1
|
Ostroverkhova D, Tyryshkin K, Beach AK, Moore EA, Masoudi-Sobhanzadeh Y, Barbari SR, Rogozin IB, Shaitan KV, Panchenko AR, Shcherbakova PV. DNA polymerase ε and δ variants drive mutagenesis in polypurine tracts in human tumors. Cell Rep 2024; 43:113655. [PMID: 38219146 PMCID: PMC10830898 DOI: 10.1016/j.celrep.2023.113655] [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: 07/14/2023] [Revised: 11/07/2023] [Accepted: 12/19/2023] [Indexed: 01/16/2024] Open
Abstract
Alterations in the exonuclease domain of DNA polymerase ε cause ultramutated cancers. These cancers accumulate AGA>ATA transversions; however, their genomic features beyond the trinucleotide motifs are obscure. We analyze the extended DNA context of ultramutation using whole-exome sequencing data from 524 endometrial and 395 colorectal tumors. We find that G>T transversions in POLE-mutant tumors predominantly affect sequences containing at least six consecutive purines, with a striking preference for certain positions within polypurine tracts. Using this signature, we develop a machine-learning classifier to identify tumors with hitherto unknown POLE drivers and validate two drivers, POLE-E978G and POLE-S461L, by functional assays in yeast. Unlike other pathogenic variants, the E978G substitution affects the polymerase domain of Pol ε. We further show that tumors with POLD1 drivers share the extended signature of POLE ultramutation. These findings expand the understanding of ultramutation mechanisms and highlight peculiar mutagenic properties of polypurine tracts in the human genome.
Collapse
Affiliation(s)
- Daria Ostroverkhova
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Kathrin Tyryshkin
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Annette K Beach
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Elizabeth A Moore
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yosef Masoudi-Sobhanzadeh
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Stephanie R Barbari
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada.
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
| |
Collapse
|
2
|
Voinova VV, Zhuikov VA, Zhuikova YV, Sorokina AA, Makhina TK, Bonartseva GA, Parshina EY, Hossain MA, Shaitan KV, Pryadko AS, Chernozem RV, Mukhortova YR, Shlapakova LE, Surmenev RA, Surmeneva MA, Bonartsev AP. Adhesion of Escherichia coli and Lactobacillus fermentum to Films and Electrospun Fibrous Scaffolds from Composites of Poly(3-hydroxybutyrate) with Magnetic Nanoparticles in a Low-Frequency Magnetic Field. Int J Mol Sci 2023; 25:208. [PMID: 38203380 PMCID: PMC10778586 DOI: 10.3390/ijms25010208] [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: 11/01/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
The ability of materials to adhere bacteria on their surface is one of the most important aspects of their development and application in bioengineering. In this work, the effect of the properties of films and electrospun scaffolds made of composite materials based on biosynthetic poly(3-hydroxybutyrate) (PHB) with the addition of magnetite nanoparticles (MNP) and their complex with graphene oxide (MNP/GO) on the adhesion of E. coli and L. fermentum under the influence of a low-frequency magnetic field and without it was investigated. The physicochemical properties (crystallinity; surface hydrophilicity) of the materials were investigated by X-ray structural analysis, differential scanning calorimetry and "drop deposition" methods, and their surface topography was studied by scanning electron and atomic force microscopy. Crystal violet staining made it possible to reveal differences in the surface charge value and to study the adhesion of bacteria to it. It was shown that the differences in physicochemical properties of materials and the manifestation of magnetoactive properties of materials have a multidirectional effect on the adhesion of model microorganisms. Compared to pure PHB, the adhesion of E. coli to PHB-MNP/GO, and for L. fermentum to both composite materials, was higher. In the magnetic field, the adhesion of E. coli increased markedly compared to PHB-MNP/GO, whereas the effect on the adhesion of L. fermentum was reversed and was only evident in samples with PHB-MNP. Thus, the resultant factors enhancing and impairing the substrate binding of Gram-negative E. coli and Gram-positive L. fermentum turned out to be multidirectional, as they probably have different sensitivity to them. The results obtained will allow for the development of materials with externally controlled adhesion of bacteria to them for biotechnology and medicine.
Collapse
Affiliation(s)
- Vera V. Voinova
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (V.V.V.); (A.A.S.); (E.Y.P.); (M.A.H.); (K.V.S.)
| | - Vsevolod A. Zhuikov
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow 119071, Russia; (V.A.Z.); (Y.V.Z.); (T.K.M.); (G.A.B.)
| | - Yulia V. Zhuikova
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow 119071, Russia; (V.A.Z.); (Y.V.Z.); (T.K.M.); (G.A.B.)
| | - Anastasia A. Sorokina
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (V.V.V.); (A.A.S.); (E.Y.P.); (M.A.H.); (K.V.S.)
| | - Tatiana K. Makhina
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow 119071, Russia; (V.A.Z.); (Y.V.Z.); (T.K.M.); (G.A.B.)
| | - Garina A. Bonartseva
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow 119071, Russia; (V.A.Z.); (Y.V.Z.); (T.K.M.); (G.A.B.)
| | - Evgeniia Yu. Parshina
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (V.V.V.); (A.A.S.); (E.Y.P.); (M.A.H.); (K.V.S.)
| | - Muhammad Asif Hossain
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (V.V.V.); (A.A.S.); (E.Y.P.); (M.A.H.); (K.V.S.)
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (V.V.V.); (A.A.S.); (E.Y.P.); (M.A.H.); (K.V.S.)
| | - Artyom S. Pryadko
- Physical Materials Science and Composite Materials Center, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia; (A.S.P.); (Y.R.M.); (L.E.S.); (R.A.S.); (M.A.S.)
| | - Roman V. Chernozem
- International Research and Development Center “Piezo- and Magnetoelectric Materials”, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia;
| | - Yulia R. Mukhortova
- Physical Materials Science and Composite Materials Center, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia; (A.S.P.); (Y.R.M.); (L.E.S.); (R.A.S.); (M.A.S.)
- International Research and Development Center “Piezo- and Magnetoelectric Materials”, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia;
| | - Lada E. Shlapakova
- Physical Materials Science and Composite Materials Center, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia; (A.S.P.); (Y.R.M.); (L.E.S.); (R.A.S.); (M.A.S.)
| | - Roman A. Surmenev
- Physical Materials Science and Composite Materials Center, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia; (A.S.P.); (Y.R.M.); (L.E.S.); (R.A.S.); (M.A.S.)
- International Research and Development Center “Piezo- and Magnetoelectric Materials”, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia;
| | - Maria A. Surmeneva
- Physical Materials Science and Composite Materials Center, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia; (A.S.P.); (Y.R.M.); (L.E.S.); (R.A.S.); (M.A.S.)
- International Research and Development Center “Piezo- and Magnetoelectric Materials”, Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia;
| | - Anton P. Bonartsev
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (V.V.V.); (A.A.S.); (E.Y.P.); (M.A.H.); (K.V.S.)
| |
Collapse
|
3
|
Bagrov DV, Adlerberg VV, Skryabin GO, Nikishin II, Galetsky SA, Tchevkina EM, Kirpichnikov MP, Shaitan KV. AFM-TEM correlation microscopy and its application to lipid nanoparticles. Microsc Res Tech 2023. [PMID: 37125595 DOI: 10.1002/jemt.24336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 11/17/2022] [Revised: 03/04/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
So far, only a few articles have demonstrated the possibility of correlated AFM-TEM imaging - sequential imaging of the same individual objects using atomic-force microscopy (AFM) and transmission electron microscopy (TEM). The current work contributes to the development of this approach by giving a step-by-step procedure, which yields pairs of correlated AFM-TEM images. We describe the application of correlation AFM-TEM microscopy to lipid nanoparticles (small extracellular vesicles and liposomes). The sizes of individual particles measured by the two methods were in good agreement, taking the tip broadening into account. The correlated AFM-TEM imaging can be valuable for single-particle analysis and nanometrology.
Collapse
Affiliation(s)
- Dmitry V Bagrov
- Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir V Adlerberg
- Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Gleb O Skryabin
- Department of oncogene regulation, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Igor I Nikishin
- Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Sergey A Galetsky
- Department of oncogene regulation, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Elena M Tchevkina
- Department of oncogene regulation, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Mikhail P Kirpichnikov
- Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin V Shaitan
- Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
4
|
Zharkova II, Volkov AV, Muraev AA, Makhina TK, Voinova VV, Ryabova VM, Gazhva YV, Kashirina AS, Kashina AV, Bonartseva GA, Zhuikov VA, Shaitan KV, Kirpichnikov MP, Ivanov SY, Bonartsev AP. Poly(3-hydroxybutyrate) 3D-Scaffold-Conduit for Guided Tissue Sprouting. Int J Mol Sci 2023; 24:ijms24086965. [PMID: 37108133 PMCID: PMC10138660 DOI: 10.3390/ijms24086965] [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: 11/15/2022] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Scaffold biocompatibility remains an urgent problem in tissue engineering. An especially interesting problem is guided cell intergrowth and tissue sprouting using a porous scaffold with a special design. Two types of structures were obtained from poly(3-hydroxybutyrate) (PHB) using a salt leaching technique. In flat scaffolds (scaffold-1), one side was more porous (pore size 100-300 μm), while the other side was smoother (pore size 10-50 μm). Such scaffolds are suitable for the in vitro cultivation of rat mesenchymal stem cells and 3T3 fibroblasts, and, upon subcutaneous implantation to older rats, they cause moderate inflammation and the formation of a fibrous capsule. Scaffold-2s are homogeneous volumetric hard sponges (pore size 30-300 μm) with more structured pores. They were suitable for the in vitro culturing of 3T3 fibroblasts. Scaffold-2s were used to manufacture a conduit from the PHB/PHBV tube with scaffold-2 as a filler. The subcutaneous implantation of such conduits to older rats resulted in gradual soft connective tissue sprouting through the filler material of the scaffold-2 without any visible inflammatory processes. Thus, scaffold-2 can be used as a guide for connective tissue sprouting. The obtained data are advanced studies for reconstructive surgery and tissue engineering application for the elderly patients.
