V Petoukhov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia
| | - Alexander M Gordienko
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia
| | - Valentin A Manuvera
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, 119435, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, 141701, Russia
| | - Vassili N Lazarev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, 119435, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Rakitina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- National Research Centre "Kurchatov Institute", Moscow, 123182, Russia
| | - Andrey A Mozhaev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Georgy S Peters
- National Research Centre "Kurchatov Institute", Moscow, 123182, Russia
| | - Eleonora V Shtykova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia.
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Smirnova EV, Rakitina TV, Ziganshin RH, Saratov GA, Arapidi GP, Belogurov AA, Kudriaeva AA. Identification of Myelin Basic Protein Proximity Interactome Using TurboID Labeling Proteomics. Cells 2023; 12:cells12060944. [PMID: 36980286 PMCID: PMC10047773 DOI: 10.3390/cells12060944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Myelin basic protein (MBP) is one of the key structural elements of the myelin sheath and has autoantigenic properties in multiple sclerosis (MS). Its intracellular interaction network is still partially deconvoluted due to the unfolded structure, abnormally basic charge, and specific cellular localization. Here we used the fusion protein of MBP with TurboID, an engineered biotin ligase that uses ATP to convert biotin to reactive biotin-AMP that covalently attaches to nearby proteins, to determine MBP interactome. Despite evident benefits, the proximity labeling proteomics technique generates high background noise, especially in the case of proteins tending to semi-specific interactions. In order to recognize unique MBP partners, we additionally mapped protein interaction networks for deaminated MBP variant and cyclin-dependent kinase inhibitor 1 (p21), mimicking MBP in terms of natively unfolded state, size and basic amino acid clusters. We found that in the plasma membrane region, MBP is colocalized with adhesion proteins occludin and myelin protein zero-like protein 1, solute carrier family transporters ZIP6 and SNAT1, Eph receptors ligand Ephrin-B1, and structural components of the vesicle transport machinery-synaptosomal-associated protein 23 (SNAP23), vesicle-associated membrane protein 3 (VAMP3), protein transport protein hSec23B and cytoplasmic dynein 1 heavy chain 1. We also detected that MBP potentially interacts with proteins involved in Fe2+ and lipid metabolism, namely, ganglioside GM2 activator protein, long-chain-fatty-acid-CoA ligase 4 (ACSL4), NADH-cytochrome b5 reductase 1 (CYB5R1) and metalloreductase STEAP3. Assuming the emerging role of ferroptosis and vesicle cargo docking in the development of autoimmune neurodegeneration, MBP may recruit and regulate the activity of these processes, thus, having a more inclusive role in the integrity of the myelin sheath.
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Affiliation(s)
- Evgeniya V Smirnova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Tatiana V Rakitina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Rustam H Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - George A Saratov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
| | - Georgij P Arapidi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Alexey A Belogurov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Department of Biological Chemistry, Evdokimov Moscow State University of Medicine and Dentistry, Ministry of Health of Russian Federation, 127473 Moscow, Russia
| | - Anna A Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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Shilova SA, Khrenova MG, Matyuta IO, Nikolaeva AY, Rakitina TV, Klyachko NL, Minyaev ME, Boyko KM, Popov VO, Bezsudnova EY. To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense. Molecules 2023; 28:molecules28052109. [PMID: 36903355 PMCID: PMC10003956 DOI: 10.3390/molecules28052109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
Pyridoxal-5'-phosphate (PLP)-dependent transaminases are highly efficient biocatalysts for stereoselective amination. D-amino acid transaminases can catalyze stereoselective transamination producing optically pure D-amino acids. The knowledge of substrate binding mode and substrate differentiation mechanism in D-amino acid transaminases comes down to the analysis of the transaminase from Bacillus subtilis. However, at least two groups of D-amino acid transaminases differing in the active site organization are known today. Here, we present a detailed study of D-amino acid transaminase from the gram-negative bacterium Aminobacterium colombiense with a substrate binding mode different from that for the transaminase from B. subtilis. We study the enzyme using kinetic analysis, molecular modeling, and structural analysis of holoenzyme and its complex with D-glutamate. We compare the multipoint binding of D-glutamate with the binding of other substrates, D-aspartate and D-ornithine. QM/MM MD simulation reveals that the substrate can act as a base and its proton can be transferred from the amino group to the α-carboxylate group. This process occurs simultaneously with the nucleophilic attack of the PLP carbon atom by the nitrogen atom of the substrate forming gem-diamine at the transimination step. This explains the absence of the catalytic activity toward (R)-amines that lack an α-carboxylate group. The obtained results clarify another substrate binding mode in D-amino acid transaminases and underpinned the substrate activation mechanism.
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Affiliation(s)
- Sofia A. Shilova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ilya O. Matyuta
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alena Y. Nikolaeva
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Tatiana V. Rakitina
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Natalia L. Klyachko
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Mikhail E. Minyaev
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ekaterina Yu. Bezsudnova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Correspondence:
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Petrenko DE, Karlinsky DM, Gordeeva VD, Arapidi GP, Britikova EV, Britikov VV, Nikolaeva AY, Boyko KM, Timofeev VI, Kuranova IP, Mikhailova AG, Bocharov EV, Rakitina TV. Crystal Structure of Inhibitor-Bound Bacterial Oligopeptidase B in the Closed State: Similarity and Difference between Protozoan and Bacterial Enzymes. Int J Mol Sci 2023; 24:ijms24032286. [PMID: 36768612 PMCID: PMC9917282 DOI: 10.3390/ijms24032286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/20/2022] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
The crystal structure of bacterial oligopeptidase B from Serratia proteamaculans (SpOpB) in complex with a chloromethyl ketone inhibitor was determined at 2.2 Å resolution. SpOpB was crystallized in a closed (catalytically active) conformation. A single inhibitor molecule bound simultaneously to the catalytic residues S532 and H652 mimicked a tetrahedral intermediate of the catalytic reaction. A comparative analysis of the obtained structure and the structure of OpB from Trypanosoma brucei (TbOpB) in a closed conformation showed that in both enzymes, the stabilization of the D-loop (carrying the catalytic D) in a position favorable for the formation of a tetrahedral complex occurs due to interaction with the neighboring loop from the β-propeller. However, the modes of interdomain interactions were significantly different for bacterial and protozoan OpBs. Instead of a salt bridge (as in TbOpB), in SpOpB, a pair of polar residues following the catalytic D617 and a pair of neighboring arginine residues from the β-propeller domain formed complementary oppositely charged surfaces. Bioinformatics analysis and structural modeling show that all bacterial OpBs can be divided into two large groups according to these two modes of D-loop stabilization in closed conformations.
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Affiliation(s)
| | - David M. Karlinsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Veronika D. Gordeeva
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Georgij P. Arapidi
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Phystech School of Biological and Medical Physics, 117303 Moscow, Russia
| | - Elena V. Britikova
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Vladimir V. Britikov
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | | | - Konstantin M. Boyko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Vladimir I. Timofeev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics” of the Russian Academy of Sciences, 119333 Moscow, Russia
| | - Inna P. Kuranova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics” of the Russian Academy of Sciences, 119333 Moscow, Russia
| | - Anna G. Mikhailova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Eduard V. Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Phystech School of Biological and Medical Physics, 117303 Moscow, Russia
| | - Tatiana V. Rakitina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
- Correspondence:
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Gaponov YA, Timofeev VI, Agapova YK, Bocharov EV, Shtykova EV, Rakitina TV. Comparative structural analysis of a histone-like protein from Spiroplasma melliferum in the crystalline state and in solution. Mendeleev Communications 2022. [DOI: 10.1016/j.mencom.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Babakhanova S, Jung EE, Namikawa K, Zhang H, Wang Y, Subach OM, Korzhenevskiy DA, Rakitina TV, Xiao X, Wang W, Shi J, Drobizhev M, Park D, Eisenhard L, Tang H, Köster RW, Subach FV, Boyden ES, Piatkevich KD. Rapid directed molecular evolution of fluorescent proteins in mammalian cells. Protein Sci 2022; 31:728-751. [PMID: 34913537 PMCID: PMC8862398 DOI: 10.1002/pro.4261] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/24/2021] [Accepted: 12/14/2021] [Indexed: 12/31/2022]
Abstract
In vivo imaging of model organisms is heavily reliant on fluorescent proteins with high intracellular brightness. Here we describe a practical method for rapid optimization of fluorescent proteins via directed molecular evolution in cultured mammalian cells. Using this method, we were able to perform screening of large gene libraries containing up to 2 × 107 independent random genes of fluorescent proteins expressed in HEK cells, completing one iteration of directed evolution in a course of 8 days. We employed this approach to develop a set of green and near-infrared fluorescent proteins with enhanced intracellular brightness. The developed near-infrared fluorescent proteins demonstrated high performance for fluorescent labeling of neurons in culture and in vivo in model organisms such as Caenorhabditis elegans, Drosophila, zebrafish, and mice. Spectral properties of the optimized near-infrared fluorescent proteins enabled crosstalk-free multicolor imaging in combination with common green and red fluorescent proteins, as well as dual-color near-infrared fluorescence imaging. The described method has a great potential to be adopted by protein engineers due to its simplicity and practicality. We also believe that the new enhanced fluorescent proteins will find wide application for in vivo multicolor imaging of small model organisms.
