1
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Maluchenko NV, Korovina AN, Saulina AA, Studitsky VM, Feofanov AV. [The Role of the WGR Domain in the Functions of PARP1 and PARP2]. Mol Biol (Mosk) 2023; 57:782-791. [PMID: 37752643 DOI: 10.31857/s0026898423050129, edn: ejblxo] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/02/2023] [Indexed: 09/28/2023]
Abstract
The PARP1 and PARP2 proteins are members of the poly(ADP-ribose) polymerase family involved in the regulation of DNA repair and replication, RNA processing, ribosome biogenesis, transcription, cell division, and cell death. PARP1 and PARP2 are promising targets for the development of anticancer drugs and can be used in the treatment of cardiovascular, neurodegenerative, and other disorders. The WGR domain has been shown to play a central role in the functioning of PARP1 and PARP2 proteins. This review considers the mechanisms of functioning of WGR domains in the PARP1 and PARP2 proteins, which have several similar and specialized properties. Understanding these processes is of great interest to fundamental science and can contribute to the development of more effective and selective inhibitors of PARP1 and PARP2.
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Affiliation(s)
- N V Maluchenko
- Department of Biology, Moscow State University, Moscow, 119234 Russia
| | - A N Korovina
- Department of Biology, Moscow State University, Moscow, 119234 Russia
| | - A A Saulina
- Department of Biology, Moscow State University, Moscow, 119234 Russia
| | - V M Studitsky
- Department of Biology, Moscow State University, Moscow, 119234 Russia
- Fox Chase Cancer Center, Philadelphia, PA 19111-2497 United States
| | - A V Feofanov
- Department of Biology, Moscow State University, Moscow, 119234 Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
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2
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Afonin DA, Geras’kina OV, Loseva TV, Kirpichnikov MP, Studitsky VM, Feofanov AV. Structure and Affinity of Complexes between the DNA-Binding Domain of Swi4 and DNA. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922050037] [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: 12/24/2022] Open
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3
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Gerasimova NS, Korovina AN, Afonin DA, Shaytan KV, Feofanov AV, Studitsky VM. Analysis of Structure of Elongation Complexes in Polyacrylamide Gel with Förster Resonance Energy Transfer Technique. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922020063] [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: 11/23/2022] Open
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4
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Sidorova MV, Bibilashvili RS, Avdeev DV, Kozhokar US, Palkeeva ME, Ovchinnikov MV, Molokoedov AS, Shirokov DA, Semyonova AV, Uvarova VI, Kulyaev PO, Khvatov EV, Ignatova AA, Feofanov AV, Osolodkin DI, Porozov YB, Kozlovskaya LI, Ishmukhametov AA, Parfyonova YV, Egorov AM. Properties and Activity of Peptide Derivatives of ACE2 Cellular Receptor and Their Interaction with SARS-CoV-2 S Protein Receptor-Binding Domain. DOKL BIOCHEM BIOPHYS 2022; 507:237-241. [PMID: 36580213 PMCID: PMC9798946 DOI: 10.1134/s1607672922060126] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/30/2022]
Abstract
The aim of this work was to design and characterize peptides based on the α-helices h1 and h2 of the ACE2 receptor, forming the interaction interface between the receptor-binding domain (RBD) of the SARS-CoV-2 S protein and the cellular ACE2 receptor. Monomeric and heterodimeric peptides connected by disulfide bonds at different positions were synthesized. Solubility, RBD-binding affinity, and peptide helicity were experimentally measured, and molecular dynamics simulation was performed in various solvents. It was established that the preservation of the helical conformation is a necessary condition for the binding of peptides to RBD. The peptides have a low degree of helicity and low affinity for RBD in water. Dimeric peptides have a higher degree of helicity than monomeric ones, probably due to the mutual influence of helices. The degree of helicity of the peptides in trifluoroethanol is the highest; however, for in vitro studies, the most suitable solvent is a water-ethanol mixture.
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Affiliation(s)
- M. V. Sidorova
- Chazov National Medical Research Center for Cardiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - R. S. Bibilashvili
- Chazov National Medical Research Center for Cardiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - D. V. Avdeev
- Chazov National Medical Research Center for Cardiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - U. S. Kozhokar
- Chazov National Medical Research Center for Cardiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - M. E. Palkeeva
- Chazov National Medical Research Center for Cardiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - M. V. Ovchinnikov
- Chazov National Medical Research Center for Cardiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - A. S. Molokoedov
- Chazov National Medical Research Center for Cardiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - D. A. Shirokov
- Federal Research and Clinical Center of Physical Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia ,Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | - A. V. Semyonova
- Federal Research and Clinical Center of Physical Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - V. I. Uvarova
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of the Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia
| | - P. O. Kulyaev
- Sirius University of Science and Technology, Sochi, Russia
| | - E. V. Khvatov
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of the Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia
| | - A. A. Ignatova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - D. I. Osolodkin
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of the Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia ,Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Yu. B. Porozov
- Sirius University of Science and Technology, Sochi, Russia ,Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - L. I. Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of the Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia ,Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - A. A. Ishmukhametov
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of the Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia ,Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Ye. V. Parfyonova
- Chazov National Medical Research Center for Cardiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - A. M. Egorov
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of the Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia ,Lomonosov Moscow State University, Moscow, Russia
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5
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Danilova ND, Geraskina OV, Diuvenji EV, Feofanov AV, Plakunov VK, Gannesen AV. Inhibitory Effect of Norepinephrine on Biofilm Growth of the Human Skin Commensal Kytococcus schroeteri H01. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721050039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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6
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Efremenko AV, Dyakova ED, Ostroverkhov PV, Kirin NS, Mironov AF, Grin MA, Feofanov AV. Intracellular Localization and the Mechanisms of Photodynamic Action of 131-[2-(Guanidinyl)ethylamino] Chlorin e6 Dimethyl Ester. Russ J Bioorg Chem 2021. [DOI: 10.1134/s1068162021040087] [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: 11/23/2022]
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7
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Abstract
Poly(ADP-ribosyl)ation plays a key role in cellular metabolism. Covalent poly(ADP-ribosyl)ation affects the activity of the proteins engaged in DNA repair, chromatin structure regulation, gene expression, RNA processing, ribosome biogenesis, and protein translation. Non-covalent PAR-dependent interactions are involved in the various types of cellular response to stress and viral infection, such as inflammation, hormonal signaling, and the immune response. The review discusses how structurally different poly(ADP-ribose) (PAR) molecules composed of identical monomers can differentially participate in various cellular processes acting as the so-called "PAR code." The article describes the ability of PAR polymers to form functional biomolecular clusters through a phase-separation in response to various signals. This phase-separation contributes to rapid spatial segregation of biochemical processes and effective recruitment of the necessary components. The cellular PAR level is tightly controlled by a network of regulatory proteins: PAR code writers, readers, and erasers. Impaired PAR metabolism is associated with the development of pathological processes causing oncological, cardiovascular, and neurodegenerative diseases. Pharmacological correction of the PAR level may represent a new approach to the treatment of various diseases.