Collapse
Affiliation(s)
- Irina I Zharkova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1-12, Moscow 119234, Russia
| | - Aleksey V Volkov
- Federal State Budgetary Institution "N.N. Priorov National Medical Research Center of Traumatology and Orthopedics", Ministry of Health of the Russian Federation, Priorova Str. 10, Moscow 127299, Russia
- Department of Oral and Maxillofacial Surgery and Surgical Dentistry, Medical Institute, RUDN Universiry, Miklukho-Maklaya Str., Moscow 6117198, Russia
| | - Aleksandr A Muraev
- Department of Oral and Maxillofacial Surgery and Surgical Dentistry, Medical Institute, RUDN Universiry, Miklukho-Maklaya Str., Moscow 6117198, Russia
| | - Tatiana K Makhina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow 119071, Russia
| | - Vera V Voinova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1-12, Moscow 119234, Russia
| | - Valentina M Ryabova
- Department of Oral and Maxillofacial Surgery and Surgical Dentistry, Medical Institute, RUDN Universiry, Miklukho-Maklaya Str., Moscow 6117198, Russia
- Federal State Budgetary Educational Institution of Higher Education "Privolzhsky Research Medical University", Ministry of Health of the Russian Federation, Minin and Pozharsky pl., 10/1, Nizhny Novgorod 603005, Russia
| | - Yulia V Gazhva
- Department of Oral and Maxillofacial Surgery and Surgical Dentistry, Medical Institute, RUDN Universiry, Miklukho-Maklaya Str., Moscow 6117198, Russia
- Federal State Budgetary Educational Institution of Higher Education "Privolzhsky Research Medical University", Ministry of Health of the Russian Federation, Minin and Pozharsky pl., 10/1, Nizhny Novgorod 603005, Russia
| | - Alena S Kashirina
- Federal State Budgetary Educational Institution of Higher Education "Privolzhsky Research Medical University", Ministry of Health of the Russian Federation, Minin and Pozharsky pl., 10/1, Nizhny Novgorod 603005, Russia
| | - Aleksandra V Kashina
- Federal State Budgetary Educational Institution of Higher Education "Privolzhsky Research Medical University", Ministry of Health of the Russian Federation, Minin and Pozharsky pl., 10/1, Nizhny Novgorod 603005, Russia
| | - Garina A Bonartseva
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow 119071, Russia
| | - Vsevolod A Zhuikov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow 119071, Russia
| | - Konstantin V Shaitan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1-12, Moscow 119234, Russia
| | - Mikhail P Kirpichnikov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1-12, Moscow 119234, Russia
| | - Sergey Yu Ivanov
- Department of Oral and Maxillofacial Surgery and Surgical Dentistry, Medical Institute, RUDN Universiry, Miklukho-Maklaya Str., Moscow 6117198, Russia
- Department of Oral and Maxillofacial Surgery, Sechenov University, Trubetskaya Str., 8-2, Moscow 119991, Russia
| | - Anton P Bonartsev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1-12, Moscow 119234, Russia
| |
Collapse
|
5
|
Moiseenko AV, Bagrov DV, Vorovitch MF, Uvarova VI, Veselov MM, Kashchenko AV, Ivanova AL, Osolodkin DI, Egorov AM, Ishmukhametov AA, Shaitan KV, Sokolova OS. Size Distribution of Inactivated Tick-Borne Encephalitis Virus Particles Revealed by a Comprehensive Physicochemical Approach. Biomedicines 2022; 10:biomedicines10102478. [PMID: 36289740 PMCID: PMC9598892 DOI: 10.3390/biomedicines10102478] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 11/24/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is an enveloped RNA virus, a member of the genus Flavivirus (family Flaviviridae). Here, we provide a detailed analysis of the size and structure of the inactivated TBEV vaccine strain Sofjin-Chumakov. Four analytical methods were used to analyze individual TBEV particles—negative staining TEM, cryo-EM, atomic force microscopy (AFM), and nanoparticle tracking analysis (NTA). All methods confirmed that the particles were monodisperse and that their mean size was ~50 nm. Cryo-EM data allowed us to obtain a 3D electron density model of the virus with clearly distinguishable E protein molecules. STEM-EELS analysis detected phosphorus in the particles, which was interpreted as an indicator of RNA presence. Altogether, the described analytical procedures can be valuable for the characterization of inactivated vaccine virus samples.
Collapse
Affiliation(s)
- Andrey V. Moiseenko
- Department of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Dmitry V. Bagrov
- Department of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Mikhail F. Vorovitch
- FSASI “Chumakov FSC R&D IBP RAS” (Institute of Poliomyelitis), Moscow 108819, Russia
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Victoria I. Uvarova
- FSASI “Chumakov FSC R&D IBP RAS” (Institute of Poliomyelitis), Moscow 108819, Russia
| | - Maxim M. Veselov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119234, Russia
| | | | - Alla L. Ivanova
- FSASI “Chumakov FSC R&D IBP RAS” (Institute of Poliomyelitis), Moscow 108819, Russia
| | - Dmitry I. Osolodkin
- FSASI “Chumakov FSC R&D IBP RAS” (Institute of Poliomyelitis), Moscow 108819, Russia
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Alexey M. Egorov
- FSASI “Chumakov FSC R&D IBP RAS” (Institute of Poliomyelitis), Moscow 108819, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Aydar A. Ishmukhametov
- FSASI “Chumakov FSC R&D IBP RAS” (Institute of Poliomyelitis), Moscow 108819, Russia
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | | | - Olga S. Sokolova
- Faculty of Biology, MSU-BIT Shenzhen University, 1 International University Park Road, Dayun New Town, Longgang District, Shenzhen 518172, China
- Correspondence:
| |
Collapse
|
6
|
Pryadko A AS, Mukhortova YR, Chernozem RV, Pariy I, Alipkina SI, Zharkova II, Dudun AA, Zhuikov VA, Moisenovich AM, Bonartseva GA, Voinova VV, Chesnokova DV, Ivanov AA, Travnikova DY, Shaitan KV, Bonartsev AP, Wagner DV, Shlapakova LE, Surmenev RA, Surmeneva MA. Electrospun Magnetic Composite Poly-3-hydroxybutyrate/Magnetite Scaffolds for Biomedical Applications: Composition, Structure, Magnetic Properties, and Biological Performance. ACS Appl Bio Mater 2022; 5:3999-4019. [PMID: 35925883 DOI: 10.1021/acsabm.2c00496] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 11/30/2022]
Abstract
Magnetically responsive composite polymer scaffolds have good potential for a variety of biomedical applications. In this work, electrospun composite scaffolds made of polyhydroxybutyrate (PHB) and magnetite (Fe3O4) particles (MPs) were studied before and after degradation in either PBS or a lipase solution. MPs of different sizes with high saturation magnetization were synthesized by the coprecipitation method followed by coating with citric acid (CA). Nanosized MPs were prone to magnetite-maghemite phase transformation during scaffold fabrication, as revealed by Raman spectroscopy; however, for CA-functionalized nanoparticles, the main phase was found to be magnetite, with some traces of maghemite. Submicron MPs were resistant to the magnetite-maghemite phase transformation. MPs did not significantly affect the morphology and diameter of PHB fibers. The scaffolds containing CA-coated MPs lost 0.3 or 0.2% of mass in the lipase solution and PBS, respectively, whereas scaffolds doped with unmodified MPs showed no mass changes after 1 month of incubation in either medium. In all electrospun scaffolds, no alterations of the fiber morphology were observed. Possible mechanisms of the crystalline-lamellar-structure changes in hybrid PHB/Fe3O4 scaffolds during hydrolytic and enzymatic degradation are proposed. It was revealed that particle size and particle surface functionalization affect the mechanical properties of the hybrid scaffolds. The addition of unmodified MPs increased scaffolds' ultimate strength but reduced elongation at break after the biodegradation, whereas simultaneous increases in both parameters were observed for composite scaffolds doped with CA-coated MPs. The highest saturation magnetization─higher than that published in the literature─was registered for composite PHB scaffolds doped with submicron MPs. All PHB scaffolds proved to be biocompatible, and the ones doped with nanosized MPs yielded faster proliferation of rat mesenchymal stem cells. In addition, all electrospun scaffolds were able to support angiogenesis in vivo at 30 days after implantation in Wistar rats.