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Petrenko DE, Timofeev VI, Britikov VV, Britikova EV, Kleymenov SY, Vlaskina AV, Kuranova IP, Mikhailova AG, Rakitina TV. First Crystal Structure of Bacterial Oligopeptidase B in an Intermediate State: The Roles of the Hinge Region Modification and Spermine. Biology (Basel) 2021; 10:biology10101021. [PMID: 34681120 PMCID: PMC8533160 DOI: 10.3390/biology10101021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Oligopeptidase B is a two-domain, trypsin-like peptidase from parasitic protozoa and bacteria which belongs to the least studied group of prolyloligopeptidases. In this study, we describe for the first time a crystal structure of bacterial oligopeptidase B and compare it with those of protozoan oligopeptidases B and related prolyloligopeptidases. The enzyme was crystallized in the presence of spermine and contained a modified sequence of the interdomain linker. Both factors were key for crystallization. The structure showed an uncommon intermediate conformation with a domain arrangement intermediate between open and closed conformations found in the crystals of ligand-free and inhibitor-bound prolyloligopeptidases, respectively. To evaluate the impact of the modification and spermine in the obtained conformation, small-angle X-ray scattering was applied, which showed that in solution wild-type enzymes adopt the open conformation and spermine causes a transition to the intermediate state, while the modification is associated with a partial transition. We suggest that spermine-dependent conformational transition replicates the behavior of the enzyme in bacterial cells and the intermediate state, which is rarely detected in vitro, and might be widely distributed in vivo, and so should be considered during computational studies, including those aimed wanting to develop the small molecule inhibitors targeting prolyloligopeptidases. Abstract Oligopeptidase B (OpB) is a two-domain, trypsin-like serine peptidase belonging to the S9 prolyloligopeptidase (POP) family. Two domains are linked by a hinge region that participates in the transition of the enzyme between two major states—closed and open—in which domains and residues of the catalytic triad are located close to each other and separated, respectively. In this study, we described, for the first time, a structure of OpB from bacteria obtained for an enzyme from Serratia proteomaculans with a modified hinge region (PSPmod). PSPmod was crystallized in a conformation characterized by a disruption of the catalytic triad together with a domain arrangement intermediate between open and closed states found in crystals of ligand-free and inhibitor-bound POP, respectively. Two additional derivatives of PSPmod were crystallized in the same conformation. Neither wild-type PSP nor its corresponding mutated variants were susceptible to crystallization, indicating that the hinge region modification was key in the crystallization process. The second key factor was suggested to be polyamine spermine since all crystals were grown in its presence. The influences of the hinge region modification and spermine on the conformational state of PSP in solution were evaluated by small-angle X-ray scattering. SAXS showed that, in solution, wild-type PSP adopted the open state, spermine caused the conformational transition to the intermediate state, and spermine-free PSPmod contained molecules in the open and intermediate conformations in dynamic equilibrium.
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Affiliation(s)
- Dmitry E. Petrenko
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (D.E.P.); (A.V.V.)
| | - Vladimir I. Timofeev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, 117997 Moscow, Russia;
- Federal Scientific Research Center “Crystallography and Photonics”, RAS, 119333 Moscow, Russia;
- Correspondence: (V.I.T.); (T.V.R.)
| | - Vladimir V. Britikov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (V.V.B.); (E.V.B.)
| | - Elena V. Britikova
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (V.V.B.); (E.V.B.)
| | - Sergey Y. Kleymenov
- Bach Institute of Biochemistry, Federal Research Center “Fundamentals of Biotechnology”, RAS, 119071 Moscow, Russia;
- Koltzov Institute of Developmental Biology, RAS, 119334 Moscow, Russia
| | - Anna V. Vlaskina
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (D.E.P.); (A.V.V.)
| | - Inna P. Kuranova
- Federal Scientific Research Center “Crystallography and Photonics”, RAS, 119333 Moscow, Russia;
| | - Anna G. Mikhailova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, 117997 Moscow, Russia;
| | - Tatiana V. Rakitina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, 117997 Moscow, Russia;
- Correspondence: (V.I.T.); (T.V.R.)
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Bakunova AK, Nikolaeva AY, Rakitina TV, Isaikina TY, Khrenova MG, Boyko KM, Popov VO, Bezsudnova EY. The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme. Molecules 2021; 26:molecules26165053. [PMID: 34443642 PMCID: PMC8401098 DOI: 10.3390/molecules26165053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 02/02/2023] Open
Abstract
Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.
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Affiliation(s)
- Alina K. Bakunova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Alena Yu. Nikolaeva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Tatiana V. Rakitina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia
| | - Tatiana Y. Isaikina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
- Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory 1/3, 119991 Moscow, Russia
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Ekaterina Yu. Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
- Correspondence: author E-mail:
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11
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Bezsudnova EY, Nikolaeva AY, Bakunova AK, Rakitina TV, Suplatov DA, Popov VO, Boyko KM. Probing the role of the residues in the active site of the transaminase from Thermobaculum terrenum. PLoS One 2021; 16:e0255098. [PMID: 34324538 PMCID: PMC8320979 DOI: 10.1371/journal.pone.0255098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/11/2021] [Indexed: 11/28/2022] Open
Abstract
Creating biocatalysts for (R)-selective amination effectively is highly desirable in organic synthesis. Despite noticeable progress in the engineering of (R)-amine activity in pyridoxal-5’-phosphate-dependent transaminases of fold type IV, the specialization of the activity is still an intuitive task, as there is poor understanding of sequence-structure-function relationships. In this study, we analyzed this relationship in transaminase from Thermobaculum terrenum, distinguished by expanded substrate specificity and activity in reactions with L-amino acids and (R)-(+)-1-phenylethylamine using α-ketoglutarate and pyruvate as amino acceptors. We performed site-directed mutagenesis to create a panel of the enzyme variants, which differ in the active site residues from the parent enzyme to a putative transaminase specific to (R)-primary amines. The variants were examined in the overall transamination reactions and half-reaction with (R)-(+)-1-phenylethylamine. A structural analysis of the most prominent variants revealed a spatial reorganization in the active sites, which caused changes in activity. Although the specialization to (R)-amine transaminase was not implemented, we succeeded in understanding the role of the particular active site residues in expanding substrate specificity of the enzyme. We showed that the specificity for (R)-(+)-1-phenylethylamine in transaminase from T. terrenum arises without sacrificing the specificity for L-amino acids and α-ketoglutarate and in consensus with it.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Alena Yu Nikolaeva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Alina K Bakunova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatiana V Rakitina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation.,Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry A Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, Russian Federation
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
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12
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Muslinkina L, Pletnev VZ, Pletneva NV, Ruchkin DA, Kolesov DV, Bogdanov AM, Kost LA, Rakitina TV, Agapova YK, Shemyakina II, Chudakov DM, Pletnev S. Two independent routes of post-translational chemistry in fluorescent protein FusionRed. Int J Biol Macromol 2020; 155:551-559. [PMID: 32243936 DOI: 10.1016/j.ijbiomac.2020.03.244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/27/2020] [Accepted: 03/29/2020] [Indexed: 10/24/2022]
Abstract
The crystal structure of monomeric red fluorescent protein FusionRed (λex/λem 580/608 mn) has been determined at 1.09 Å resolution and revealed two alternative routes of post-translational chemistry, resulting in distinctly different products. The refinement occupancies suggest the 60:40 ratio of the mature Met63-Tyr64-Gly65 chromophore and uncyclized chromophore-forming tripeptide with the protein backbone cleaved between Met63 and the preceding Phe62 and oxidized Cα-Cβ bond of Tyr64. We analyzed the structures of FusionRed and several related red fluorescent proteins, identified structural elements causing hydrolysis of the peptide bond, and verified their impact by single point mutagenesis. These findings advance the understanding of the post-translational chemistry of GFP-like fluorescent proteins beyond the canonical cyclization-dehydration-oxidation mechanism. They also show that impaired cyclization does not prevent chromophore-forming tripeptide from further transformations enabled by the same set of catalytic residues. Our mutagenesis efforts resulted in inhibition of the peptide backbone cleavage, and a FusionRed variant with ~30% improved effective brightness.
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Affiliation(s)
- Liya Muslinkina
- Basic Science Program, Frederick National Laboratory for Cancer Research, Argonne, IL 60439, USA
| | - Vladimir Z Pletnev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nadya V Pletneva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Ruchkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Danila V Kolesov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Lubov A Kost
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V Rakitina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yulia K Agapova
- National Research Center "Kurchatov Institute," Moscow, Russia
| | - Irina I Shemyakina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergei Pletnev
- Basic Science Program, Frederick National Laboratory for Cancer Research, Argonne, IL 60439, USA.
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13
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Barykina NV, Sotskov VP, Gruzdeva AM, Wu YK, Portugues R, Subach OM, Chefanova ES, Plusnin VV, Ivashkina OI, Anokhin KV, Vlaskina AV, Korzhenevskiy DA, Nikolaeva AY, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Subach FV. FGCaMP7, an Improved Version of Fungi-Based Ratiometric Calcium Indicator for In Vivo Visualization of Neuronal Activity. Int J Mol Sci 2020; 21:ijms21083012. [PMID: 32344594 PMCID: PMC7215472 DOI: 10.3390/ijms21083012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 01/06/2023] Open
Abstract
Genetically encoded calcium indicators (GECIs) have become a widespread tool for the visualization of neuronal activity. As compared to popular GCaMP GECIs, the FGCaMP indicator benefits from calmodulin and M13-peptide from the fungi Aspergillus niger and Aspergillus fumigatus, which prevent its interaction with the intracellular environment. However, FGCaMP exhibits a two-phase fluorescence behavior with the variation of calcium ion concentration, has moderate sensitivity in neurons (as compared to the GCaMP6s indicator), and has not been fully characterized in vitro and in vivo. To address these limitations, we developed an enhanced version of FGCaMP, called FGCaMP7. FGCaMP7 preserves the ratiometric phenotype of FGCaMP, with a 3.1-fold larger ratiometric dynamic range in vitro. FGCaMP7 demonstrates 2.7- and 8.7-fold greater photostability compared to mEGFP and mTagBFP2 fluorescent proteins in vitro, respectively. The ratiometric response of FGCaMP7 is 1.6- and 1.4-fold higher, compared to the intensiometric response of GCaMP6s, in non-stimulated and stimulated neuronal cultures, respectively. We reveal the inertness of FGCaMP7 to the intracellular environment of HeLa cells using its truncated version with a deleted M13-like peptide; in contrast to the similarly truncated variant of GCaMP6s. We characterize the crystal structure of the parental FGCaMP indicator. Finally, we test the in vivo performance of FGCaMP7 in mouse brain using a two-photon microscope and an NVista miniscope; and in zebrafish using two-color ratiometric confocal imaging.