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Affiliation(s)
- N. V. Maluchenko
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
| | - D. O. Koshkina
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
| | - A. V. Feofanov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - V. M. Studitsky
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
- Fox Chase Cancer Center, Philadelphia, PA, 19111-2497 USA
| | - M. P. Kirpichnikov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
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8
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Primak AL, Skutel MA, Nekrasova OV, Arseniev AS, Kirpichnikov MP, Feofanov AV. Kv1 Potassium Channel Ligands Based on Hongotoxin 1 and Red Fluorescent Protein. Russ J Bioorg Chem 2020. [DOI: 10.1134/s1068162020060266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Maluchenko NV, Sultanov DS, Kotova EY, Kirpichnikov MP, Studitsky VM, Feofanov AV. Histone Tails Promote PARP1-Dependent Structural Rearrangements in Nucleosomes. DOKL BIOCHEM BIOPHYS 2020; 489:377-379. [PMID: 32130604 DOI: 10.1134/s1607672919060061] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Indexed: 12/28/2022]
Abstract
PARP 1 alters the wrapping of nucleosomal DNA on the histone octamer, thereby modulating the accessibility of different genome sites to nuclear protein factors. Here, we show that non-structured histone tails are involved in the PARP1-induced structural rearrangements in nucleosomes, facilitate and stabilize them, but do not affect the enzymatic activity of PARP1.
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Affiliation(s)
| | | | | | - M P Kirpichnikov
- Moscow State University, 119234, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - V M Studitsky
- Moscow State University, 119234, Moscow, Russia.,Fox Chase Cancer Center, Philadelphia, USA
| | - A V Feofanov
- Moscow State University, 119234, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
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10
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Bonartsev AP, Voinova VV, Kuznetsova ES, Zharkova II, Makhina TK, Myshkina VL, Chesnokova DV, Kudryashova KS, Feofanov AV, Shaitan KV, Bonartseva GA. BSA Adsorption on Porous Scaffolds Prepared from BioPEGylated Poly(3-Hydroxybutyrate). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818040038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Lyukmanova EN, Bychkov ML, Sharonov GV, Efremenko AV, Shulepko MA, Kulbatskii DS, Shenkarev ZO, Feofanov AV, Dolgikh DA, Kirpichnikov MP. Human secreted proteins SLURP-1 and SLURP-2 control the growth of epithelial cancer cells via interactions with nicotinic acetylcholine receptors. Br J Pharmacol 2018; 175:1973-1986. [PMID: 29505672 DOI: 10.1111/bph.14194] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 02/19/2018] [Accepted: 02/22/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND AND PURPOSE Nicotinic acetylcholine receptors (nAChRs) are a promising target for development of new anticancer therapies. Here we have investigated the effects of the endogenous human proteins SLURP-1 and SLURP-2, antagonists of nAChRs, on human epithelial cancer cells. EXPERIMENTAL APPROACH Growth of epithelial cancer cells (A431, SKBR3, MCF-7, A549, HT-29) exposed to SLURP-1, SLURP-2, mecamylamine, atropine, timolol and gefitinib was measured by the WST-1 test. Expression levels of SLURP-1, α7-nAChR and EGF receptors and their distribution in cancer cells were studied by confocal microscopy and flow cytometry. Secretion of endogenous SLURP-1 by A431 cells under treatment with recombinant SLURP-1 was analysed by Western-blotting. KEY RESULTS SLURP-1 and SLURP-2 significantly inhibited growth of A431, SKBR3, MCF-7 and HT-29 cells at concentrations above 1 nM, to 40-70% of the control, in 24 h. Proliferation of A549 cells was inhibited only by SLURP-1. The anti-proliferative activity of SLURPs on A431 cells was associated with nAChRs, but not with β-adrenoceptors or EGF receptors. Action of gefitinib and SLURPs was additive and resulted almost complete inhibition of A431 cell proliferation during 24 h. Exposure of A431 cells to recombinant SLURP-1 down-regulated α7-nAChR expression and induced secretion of endogenous SLURP-1 from intracellular depots, increasing its concentration in the extracellular media. CONCLUSIONS AND IMPLICATIONS SLURPs inhibit growth of epithelial cancer cells in vitro and merit further investigation as potential agents for anticancer therapy. LINKED ARTICLES This article is part of a themed section on Nicotinic Acetylcholine Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.11/issuetoc.