Collapse
Affiliation(s)
- Artyom S Pryadko A
- Physical Materials Science and Composite Materials Center, Research School of Chemistry & Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Yulia R Mukhortova
- Physical Materials Science and Composite Materials Center, Research School of Chemistry & Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Roman V Chernozem
- Physical Materials Science and Composite Materials Center, Research School of Chemistry & Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Igor Pariy
- Physical Materials Science and Composite Materials Center, Research School of Chemistry & Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Svetlana I Alipkina
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow 119234, Russia
| | - Irina I Zharkova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow 119234, Russia
| | - Andrey A Dudun
- Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave 33, Bldg. 2, Moscow 119071, Russia
| | - Vsevolod A Zhuikov
- Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave 33, Bldg. 2, Moscow 119071, Russia
| | - Anastasia M Moisenovich
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow 119234, Russia
| | - Garina A Bonartseva
- Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave 33, Bldg. 2, Moscow 119071, Russia
| | - Vera V Voinova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow 119234, Russia
| | - Dariana V Chesnokova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow 119234, Russia
| | - Alexey A Ivanov
- Physical Materials Science and Composite Materials Center, Research School of Chemistry & Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Daria Yu Travnikova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow 119234, Russia
| | - Konstantin V Shaitan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow 119234, Russia
| | - Anton P Bonartsev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow 119234, Russia
| | - Dmitry V Wagner
- National Research Tomsk State University, Tomsk 634050, Russia
| | - Lada E Shlapakova
- Physical Materials Science and Composite Materials Center, Research School of Chemistry & Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Roman A Surmenev
- Physical Materials Science and Composite Materials Center, Research School of Chemistry & Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Maria A Surmeneva
- Physical Materials Science and Composite Materials Center, Research School of Chemistry & Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| |
Collapse
|
7
|
Efremov YM, Bagrov DV, Kirpichnikov MP, Shaitan KV. Corrigendum to "Application of the Johnson-Kendall-Roberts model in AFM-based mechanical measurements on cells and gel" [Colloids Surf. B Biointerfaces 134 (2015) 131-139]. Colloids Surf B Biointerfaces 2022; 216:112586. [PMID: 35636329 DOI: 10.1016/j.colsurfb.2022.112586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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)
- Yu M Efremov
- Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1/73, Moscow 119234, Russia.
| | - D V Bagrov
- Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1/73, Moscow 119234, Russia
| | - M P Kirpichnikov
- Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1/73, Moscow 119234, Russia
| | - K V Shaitan
- Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1/73, Moscow 119234, Russia
| |
Collapse
|
8
|
Chernozem RV, Pariy IO, Pryadko A, Bonartsev AP, Voinova VV, Zhuikov VA, Makhina TK, Bonartseva GA, Shaitan KV, Shvartsman VV, Lupascu DC, Romanyuk KN, Kholkin AL, Surmenev RA, Surmeneva MA. A comprehensive study of the structure and piezoelectric response of biodegradable polyhydroxybutyrate-based films for tissue engineering applications. Polym J 2022. [DOI: 10.1038/s41428-022-00662-8] [Citation(s) in RCA: 1] [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: 11/09/2022]
|
9
|
Bozdaganyan ME, Shaitan KV, Kirpichnikov MP, Sokolova OS, Orekhov PS. Computational Analysis of Mutations in the Receptor-Binding Domain of SARS-CoV-2 Spike and Their Effects on Antibody Binding. Viruses 2022; 14:v14020295. [PMID: 35215888 PMCID: PMC8874930 DOI: 10.3390/v14020295] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Currently, SARS-CoV-2 causing coronavirus disease 2019 (COVID-19) is responsible for one of the most deleterious pandemics of our time. The interaction between the ACE2 receptors at the surface of human cells and the viral Spike (S) protein triggers the infection, making the receptor-binding domain (RBD) of the SARS-CoV-2 S-protein a focal target for the neutralizing antibodies (Abs). Despite the recent progress in the development and deployment of vaccines, the emergence of novel variants of SARS-CoV-2 insensitive to Abs produced in response to the vaccine administration and/or monoclonal ones represent a potential danger. Here, we analyzed the diversity of neutralizing Ab epitopes and assessed the possible effects of single and multiple mutations in the RBD of SARS-CoV-2 S-protein on its binding affinity to various antibodies and the human ACE2 receptor using bioinformatics approaches. The RBD-Ab complexes with experimentally resolved structures were grouped into four clusters with distinct features at sequence and structure level. The performed computational analysis indicates that while single amino acid replacements in RBD may only cause partial impairment of the Abs binding, moreover, limited to specific epitopes, the variants of SARS-CoV-2 with multiple mutations, including some which were already detected in the population, may potentially result in a much broader antigenic escape. Further analysis of the existing RBD variants pointed to the trade-off between ACE2 binding and antigenic escape as a key limiting factor for the emergence of novel SAR-CoV-2 strains, as the naturally occurring mutations in RBD tend to reduce its binding affinity to Abs but not to ACE2. The results provide guidelines for further experimental studies aiming to identify high-risk RBD mutations that allow for an antigenic escape.
Collapse
Affiliation(s)
- Marine E. Bozdaganyan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (K.V.S.); (M.P.K.)
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (K.V.S.); (M.P.K.)
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (K.V.S.); (M.P.K.)
| | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (K.V.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Correspondence: (O.S.S.); (P.S.O.)
| | - Philipp S. Orekhov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (K.V.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
- Correspondence: (O.S.S.); (P.S.O.)
| |
Collapse
|
10
|
Orekhov PS, Bozdaganyan ME, Voskoboynikova N, Mulkidjanian AY, Karlova MG, Yudenko A, Remeeva A, Ryzhykau YL, Gushchin I, Gordeliy VI, Sokolova OS, Steinhoff HJ, Kirpichnikov MP, Shaitan KV. Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review. Nanomaterials 2022; 12:nano12030361. [PMID: 35159706 PMCID: PMC8838559 DOI: 10.3390/nano12030361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene–maleic acid (SMA), diisobutylene–maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without the need for classical detergents. Within the particular experimental setup, they form disc-shaped nanoparticles with a narrow size distribution, which serve as a suitable platform for diverse kinds of spectroscopy and other biophysical techniques that require relatively small, homogeneous, water-soluble particles of separate membrane proteins in their native lipid environment. In recent years, copolymer-encased nanolipoparticles have been proven as suitable protein carriers for various structural biology applications, including cryo-electron microscopy (cryo-EM), small-angle scattering, and conventional and single-molecule X-ray diffraction experiments. Here, we review the current understanding of how such nanolipoparticles are formed and organized at the molecular level with an emphasis on their chemical diversity and factors affecting their size and solubilization efficiency.
Collapse
Affiliation(s)
- Philipp S. Orekhov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
- Correspondence: (P.S.O.); (K.V.S.)
| | - Marine E. Bozdaganyan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Natalia Voskoboynikova
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria G. Karlova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Yury L. Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Valentin I. Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Heinz-Jürgen Steinhoff
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Mikhail P. Kirpichnikov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Correspondence: (P.S.O.); (K.V.S.)
| |
Collapse
|
11
|
Dudun AA, Akoulina EA, Zhuikov VA, Makhina TK, Voinova VV, Belishev NV, Khaydapova DD, Shaitan KV, Bonartseva GA, Bonartsev AP. Competitive Biosynthesis of Bacterial Alginate Using Azotobacter vinelandii 12 for Tissue Engineering Applications. Polymers (Basel) 2021; 14:polym14010131. [PMID: 35012152 PMCID: PMC8747204 DOI: 10.3390/polym14010131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/17/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
This study investigated the effect of various cultivation conditions (sucrose/phosphate concentrations, aeration level) on alginate biosynthesis using the bacterial producing strain Azotobacter vinelandii 12 by the full factorial design (FFD) method and physicochemical properties (e.g., rheological properties) of the produced bacterial alginate. We demonstrated experimentally the applicability of bacterial alginate for tissue engineering (the cytotoxicity testing using mesenchymal stem cells (MSCs)). The isolated synthesis of high molecular weight (Mw) capsular alginate with a high level of acetylation (25%) was achieved by FFD method under a low sucrose concentration, an increased phosphate concentration, and a high aeration level. Testing the viscoelastic properties and cytotoxicity showed that bacterial alginate with a maximal Mw (574 kDa) formed the densest hydrogels (which demonstrated relatively low cytotoxicity for MSCs in contrast to bacterial alginate with low Mw). The obtained data have shown promising prospects in controlled biosynthesis of bacterial alginate with different physicochemical characteristics for various biomedical applications including tissue engineering.
Collapse
Affiliation(s)
- Andrei A. Dudun
- Research Center of Biotechnology of the Russian Academy of Sciences Leninsky Ave, 33, Bld. 2, 119071 Moscow, Russia; (A.A.D.); (V.A.Z.); (T.K.M.); (G.A.B.)
| | - Elizaveta A. Akoulina
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - Vsevolod A. Zhuikov
- Research Center of Biotechnology of the Russian Academy of Sciences Leninsky Ave, 33, Bld. 2, 119071 Moscow, Russia; (A.A.D.); (V.A.Z.); (T.K.M.); (G.A.B.)
| | - Tatiana K. Makhina
- Research Center of Biotechnology of the Russian Academy of Sciences Leninsky Ave, 33, Bld. 2, 119071 Moscow, Russia; (A.A.D.); (V.A.Z.); (T.K.M.); (G.A.B.)
| | - Vera V. Voinova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - Nikita V. Belishev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - Dolgor D. Khaydapova
- Department of Soil Physics and Reclamation, Soil Science Faculty, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia;
| | - Konstantin V. Shaitan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - Garina A. Bonartseva
- Research Center of Biotechnology of the Russian Academy of Sciences Leninsky Ave, 33, Bld. 2, 119071 Moscow, Russia; (A.A.D.); (V.A.Z.); (T.K.M.); (G.A.B.)
| | - Anton P. Bonartsev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (V.V.V.); (N.V.B.); (K.V.S.)