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Affiliation(s)
- Natalia V. Barykina
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia; (N.V.B.); (O.I.I.); (K.V.A.)
| | - Vladimir P. Sotskov
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
| | - Anna M. Gruzdeva
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; (Y.K.W.); (R.P.)
| | - You Kure Wu
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; (Y.K.W.); (R.P.)
| | - Ruben Portugues
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; (Y.K.W.); (R.P.)
- Institute of Neuroscience, Technical University of Munich, 80802 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Elizaveta S. Chefanova
- Department of NBIC-technologies, Moscow Institute of Physics and Technology, 123182 Moscow, Russia;
| | - Viktor V. Plusnin
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Department of NBIC-technologies, Moscow Institute of Physics and Technology, 123182 Moscow, Russia;
| | - Olga I. Ivashkina
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia; (N.V.B.); (O.I.I.); (K.V.A.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Konstantin V. Anokhin
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia; (N.V.B.); (O.I.I.); (K.V.A.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Dmitry A. Korzhenevskiy
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Tatiana V. Rakitina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Laboratory of Hormonal Regulation Proteins, M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Anna M. Varizhuk
- Department of Biophysics, Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.M.V.); (G.E.P.)
- Department of Biophysics, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119435 Moscow, Russia
| | - Galina E. Pozmogova
- Department of Biophysics, Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.M.V.); (G.E.P.)
- Department of Biophysics, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119435 Moscow, Russia
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Correspondence: ; Tel.: +07-499-196-7100-3389
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Subach OM, Sotskov VP, Plusnin VV, Gruzdeva AM, Barykina NV, Ivashkina OI, Anokhin KV, Nikolaeva AY, Korzhenevskiy DA, Vlaskina AV, Lazarenko VA, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Podgorny OV, Piatkevich KD, Boyden ES, Subach FV. Novel Genetically Encoded Bright Positive Calcium Indicator NCaMP7 Based on the mNeonGreen Fluorescent Protein. Int J Mol Sci 2020; 21:ijms21051644. [PMID: 32121243 PMCID: PMC7084697 DOI: 10.3390/ijms21051644] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 12/21/2022] Open
Abstract
Green fluorescent genetically encoded calcium indicators (GECIs) are the most popular tool for visualization of calcium dynamics in vivo. However, most of them are based on the EGFP protein and have similar molecular brightnesses. The NTnC indicator, which is composed of the mNeonGreen fluorescent protein with the insertion of troponin C, has higher brightness as compared to EGFP-based GECIs, but shows a limited inverted response with an ΔF/F of 1. By insertion of a calmodulin/M13-peptide pair into the mNeonGreen protein, we developed a green GECI called NCaMP7. In vitro, NCaMP7 showed positive response with an ΔF/F of 27 and high affinity (Kd of 125 nM) to calcium ions. NCaMP7 demonstrated a 1.7-fold higher brightness and similar calcium-association/dissociation dynamics compared to the standard GCaMP6s GECI in vitro. According to fluorescence recovery after photobleaching (FRAP) experiments, the NCaMP7 design partially prevented interactions of NCaMP7 with the intracellular environment. The NCaMP7 crystal structure was obtained at 1.75 Å resolution to uncover the molecular basis of its calcium ions sensitivity. The NCaMP7 indicator retained a high and fast response when expressed in cultured HeLa and neuronal cells. Finally, we successfully utilized the NCaMP7 indicator for in vivo visualization of grating-evoked and place-dependent neuronal activity in the visual cortex and the hippocampus of mice using a two-photon microscope and an NVista miniscope, respectively.
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Affiliation(s)
- Oksana M. Subach
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Vladimir P. Sotskov
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
| | - Viktor V. Plusnin
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Anna M. Gruzdeva
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
| | - Natalia V. Barykina
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Olga I. Ivashkina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Konstantin V. Anokhin
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Alena Y. Nikolaeva
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Dmitry A. Korzhenevskiy
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Anna V. Vlaskina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Vladimir A. Lazarenko
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia;
| | - Tatiana V. Rakitina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia;
| | - Anna M. Varizhuk
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (A.M.V.); (G.E.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Galina E. Pozmogova
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (A.M.V.); (G.E.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Oleg V. Podgorny
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia;
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- N.K. Koltzov Institute of Developmental Biology, RAS, Moscow 119334, Russia
| | - Kiryl D. Piatkevich
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (K.D.P.); (E.S.B.)
- School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Edward S. Boyden
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (K.D.P.); (E.S.B.)
| | - Fedor V. Subach
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Correspondence: ; Tel.: +07-499-196 7100-3389
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15
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Akparov VK, Timofeev VI, Konstantinova GE, Khaliullin IG, Kuranova IP, Rakitina TV, Švedas V. 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. PLoS One 2019; 14:e0226636. [PMID: 31887148 PMCID: PMC6937156 DOI: 10.1371/journal.pone.0226636] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/27/2019] [Indexed: 01/03/2023] Open
Abstract
The carboxypeptidase T (CPT) from Thermoactinomyces vulgaris has an active site structure and 3D organization similar to pancreatic carboxypeptidases A and B (CPA and CPB), but differs in broader substrate specificity. The crystal structures of CPT complexes with the transition state analogs N-sulfamoyl-L-leucine and N-sulfamoyl-L-glutamate (SLeu and SGlu) were determined and compared with previously determined structures of CPT complexes with N-sulfamoyl-L-arginine and N-sulfamoyl-L-phenylalanine (SArg and SPhe). The conformations of residues Tyr255 and Glu270, the distances between these residues and the corresponding ligand groups, and the Zn-S gap between the zinc ion and the sulfur atom in the ligand's sulfamoyl group that simulates a distance between the zinc ion and the tetrahedral sp3-hybridized carbon atom of the converted peptide bond, vary depending on the nature of the side chain in the substrate's C-terminus. The increasing affinity of CPT with the transition state analogs in the order SGlu, SArg, SPhe, SLeu correlates well with a decreasing Zn-S gap in these complexes and the increasing efficiency of CPT-catalyzed hydrolysis of the corresponding tripeptide substrates (ZAAL > ZAAF > ZAAR > ZAAE). Thus, the side chain of the ligand that interacts with the primary specificity pocket of CPT, determines the geometry of the transition complex, the relative orientation of the bond to be cleaved by the catalytic groups of the active site and the catalytic properties of the enzyme. In the case of CPB, the relative orientation of the catalytic amino acid residues, as well as the distance between Glu270 and SArg/SPhe, is much less dependent on the nature of the corresponding side chain of the substrate. The influence of the nature of the substrate side chain on the structural organization of the transition state determines catalytic activity and broad substrate specificity of the carboxypeptidase T.