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Affiliation(s)
- E N Lyukmanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation.,Lomonosov Moscow State University, Moscow, Russian Federation.,Moscow Institute of Physics and Technology, Moscow Region, Russian Federation
| | - M L Bychkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation.,Lomonosov Moscow State University, Moscow, Russian Federation
| | - G V Sharonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation.,Lomonosov Moscow State University, Moscow, Russian Federation
| | - A V Efremenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation.,Lomonosov Moscow State University, Moscow, Russian Federation
| | - M A Shulepko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation.,Lomonosov Moscow State University, Moscow, Russian Federation
| | - D S Kulbatskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation.,Lomonosov Moscow State University, Moscow, Russian Federation
| | - Z O Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation.,Lomonosov Moscow State University, Moscow, Russian Federation.,Moscow Institute of Physics and Technology, Moscow Region, Russian Federation
| | - A V Feofanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation.,Lomonosov Moscow State University, Moscow, Russian Federation
| | - D A Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation.,Lomonosov Moscow State University, Moscow, Russian Federation
| | - M P Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation.,Lomonosov Moscow State University, Moscow, Russian Federation
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12
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Shulepko MA, Lyukmanova EN, Shenkarev ZO, Dubovskii PV, Astapova MV, Feofanov AV, Arseniev AS, Utkin YN, Kirpichnikov MP, Dolgikh DA. Towards universal approach for bacterial production of three-finger Ly6/uPAR proteins: Case study of cytotoxin I from cobra N. oxiana. Protein Expr Purif 2016; 130:13-20. [PMID: 27702601 DOI: 10.1016/j.pep.2016.09.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 08/01/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 01/26/2023]
Abstract
Cytotoxins or cardiotoxins is a group of polycationic toxins from cobra venom belonging to the 'three-finger' protein superfamily (Ly6/uPAR family) which includes small β-structural proteins (60-90 residues) with high disulfide bond content (4-5 disulfides). Due to a high cytotoxic activity for cancer cells, cytotoxins are considered as potential anticancer agents. Development of the high-throughput production methods is required for the prospective applications of cytotoxins. Here, efficient approach for bacterial production of recombinant analogue of cytotoxin I from N. oxiana containing additional N-terminal Met-residue (rCTX1) was developed. rCTX1 was produced in the form of E. coli inclusion bodies. Refolding in optimized conditions provided ∼6 mg of correctly folded protein from 1 L of bacterial culture. Cytotoxicity of rCTX1 for C6 rat glioma cells was found to be similar to the activity of wild type CTX1. The milligram quantities of 13C,15N-labeled rCTX1 were obtained. NMR study confirmed the similarity of the spatial structures of recombinant and wild-type toxins. Additional Met residue does not perturb the overall structure of the three-finger core. The analysis of available data for different Ly6/uPAR proteins of snake and human origin revealed that efficiency of their folding in vitro is correlated with the number of proline residues in the third loop and the surface area of hydrophobic residues buried within the protein interior. The obtained data indicate that hydrophobic core is important for the folding of proteins with high disulfide bond content. Developed expression method opens new possibilities for structure-function studies of CTX1 and other related three-finger proteins.
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Affiliation(s)
- M A Shulepko
- Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, 117997, Moscow, Russia
| | - E N Lyukmanova
- Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, 117997, Moscow, Russia.
| | - Z O Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, 117997, Moscow, Russia; Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, Moscow Region, 141700, Russia
| | - P V Dubovskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, 117997, Moscow, Russia
| | - M V Astapova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, 117997, Moscow, Russia
| | - A V Feofanov
- Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, 117997, Moscow, Russia
| | - A S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, 117997, Moscow, Russia; Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, Moscow Region, 141700, Russia
| | - Y N Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, 117997, Moscow, Russia
| | - M P Kirpichnikov
- Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, 117997, Moscow, Russia
| | - D A Dolgikh
- Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, 117997, Moscow, Russia
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13
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Nekrasova OV, Volyntseva AD, Kudryashova KS, Novoseletsky VN, Lyapina EA, Illarionova AV, Yakimov SA, Korolkova YV, Shaitan KV, Kirpichnikov MP, Feofanov AV. Complexes of Peptide Blockers with Kv1.6 Pore Domain: Molecular Modeling and Studies with KcsA-Kv1.6 Channel. J Neuroimmune Pharmacol 2016; 12:260-276. [PMID: 27640211 DOI: 10.1007/s11481-016-9710-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 06/21/2016] [Accepted: 09/09/2016] [Indexed: 11/25/2022]
Abstract
Potassium voltage-gated Kv1.6 channel, which is distributed primarily in neurons of central and peripheral nervous systems, is of significant physiological importance. To date, several high-affinity Kv1.6-channel blockers are known, but the lack of selective ones among them hampers the studies of tissue localization and functioning of Kv1.6 channels. Here we present an approach to advanced understanding of interactions of peptide toxin blockers with a Kv1.6 pore. It combines molecular modeling studies and an application of a new bioengineering system based on a KcsA-Kv1.6 hybrid channel for the quantitative fluorescent analysis of blocker-channel interactions. Using this system we demonstrate that peptide toxins agitoxin 2, kaliotoxin1 and OSK1 have similar high affinity to the extracellular vestibule of the K+-conducting pore of Kv1.6, hetlaxin is a low-affinity ligand, whereas margatoxin and scyllatoxin do not bind to Kv1.6 pore. Binding of toxins to Kv1.6 pore has considerable inverse dependence on the ionic strength. Model structures of KcsA-Kv1.6 and Kv1.6 complexes with agitoxin 2, kaliotoxin 1 and OSK1 were obtained using homology modeling and molecular dynamics simulation. Interaction interfaces, which are formed by 15-19 toxin residues and 10 channel residues, are described and compared. Specific sites of Kv1.6 pore recognition are identified for targeting of peptide blockers. Analysis of interactions between agitoxin 2 derivatives with point mutations (S7K, S11G, L19S, R31G) and KcsA-Kv1.6 confirms reliability of the calculated complex structure.