- Correspondence: ; Tel.: +7-4959306306
| |
Collapse
|
12
|
Bagrov DV, Glukhov GS, Moiseenko AV, Karlova MG, Litvinov DS, Zaitsev PА, Kozlovskaya LI, Shishova AA, Kovpak AA, Ivin YY, Piniaeva AN, Oksanich AS, Volok VP, Osolodkin DI, Ishmukhametov AA, Egorov AM, Shaitan KV, Kirpichnikov MP, Sokolova OS. Structural characterization of β-propiolactone inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) particles. Microsc Res Tech 2021; 85:562-569. [PMID: 34498784 PMCID: PMC8646525 DOI: 10.1002/jemt.23931] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/22/2021] [Indexed: 12/23/2022]
Abstract
The severe COVID‐19 pandemic drives the research toward the SARS‐CoV‐2 virion structure and the possible therapies against it. Here, we characterized the β‐propiolactone inactivated SARS‐CoV‐2 virions using transmission electron microscopy (TEM) and atomic force microscopy (AFM). We compared the SARS‐CoV‐2 samples purified by two consecutive chromatographic procedures (size exclusion chromatography [SEC], followed by ion‐exchange chromatography [IEC]) with samples purified by ultracentrifugation. The samples prepared using SEC and IEC retained more spikes on the surface than the ones prepared using ultracentrifugation, as confirmed by TEM and AFM. TEM showed that the spike (S) proteins were in the pre‐fusion conformation. Notably, the S proteins could be recognized by specific monoclonal antibodies. Analytical TEM showed that the inactivated virions retained nucleic acid. Altogether, we demonstrated that the inactivated SARS‐CoV‐2 virions retain the structural features of native viruses and provide a prospective vaccine candidate.
Collapse
Affiliation(s)
- Dmitry V Bagrov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Grigory S Glukhov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Andrey V Moiseenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Maria G Karlova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Daniil S Litvinov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr А Zaitsev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Liubov I Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anna A Shishova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anastasia A Kovpak
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia
| | - Yury Y Ivin
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia
| | - Anastasia N Piniaeva
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia
| | | | - Viktor P Volok
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia
| | - Dmitry I Osolodkin
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Aydar A Ishmukhametov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey M Egorov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Konstantin V Shaitan
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | | | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Biology Department, MSU-BIT University, Shenzhen, China
| |
Collapse
|
13
|
Kozlovskaya LI, Piniaeva AN, Ignatyev GM, Gordeychuk IV, Volok VP, Rogova YV, Shishova AA, Kovpak AA, Ivin YY, Antonova LP, Mefyod KM, Prokosheva LS, Sibirkina AS, Tarasova YY, Bayurova EO, Gancharova OS, Illarionova VV, Glukhov GS, Sokolova OS, Shaitan KV, Moysenovich AM, Gulyaev SA, Gulyaeva TV, Moroz AV, Gmyl LV, Ipatova EG, Kirpichnikov MP, Egorov AM, Siniugina AA, Ishmukhametov AA. Long-term humoral immunogenicity, safety and protective efficacy of inactivated vaccine against COVID-19 (CoviVac) in preclinical studies. Emerg Microbes Infect 2021; 10:1790-1806. [PMID: 34427172 PMCID: PMC8439218 DOI: 10.1080/22221751.2021.1971569] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The unprecedented in recent history global COVID-19 pandemic urged the implementation of all existing vaccine platforms to ensure the availability of the vaccines against COVID-19 to every country in the world. Despite the multitude of high-quality papers describing clinical trials of different vaccine products, basic detailed data on general toxicity, reproductive toxicity, immunogenicity, protective efficacy and durability of immune response in animal models are scarce. Here, we developed a β-propiolactone-inactivated whole virion vaccine CoviVac and assessed its safety, protective efficacy, immunogenicity and stability of the immune response in rodents and non-human primates. The vaccine showed no signs of acute/chronic, reproductive, embryo- and fetotoxicity, or teratogenic effects, as well as no allergenic properties in studied animal species. The vaccine induced stable and robust humoral immune response both in form of specific anti-SARS-CoV-2 IgG and NAbs in mice, Syrian hamsters, and common marmosets. The NAb levels did not decrease significantly over the course of one year. The course of two immunizations protected Syrian hamsters from severe pneumonia upon intranasal challenge with the live virus. Robustness of the vaccine manufacturing process was demonstrated as well. These data encouraged further evaluation of CoviVac in clinical trials.
Collapse
Affiliation(s)
- Liubov I Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anastasia N Piniaeva
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Georgy M Ignatyev
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Ilya V Gordeychuk
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Viktor P Volok
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yulia V Rogova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Anna A Shishova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anastasia A Kovpak
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Yury Yu Ivin
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Liliya P Antonova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Kirill M Mefyod
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Lyubov S Prokosheva
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Anna S Sibirkina
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Yuliya Yu Tarasova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina O Bayurova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Olga S Gancharova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Victoria V Illarionova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Grigory S Glukhov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga S Sokolova
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Stanislav A Gulyaev
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V Gulyaeva
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Andrey V Moroz
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Larissa V Gmyl
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Elena G Ipatova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | | | - Alexey M Egorov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aleksandra A Siniugina
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Aydar A Ishmukhametov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| |
Collapse
|
14
|
Zhuikov VA, Akoulina EA, Chesnokova DV, Wenhao Y, Makhina TK, Demyanova IV, Zhuikova YV, Voinova VV, Belishev NV, Surmenev RA, Surmeneva MA, Bonartseva GA, Shaitan KV, Bonartsev AP. The Growth of 3T3 Fibroblasts on PHB, PLA and PHB/PLA Blend Films at Different Stages of Their Biodegradation In Vitro. Polymers (Basel) 2020; 13:polym13010108. [PMID: 33383857 PMCID: PMC7795568 DOI: 10.3390/polym13010108] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 11/19/2022] Open
Abstract
Over the past century there was a significant development and extensive application of biodegradable and biocompatible polymers for their biomedical applications. This research investigates the dynamic change in properties of biodegradable polymers: poly(3-hydroxybutyrate (PHB), poly-l-lactide (PLA), and their 50:50 blend (PHB/PLA)) during their hydrolytic non-enzymatic (in phosphate buffered saline (PBS), at pH = 7.4, 37 °C) and enzymatic degradation (in PBS supplemented with 0.25 mg/mL pancreatic lipase). 3T3 fibroblast proliferation on the polymer films experiencing different degradation durations was also studied. Enzymatic degradation significantly accelerated the degradation rate of polymers compared to non-enzymatic hydrolytic degradation, whereas the seeding of 3T3 cells on the polymer films accelerated only the PLA molecular weight loss. Surprisingly, the immiscible nature of PHB/PLA blend (showed by differential scanning calorimetry) led to a slower and more uniform enzymatic degradation in comparison with pure polymers, PHB and PLA, which displayed a two-stage degradation process. PHB/PLA blend also displayed relatively stable cell viability on films upon exposure to degradation of different durations, which was associated with the uneven distribution of cells on polymer films. Thus, the obtained data are of great benefit for designing biodegradable scaffolds based on polymer blends for tissue engineering.
Collapse
Affiliation(s)
- Vsevolod A. Zhuikov
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave, 33, Bld. 2, 119071 Moscow, Russia; (V.A.Z.); (T.K.M.); (Y.V.Z.); (G.A.B.)
| | - Elizaveta A. Akoulina
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (D.V.C.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - Dariana V. Chesnokova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (D.V.C.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - You Wenhao
- Biological Faculty, Shenzhen MSU-BIT University, No.299, Ruyi Road, Longgang District, Shenzhen 518172, China; (Y.W.); (I.V.D.)
| | - Tatiana K. Makhina
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave, 33, Bld. 2, 119071 Moscow, Russia; (V.A.Z.); (T.K.M.); (Y.V.Z.); (G.A.B.)
| | - Irina V. Demyanova
- Biological Faculty, Shenzhen MSU-BIT University, No.299, Ruyi Road, Longgang District, Shenzhen 518172, China; (Y.W.); (I.V.D.)
| | - Yuliya V. Zhuikova
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave, 33, Bld. 2, 119071 Moscow, Russia; (V.A.Z.); (T.K.M.); (Y.V.Z.); (G.A.B.)
| | - Vera V. Voinova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (D.V.C.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - Nikita V. Belishev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (D.V.C.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - Roman A. Surmenev
- National Research Tomsk Polytechnic University, Lenin Ave, 30, 634050 Tomsk, Russia; (R.A.S.); (M.A.S.)
| | - Maria A. Surmeneva
- National Research Tomsk Polytechnic University, Lenin Ave, 30, 634050 Tomsk, Russia; (R.A.S.); (M.A.S.)
| | - Garina A. Bonartseva
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave, 33, Bld. 2, 119071 Moscow, Russia; (V.A.Z.); (T.K.M.); (Y.V.Z.); (G.A.B.)
| | - Konstantin V. Shaitan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (D.V.C.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - Anton P. Bonartsev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (D.V.C.); (V.V.V.); (N.V.B.); (K.V.S.)