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Affiliation(s)
- Valery Kh. Akparov
- Protein Chemistry Department, Federal Institution "State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", Moscow, Russia
- Protein Factory, National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Vladimir I. Timofeev
- Laboratory of X-ray analysis methods and synchrotron radiation, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
- Kurchatov center of synchrotron-neutron research, National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Galina E. Konstantinova
- Protein Chemistry Department, Federal Institution "State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", Moscow, Russia
| | - Ilyas G. Khaliullin
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
| | - Inna P. Kuranova
- Laboratory of X-ray analysis methods and synchrotron radiation, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
- Kurchatov center of synchrotron-neutron research, National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Tatiana V. Rakitina
- Protein Factory, National Research Centre “Kurchatov Institute”, Moscow, Russia
- Laboratory of Hormonal Regulation Proteins, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vytas Švedas
- Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
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16
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Petrenko DE, Mikhailova AG, Timofeev VI, Agapova YК, Karlinsky DM, Komolov AS, Korzhenevskiy DA, Vlaskina AV, Rumsh LD, Rakitina TV. 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. J Biomol Struct Dyn 2019; 38:4868-4882. [PMID: 31724904 DOI: 10.1080/07391102.2019.1692694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Oligopeptidases B (OpdBs) are trypsin-like peptidases from protozoa and bacteria that belong to the prolyl oligopeptidase (POP) family. All POPs consist of C-terminal catalytic domain and N-terminal β-propeller domain and exist in two major conformations: closed (active), where the domains and residues of the catalytic triad are positioned close to each other, and open (non-active), where two domains and residues of the catalytic triad are separated. The interdomain interface, particularly, one of its salt bridges (SB1), plays a role in the transition between these two conformations. However, due to double amino acid substitution (E/R and R/Q), this functionally important SB1 is absent in γ-proteobacterial OpdBs including peptidase from Serratia proteamaculans (PSP). In this study, molecular dynamics was used to analyze inter- and intradomain interactions stabilizing PSP in the closed conformation, in which catalytic H652 is located close to other residues of the catalytic triad. The 3D models of either wild-type PSP or of mutant PSPs carrying activating mutations E125A and D649A in complexes with peptide-substrates were subjected to the analysis. The mechanism that regulates transition of H652 from active to non-active conformation upon domain separation in PSP and other γ-proteobacterial OpdB was proposed. The complex network of polar interactions within H652-loop/C-terminal α-helix and between these areas and β-propeller domain, established in silico, was in a good agreement with both previously published results on the effects of single-residue mutations and new data on the effects of the activating mutations on each other and on the low active mutant PSP-K655A.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dmitry E Petrenko
- National Research Center "Kurchatov Institute", Moscow, Russian Federation
| | - Anna G Mikhailova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir I Timofeev
- National Research Center "Kurchatov Institute", Moscow, Russian Federation.,Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russian Federation
| | - Yulia К Agapova
- National Research Center "Kurchatov Institute", Moscow, Russian Federation
| | - David M Karlinsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Aleksandr S Komolov
- National Research Center "Kurchatov Institute", Moscow, Russian Federation.,Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russian Federation
| | | | - Anna V Vlaskina
- National Research Center "Kurchatov Institute", Moscow, Russian Federation
| | - Lev D Rumsh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatiana V Rakitina
- National Research Center "Kurchatov Institute", Moscow, Russian Federation.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
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17
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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: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Zeifman YS, Boyko KM, Nikolaeva AY, Timofeev VI, Rakitina TV, Popov VO, Bezsudnova EY. Functional characterization of PLP fold type IV transaminase with a mixed type of activity from Haliangium ochraceum. Biochim Biophys Acta Proteins Proteom 2019; 1867:575-585. [PMID: 30902765 DOI: 10.1016/j.bbapap.2019.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/01/2019] [Accepted: 03/16/2019] [Indexed: 12/11/2022]
Abstract
Pyridoxal-5'-phosphate (PLP)-dependent transaminases are industrially important enzymes catalyzing the stereoselective amination of ketones and keto acids. Transaminases of PLP fold type IV are characterized by (R)- or (S)-stereoselective transfer of amino groups, depending on the substrate profile of the enzyme. PLP fold type IV transaminases include branched-chain amino acid transaminases (BCATs), D-amino acid transaminases and (R)-amine:pyruvate transaminases. Recently, transaminases with a mixed type of activity were identified and characterized. Here, we report biochemical and structural characterization of a transaminase from myxobacterium Haliangium ochraceum (Hoch3033), which is active towards keto analogs of branched-chain amino acids (specific substrates for BCATs) and (R)-(+)-α-methylbenzylamine (specific substrate for (R)-amine:pyruvate transaminases). The enzyme is characterized by an alkaline pH optimum (pH 10.0-10.5) and a tolerance to high salt concentrations (up to 2 M NaCl). The structure of Hoch3033 was determined at 2.35 Å resolution. The overall fold of the enzyme was similar to those of known enzymes of PLP fold type IV. The mixed type of activity of Hoch3033 was implemented within the BCAT-like active site. However, in the active site of Hoch3033, we observed substitutions of specificity-determining residues that are important for substrate binding in canonical BCATs. We suggest that these changes result in the loss of activity towards α-ketoglutarate and increase the affinity towards (R)-(+)-α-methylbenzylamine. These results complement our knowledge of the catalytic diversity of transaminases and indicate the need for further research to understand the structural basis of substrate specificity in these enzymes.
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Affiliation(s)
- Yulia S Zeifman
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation; Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation.
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation; Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation
| | - Alena Yu Nikolaeva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation; Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation
| | - Vladimir I Timofeev
- Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation; FSRC «Crystallography and Photonics» RAS, Leninskiy Prospekt 59, 119333 Moscow, Russian Federation
| | - Tatiana V Rakitina
- Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation; Shemyakin&Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, 117997 Moscow, Russian Federation
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation; Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation
| | - Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation
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19
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Akparov VK, Timofeev VI, Khaliullin IG, Konstantinova GE, Kuranova IP, Rakitina TV, Švedas VK. Mobile Loop in the Active Site of Metallocarboxypeptidases as an Underestimated Determinant of Substrate Specificity. Biochemistry (Mosc) 2019; 83:1594-1602. [PMID: 30878033 DOI: 10.1134/s0006297918120167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
It is generally accepted that the primary specificity of metallocarboxypeptidases is mainly determined by the structure of the so-called primary specificity pocket. However, the G215S/A251G/T257A/D260G/T262D mutant of carboxypeptidase T from Thermoactinomyces vulgaris (CPT) with the primary specificity pocket fully reproducing the one in pancreatic carboxypeptidase B (CPB) retained the broad, mainly hydrophobic substrate specificity of the wild-type enzyme. In order to elucidate factors affecting substrate specificity of metallocarboxypeptidases and the reasons for the discrepancy with the established views, we have solved the structure of the complex of the CPT G215S/A251G/T257A/D260G/T262D mutant with the transition state analogue N-sulfamoyl-L-phenylalanine at a resolution of 1.35 Å and compared it with the structure of similar complex formed by CPB. The comparative study revealed a previously underestimated structural determinant of the substrate specificity of metallocarboxypeptidases and showed that even if substitution of five amino acid residues in the primary specificity pocket results in its almost complete structural correspondence to the analogous pocket in CPB, this does not lead to fundamental changes in the substrate specificity of the mutant enzyme due to the differences in the structure of the mobile loop located at the active site entrance that affects the substrate-induced conformational rearrangements of the active site.
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Affiliation(s)
- V Kh Akparov
- State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, 117545, Russia.
| | - V I Timofeev
- Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Center, Russian Academy of Sciences, Moscow, 119333, Russia. .,Kurchatov Institute National Research Center, Moscow, 123098, Russia
| | - I G Khaliullin
- Laboratory of Ion and Molecular Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, 141700, Russia.
| | - G E Konstantinova
- State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, 117545, Russia
| | - I P Kuranova
- Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Center, Russian Academy of Sciences, Moscow, 119333, Russia. .,Kurchatov Institute National Research Center, Moscow, 123098, Russia
| | - T V Rakitina
- Kurchatov Institute National Research Center, Moscow, 123098, Russia. .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Hormonal Regulation Proteins, Russian Academy of Sciences, Moscow, 117997, Russia
| | - V K Švedas
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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20
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Bezsudnova EY, Boyko KM, Nikolaeva AY, Zeifman YS, Rakitina TV, Suplatov DA, Popov VO. Biochemical and structural insights into PLP fold type IV transaminase from Thermobaculum terrenum. Biochimie 2018; 158:130-138. [PMID: 30599183 DOI: 10.1016/j.biochi.2018.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/27/2018] [Indexed: 10/27/2022]
Abstract
The high catalytic efficiency of enzymes under reaction conditions is one of the main goals in biocatalysis. Despite the dramatic progress in the development of more efficient biocatalysts by protein design, the search for natural enzymes with useful properties remains a promising strategy. The pyridoxal 5'-phosphate (PLP)-dependent transaminases represent a group of industrially important enzymes due to their ability to stereoselectively transfer amino groups between diverse substrates; however, the complex mechanism of substrate recognition and conversion makes the design of transaminases a challenging task. Here we report a detailed structural and kinetic study of thermostable transaminase from the bacterium Thermobaculum terrenum (TaTT) using the methods of enzyme kinetics, X-ray crystallography and molecular modeling. TaTT can convert L-branched-chain and L-aromatic amino acids as well as (R)-(+)-1-phenylethylamine at a high rate and with high enantioselectivity. The structures of TaTT in complex with the cofactor pyridoxal 5'-phosphate covalently bound to enzyme and in complex with its reduced form, pyridoxamine 5'-phosphate, were determined at resolutions of 2.19 Å and 1.5 Å, and deposited in the Protein Data Bank as entries 6GKR and 6Q8E, respectively. TaTT is a fold type IV PLP-dependent enzyme. In terms of structural similarity, the enzyme is close to known branched-chain amino acid aminotransferases, but differences in characteristic sequence motifs in the active site were observed in TaTT compared to canonical branched-chain amino acid aminotransferases, which can explain the improved binding of aromatic amino acids and (R)-(+)-1-phenylethylamine. This study has shown for the first time that high substrate specificity towards both various l-amino acids and (R)-primary amines can be implemented within one pyridoxal 5'-phosphate-dependent active site of fold type IV. These results complement our knowledge of the catalytic diversity of transaminases and indicate the need for further biochemical and bioinformatic studies to understand the sequence-structure-function relationship in these enzymes.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation.