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Affiliation(s)
- O V Nekrasova
- Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - A D Volyntseva
- Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119992, Russia
| | - K S Kudryashova
- Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - V N Novoseletsky
- Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119992, Russia
| | - E A Lyapina
- Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119992, Russia
| | - A V Illarionova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - S A Yakimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Yu V Korolkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - K V Shaitan
- Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119992, Russia
| | - M P Kirpichnikov
- Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - A V Feofanov
- Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119992, Russia. .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
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14
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Novoseletsky VN, Volyntseva AD, Shaitan KV, Kirpichnikov MP, Feofanov AV. Modeling of the Binding of Peptide Blockers to Voltage-Gated Potassium Channels: Approaches and Evidence. Acta Naturae 2016. [DOI: 10.32607/20758251-2016-8-2-35-46] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Modeling of the structure of voltage-gated potassium (KV) channels bound to peptide blockers aims to identify the key amino acid residues dictating affinity and provide insights into the toxin-channel interface. Computational approaches open up possibilities for in silico rational design of selective blockers, new molecular tools to study the cellular distribution and functional roles of potassium channels. It is anticipated that optimized blockers will advance the development of drugs that reduce over activation of potassium channels and attenuate the associated malfunction. Starting with an overview of the recent advances in computational simulation strategies to predict the bound state orientations of peptide pore blockers relative to KV-channels, we go on to review algorithms for the analysis of intermolecular interactions, and then take a look at the results of their application.
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15
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Volovetskiy AB, Shilyagina NY, Dudenkova VV, Pasynkova SO, Ignatova AA, Mironov AF, Grin MA, Bregadze VI, Feofanov AV, Balalaeva IV, Maslennikova AV. Study of the tissue distribution of potential boron neutron-capture therapy agents based on conjugates of chlorin e 6 aminoamide derivatives with boron nanoparticles. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916010255] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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16
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Bonartsev AP, Zharkova II, Yakovlev SG, Myshkina VL, Makhina TK, Zernov AL, Kudryashova KS, Feofanov AV, Akulina EA, Ivanova EV, Zhuikov VA, Andreeva NV, Voinova VV, Bessonov IV, Kopitsyna MN, Morozov AS, Bonartseva GA, Shaitan KV, Kirpichnikov MP. ERRATUM 3D-Scaffolds from Poly(3-hydroxybutyrate)-Poly(ethylene glycol) Copolymer for Tissue Engineering (Journal of Biomaterials and Tissue Engineering, Vol. 6(1), pp. 42–52 (2016)). J BIOMATER TISS ENG 2016. [DOI: 10.1166/jbt.2016.1492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Novoseletsky VN, Volyntseva AD, Shaitan KV, Kirpichnikov MP, Feofanov AV. Modeling of the Binding of Peptide Blockers to Voltage-Gated Potassium Channels: Approaches and Evidence. Acta Naturae 2016; 8:35-46. [PMID: 27437138 PMCID: PMC4947987] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Indexed: 11/13/2022] Open
Abstract
Modeling of the structure of voltage-gated potassium (KV) channels bound to peptide blockers aims to identify the key amino acid residues dictating affinity and provide insights into the toxin-channel interface. Computational approaches open up possibilities for in silico rational design of selective blockers, new molecular tools to study the cellular distribution and functional roles of potassium channels. It is anticipated that optimized blockers will advance the development of drugs that reduce over activation of potassium channels and attenuate the associated malfunction. Starting with an overview of the recent advances in computational simulation strategies to predict the bound state orientations of peptide pore blockers relative to KV-channels, we go on to review algorithms for the analysis of intermolecular interactions, and then take a look at the results of their application.
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Affiliation(s)
- V. N. Novoseletsky
- M.V.Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1, bldg. 12, 119992 , Moscow, Russia
| | - A. D. Volyntseva
- M.V.Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1, bldg. 12, 119992 , Moscow, Russia
| | - K. V. Shaitan
- M.V.Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1, bldg. 12, 119992 , Moscow, Russia
| | - M. P. Kirpichnikov
- M.V.Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1, bldg. 12, 119992 , Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho- Maklaya str. 16/10, 117997, Moscow, Russia
| | - A. V. Feofanov
- M.V.Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1, bldg. 12, 119992 , Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho- Maklaya str. 16/10, 117997, Moscow, Russia
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18
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Bonartsev AP, Zharkova II, Yakovlev SG, Myshkina VL, Makhina TK, Zernov AL, Kudryashova KS, Feofanov AV, Akulina EA, Ivanova EV, Zhuikov VA, Andreeva NV, Voinova VV, Bessonov IV, Kopitsyna MV, Morozov AS, Bonartseva GA, Shaitan KV, Kirpichnikov MP. 3D-Scaffolds from Poly(3-hydroxybutyrate)Poly(ethylene glycol) Copolymer for Tissue Engineering. J BIOMATER TISS ENG 2016. [DOI: 10.1166/jbt.2016.1414] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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19
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Yakubovskaya RI, Morozova NB, Pankratov AA, Kazachkina NI, Plyutinskaya AD, Karmakova TA, Andreeva TN, Venediktova YB, Plotnikova EA, Nemtsova ER, Sokolov VV, Filonenko EV, Chissov VI, Kogan BY, Butenin AV, Feofanov AV, Strakhovskaya MG. Experimental photodynamic therapy: 15 years of development. RUSS J GEN CHEM+ 2015. [DOI: 10.1134/s1070363215010405] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Kuznetsov AS, Dubovskii PV, Vorontsova OV, Feofanov AV, Efremov RG. Interaction of linear cationic peptides with phospholipid membranes and polymers of sialic acid. Biochemistry Moscow 2014; 79:459-68. [DOI: 10.1134/s0006297914050101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Shebanova AS, Bogdanov AG, Ismagulova TT, Feofanov AV, Semenyuk PI, Muronets VI, Erokhina MV, Onishchenko GE, Kirpichnikov MP, Shaitan KV. [application of the analytical transmission electron microscopy techniques for detection, identification and visualization of localization of nanoparticles of titanium and cerium oxides in mammalian cells]. Biofizika 2014; 59:348-359. [PMID: 25702487] [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: 06/04/2023]
Abstract
This work represents the results of the study on applicability of the modern methods of analytical transmission electron microscopy for detection, identification and visualization of localization of nanoparticles of titanium and cerium oxides in A549 cell, human lung adenocarcinoma cell line. A comparative analysis of images of the nanoparticles in the cells obtained in the bright field mode of transmission electron microscopy, under dark-field scanning transmission electron microscopy and high-angle annular dark field scanning transmission electron was performed. For identification of nanoparticles in the cells the analytical techniques, energy-dispersive X-ray spectroscopy and electron energy loss spectroscopy, were compared when used in the mode of obtaining energy spectrum from different particles and element mapping. It was shown that the method for electron tomography is applicable to confirm that nanoparticles are localized in the sample but not coated by contamination. The possibilities and fields of utilizing different techniques for analytical transmission electron microscopy for detection, visualization and identification of nanoparticles in the biological samples are discussed.