- Correspondence: ; Tel.: +7-4959306306
| |
Collapse
|
15
|
Moysenovich AM, Moisenovich MM, Sudina AK, Tatarskiy VV, Khamidullina AI, Yastrebova MA, Davydova LI, Bogush VG, Debabov VG, Arkhipova AY, Shaitan KV, Shtil AA, Demina IA. Recombinant Spidroin Films Attenuate Individual Markers of Glucose Induced Aging in NIH 3T3 Fibroblasts. Biochemistry (Mosc) 2020; 85:808-819. [PMID: 33040725 DOI: 10.1134/s0006297920070093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effect of bioresorbable materials on aging in cultured mouse NIH 3T3 fibroblasts treated with elevated glucose concentration was investigated. The cells were grown on films produced from the silkworm fibroin and rS1/9, a recombinant analog of Nephila clavipes spidroin 1. Exposure to 50 mM glucose of the cells grown on uncoated glass support resulted in the cell growth retardation. The average areas of the cells and nuclei and the percentage of apoptotic cells increased, whereas the amount of soluble collagen decreased. In contrast, on the fibroin and spidroin films, the cell density and the percentage of 5-bromo-2'-deoxyuridine (BrdU)-positive cells were higher vs. the cells grown on the glass support. The films protected NIH 3T3 fibroblasts from the glucose-induced death. The most prominent effects on the cell density, BrdU incorporation, and apoptosis prevention were observed in the cells cultured on spidroin films. Unlike the cells grown on glass support (decrease in the soluble collagen production) or fibroin (no effect), production of soluble collagen by the cells grown on spidroin films increased after cell exposure to 50 mM glucose. Molecular analysis demonstrated that 50 mM glucose upregulated phosphorylation of the NFκB heterodimer p65 subunit in the cells grown on the glass support. The treatment of cells grown on fibroin films with 5.5 mM or 50 mM glucose had no effect on p65 phosphorylation. The same treatment decreased p65 phosphorylation in the cells on the spidroin films. These results demonstrate the anti-aging efficacy of biomaterials derived from the silk proteins and suggest that spidroin is more advantageous for tissue engineering and therapy than fibroin.
Collapse
Affiliation(s)
- A M Moysenovich
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - M M Moisenovich
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - A K Sudina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - V V Tatarskiy
- Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.,National University of Science and Technology "MISiS", Moscow, 119049, Russia
| | - A I Khamidullina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - M A Yastrebova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - L I Davydova
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Moscow, 117519, Russia.,NRC "Kurchatov Institute", Moscow, 123182, Russia
| | - V G Bogush
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Moscow, 117519, Russia.,NRC "Kurchatov Institute", Moscow, 123182, Russia
| | - V G Debabov
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Moscow, 117519, Russia.,NRC "Kurchatov Institute", Moscow, 123182, Russia
| | - A Yu Arkhipova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.,Moscow Regional Research and Clinical Institute (MONIKI), Moscow, 129110, Russia
| | - K V Shaitan
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.,Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - A A Shtil
- Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - I A Demina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.,Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia
| |
Collapse
|
16
|
Moisenovich MM, Silachev DN, Moysenovich AM, Arkhipova AY, Shaitan KV, Bogush VG, Debabov VG, Latanov AV, Pevzner IB, Zorova LD, Babenko VA, Plotnikov EY, Zorov DB. Effects of Recombinant Spidroin rS1/9 on Brain Neural Progenitors After Photothrombosis-Induced Ischemia. Front Cell Dev Biol 2020; 8:823. [PMID: 33015039 PMCID: PMC7505932 DOI: 10.3389/fcell.2020.00823] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 08/03/2020] [Indexed: 12/31/2022] Open
Abstract
The existence of niches of stem cells residence in the ventricular-subventricular zone and the subgranular zone in the adult brain is well-known. These zones are the sites of restoration of brain function after injury. Bioengineered scaffolds introduced in the damaged loci were shown to support neurogenesis to the injury area, thus representing a strategy to treat acute neurodegeneration. In this study, we explored the neuroprotective activity of the recombinant analog of Nephila clavipes spidroin 1 rS1/9 after its introduction into the ischemia-damaged brain. We used nestin-green fluorescent protein (GFP) transgenic reporter mouse line, in which neural stem/progenitor cells are easily visualized and quantified by the expression of GFP, to determine the alterations in the dentate gyrus (DG) after focal ischemia in the prefrontal cortex. Changes in the proliferation of neural stem/progenitor cells during the first weeks following photothrombosis-induced brain ischemia and in vitro effects of spidroin rS1/9 in rat primary neuronal cultures were the subject of the study. The introduction of microparticles of the recombinant protein rS1/9 into the area of ischemic damage to the prefrontal cortex leads to a higher proliferation rate and increased survival of progenitor cells in the DG of the hippocampus which functions as a niche of brain stem cells located at a distance from the injury zone. rS1/9 also increased the levels of a mitochondrial probe in DG cells, which may report on either an increased number of mitochondria and/or of the mitochondrial membrane potential in progenitor cells. Apparently, the stimulation of progenitor cells was caused by formed biologically active products stemming from rS1/9 biodegradation which can also have an effect upon the growth of primary cortical neurons, their adhesion, neurite growth, and the formation of a neuronal network. The high biological activity of rS1/9 suggests it as an excellent material for therapeutic usage aimed at enhancing brain plasticity by interacting with stem cell niches. Substances formed from rS1/9 can also be used to enhance primary neuroprotection resulting in reduced cell death in the injury area.
Collapse
Affiliation(s)
| | - Denis N. Silachev
- Laboratory of Mitochondrial Structure and Function, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Moscow, Russia
- Histology, Embryology and Cytology Department, Peoples’ Friendship University of Russia, Moscow, Russia
| | | | | | | | - Vladimir G. Bogush
- National Research Center “Kurchatov Institute” – GOSNIIGENETIKA, Moscow, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Vladimir G. Debabov
- National Research Center “Kurchatov Institute” – GOSNIIGENETIKA, Moscow, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | | | - Irina B. Pevzner
- Laboratory of Mitochondrial Structure and Function, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Moscow, Russia
| | - Ljubava D. Zorova
- Laboratory of Mitochondrial Structure and Function, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Moscow, Russia
| | - Valentina A. Babenko
- Laboratory of Mitochondrial Structure and Function, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Moscow, Russia
| | - Egor Y. Plotnikov
- Laboratory of Mitochondrial Structure and Function, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Moscow, Russia
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Dmitry B. Zorov
- Laboratory of Mitochondrial Structure and Function, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Moscow, Russia
| |
Collapse
|
17
|
Volkov AV, Muraev AA, Zharkova II, Voinova VV, Akoulina EA, Zhuikov VA, Khaydapova DD, Chesnokova DV, Menshikh KA, Dudun AA, Makhina TK, Bonartseva GA, Asfarov TF, Stamboliev IA, Gazhva YV, Ryabova VM, Zlatev LH, Ivanov SY, Shaitan KV, Bonartsev AP. Poly(3-hydroxybutyrate)/hydroxyapatite/alginate scaffolds seeded with mesenchymal stem cells enhance the regeneration of critical-sized bone defect. Mater Sci Eng C Mater Biol Appl 2020; 114:110991. [PMID: 32994018 DOI: 10.1016/j.msec.2020.110991] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/08/2020] [Accepted: 04/18/2020] [Indexed: 01/13/2023]
Abstract
A critical-sized calvarial defect in rats is employed to reveal the osteoinductive properties of biomaterials. In this study, we investigate the osteogenic efficiency of hybrid scaffolds based on composites of a biodegradable and biocompatible polymer, poly(3-hydroxybutyrate) (PHB) with hydroxyapatite (HA) filled with alginate (ALG) hydrogel containing mesenchymal stem cells (MSCs) on the regeneration of the critical-sized radial defect of the parietal bone in rats. The scaffolds based on PHB and PHB/HA with desired shapes were prepared by two-stage salt leaching technique using a mold obtained by three-dimensional printing. To obtain PHB/HA/ALG/MSC scaffolds seeded with MSCs, the scaffolds were filled with ALG hydrogel containing MSCs; acellular PHB/ALG and PHB/ALG filled with empty ALG hydrogel were prepared for comparison. The produced scaffolds have high porosity and irregular interconnected pore structure. PHB/HA scaffolds supported MSC growth and induced cell osteogenic differentiation in a regular medium in vitro that was manifested by an increase in ALP activity and expression of the CD45 phenotype marker. The data of computed tomography and histological studies showed 94% and 92%, respectively, regeneration of critical-sized calvarial bone defect in vivo at 28th day after implantation of MSC-seeded PHB/HA/ALG/MSC scaffolds with 3.6 times higher formation of the main amount of bone tissue at 22-28 days in comparison with acellular PHB/HA/ALG scaffolds that was shown at the first time by fluorescent microscopy using the original technique of intraperitoneal administration of fluorescent dyes to living postoperative rats. The obtained in vivo results can be associated with the MSC-friendly microstructure and in vitro osteogenic properties of PHB/HA base-scaffolds. Thus, the obtained data demonstrate the potential of MSCs encapsulated in the bioactive biopolymer/mineral/hydrogel scaffold to improve the bone regeneration process in critical-sized bone defects.