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation; Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
| | - Alena Yu Nikolaeva
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
| | - Yulia S Zeifman
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation; Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
| | - Tatiana V Rakitina
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation; Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya Str. 16/10, 117997, Moscow, Russian Federation
| | - Dmitry A Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskiye Gory 1-73, Moscow, 119991, Russian Federation
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation; Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
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21
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Akparov VK, Timofeev VI, Kuranova IP, Rakitina TV. Crystal structure of mutant carboxypeptidase T from Thermoactinomyces vulgaris with an implanted S1' subsite from pancreatic carboxypeptidase B. Acta Crystallogr F Struct Biol Commun 2018; 74:638-643. [PMID: 30279315 PMCID: PMC6168770 DOI: 10.1107/s2053230x18011962] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/23/2018] [Indexed: 11/10/2022] Open
Abstract
A site-directed mutagenesis method has been used to obtain the G215S/A251G/T257A/D260G/T262D mutant of carboxypeptidase T from Thermoactinomyces vulgaris (CPT), in which the amino-acid residues of the S1' subsite are substituted by the corresponding residues from pancreatic carboxypeptidase B (CPB). It was shown that the mutant enzyme retained the broad, mainly hydrophobic selectivity of wild-type CPT. The mutant containing the implanted CPB S1' subsite was crystallized and its three-dimensional structure was determined at 1.29 Å resolution by X-ray crystallography. A comparison of the three-dimensional structures of CPT, the G215S/A251G/T257A/D260G/T262D CPT mutant and CPB showed that the S1' subsite of CPT has not been distorted by the mutagenesis and adequately reproduces the structure of the CPB S1' subsite. The CPB-like mutant differs from CPB in substrate selectivity owing to differences between the two enzymes outside the S1' subsite. Moreover, the difference in substrate specificity between the enzymes was shown to be affected by residues other than those that directly contact the substrate.
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Affiliation(s)
- Valery Kh. Akparov
- Protein Chemistry Department, State Research Institute for Genetics and Selection of Industrial Microorganisms, 1yi Dorozhnyi Proezd 1, Moscow 117545, Russian Federation
| | - Vladimir I. Timofeev
- X-ray Analysis Methods and Synchrotron Radiation Laboratory, Shubnikov Institute of Crystallography of Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospect 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Centre ‘Kurchatov Institute’, Akad. Kurchatova Sq. 1, Moscow 123182, Russian Federation
| | - Inna P. Kuranova
- X-ray Analysis Methods and Synchrotron Radiation Laboratory, Shubnikov Institute of Crystallography of Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospect 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Centre ‘Kurchatov Institute’, Akad. Kurchatova Sq. 1, Moscow 123182, Russian Federation
| | - Tatiana V. Rakitina
- Kurchatov Complex of NBICS-Technologies, National Research Centre ‘Kurchatov Institute’, Akad. Kurchatova Sq. 1, Moscow 123182, Russian Federation
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Bezsudnova EY, Dibrova DV, Nikolaeva AY, Rakitina TV, Popov VO. Identification of branched-chain amino acid aminotransferases active towards (R)-(+)-1-phenylethylamine among PLP fold type IV transaminases. J Biotechnol 2018; 271:26-28. [PMID: 29453991 DOI: 10.1016/j.jbiotec.2018.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/29/2017] [Accepted: 02/09/2018] [Indexed: 10/18/2022]
Abstract
New class IV transaminases with activity towards L-Leu, which is typical of branched-chain amino acid aminotransferases (BCAT), and with activity towards (R)-(+)-1-phenylethylamine ((R)-PEA), which is typical of (R)-selective (R)-amine:pyruvate transaminases, were identified by bioinformatics analysis, obtained in recombinant form, and analyzed. The values of catalytic activities in the reaction with L-Leu and (R)-PEA are comparable to those measured for characteristic transaminases with the corresponding specificity. Earlier, (R)-selective class IV transaminases were found to be active, apart from (R)-PEA, only with some other (R)-primary amines and D-amino acids. Sequences encoding new transaminases with mixed type of activity were found by searching for changes in the conserved motifs of sequences of BCAT by different bioinformatics tools.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation.
| | - Daria V Dibrova
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskie Gory 1-73, Moscow 119991, Russian Federation
| | - Alena Yu Nikolaeva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation; Kurchatov Complex of NBICS-Technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation
| | - Tatiana V Rakitina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation; Kurchatov Complex of NBICS-Technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation; Kurchatov Complex of NBICS-Technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation
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23
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Timofeev VI, Altukhov DA, Talyzina AA, Agapova YK, Vlaskina AV, Korzhenevskiy DA, Kleymenov SY, Bocharov EV, Rakitina TV. Structural plasticity and thermal stability of the histone-like protein from Spiroplasma melliferum are due to phenylalanine insertions into the conservative scaffold. J Biomol Struct Dyn 2017; 36:4392-4404. [PMID: 29283021 DOI: 10.1080/07391102.2017.1417162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The histone-like (HU) protein is one of the major nucleoid-associated proteins of the bacterial nucleoid, which shares high sequence and structural similarity with IHF but differs from the latter in DNA-specificity. Here, we perform an analysis of structural-dynamic properties of HU protein from Spiroplasma melliferum and compare its behavior in solution to that of another mycoplasmal HU from Mycoplasma gallisepticum. The high-resolution heteronuclear NMR spectroscopy was coupled with molecular-dynamics study and comparative analysis of thermal denaturation of both mycoplasmal HU proteins. We suggest that stacking interactions in two aromatic clusters in the HUSpm dimeric interface determine not only high thermal stability of the protein, but also its structural plasticity experimentally observed as slow conformational exchange. One of these two centers of stacking interactions is highly conserved among the known HU and IHF proteins. Second aromatic core described recently in IHFs and IHF-like proteins is considered as a discriminating feature of IHFs. We performed an electromobility shift assay to confirm high affinities of HUSpm to both normal and distorted dsDNA, which are the characteristics of HU protein. MD simulations of HUSpm with alanine mutations of the residues forming the non-conserved aromatic cluster demonstrate its role in dimer stabilization, as both partial and complete distortion of the cluster enhances local flexibility of HUSpm.
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Affiliation(s)
- Vladimir I Timofeev
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,b Federal Scientific Research Center 'Crystallography and Photonics' RAS , Leninskii pr., 59, Moscow 119333 , Russian Federation
| | - Dmitry A Altukhov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna A Talyzina
- c Moscow Institute of Physics and Technology , Institutskiy per., 9, Dolgoprudny, Moscow Region 141700 , Russian Federation
| | - Yulia K Agapova
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna V Vlaskina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Dmitry A Korzhenevskiy
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Sergey Yu Kleymenov
- d Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences , Leninsky Prospekt. 33, bld. 2, Moscow 119071 , Russian Federation.,e Russian Academy of Sciences, Koltzov Institute of Developmental Biology , ul. Vavilova, 26, Moscow 119334 , Russian Federation
| | - Eduard V Bocharov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,f Shemyakin&Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
| | - Tatiana V Rakitina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,f Shemyakin&Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
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Akparov VK, Timofeev VI, Khaliullin IG, Švedas V, Kuranova IP, Rakitina TV. Crystal structures of carboxypeptidase T complexes with transition-state analogs. J Biomol Struct Dyn 2017; 36:3958-3966. [DOI: 10.1080/07391102.2017.1404932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Valery Kh. Akparov
- Protein Chemistry Department, State Research Institute for Genetics and Selection of Industrial Microorganisms, 1yi Dorozhnyi Proezd, 1, Moscow 117545, Russia
| | - Vladimir I. Timofeev
- X-ray Analysis Methods and Synchrotron Radiation Laboratory, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskii Prospect 59, Moscow 119333, Russia
- Kurchatov Complex of NBICS-Technologies, National Research Center “Kurchatov Institute”, Akad. Kurchatova pl.1, Moscow 123182, Russia
| | - Ilyas G. Khaliullin
- Laboratory of Ion and Molecular Physics, Moscow Institute of Physics and Technology, Institutskii per., 9, Dolgoprudnyi, Moscow Region 141700, Russia
| | - Vytas Švedas
- Biokinetics Department, Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskie Gory 1, b.73, Moscow 119991, Russia
| | - Inna P. Kuranova
- X-ray Analysis Methods and Synchrotron Radiation Laboratory, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskii Prospect 59, Moscow 119333, Russia
- Kurchatov Complex of NBICS-Technologies, National Research Center “Kurchatov Institute”, Akad. Kurchatova pl.1, Moscow 123182, Russia
| | - Tatiana V. Rakitina
- Kurchatov Complex of NBICS-Technologies, National Research Center “Kurchatov Institute”, Akad. Kurchatova pl.1, Moscow 123182, Russia
- Laboratory of Hormonal Regulation Proteins, M.M. Shemyakin and Yu.A, Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia
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Kamashev D, Agapova Y, Rastorguev S, Talyzina AA, Boyko KM, Korzhenevskiy DA, Vlaskina A, Vasilov R, Timofeev VI, Rakitina TV. Comparison of histone-like HU protein DNA-binding properties and HU/IHF protein sequence alignment. PLoS One 2017; 12:e0188037. [PMID: 29131864 PMCID: PMC5683647 DOI: 10.1371/journal.pone.0188037] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/12/2017] [Indexed: 12/12/2022] Open
Abstract
Background The structure and function of bacterial nucleoid are controlled by histone-like proteins of HU/IHF family, omnipresent in bacteria and also founding archaea and some eukaryotes.HU protein binds dsDNA without sequence specificity and avidly binds DNA structures with propensity to be inclined such as forks, three/four-way junctions, nicks, overhangs and DNA bulges. Sequence comparison of thousands of known histone-like proteins from diverse bacteria phyla reveals relation between HU/IHF sequence, DNA–binding properties and other protein features. Methodology and principal findings Performed alignment and clusterization of the protein sequences show that HU/IHF family proteins can be unambiguously divided into three groups, HU proteins, IHF_A and IHF_B proteins. HU proteins, IHF_A and IHF_B proteins are further partitioned into several clades for IHF and HU; such a subdivision is in good agreement with bacterial taxonomy. We also analyzed a hundred of 3D fold comparative models built for HU sequences from all revealed HU clades. It appears that HU fold remains similar in spite of the HU sequence variations. We studied DNA–binding properties of HU from N. gonorrhoeae, which sequence is similar to one of E.coli HU, and HU from M. gallisepticum and S. melliferum which sequences are distant from E.coli protein. We found that in respect to dsDNA binding, only S. melliferum HU essentially differs from E.coli HU. In respect to binding of distorted DNA structures, S. melliferum HU and E.coli HU have similar properties but essentially different from M. gallisepticum HU and N. gonorrhea HU. We found that in respect to dsDNA binding, only S. melliferum HU binds DNA in non-cooperative manner and both mycoplasma HU bend dsDNA stronger than E.coli and N. gonorrhoeae. In respect to binding to distorted DNA structures, each HU protein has its individual profile of affinities to various DNA-structures with the increased specificity to DNA junction. Conclusions and significance HU/IHF family proteins sequence alignment and classification are updated. Comparative modeling demonstrates that HU protein 3D folding’s even more conservative than HU sequence. For the first time, DNA binding characteristics of HU from N. gonorrhoeae, M. gallisepticum and S. melliferum are studied. Here we provide detailed analysis of the similarity and variability of DNA-recognizing and bending of four HU proteins from closely and distantly related HU clades.