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22
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Shebanova AS, Bogdanov AG, Ismagulova TT, Feofanov AV, Semenyuk PI, Muronets VI, Erokhina MV, Onishchenko GE, Kirpichnikov MP, Shaitan KV. Application of the analytical transmission electron microscopy techniques for detection, identification and visualization of localization of nanoparticles of titanium and cerium oxides in mammalian cells. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350914020237] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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23
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Nekrasova OV, Sharonov GV, Tikhonov RV, Kolosov PM, Astapova MV, Yakimov SA, Tagvey AI, Korchagina AA, Bocharova OV, Wulfson AN, Feofanov AV, Kirpichnikov MP. Receptor-binding domain of ephrin-A1: production in bacterial expression system and activity. Biochemistry (Mosc) 2013; 77:1387-94. [PMID: 23244735 DOI: 10.1134/s0006297912120073] [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] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Eph receptor tyrosine kinases and their ligands, the ephrins, perform an important regulatory function in tissue organization, as well as participate in malignant transformation of cells. Ephrin-A1, a ligand of A class Eph receptors, is a modulator of tumor growth and progression, and the mechanism of its action needs detailed investigation. Here we report on the development of a system for bacterial expression of an ephrin-A1 receptor-binding domain (eA1), a procedure for its purification, and its renaturation with final yield of 50 mg/liter of culture. Functional activity of eA1 was confirmed by immunoblotting, laser scanning confocal microscopy, and flow cytometry. It is shown that monomeric non-glycosylated receptor-binding domain of ephrin-A1 is able to activate cellular EphA2 receptors, stimulating their phosphorylation. Ligand eA1 can be used to study the features of ephrin-A1 interactions with different A class Eph receptors. The created expression cassette is suitable for the development of ligands with increased activity and selectivity and experimental systems for the delivery of cytotoxins into tumor cells that overexpress EphA2 or other class A Eph receptors.
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Affiliation(s)
- O V Nekrasova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
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24
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Anh HN, Hoang VDM, Kudryashova KS, Nekrasova OV, Feofanov AV, Andreeva TV, Tsetlin VI, Utkin YN. Hetlaxin, a new toxin from the Heterometrus laoticus scorpion venom, interacts with voltage-gated potassium channel Kv1.3. DOKL BIOCHEM BIOPHYS 2013; 449:109-11. [DOI: 10.1134/s1607672913020142] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Indexed: 11/23/2022]
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Samsonova OV, Kudryashova KS, Feofanov AV. N-Terminal Moiety of Antimicrobial Peptide Ltc1-K Increases its Toxicity for Eukaryotic Cells. Acta Naturae 2011. [DOI: 10.32607/20758251-2011-3-2-68-78] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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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26
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Smirnova EA, Gusev AA, Zaitseva ON, Lazareva EM, Onishchenko GE, Kuznetsova EV, Tkachev AG, Feofanov AV, Kirpichnikov MP. Multi-walled Carbon Nanotubes Penetrate into Plant Cells and Affect the Growth of Onobrychis arenaria Seedlings. Acta Naturae 2011. [DOI: 10.32607/20758251-2011-3-1-99-106] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [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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27
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Ignatova AA, Maslova AS, Kirpichnikov MP, Feofanov AV. [Interaction of the photosensitizer 13,15-N-(3'-hydroxypropyl)cycloimide of chlorin p(6) with normal and cancerous blood cells]. Bioorg Khim 2010; 35:830-6. [PMID: 20208583 DOI: 10.1134/s1068162009060119] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The interaction of 13,15-N-(3'-hydroxypropyl)cycloimide of chlorin p(6) (CIC) with normal blood cells and human K562 and HL60 myeloid leukemia cells was studied. CIC was found to be bound by the erythrocyte membrane but did not penetrate into the cytoplasm. It is characterized by a diffuse distribution in the cytoplasm of normal leukocytes, whereas its diffuse distribution in K562 and HL60 cells is accompanied by perinuclear accumulation and binding to the plasma membrane. The average cytoplasmic concentration corresponding to the CIC accumulation in leukemic cells at saturation is 2.2 to 2.6 times higher than that in normal leukocytes. CIC is more intensely accumulated in granulocytes than in lymphocytes. The kinetics of the cellular uptake and efflux was characterized. The normal leukocytes and erythrocytes were found to be 1.5 times and 3 to 4 times less sensitive, respectively, to the photodynamic action of CIC than the K562 and HL60 cells.
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Nazarova AI, Feofanov AV, Karmakova TA, Sharonov GV, Pliutinskaia AD, Iakubovskaia RI, Lebedeva VS, Mironov AF, Maurizot JC, Vigny P. Effect of Substituents on Photochemical and Biological Properties of 13,15-N-Cycloimide Derivatives of Chlorin p6. Russ J Bioorg Chem 2005; 31:535-48. [PMID: 16245697 DOI: 10.1007/s11171-005-0066-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [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
The effect of electron-accepting substituents in position 3 of the chlorine p6 macrocycle in neutral and carboxyl-containing negatively charged cycloimide derivatives of chlorin p6 (CIC) on the photochemical and biological properties of these photosensitizers was studied. A relationship between the structure and properties of CICs was analyzed on the basis of information on their photoinduced cytotoxicity, efficiency of the generation of reactive oxygen species, photostability, intracellular localization, quantitative parameters of accumulation in cells, and cellular pharmacokinetics. It was shown that these compounds can be used for the development of photosensitizers with intense light absorption at 740 nm, controlled intracellular localization, and a high photodynamic activity toward tumor cells.