Collapse
Affiliation(s)
- Alexey V Volkov
- The Peoples' Friendship University of Russia, Miklukho-Maklaya St. 6, 117198 Moscow, Russia; N.N. Priorov National Medical Research Center of Traumatology and Orthopedics of the Ministry of Health of the Russian Federation, Priorova Str. 10, 127299 Moscow, Russia
| | - Alexander A Muraev
- The Peoples' Friendship University of Russia, Miklukho-Maklaya St. 6, 117198 Moscow, Russia; I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya St. 8/2, 119991, Moscow, Russia
| | - Irina I Zharkova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, bld. 12, 119234 Moscow, Russia
| | - Vera V Voinova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, bld. 12, 119234 Moscow, Russia; A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia
| | - Elizaveta A Akoulina
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, bld. 12, 119234 Moscow, Russia; A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia
| | - Vsevolod A Zhuikov
- A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia
| | - Dolgor D Khaydapova
- Faculty of Soil Science, M.V.Lomonosov Moscow State University, Leninskie gory, 1, bld. 12, 119234 Moscow, Russia
| | - Dariana V Chesnokova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, bld. 12, 119234 Moscow, Russia
| | - Ksenia A Menshikh
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, bld. 12, 119234 Moscow, Russia
| | - Andrej A Dudun
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, bld. 12, 119234 Moscow, Russia; A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia
| | - Tatiana K Makhina
- A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia
| | - Garina A Bonartseva
- A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia
| | - Teymur F Asfarov
- The Peoples' Friendship University of Russia, Miklukho-Maklaya St. 6, 117198 Moscow, Russia
| | - Ivan A Stamboliev
- The Peoples' Friendship University of Russia, Miklukho-Maklaya St. 6, 117198 Moscow, Russia
| | - Yulia V Gazhva
- Privolzhsky Research Medical University of the Ministry of Health of the Russian Federation, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia
| | - Valentina M Ryabova
- Privolzhsky Research Medical University of the Ministry of Health of the Russian Federation, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia
| | - Lubomir H Zlatev
- The Peoples' Friendship University of Russia, Miklukho-Maklaya St. 6, 117198 Moscow, Russia
| | - Sergey Y Ivanov
- The Peoples' Friendship University of Russia, Miklukho-Maklaya St. 6, 117198 Moscow, Russia; I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya St. 8/2, 119991, Moscow, Russia
| | - Konstantin V Shaitan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, bld. 12, 119234 Moscow, Russia
| | - Anton P Bonartsev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, bld. 12, 119234 Moscow, Russia; A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia.
| |
Collapse
|
18
|
Colbasevici A, Voskoboynikova N, Orekhov PS, Bozdaganyan ME, Karlova MG, Sokolova OS, Klare JP, Mulkidjanian AY, Shaitan KV, Steinhoff HJ. Lipid dynamics in nanoparticles formed by maleic acid-containing copolymers: EPR spectroscopy and molecular dynamics simulations. Biochim Biophys Acta Biomembr 2020; 1862:183207. [PMID: 31987867 DOI: 10.1016/j.bbamem.2020.183207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/11/2022]
Abstract
Amphiphilic maleic acid-containing copolymers account for a recent methodical breakthrough in the study of membrane proteins. Their application enables a detergent-free extraction of membrane proteins from lipid bilayers, yielding stable water-soluble, discoidal lipid bilayer particles with incorporated proteins, which are wrapped with copolymers. Although many studies confirm the potential of this approach for membrane protein research, the interactions between the maleic acid-containing copolymers and extracted lipids, as well as possible effects of the copolymers on lipid-embedded proteins deserve further scrutinization. Here, we combine electron paramagnetic resonance spectroscopy and coarse-grain molecular dynamics simulations to compare the distribution and dynamics of lipids in lipid particles of phospholipid bilayers encased either by an aliphatic diisobutylene/maleic acid copolymer (DIBMALPs) or by an aromatic styrene/maleic acid copolymer (SMALPs). Nitroxides located at the 5th, 12th or 16th carbon atom positions in phosphatidylcholine-based spin labels experience restrictions of their reorientational motion depending on the type of encasing copolymer. The dynamics of the lipids was less constrained in DIBMALPs than in SMALPs with the affinity of spin labeled lipids to the polymeric rim being more pronounced in SMALPs.
Collapse
Affiliation(s)
| | | | - Philipp S Orekhov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; Sechenov University, Moscow 119146, Russia; Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marine E Bozdaganyan
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Maria G Karlova
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga S Sokolova
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Johann P Klare
- Department of Physics, Osnabrueck University, 49069 Osnabrueck, Germany
| | - Armen Y Mulkidjanian
- Department of Physics, Osnabrueck University, 49069 Osnabrueck, Germany; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Konstantin V Shaitan
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | | |
Collapse
|
19
|
Bessonov IV, Rochev YA, Arkhipova АY, Kopitsyna MN, Bagrov DV, Karpushkin EA, Bibikova TN, Moysenovich AM, Soldatenko AS, Nikishin II, Kotliarova MS, Bogush VG, Shaitan KV, Moisenovich MM. Fabrication of hydrogel scaffolds via photocrosslinking of methacrylated silk fibroin. Biomed Mater 2019; 14:034102. [DOI: 10.1088/1748-605x/ab04e0] [Citation(s) in RCA: 17] [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: 12/26/2022]
|
20
|
Orekhov PS, Bozdaganyan ME, Voskoboynikova N, Mulkidjanian AY, Steinhoff HJ, Shaitan KV. Styrene/Maleic Acid Copolymers Form SMALPs by Pulling Lipid Patches out of the Lipid Bilayer. Langmuir 2019; 35:3748-3758. [PMID: 30773011 DOI: 10.1021/acs.langmuir.8b03978] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Amphiphilic copolymers composed of styrene and maleic acid (SMA) monomers caused a major methodical breakthrough in the study of membrane proteins. They were found to directly release phospholipids and membrane proteins both from artificial and natural lipid bilayers, yielding stable water-soluble discoidal SMA/lipid particles (SMALPs) of uniform size. Although many empirical studies indicate the great potency of SMALPs for membrane protein research, the mechanisms of their formation remain obscure. It is unknown which factors account for the very assembly of SMALPs and govern their uniform size. We have developed a coarse-grained (CG) molecular model of SMA copolymers based on the MARTINI CG force field and used it to probe the behavior of SMA copolymers with varying composition/charge/concentration in solution as well as their interaction with lipid membranes. First, we found that SMA copolymers tend to aggregate in solution into clusters, which could account for the uniform size of SMALPs. Next, molecular dynamics (MD) simulations showed that periodic SMA copolymers with styrene/maleic acid ratios of 2:1 ([SSM] n) and 3:1 ([SSSM] n) differently interacted with lipid bilayers. While clusters of 2:1 SMA copolymers induced membrane poration, the clusters of 3:1 SMA copolymers extracted lipid patches from the membrane yielding SMALP-like structures. Extraction of lipid patches was also observed when we simulated the behavior of 3:1 copolymers with varying lengths and statistical distribution of styrene and MA units. Analysis of MD simulation trajectories and comparison with experimental data indicate that the formation of SMALPs requires copolymer molecules with a sufficient number of units made of more than two sequential styrene monomers.
Collapse
Affiliation(s)
- Philipp S Orekhov
- Department of Biology , Lomonosov Moscow State University , Moscow 119991 , Russia
- Sechenov University , Moscow 119146 , Russia
- Moscow Institute of Physics and Technology , Dolgoprudny 141701 , Russia
| | - Marine E Bozdaganyan
- Department of Biology , Lomonosov Moscow State University , Moscow 119991 , Russia
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies , Federal Medical and Biological Agency of Russia , Moscow 123182 , Russia
| | | | | | | | - Konstantin V Shaitan
- Department of Biology , Lomonosov Moscow State University , Moscow 119991 , Russia
| |
Collapse
|
21
|
Sokolova AI, Pavlova ER, Khramova YV, Klinov DV, Shaitan KV, Bagrov DV. Imaging human keratinocytes grown on electrospun mats by scanning electron microscopy. Microsc Res Tech 2019; 82:544-549. [DOI: 10.1002/jemt.23198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/11/2018] [Accepted: 12/03/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Anastasiia I. Sokolova
- Department of Bioengineering, Faculty of BiologyLomonosov Moscow State University Moscow Russia
- Federal Research Clinical Center of Physical‐Chemical Medicine of the Federal Medical and Biological Agency of Russia Moscow Russia
| | - Elizaveta R. Pavlova
- Department of Bioengineering, Faculty of BiologyLomonosov Moscow State University Moscow Russia
- Moscow Institute of Physics and Technology Dolgoprudny Moscow Region Russia
| | - Yuliya V. Khramova
- Department of Embryology, Faculty of BiologyLomonosov Moscow State University Moscow Russia
| | - Dmitry V. Klinov
- Department of Bioengineering, Faculty of BiologyLomonosov Moscow State University Moscow Russia
| | - Konstantin V. Shaitan
- Federal Research Clinical Center of Physical‐Chemical Medicine of the Federal Medical and Biological Agency of Russia Moscow Russia
| | - Dmitry V. Bagrov
- Department of Bioengineering, Faculty of BiologyLomonosov Moscow State University Moscow Russia
- Federal Research Clinical Center of Physical‐Chemical Medicine of the Federal Medical and Biological Agency of Russia Moscow Russia
| |
Collapse
|
22
|
Orekhov P, Bothe A, Steinhoff HJ, Shaitan KV, Raunser S, Fotiadis D, Schlesinger R, Klare JP, Engelhard M. Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers. Photochem Photobiol 2018; 93:796-804. [PMID: 28500714 DOI: 10.1111/php.12763] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/02/2017] [Indexed: 12/28/2022]
Abstract
Archaeal photoreceptors consist of sensory rhodopsins in complex with their cognate transducers. After light excitation, a two-component signaling chain is activated, which is homologous to the chemotactic signaling cascades in enterobacteria. The latter system has been studied in detail. From structural and functional studies, a picture emerges which includes stable signaling complexes, which assemble to receptor arrays displaying hexagonal structural elements. At this higher order structural level, signal amplification and sensory adaptation occur. Here, we describe electron microscopy data, which show that also the archaeal phototaxis receptors sensory rhodopsin I and II in complex with their cognate transducers can form hexagonal lattices even in the presence of a detergent. This result could be confirmed by molecular dynamics calculations, which revealed similar structural elements. Calculations of the global modes of motion displayed one mode, which resembles the "U"-"V" transition of the NpSRII:NpHtrII complex, which was previously argued to represent a functionally relevant global conformational change accompanying the activation process [Ishchenko et al. (2013) J. Photochem. Photobiol. B 123, 55-58]. A model of cooperativity at the transmembrane level is discussed.