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Affiliation(s)
- Dmitri Kamashev
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
- * E-mail:
| | - Yulia Agapova
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
| | - Sergey Rastorguev
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
| | - Anna A. Talyzina
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Konstantin M. Boyko
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry A. Korzhenevskiy
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
| | - Anna Vlaskina
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
| | - Raif Vasilov
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
| | - Vladimir I. Timofeev
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
- Federal Scientific Research Center “Crystallography and Photonics”, RAS, Moscow, Russian Federation
| | - Tatiana V. Rakitina
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
- Shemyakin&Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russian Federation
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26
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Mikhailova AG, Rakitina TV, Timofeev VI, Karlinsky DM, Korzhenevskiy DA, Agapova YК, Vlaskina AV, Ovchinnikova MV, Gorlenko VA, Rumsh LD. Activity modulation of the oligopeptidase B from Serratia proteamaculans by site-directed mutagenesis of amino acid residues surrounding catalytic triad histidine. Biochimie 2017; 139:125-136. [DOI: 10.1016/j.biochi.2017.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 11/16/2022]
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27
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Altukhov DA, Talyzina AA, Agapova YK, Vlaskina AV, Korzhenevskiy DA, Bocharov EV, Rakitina TV, Timofeev VI, Popov VO. Enhanced conformational flexibility of the histone-like (HU) protein from Mycoplasma gallisepticum. J Biomol Struct Dyn 2016; 36:45-53. [PMID: 27884082 DOI: 10.1080/07391102.2016.1264893] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The histone-like (HU) protein is one of the major nucleoid-associated proteins involved in DNA supercoiling and compaction into bacterial nucleoid as well as in all DNA-dependent transactions. This small positively charged dimeric protein binds DNA in a non-sequence specific manner promoting DNA super-structures. The majority of HU proteins are highly conserved among bacteria; however, HU protein from Mycoplasma gallisepticum (HUMgal) has multiple amino acid substitutions in the most conserved regions, which are believed to contribute to its specificity to DNA targets unusual for canonical HU proteins. In this work, we studied the structural dynamic properties of the HUMgal dimer by NMR spectroscopy and MD simulations. The obtained all-atom model displays compliance with the NMR data and confirms the heterogeneous backbone flexibility of HUMgal. We found that HUMgal, being folded into a dimeric conformation typical for HU proteins, has a labile α-helical body with protruded β-stranded arms forming DNA-binding domain that are highly flexible in the absence of DNA. The amino acid substitutions in conserved regions of the protein are likely to affect the conformational lability of the HUMgal dimer that can be responsible for complex functional behavior of HUMgal in vivo, e.g. facilitating its spatial adaptation to non-canonical DNA-targets.
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Affiliation(s)
- Dmitry A Altukhov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna A Talyzina
- b Moscow Institute of Physics and Technology , Institutskiy per., 9, Dolgoprudny, Moscow Region 141700 , Russian Federation
| | - Yulia K Agapova
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna V Vlaskina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Dmitry A Korzhenevskiy
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Eduard V Bocharov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,c Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
| | - Tatiana V Rakitina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,c Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
| | - Vladimir I Timofeev
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,d Federal Scientific Research Center 'Crystallography and Photonics' RAS , Leninskii pr., 59, Moscow 119333 , Russian Federation
| | - Vladimir O Popov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,e Bach Institute of Biochemistry , Research Center of Biotechnology of the Russian Academy of Sciences , Leninsky Prospekt. 33, bld. 2, Moscow 119071 , Russian Federation
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28
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Mikhailova AG, Nekrasov AN, Zinchenko AA, Rakitina TV, Korzhenevsky DA, Lipkin AV, Razguljaeva OA, Ovchinnikova MV, Gorlenko VA, Rumsh LD. Truncated Variants of Serratia proteamaculans Oligopeptidase B Having Different Activities. Biochemistry (Mosc) 2016; 80:1331-43. [PMID: 26567578 DOI: 10.1134/s0006297915100156] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Treatment of native psychrophilic oligopeptidase B from Serratia proteamaculans (PSP, 78 kDa) with chymotrypsin (soluble or immobilized on modified porous glass MPG-PA) in the presence of 50% glycerol leads to production of a truncated enzyme form (PSP-Chtr, ~66 kDa), which retains activity toward the low molecular weight substrate of PSP, BAPNA, but in contrast to PSP, is active toward the protein substrate azocasein. It has been shown by MALDI-TOF mass-spectrometry that PSP-Chtr lacks the N-terminal region of the molecule that envelops the catalytic domain of PSP and supposedly prevents hydrolysis of high molecular weight substrates. It has also been established that the lacking fragment corresponds to the N-terminal highest rank element of the informational structure of PSP. This finding confirms the usefulness of the method of informational structure analysis for protein engineering of enzymes. A similar treatment of PSP with immobilized trypsin also led to production of a stable truncated enzyme form (PSP-Tr, ~75 kDa) which lacked 22 C-terminal amino acid residues and completely lost enzymatic activity, presumably because of changes in the nearest environment of His652 of the catalytic triad.
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Affiliation(s)
- A G Mikhailova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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Rakitina TV, Zeifman AA, Novikov FN, Stroganov OV, Stroylov VS, Svitanko IV, Frank-Kamenetskii A, Chilov GG. Novel PARP1 inhibitors potentiate doxorubicin antitumor activity in vitro. Mendeleev Communications 2015. [DOI: 10.1016/j.mencom.2015.09.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Boyko KM, Gorbacheva MA, Rakitina TV, Korzhenevsky DA, Dorovatovsky PV, Lipkin AV, Popov VO. Identification of the ligand in the structure of the protein with unknown function STM4435 from Salmonella typhimurium. DOKL BIOCHEM BIOPHYS 2014; 457:121-4. [PMID: 25172330 DOI: 10.1134/s1607672914040012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Indexed: 01/09/2023]
Abstract
The unidentified ligand, which is present in the crystal of the protein with unknown function STM4435 from Salmonella typhimurium, was identified using a combination of high-resolution X-ray crystallography and accurate-mass time-of-flight mass spectrometry. The identified glycerol was present as a component of the solutions used for the isolation and crystallization of the protein and serves as the ligand mimicking the natural metabolite, presumably, 2-keto-myo-isonitol, which is indicative of the involvement of STM4435 in the myo-isonitol catabolism. The results of the present study show that this approach holds promise in complex studies aimed at determining, refining, or confirming the protein functions.
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Affiliation(s)
- K M Boyko
- Bach Institute of Biochemistry, Russian Academy of Sciences, Leninskii pr. 33, Moscow, 119071, Russia,
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31
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Minkevich NI, Rakitina TV, Bogachuk AP, Radchenko VV, Surina EA, Morozova-Roche LA, Yanamandra K, Iomdina EN, Babichenko II, Kostanian IA, Lipkin VM. [Amyloid-like fibrils forming and fibroblasts destruction in Tenon's capsule in progressive myopia as a result of pigment epithelium derived factor resistance to restricted proteolysis]. Bioorg Khim 2013; 38:683-90. [PMID: 23547472 DOI: 10.1134/s1068162012060118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have shown previously the presence of full length (50 kD) and truncated proteolytic form (45 kD) of pigment epithelium derived factor (PEDF) in the eye Tenon's capsule in progressive myopia. The full length PEDF is prevalent in myopia that correlates with breach in collagen fibrils forming. Immunohistochemical analysis of Tenon's capsule with polyclonal antibodies to PEDF revealed PEDF in control group being exclusively inside fibroblasts, whereas in myopia, PEDF was distributed extracellularly as halo around blasted fibroblasts. By means of atomic force microscopy and immunodot analysis with anti amyloid fibrils antibodies the ability was studied of recombinant PEDF fragments to form fibrils. Only full length PEDF was shown to form amyloid like fibril structures, but not the truncated form. Accumulation offibrils results in fibroblasts destruction and might be the cause of changes in biochemical and morphological structure of Tenon's capsule observed in myopia.