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29
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Sharonov GV, Feofanov AV, Bocharova OV, Astapova MV, Dedukhova VI, Chernyak BV, Dolgikh DA, Arseniev AS, Skulachev VP, Kirpichnikov MP. Comparative analysis of proapoptotic activity of cytochrome c mutants in living cells. Apoptosis 2005; 10:797-808. [PMID: 16133870 DOI: 10.1007/s10495-005-0366-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [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: 10/25/2022]
Abstract
A non-traumatic electroporation procedure was developed to load exogenous cytochrome c into the cytoplasm and to study the apoptotic effect of cytochrome c, its K72-substitued mutants and "yeast --> horse" hybrid cytochrome c in living WEHI-3 cells. The minimum apoptosis-activating intracellular concentration of horse heart cytochrome c was estimated to be 2.7 +/- 0.5 microM (47 +/- 9 fg/cell). The equieffective concentrations of the K72A-, K72E- and K72L-substituted mutants of cytochrome c were five-, 15- and 70-fold higher. The "yeast --> horse" hybrid created by introducing S2D, K4E, A7K, T8K, and K11V substitutions (horse protein numbering) and deleting five N-terminal residues in yeast cytochrome c did not evoke apoptotic activity in mammalian cells. The apoptotic function of cytochrome c was abolished by the K72W substitution. The K72W-substituted cytochrome c possesses reduced affinity to the apoptotic protease activating factor-1 (Apaf-1) and forms an inactive complex. This mutant is competent as a respiratory-chain electron carrier and well suited for knock-in studies of cytochrome c-mediated apoptosis.
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Affiliation(s)
- G V Sharonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia
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30
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Feofanov AV, Sharonov GV, Dubinnyi MA, Astapova MV, Kudelina IA, Dubovskii PV, Rodionov DI, Utkin YN, Arseniev AS. Comparative Study of Structure and Activity of Cytotoxins from Venom of the Cobras Naja oxiana, Naja kaouthia, and Naja haje. Biochemistry (Moscow) 2004; 69:1148-57. [PMID: 15527416 DOI: 10.1023/b:biry.0000046890.46901.7e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [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
Cytotoxins are positively charged polypeptides that constitute about 60% of all proteins in cobra venom; they have a wide spectrum of biological activities. By CD spectroscopy, cytotoxins CT1 and CT2 Naja oxiana, CT3 Naja kaouthia, and CT1 and CT2 Naja haje were shown to have similar secondary structure in an aqueous environment, with dominating beta-sheet structure, and to vary in the twisting angle of the beta-sheet and the conformation of disulfide groups. Using dodecylphosphocholine micelles and liposomes, CT1 and CT2 Naja oxiana were shown to incorporate into lipid structures without changes in the secondary structure of the peptides. The binding of CT1 and CT2 Naja oxiana with liposomes was associated with an increase in the beta-sheet twisting and a sign change of the dihedral angle of one disulfide group. The cytotoxins were considerably different in cytotoxicity and cooperativity of the effect on human promyelocytic leukemia cells HL60, mouse myelomonocytic cells WEHI-3, and human erythroleukemic cells K562. The most toxic CT2 Naja oxiana and CT3 Naja kaouthia possessed low cooperativity of interaction (Hill coefficient h = 0.6-0.8), unlike 10-20-fold less toxic CT1 and CT2 Naja haje (h = 1.2-1.7). CT1 Naja oxiana has an intermediate position on the cytotoxicity scale and is characterized by h = 0.5-0.8. The cytotoxins under study induced necrosis of HL60 cells and failed to activate apoptosis. The differences in cytotoxicity are supposed to be related not with features of the secondary structure of the peptides, but with interactions of side chains of variable amino acid residues with lipids and/or membrane proteins.
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Affiliation(s)
- A V Feofanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Mikklukho-Maklaya 16/10, Moscow 117997, Russia.
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31
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Feofanov AV, Nazarova AI, Karmakova TA, Pliutinskaia AD, Grishin AI, Iakubovskaia RI, Lebedeva VS, Ruziev RD, Mironov AF, Maurizot JC, Vigny P. [Photobiological properties of 13,15-N-(carboxymethyl)- and 13,15-N-(2-carboxyethyl)cycloimide derivatives of chlorin p6]. Bioorg Khim 2004; 30:417-28. [PMID: 15469017] [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: 04/30/2023]
Abstract
Lipophilic derivatives of chlorin p6, 13,15-N-(carboxymethyl)cycloimide methyl ester (CIC1) and 13,15-N-(2-carboxyethyl)cycloimide methyl ester (CIC2), were shown to absorb light in 710 nm region and to be efficient IR photosensitizers. They exhibit similar phototoxicities on the cells of A549 human lung adenocarcinoma, which are 40- and 100-fold higher than those of chlorin p6 and the clinically used Photogem, respectively, and are not toxic in the absence of light irradiation. The confocal spectral imaging technique allowed us to demonstrate that the high phototoxicity of CIC1 and CIC2 is due to their ability to readily penetrate to cells and to be bound to the cell membranes and lipid-containing structures in the monomeric photoactive form. Under the irradiation, the membrane-bound CIC1 and CIC2 are characterized by high quantum yields of singlet oxygen generation (0.6 and 0.65, respectively) and the inability to produce hydroxyl radicals. A 1.5-microM content of CIC1 and CIC2 in the incubation medium provides for their average cytoplasmic concentrations of 21 and 16.5 microM, respectively. The incubation times to achieve 50% level of maximum accumulation for CIC1 and CIC2 in A549 cells are 30 +/- 6 and 24 +/- 12 min, and the times for 50% release of the dyes from the cells are 17 +/- 4 and 50 +/- 10 min, respectively. A diffuse distribution with the predominant accumulation in the membranes of the Golgi apparatus and mitochondria is characteristic of both CIC2 and CIC1, whereas, in addition, CIC1 is considerably accumulated in lipid droplets (cellular organelles responsible for the storage and metabolism of neutral lipids and steryl esters). Our results demonstrate that changes in the structure of the imide substituent could affect the intracellular localization and the rate of release of chlorin p6 cycloimide derivatives from cells while preserving their high photodynamic activity.