Collapse
Affiliation(s)
- Philipp Orekhov
- Department of Physics, University of Osnabrück, Osnabrück, Germany.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Arne Bothe
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | | | - Stefan Raunser
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Ramona Schlesinger
- Department of Physics, Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Johann P Klare
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Martin Engelhard
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| |
Collapse
|
23
|
Bonartsev AP, Zernov AL, Yakovlev SG, Zharkova II, Myshkina VL, Mahina TK, Bonartseva GA, Andronova NV, Smirnova GB, Borisova JA, Kalishjan MS, Shaitan KV, Treshalina HM. New Poly(3-hydroxybutyrate) Microparticles with Paclitaxel Sustained Release for Intraperitoneal Administration. Anticancer Agents Med Chem 2017; 17:434-441. [PMID: 27141874 DOI: 10.2174/1871520615666160504095433] [Citation(s) in RCA: 7] [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] [Received: 11/09/2015] [Revised: 03/29/2016] [Accepted: 04/30/2016] [Indexed: 11/22/2022]
Abstract
BACKGROUND Poly(hydroxyalkanoates) (PHA) have recently attracted increasing attention due to their biodegradability and high biocompatibility, which makes them suitable for the development of new prolong drug formulations. OBJECTIVE This study was conducted to develop new prolong paclitaxel (PTX) formulation based on poly(3- hydroxybutyrate) (PHB) microparticles. METHOD PHB microparticles loaded with antitumor cytostatic drug PTX were obtained by spray-drying method using Nano Spray Dryer B-90. The PTX release kinetics in vitro from PHB microparticles and their cytotoxity on murine hepatoma cell line MH-22a were studied. Microparticles antitumor activity in vivo was studied using intraperitoneally (i.p.) transplanted tumor models: murine Lewis lung carcinoma and xenografts of human breast cancer RMG1. RESULTS Uniform PTX release from PHB-microparticles during 2 months was observed. PTX-loaded PHB microparticles have demonstrated a significant antitumor activity versus pure drug both in vitro in murine hepatoma cells and in vivo when administered i.p. to mice with murine Lewis lung carcinoma and xenografts of human breast cancer RMG1. CONCLUSION The developed technique of PTX sustained delivery from PHB-microparticles has therapeutic potential as prolong anticancer drug formulation.
Collapse
Affiliation(s)
- Anton P Bonartsev
- Faculty of Biology, Moscow State University, Leninskie gory, 1-12, Moscow 119991, Russian Federation
| | - Anton L Zernov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Sergey G Yakovlev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Irina I Zharkova
- Faculty of Biology, Moscow State University, Moscow, Russian Federation
| | - Vera L Myshkina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatiana K Mahina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Garina A Bonartseva
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Natalia V Andronova
- Federal State Budgetary Institution «N.N. Blokhin Russian Cancer Research Center», Moscow, Russian Federation
| | - Galina B Smirnova
- Federal State Budgetary Institution «N.N. Blokhin Russian Cancer Research Center», Moscow, Russian Federation
| | - Juliya A Borisova
- Federal State Budgetary Institution «N.N. Blokhin Russian Cancer Research Center», Moscow, Russian Federation
| | - Mikhail S Kalishjan
- Federal State Budgetary Institution «N.N. Blokhin Russian Cancer Research Center», Moscow, Russian Federation
| | | | - Helena M Treshalina
- Federal State Budgetary Institution «N.N. Blokhin Russian Cancer Research Center», Moscow, Russian Federation
| |
Collapse
|
24
|
Moldogazieva NT, Shaitan KV, Antonov MY, Mokhosoev IM, Levtsova OV, Terentiev AA. Human EGF-derived direct and reverse short linear motifs: conformational dynamics insight into the receptor-binding residues. J Biomol Struct Dyn 2017; 36:1286-1305. [PMID: 28447543 DOI: 10.1080/07391102.2017.1321502] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Short linear motifs (SLiMs) have been recognized to perform diverse functions in a variety of regulatory proteins through the involvement in protein-protein interactions, signal transduction, cell cycle regulation, protein secretion, etc. However, detailed molecular mechanisms underlying their functions including roles of definite amino acid residues remain obscure. In our previous studies, we demonstrated that conformational dynamics of amino acid residues in oligopeptides derived from regulatory proteins such as alpha-fetoprotein (AFP), carcino-embryonic antigen (CEA), and pregnancy specific β1-glycoproteins (PSGs) contributes greatly to their biological activities. In the present work, we revealed the 22-member linear modules composed of direct and reverse AFP14-20-like heptapeptide motifs linked by CxxGY/FxGx consensus motif within epidermal growth factor (EGF), growth factors of EGF family and numerous regulatory proteins containing EGF-like modules. We showed, first, the existence of similarity in amino acid signatures of both direct and reverse motifs in terms of their physicochemical properties. Second, molecular dynamics (MD) simulation study demonstrated that key receptor-binding residues in human EGF in the aligned positions of the direct and reverse motifs may have similar distribution of conformational probability densities and dynamic behavior despite their distinct physicochemical properties. Third, we found that the length of a polypeptide chain (from 7 to 53 residues) has no effect, while disulfide bridging and backbone direction significantly influence the conformational distribution and dynamics of the residues. Our data may contribute to the atomic level structure-function analysis and protein structure decoding; additionally, they may provide a basis for novel protein/peptide engineering and peptide-mimetic drug design.
Collapse
Affiliation(s)
- Nurbubu T Moldogazieva
- a Department of Biochemistry and Molecular Biology , N.I. Pirogov Russian National Research Medical University , 1 Ostrovityanov str., Moscow 117997 , Russian Federation
| | - Konstantin V Shaitan
- b Faculty of Biology, Department of Bioengineering , M.V. Lomonosov Moscow State University , 1 Vorobyevy Gory, Moscow 119991 , Russian Federation
| | - Mikhail Yu Antonov
- c M.K. Ammosov North-Eastern Federal University , 58 Belinskiy str., Yakutsk 677980 , Republic of Sakha (Yakutia) , Russian Federation
| | - Innokenty M Mokhosoev
- a Department of Biochemistry and Molecular Biology , N.I. Pirogov Russian National Research Medical University , 1 Ostrovityanov str., Moscow 117997 , Russian Federation
| | - Olga V Levtsova
- b Faculty of Biology, Department of Bioengineering , M.V. Lomonosov Moscow State University , 1 Vorobyevy Gory, Moscow 119991 , Russian Federation
| | - Alexander A Terentiev
- a Department of Biochemistry and Molecular Biology , N.I. Pirogov Russian National Research Medical University , 1 Ostrovityanov str., Moscow 117997 , Russian Federation
| |
Collapse
|
25
|
Pavlova ER, Bagrov DV, Kopitsyna MN, Shchelokov DA, Bonartsev AP, Zharkova II, Mahina TK, Myshkina VL, Bonartseva GA, Shaitan KV, Klinov DV. Poly(hydroxybutyrate-co
-hydroxyvalerate) and bovine serum albumin blend prepared by electrospinning. J Appl Polym Sci 2017. [DOI: 10.1002/app.45090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Elizaveta R. Pavlova
- Federal Research Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency of Russia; 1a Malaya Pirogovskaya Street 119435 Moscow Russian Federation
- Moscow Institute of Physics and Technology; 9 Institutsky Per. 141700 Dolgoprudny Moscow Region Russian Federation
| | - Dmitry V. Bagrov
- Federal Research Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency of Russia; 1a Malaya Pirogovskaya Street 119435 Moscow Russian Federation
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University; 119234 Leninskie gory, 1, Bld. 12 Moscow Russian Federation
| | - Maria N. Kopitsyna
- Bauman Moscow State Technical University; 105005 2-ya Baumanskaya Street, 5 Moscow Russian Federation
| | - Dmitry A. Shchelokov
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University; 119234 Leninskie gory, 1, Bld. 12 Moscow Russian Federation
| | - Anton P. Bonartsev
- A. N. Bach Institute of Biochemistry RAS; Leninsky Avenue, 33-2 119071 Moscow Russian Federation
| | - Irina I. Zharkova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University; 119234 Leninskie gory, 1, Bld. 12 Moscow Russian Federation
| | - Tatiana K. Mahina
- A. N. Bach Institute of Biochemistry RAS; Leninsky Avenue, 33-2 119071 Moscow Russian Federation
| | - Vera L. Myshkina
- A. N. Bach Institute of Biochemistry RAS; Leninsky Avenue, 33-2 119071 Moscow Russian Federation
| | - Galina A. Bonartseva
- A. N. Bach Institute of Biochemistry RAS; Leninsky Avenue, 33-2 119071 Moscow Russian Federation
| | - Konstantin V. Shaitan
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University; 119234 Leninskie gory, 1, Bld. 12 Moscow Russian Federation
| | - Dmitry V. Klinov
- Federal Research Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency of Russia; 1a Malaya Pirogovskaya Street 119435 Moscow Russian Federation
| |
Collapse
|
26
|
Allard-Vannier E, Hervé-Aubert K, Kaaki K, Blondy T, Shebanova A, Shaitan KV, Ignatova AA, Saboungi ML, Feofanov AV, Chourpa I. Folic acid-capped PEGylated magnetic nanoparticles enter cancer cells mostly via clathrin-dependent endocytosis. Biochim Biophys Acta Gen Subj 2016; 1861:1578-1586. [PMID: 27919801 DOI: 10.1016/j.bbagen.2016.11.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/18/2016] [Accepted: 11/19/2016] [Indexed: 11/16/2022]
Abstract
BACKGROUND This work is focused on mechanisms of uptake in cancer cells of rationally designed, covalently assembled nanoparticles, made of superparamagnetic iron oxide nanoparticles (SPIONs), fluorophores (doxorubicin or Nile Blue), polyethylene glycol (PEG) and folic acid (FA), referred hereinafter as SFP-FA. METHODS SFP-FA were characterized by DLS, zetametry and fluorescence spectroscopy. The SFP-FA uptake in cancer cells was monitored using fluorescence-based methods like fluorescence-assisted cell sorting, CLSM with single-photon and two-photon excitation. The SFP-FA endocytosis was also analyzed with electron microscopy approaches: TEM, HAADF-STEM and EELS. RESULTS The SFP-FA have zeta potential below -6mW and stable hydrodynamic diameter close to 100nm in aqueous suspensions of pH range from 5 to 8. They contain ca. 109 PEG-FA, 480 PEG-OCH3 and 22-27 fluorophore molecules per SPION. The fluorophores protected under the PEG shell allows a reliable detection of intracellular NPs. SFP-FA readily enter into all the cancer cell lines studied and accumulate in lysosomes, mostly via clathrin-dependent endocytosis, whatever the FR status on the cells. CONCLUSIONS The present study highlights the advantages of rational design of nanosystems as well as the possible involvement of direct molecular interactions of PEG and FA with cellular membranes, not limited to FA-FR recognition, in the mechanisms of their endocytosis. GENERAL SIGNIFICANCE Composition, magnetic and optical properties of the SFP-FA as well their ability to enter cancer cells are promising for their applications in cancer theranosis. Combination of complementary analytical approaches is relevant to understand the nanoparticles behavior in suspension and in contact with cells.