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32
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Pagaev RM, Kakuev DL, Pozdeev VI, Kutuzov MA, Rakitina TV, Lipkin VM. The light chain of the dynein complex DYNLRB1 interacts with NDP-kinase a from bovine retina. DOKL BIOCHEM BIOPHYS 2013; 447:286-8. [PMID: 23288570 DOI: 10.1134/s1607672912060051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Indexed: 01/14/2023]
Affiliation(s)
- R M Pagaev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
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Rakitina TV, Zeifman AA, Titov IY, Svitanko IV, Lipkin AV, Stroylov VS, Stroganov OV, Novikov FN, Chilov GG. Efficacy of Novel Syk-Kinase Inhibitors MT-SYK-03 and MT-SYK-322 in Cellular Models of Autoimmunity and Cancer. Mendeleev Communications 2012. [DOI: 10.1016/j.mencom.2012.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Zeifman AA, Titov IY, Svitanko IV, Rakitina TV, Lipkin AV, Stroylov VS, Stroganov OV, Novikov FN, Chilov GG. Rational design and synthesis of novel Syk-kinase inhibitors. Mendeleev Communications 2012. [DOI: 10.1016/j.mencom.2012.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Stroylov VS, Rakitina TV, Novikov FN, Stroganov OV, Chilova GG, Lipkin AV. Novel fragment-like inhibitors of EphA2 obtained by experimental screening and modelling. Mendeleev Communications 2010. [DOI: 10.1016/j.mencom.2010.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Rakitina TV, Bogatova OV, Smirnova EV, Pozdeev VI, Kostanian IA, Lipkin VM. [Haponin (eIF1AD) interacts with glyceraldehyde 3-phosphate dehydrogenase in the CHO-K1 cell line]. Bioorg Khim 2010; 36:312-8. [PMID: 20644585 DOI: 10.1134/s1068162010030027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Haponin (HLDF-alike protein) was previously identified from the human promyelocytic leukemia HL-60 cell line. For the functional study of this protein, we obtained recombinant haponin with an N-terminal hexahistidine tag using a baculovirus expression system. Antibodies against 6xHis-haponin were produced, and the expression of endogenous haponin was demonstrated in mammalian cell lines of different origin. Using affinity chromatography and immunoprecipitation methods, we have shown that in CHO-K1 cells haponin interacts with glyceraldehyde 3-phosphate dehydrogenase (GAPDH), which is one of the vital glycolytic enzymes with a diverse set of noncanonical functions.
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Rakitina TV, Yudkina OV, Smirnova EV, Lipkin AV. Protein Tyrosine Kinase Panel As a Tool for Anticancer Drug Design. Acta Naturae 2009. [DOI: 10.32607/actanaturae.10781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Rakitina TV, Vasilevskaya IA, O'Dwyer PJ. Inhibition of G1/S transition potentiates oxaliplatin-induced cell death in colon cancer cell lines. Biochem Pharmacol 2007; 73:1715-26. [PMID: 17343830 DOI: 10.1016/j.bcp.2007.01.037] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 01/29/2007] [Accepted: 01/31/2007] [Indexed: 11/17/2022]
Abstract
In a series of colorectal cancer cell lines, both necrosis and apoptosis were induced upon exposure to oxaliplatin, and enhanced by co-administration of the Hsp90 inhibitor 17-AAG. We analyzed the effects of these interventions on the cell cycle, and found that oxaliplatin treatment caused G1 and G2 arrest in HCT116 cells, and S-phase accumulation in two p53-deficient cell lines (HT29 and DLD1). Addition of 17-AAG enhanced cell cycle effects of oxaliplatin in HCT116, and induced G1 arrest and decrease in S-phase population in the other cell lines. Analysis of cell cycle proteins revealed that the major difference between the cell lines was that in HCT116, 17-AAG resulted in profound inhibition of expression and phosphorylation of late G1 proteins cyclin E and cdk2, with no effect on p21/WAF1 induction. Consistent with these, an HCT116 p53(-/-) line, lacking p21, showed resistance to oxaliplatin, failure to enter apoptosis, and an accumulation of cells in S-phase. Introduction of p21 in these cells caused reversal of that phenotype, including restoration of the G1 block and re-sensitization to oxaliplatin. Inhibition of G1/S progression using cdk2 inhibitor also enhanced oxaliplatin cytotoxicity. We conclude that in colon cancer cells with impaired p53 function, interventions directed to cycle arrest in G1 may potentiate oxaliplatin activity.
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Affiliation(s)
- Tatiana V Rakitina
- Abramson Family Cancer Center, University of Pennsylvania, 1020 BRB II/III, 421 Curie Blvd, Philadelphia, PA 19104, USA
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Gibanova NV, Rakitina TV, Lipkin VM, Kostanyan IA. Granulocyte differentiation inducer, hexapeptide HLDF-6, decreases cytotoxic effect of tumor necrosis factor on HL-60 cell line. Biochemistry (Mosc) 2007; 72:49-60. [PMID: 17309437 DOI: 10.1134/s0006297907010063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The effect of hexapeptide HLDF-6, the granulocytic differentiation inducer, on the tumor necrosis factor alpha (TNF-alpha)-induced differentiation and apoptosis of human promyelocytic leukemia HL-60 cells has been investigated. Costimulation of HL-60 cells with HLDF-6 and TNF-alpha enhanced granulocyte differentiation, whereas the level of monocyte differentiation remained unchanged; however, the cytotoxic action of TNF-alpha on these cells decreased. The protective effect of HLDF-6 peptide did not depend on activation of NF-kappaB (nuclear transcription factor). Since HLDF-6 peptide decreases the number of cells entering apoptosis caused by C(2)-ceramide, a mediator of TNF-induced apoptosis, and also reduces TNF-alpha-mediated activation of caspase-3, we have proposed the hypothesis that HLDF-6 increases resistance of HL-60 cells to the TNF-alpha cytotoxic effect due to inhibition of some stages of mitochondria-dependent apoptotic signaling.
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Affiliation(s)
- N V Gibanova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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Gibanova NV, Rakitina TV, Shingarova LN, Kostanyan IA. Protective effect of the hexapeptide TGENHR on the TNF-induced death of HL-60 cells. DOKL BIOCHEM BIOPHYS 2007; 410:313-6. [PMID: 17286111 DOI: 10.1134/s1607672906050164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- N V Gibanova
- Shemvakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997 Russia
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Gibanova NV, Rakitina TV, Zhokhov SS, Pustoshilova NM, Lipkin VM, Kostanian IA. [L-Glutamic acid modulates the cytotoxic effect of tumor necrosis factor in the HL-60 cell line]. Bioorg Khim 2005; 31:602-8. [PMID: 16363132 DOI: 10.1007/s11171-005-0074-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
L-Glutamic acid was shown to increase the stability of cells of the HL-60 line of human promyelocyte leukemia to the cytotoxic action of tumor necrosis factor alpha (TNF-alpha) due to the inhibition of apoptotic and NF-kappaB-activating cascades induced by this cytokine. At the same time, L-glutamic acid increases the TNF-alpha-mediated differentiating signal and the accompanying enhancement of the phosphatidylinositol-specific phospholipase C activity. Therefore, it is a promising agent for the reduction of total toxicity and inflammatory processes during treatment with TNF-alpha. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2005, vol. 31, no. 6; see also http://www.maik.ru.
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Alshibaia MM, Kovalenko OA, Dorofeev AV, Rakitina TV, Dzhangveladze TN, Musin DE. [Surgical remodeling of the left ventricle in ischemic cardiomyopathy]. Vestn Ross Akad Med Nauk 2005:53-8. [PMID: 15909832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The paper covers early and long-term results of left ventricle geometric reconstruction and myocardial revascularization in 44 patients with ischemic cardiomyopathy. The authors have established clinical and hemodynamic criteria of ischemic cardiomyopathy, indications for surgical treatment and a surgical technique. The article presents a new approach to correction of mitral insufficiency in the given category of patients. According to the results of the study, the necessary conditions for a surgical intervention to be successful are: intraoperative monitoring of central hemodynamics using Swan-Ganz catheter, evaluation of myocardial contractile function by means of transoesophageal echocardiography and wide use of preoperative intraaortic balloon pumping. Geometric reconstruction results in normalization of left ventricle shape and its end-systolic and end-diastolic volumes, marked increase of ejection fraction and improvement of central hemodynamics. The stability of the long-term results has been confirmed in a 4-year follow-up.
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Smirnova EV, Garkovenko AV, Rakitina TV, Berezhnoĭ SN, Astapova MV, Surina EA, Babichenko II, Kostanian IA, Lipkin VM. [Precursors of HLDF differentiation factor and ribosomal protein RPS21 have a common N-terminal sequence]. Bioorg Khim 2004; 30:130-40. [PMID: 15143667 DOI: 10.1023/b:rubi.0000023095.43172.c8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The mature differentiation factor HLDF, isolated from culture fluid, comprises 54 aa, whereas the open reading frame of mRNA encodes a 97-aa protein. We presumed that the protein translation begins from the first ATG codon, whose environment mostly meets the requirements for the initiation point. Two more ATG triplets are localized in positions 48-50 and 100-102, i.e., in the area preceding the cDNA fragment that encodes the N-terminal fragment of the mature protein. The mRNAs of HLDF and the S21 ribosomal protein have previously been shown to be highly homologous, and, therefore, their differences appear to be derived from two point deletions in the cDNA of the HLDF-encoding sequence (a G residue in position 112 and a C residue in position 224). As a result, the mature differentiation factor and RPS21 may be the products of translation from different open reading frames, the differentiation factor may be synthesized in the cell as a precursor, and its N-terminal sequence may be identical to that of RPS21. To test this hypothesis, we prepared recombinant RPS21 and the polyclonal antibodies to HLDF, full-size RPS21, and the C-terminal RPS21 peptide. Immunochemical staining by specially produced antibodies of native HL-60 cells and the same cells brought into apoptosis or differentiation confirmed that the precursor of the differentiation factor and the ribosomal S21 protein have a common N-terminal sequence and different cellular localizations. Neither an intron-containing gene nor a pseudogene with the nucleotide sequence corresponding to the HLDF cDNA was detected in the human genome or in the HL-60 cell line genome. On the basis of these facts, we propose a hypothesis of the molecular mechanism of the HLDF mRNA biosynthesis by means of posttranslational modifications of pre-mRNA of RPS21. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 2; see also http://www.maik.ru.