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Feofanov AV, Grichine AI, Shitova LA, Karmakova TA, Yakubovskaya RI, Egret-Charlier M, Vigny P. Confocal raman microspectroscopy and imaging study of theraphthal in living cancer cells. Biophys J 2000; 78:499-512. [PMID: 10620313 PMCID: PMC1300657 DOI: 10.1016/s0006-3495(00)76612-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [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: 12/23/2022] Open
Abstract
Binary systems combining a transition metal complex and ascorbate have been proposed recently for catalytic therapy of malignant tumors. The killing effect on tumor cells is achieved by production of free radicals in the course of accelerated oxidation of ascorbate by dioxygen in the presence of transition metal complexes. Further progress in the development of binary catalytic systems (BCSs) requires a special method for their investigation in cells and tissues, because neither component of BCSs fluoresces. Here a resonance Raman confocal spectral imaging (RR CSI) technique was introduced as a unique approach to monitor quantitatively the transition metal complexes within living cells. Intracellular accumulation, localization, and retention of theraphthal (TP), a catalyst of the advanced TP/ascorbate BCS, were investigated in A549 cells with the RR CSI technique. The cellular analysis was complemented with the detailed study of molecular interactions of TP in solution and environmental factors affecting the RR spectrum of TP. TP does not penetrate into membranes, it binds very weakly to DNA and RNA, but it readily forms complexes with proteins. Binding with Ca(2+) cations and decreasing pH below 6 induce aggregation of TP. By analyzing RR spectra recorded from every point within a TP-treated cell, three states of the agent were discriminated, namely, monomeric TP in polar environment, TP bound to proteins, and aggregated TP. Their cytoplasmic and nuclear distributions were mapped at different stages of uptake and efflux. By introducing organelle-selective fluorescent probes into drug-treated cells and measuring intracellular localization of both the probe and the drug, compartmentation of TP was revealed. Cell growth suppression by the TP/ascorbate system was measured, and probable molecular and organelle targets of radical damage were characterized.
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Affiliation(s)
- A V Feofanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 17871 Moscow, Russia.
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33
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Feofanov AV, Grishin AI, Kudelina IA, Shitova LA, Karmakova TA, Iakubovskaia RI, Egret-Charlier M, Vigny P. [Study of localization and molecular interactions of biologically active compounds in living cells and tissue slices based on confocal microspectroscopy and reconstruction of the spectral images]. Bioorg Khim 1999; 25:892-902. [PMID: 10734550] [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] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
The confocal spectral imaging (CSI) technique is described, its basic principles are considered, and a brief review of its applications to the study of biologically active compounds (BAC) within living cells and in tissue slices is presented. This technique is based on measurements and analysis of fluorescence or resonance Raman spectra in each point of the specimen under microscope with a three-dimensional resolution of about cubic micrometer. This technique is applicable to the study of stained fluorescent and nonfluorescent compounds. Unlike the conventional approaches based on the optical microscopy, the CSI technique opens the opportunity for the identification of complexes and microenvironment of BAC in intact cells and thin tissue slices (slices or sections), as well as for the analysis of localization and distribution of compounds of interest and their complexes in cellular organelles and tissue structures. The use of CSI technique in combination with the conventional biochemical and cytological methods makes it possible to significantly expand the informativeness of investigation of modes of action of new BAC.
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Affiliation(s)
- A V Feofanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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34
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Fleury F, Ianoul A, Kryukov E, Sukhanova A, Kudelina I, Wynne-Jones A, Bronstein IB, Maizieres M, Berjot M, Dodson GG, Wilkinson AJ, Holden JA, Feofanov AV, Alix AJ, Jardillier JC, Nabiev I. Raman and CD spectroscopy of recombinant 68-kDa DNA human topoisomerase I and its complex with suicide DNA-substrate. Biochemistry 1998; 37:14630-42. [PMID: 9772192 DOI: 10.1021/bi9806495] [Citation(s) in RCA: 12] [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: 11/29/2022]
Abstract
N-terminally truncated recombinant 68-kDa human topoisomerase (topo) I exhibits the same DNA-driving activities as the wild-type protein. In the present study, Raman and circular dichroism techniques were employed for detailed structural characterization of the 68-kDa human topo I and its transformations induced by the suicide sequence-specific oligonucleotide (solig) binding and cleavage. Spectroscopic data combined with statistical prediction techniques were employed to construct a model of the secondary structure distribution along the primary protein structure in solution. The 68-kDa topo I was found to consist of ca. 59% alpha-helix, 24% beta-strand and/or sheets, and 17% other structures. A secondary structure transition of the 68-kDa topo I was found to accompany solig binding and cleavage. Nearly 15% of the alpha-helix of 68-kDa topo I is transferred within the other structures when in the complex with its DNA substrate. Raman spectroscopy analysis also shows redistribution of the structural rotamers of the 68-kDa topo I disulfide bonds and significant changes in the H-bonding of the Tyr residues and in the microenvironment/conformation of the Trp side chains. No structural modifications of the DNA substrate were detected by spectroscopic techniques. The data presented provide the first direct experimental evidence of the human topo I conformational transition after the cleavage step in the reaction of binding and cleavage of DNA substrate by the enzyme. This evidence supports the model of the enzyme function requiring the protein conformational transition. The most probable location of the enzyme transformations was the core and the C-terminal conservative 68-kDa topo I structural domains. By contrast, the linker domain was found to have an extremely low potential for solig-induced structural transformations. The pattern of redistribution of protein secondary structures induced by solig binding and covalent suicide complex formation supports the model of an intramolecular bipartite mode of topo I/DNA interaction in the substrate binding and cleavage reaction.
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Affiliation(s)
- F Fleury
- Institut Fédératif de Recherche "Biomolécules", Université de Reims Champagne-Ardenne, France
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35
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Oleĭnikov VA, Feofanov AV, Shiian SD, Tuzikov AB, Kriukov EI, Ianul' AI, Bovin NB, Nabiev IR. [Surface enhanced Raman spectroscopy for characterization of structural characteristics of carbon chains in alpha1-acid glycoprotein and pseudoglycoproteins]. Bioorg Khim 1998; 24:412-21. [PMID: 9702351] [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] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Surface-enhanced Raman scattering (SERS) spectroscopy was used to study the structure of carbohydrate chains in glycosylated forms of alpha 1-acid glycoprotein (AGP) and in pseudoglycoproteins obtained by transferring the carbohydrate chains of AGP to a polyacrylamide carrier. It was found that AGP-D glycoform and pseudoglycoproteins containing three or more glycans per molecule, which possess high immunomodulating activity, have a specific spatial organization of carbohydrate chains. This organization is maintained by the interaction of neighboring glycans with each other and does not depend on the nature of the carrier (whether it is polypeptide or polyacrylamide).
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Affiliation(s)
- V A Oleĭnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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Feofanov AV, Oleĭnikov VA, Tuzikov AB, Ianul' AI, Kriukov EI, Bovin NV, Nabiev IR. [Study of sialated neoglycoconjugates by surface enhanced Raman scattering spectroscopy]. Bioorg Khim 1997; 23:910-8. [PMID: 9518432] [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] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Neoglycoconjugates based on polyacrylamide and sialic acid with N-acetylneuraminic acid or sialooligosaccharides as side chains were studied by surface-enhanced Raman scattering (SERS) spectroscopy. It had previously been found that these polymers can effectively inhibit influenza virus adhesion. This study revealed the possibility to evaluate, based on the intensity of SERS signals, the overall availability for interaction and the conformational freedom of sialic acid residues in glycoconjugates. The dependence of these two factors on the structure and density of sialylated side chains was studied. The uniformity of distribution of sialylated side chains in conjugates was shown. Comparison of the results of the SERS spectroscopic study of the conjugates and the data on their inhibitory effect on the adhesion of specific strains of influenza virus allowed the identification of the conjugates for which the availability and conformational freedom of sialic acid are the main factors determining their inhibitory properties. A conclusion was also reached about the predominance of one of the mechanisms (competitive inhibition or steric stabilization) in the inhibitory properties of the specific conjugates.
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Affiliation(s)
- A V Feofanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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37
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Feofanov AV, Baranov AV, Fleury F, Riou JF, Nabiev IR, Manfait M. DNA topoisomerase I changes the mode of interaction between camptothecin drugs and DNA as probed by UV-resonance Raman spectroscopy. FEBS Lett 1996; 396:289-92. [PMID: 8915005 DOI: 10.1016/0014-5793(96)01118-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [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: 02/03/2023]
Abstract
Pronounced differences of interactions of camptothecin (CPT) and its derivative 7-ethyl-10-[4-(1-piperidino)-1-piperidino]carbonyloxycamptothecin (CPT11), inhibitors of DNA topoisomerase I, with oligonucleotides were found using UV resonance Raman spectroscopy. 30-mer oligonucleotides were derived from the sequences of the topoisomerase I-induced and CPT-enhanced cleavage sites in SV40 DNA. CPT induces well-defined alterations of the oligo structure, whereas CPT11 interacts with oligonucleotides more weakly and in another manner than CPT. Formation of cleavable ternary complexes between CPT11, topoisomerase I and oligonucleotides causes CPT11 to interact with oligonucleotides in the same fashion as was found for its parent compound CPT, and enhances this interaction as compared to CPT-oligonucleotide complexes. The data present evidence of molecular interactions of CPT11 with both other partners (topoisomerase I and oligonucleotide) of the ternary cleavable complex at the oligonucleotide-enzyme interface.
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Affiliation(s)
- A V Feofanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
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Kryukov EV, Feofanov AV, Oleinikov VA, Vereshchetin VP, Zaitsev SY, Gromov SP, Fedorova OA, Maskevich SA, Kivach LN, Zubov VP, Nabiev IR, Alfimov MV. Aggregation and photoisomerization of amphiphilic crown-ether styryl dye in monolayers at the interface. Russ Chem Bull 1996. [DOI: 10.1007/bf01435383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Efremov RG, Feofanov AV, Dzhandzhugazyan KN, Modyanov NN, Nabiev IR. Study of ATP binding in the active site of Na+,K(+)-ATPase as probed by ultraviolet resonance Raman spectroscopy. FEBS Lett 1990; 260:257-60. [PMID: 2153587 DOI: 10.1016/0014-5793(90)80117-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [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: 12/30/2022]
Abstract
The ultraviolet resonance Raman (UV RR) spectra of functional ATP/membrane-bound Na+,K+-ATPase complexes have been obtained. The substrate binding in the enzyme active site has been shown to be accompanied with significant changes in the electronic vibrational structure of the adenine ring. From the spectral analysis of ATP, 8-Br-ATP and 6-NHMe-adenine at various pH values the conclusion was made that N1 and the NH2 group and, probably, N7 of the substrate adenine part, interact with the protein surroundings via hydrogen bonds.
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Affiliation(s)
- R G Efremov
- Shemyakin Institute of Bioorganic Chemistry, USSR Academy of Science, Moscow
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