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Affiliation(s)
- E V Smirnova
- Shemyakin-Ovchinnikov, Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow, 117997 Russia
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Vasilevskaya IA, Rakitina TV, O'Dwyer PJ. Quantitative effects on c-Jun N-terminal protein kinase signaling determine synergistic interaction of cisplatin and 17-allylamino-17-demethoxygeldanamycin in colon cancer cell lines. Mol Pharmacol 2004; 65:235-43. [PMID: 14722256 DOI: 10.1124/mol.65.1.235] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We investigated the effects of cisplatin and the hsp90 inhibitor 17-allylamino-17-demethoxygeldanamycin (17-AAG) in combination in a panel of human colon adenocarcinoma cell lines that differ in their p53 and mismatch repair status. Analysis of cytotoxicity after combined treatment revealed additive effects of cisplatin and 17-AAG in the HCT 116, DLD1, and SW480 cell lines and antagonism in HT-29 cells. Clonogenic assays demonstrated antagonism in HT-29, an additive effect in SW480, and synergism in HCT 116 and DLD1 cell lines. Analysis of signaling pathways revealed that cisplatin-induced activation of c-Jun N-terminal kinase (JNK) was fully blocked by 17-AAG in HT-29 and SW480 cells, whereas in HCT 116 and DLD1 cells it was inhibited only partially. The activation of caspases was also more pronounced in DLD1 and HCT 116 cell lines. These data suggested that a minimal level of apoptotic signaling through JNK was required for synergism with this combination. To test this hypothesis, we used the specific JNK inhibitor SP600125; when JNK was inhibited pharmacologically in HCT 116 and DLD1 cells, they demonstrated increased survival in clonogenic assays. Alternatively, sustained activation of JNK pathway led to an increase of the cytotoxicity of the cisplatin/17-AAG combination in HT-29 cells. Taken together, these data suggest that the synergistic interaction of this combination in colon cancer cell lines depends on the effect exerted by 17-AAG on cisplatin-induced signaling through JNK and associated pathways leading to cell death. An implication of that finding is that quantitative effects of signaling inhibitors may be critical for their ability to reverse cisplatin resistance.
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Rakitina TV, Vasilevskaya IA, O'Dwyer PJ. Additive interaction of oxaliplatin and 17-allylamino-17-demethoxygeldanamycin in colon cancer cell lines results from inhibition of nuclear factor kappaB signaling. Cancer Res 2003; 63:8600-5. [PMID: 14695170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Elucidation of the mechanism by which oxaliplatin induces cell death is essential to enhancing its action. We investigated the effects of oxaliplatin and 17-allylamino-17-demethoxygeldanamycin (17-AAG) in a panel of four colon adenocarcinoma cell lines. Cytotoxicity assays demonstrated at least additivity in three of the cell lines. Activation of the c-Jun NH(2)-terminal kinase pathway by oxaliplatin does not determine cytotoxicity. Activation of p38 was shown to be a key proapoptotic mediator of oxaliplatin-induced cell death. Modulation of extracellular signal-regulated kinase and AKT signaling had no impact on oxaliplatin toxicity in these cells. Nuclear factor (NF)-kappaB was constitutively active in all of the cell lines and was inhibited by 17-AAG. Down-regulation of NF-kappaB transactivation by pharmacological inhibitors enhanced oxaliplatin cytotoxicity. These data support an interaction between 17-AAG and components of the NF-kappaB pathway in the modulation of oxaliplatin sensitivity in colon cancer cells.
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Affiliation(s)
- Tatiana V Rakitina
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Vasilevskaya IA, Rakitina TV, O'Dwyer PJ. Geldanamycin and its 17-allylamino-17-demethoxy analogue antagonize the action of Cisplatin in human colon adenocarcinoma cells: differential caspase activation as a basis for interaction. Cancer Res 2003; 63:3241-6. [PMID: 12810654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Several chaperone-binding drugs based on geldanamycin (GA) have been synthesized, and one of them, 17-allylamino-17-demethoxygeldanamycin (17-AAG), is being developed in the clinic. Interest in the use of 17-AAG in combination with cytotoxic drugs led us to study both GA and 17-AAG with cisplatin (DDP) in the human colon adenocarcinoma cell lines HT29 and HCT116. We performed isobologram analysis of combinations of DDP with GA or 17-AAG in these cell lines using the standard 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay to evaluate cell survival. In HCT116, the effects of GA and 17-AAG with DDP were additive and schedule dependent. In HT29 both GA and 17-AAG antagonized DDP effects resulting in cytotoxicity less than expected. We hypothesized that the antagonism in HT29 cells might be a consequence of altered p53 function in this cell line. Accordingly, we tested GA/17-AAG and DDP in combination in the HCTp5.2 cell line, which expresses a dominant-negative form of p53. In these cells too, the GA analogues antagonized DDP, suggesting a role for p53 in the observed effects. Investigation of the DDP-induced signaling pathways revealed that ansamycins block the activation of mitogen-activated protein kinase and c-Jun NH(2)-terminal kinase pathways and c-Jun expression in HT29 cells while exerting incomplete inhibitory effects in HCT116 and HCTp5.2 cell lines. Therefore, effects on signaling are thought not to underlay the antagonism in the latter model. The ansamycins inhibited DDP-induced activation of caspases 8 and 3 in HT29 and HCTp5.2 but not in HCT116 cells, which we postulate to be the basis for higher survival of p53-deficient cells when treated with combinations of the two drugs.
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Affiliation(s)
- Irina A Vasilevskaya
- University of Pennsylvania Cancer Center, Philadelphia, Pennsylvania 19104, USA.
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Smirnova EV, Rakitina TV, Evtodienko AI, Kostanian IA, Lipkin VM. Cloning and characterization of the human ribosomal protein S21 gene [. Bioorg Khim 2000; 26:392-6. [PMID: 10900511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
A full-size functional gene encoding the human ribosomal protein S21 was cloned and characterized. Its nucleotide sequence, exon-intron organization, and transcription initiation site were determined. The gene comprises 1417 bp and is composed of six exons and five introns. Like most known genes of mammalian ribosomal proteins, it lacks the canonical TATA- and CAAT sequences in the promoter region and harbors potential binding sites for transcription factors both upstream and downstream the transcription initiation site. The first intron of the rpS21 gene is located in the 5'-untranslated region. The transcription initiation site is at a 53-bp distance from the ATG codon, and the initiation cytidine is surrounded by polypyrimidine tracts. The 5'-flanking region contains two repeats belonging to the Alu-S and Alu-J families.
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Feshchenko EA, Andreeva SG, Suslova VA, Rakitina TV, Smirnova EV, Bystrov NS, Zagranichnyĭ VE, Lipkin VM. [Nucleotide sequence of cDNA and organization of the gene for alpha-subunit of photoreceptor phosphodiesterase of cyclic GMP in human retinal cones]. Bioorg Khim 1997; 23:83-90. [PMID: 9157849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Five clones were isolated from a human retina cDNA library whose cDNA inserts allowed reconstruction of the total sequence of the human clone cGMP phosphodiesterase alpha'-subunit cDNA comprising 3455 bp. The protein's deduced sequence contains 858 amino acids residues with molecular mass 99,169 Da. A substantial homology was revealed between the amino acid sequence of the human cones cGMP-phosphodiesterase alpha'-subunit and the corresponding sequences of alpha, beta, and alpha' subunits of visual cGMP-phosphodiesterase of bovine, murine, chicken and human retinas. Four recombinant bacteriophages were isolated from a genomic library whose inserts made it possible to reconstruct a 32-kb fragment of the human cones cGMP-phosphodiesterase alpha'-subunit gene. 5'-Flanking region of the gene and first 14 exons, encoding an N-terminal segment of the protein, along with the adjacent intron segments were sequenced.
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Khramtsov NV, Feshchenko EA, Suslova VA, Shmukler BE, Terpugov BE, Rakitina TV, Atabekova NV, Lipkin VM. The human rod photoreceptor cGMP phosphodiesterase beta-subunit. Structural studies of its cDNA and gene. FEBS Lett 1993; 327:275-8. [PMID: 8394243 DOI: 10.1016/0014-5793(93)81003-i] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
cDNA clones encoding the beta-subunit of the photoreceptor cGMP phosphodiesterase (PDE) were isolated from a human retina library and their sequence was determined. The encoded polypeptide consists of 854 amino acid residues with a calculated molecular mass of 98,416 Da. Alignment of the deduced amino acid sequence with the earlier analysed alpha-, beta- and alpha'-subunits of bovine and mouse PDEs demonstrates a high homology. Two overlapping recombinant lambda phage clones containing 26 kb of the human PDE beta-subunit gene were isolated from the genomic library. A total nucleotide sequence of exons 4-22 of the PDE beta-subunit gene was established which completely corresponded to the cDNA structure. According to sequence analysis no potential possibility for alternative splicing of the beta-subunit gene was observed between exons 20 and 21 which led to the formation of the beta'-subunit as described for mouse PDE. Polymerase chain reaction (PCR) experiments also confirm the absence of the PDE beta'-subunit in human retina.
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Affiliation(s)
- N V Khramtsov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow
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