Collapse
Affiliation(s)
- Emilie Allard-Vannier
- Université François Rabelais de Tours, EA 6295 Nanomédicaments et Nanosondes, UFR des Sciences Pharmaceutiques, 31 avenue Monge, F-37200 Tours, France
| | - Katel Hervé-Aubert
- Université François Rabelais de Tours, EA 6295 Nanomédicaments et Nanosondes, UFR des Sciences Pharmaceutiques, 31 avenue Monge, F-37200 Tours, France
| | - Karine Kaaki
- Université François Rabelais de Tours, EA 6295 Nanomédicaments et Nanosondes, UFR des Sciences Pharmaceutiques, 31 avenue Monge, F-37200 Tours, France
| | - Thibaut Blondy
- Université François Rabelais de Tours, EA 6295 Nanomédicaments et Nanosondes, UFR des Sciences Pharmaceutiques, 31 avenue Monge, F-37200 Tours, France
| | - Anastasia Shebanova
- Biological Faculty, Lomonosov Moscow State University, Vorobyevi Gori 1, Moscow 119992, Russia
| | - Konstantin V Shaitan
- Biological Faculty, Lomonosov Moscow State University, Vorobyevi Gori 1, Moscow 119992, Russia
| | - Anastasia A Ignatova
- Biological Faculty, Lomonosov Moscow State University, Vorobyevi Gori 1, Moscow 119992, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Marie-Louise Saboungi
- MPMC-Université Pierre et Marie Curie, Case courrier 115, 4 place Jussieu, F-75252 Paris - Cedex 5, France; Functional Nano & Soft Materials Laboratory (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Alexey V Feofanov
- Biological Faculty, Lomonosov Moscow State University, Vorobyevi Gori 1, Moscow 119992, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Igor Chourpa
- Université François Rabelais de Tours, EA 6295 Nanomédicaments et Nanosondes, UFR des Sciences Pharmaceutiques, 31 avenue Monge, F-37200 Tours, France.
| |
Collapse
|
27
|
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.
Collapse
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.
| |
Collapse
|
28
|
Ermakova NP, Bonartsev AP, Zernov AL, Konyaeva OI, Kulbachevskaya NY, Merkulova IB, Abramovac TV, Chaley VA, Zharkova II, Yakovlev SG, Myshkina VL, Mahina TK, Bonartseva GA, Shaitan KV, Bukhman VM. Preclinical Toxicity of Paclitaxel Biopolymer Formulation. Anticancer Agents Med Chem 2016; 17:1661-1668. [PMID: 27539319 DOI: 10.2174/1871520616666160817104529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 12/03/2015] [Revised: 06/22/2016] [Accepted: 08/11/2016] [Indexed: 11/22/2022]
Abstract
BACKGROUND Poly(hydroxyalkanoates) (PHA) have recently attracted increasing attention due to their biodegradability and high biocompatibility, which makes them suitable for the development of new prolong drug formulations. OBJECTIVE A preclinical toxicology study of paclitaxel biopolymer formulation (PBF) (paclitaxel-loaded poly(3- hydroxybutyrate) (PHB) microparticles) was done in order to assess its safety and to forecast side and toxic effects in a clinical study on patients. METHOD PHB microparticles loaded with antitumor cytostatic drug PTX were obtained by spray-drying method using Nano Spray Dryer B-90. The comprehensive study of cytotoxicity (on bone marrow stem cells), acute and chronic toxicity, allergenic and pyrogenic properties, histological investigation (in mice, rats and rabbits) of obtained PBF was carried out. RESULTS The acute toxicity study showed that PBF is much less toxic in equivalent PTX-content doses than PTX in conventional formulation when administered intraperitoneally to mice and rats. However, the chronic toxicity study showed that at intraperitoneal administration PBF has distinct cumulative properties and toxic effects that prevent PBF from clinical testing in current composition. CONCLUSION Thus, the PBF as a prolong drug needs to correct its parameters for further drug formulation development.
Collapse
Affiliation(s)
- Nadezhda P Ermakova
- FGBU N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Moscow. Russian Federation
| | - Anton P Bonartsev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow. Russian Federation
| | - Anton L Zernov
- A.N. Bach Institute of Biochemistry, The Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow. Russian Federation
| | - Olga I Konyaeva
- FGBU N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Moscow. Russian Federation
| | - Natalia Y Kulbachevskaya
- FGBU N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Moscow. Russian Federation
| | - Irina B Merkulova
- FGBU N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Moscow. Russian Federation
| | - Tatiana V Abramovac
- FGBU N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Moscow. Russian Federation
| | - Vera A Chaley
- FGBU N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Moscow. Russian Federation
| | - Irina I Zharkova
- Department of Bioengineering, Faculty of Biology, Moscow State University, P.O. Box: 119991, Moscow. Russian Federation
| | - Sergey G Yakovlev
- A.N. Bach Institute of Biochemistry, The Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow. Russian Federation
| | - Vera L Myshkina
- A.N. Bach Institute of Biochemistry, The Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow. Russian Federation
| | - Tatiana K Mahina
- A.N. Bach Institute of Biochemistry, The Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow. Russian Federation
| | - Garina A Bonartseva
- A.N. Bach Institute of Biochemistry, The Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow. Russian Federation
| | - Konstantin V Shaitan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow. Russian Federation
| | - Vladimir M Bukhman
- FGBU N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Moscow. Russian Federation
| |
Collapse
|
29
|
Bonartsev AP, Zharkova II, Yakovlev SG, Myshkina VL, Mahina TK, Voinova VV, Zernov AL, Zhuikov VA, Akoulina EA, Ivanova EV, Kuznetsova ES, Shaitan KV, Bonartseva GA. Biosynthesis of poly(3-hydroxybutyrate) copolymers by Azotobacter chroococcum 7B: A precursor feeding strategy. Prep Biochem Biotechnol 2016; 47:173-184. [PMID: 27215309 DOI: 10.1080/10826068.2016.1188317] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 12/24/2022]
Abstract
A precursor feeding strategy for effective biopolymer producer strain Azotobacter chroococcum 7B was used to synthesize various poly(3-hydroxybutyrate) (PHB) copolymers. We performed experiments on biosynthesis of PHB copolymers by A. chroococcum 7B using various precursors: sucrose as the primary carbon source, various carboxylic acids and ethylene glycol (EG) derivatives [diethylene glycol (DEG), triethylene glycol (TEG), poly(ethylene glycol) (PEG) 300, PEG 400, PEG 1000] as additional carbon sources. We analyzed strain growth parameters including biomass and polymer yields as well as molecular weight and monomer composition of produced copolymers. We demonstrated that A. chroococcum 7B was able to synthesize copolymers using carboxylic acids with the length less than linear 6C, including poly(3-hydroxybutyrate-co-3-hydroxy-4-methylvalerate) (PHB-4MHV) using Y-shaped 6C 3-methylvaleric acid as precursor as well as EG-containing copolymers: PHB-DEG, PHB-TEG, PHB-PEG, and PHB-HV-PEG copolymers using short-chain PEGs (with n ≤ 9) as precursors. It was shown that use of the additional carbon sources caused inhibition of cell growth, decrease in polymer yields, fall in polymer molecular weight, decrease in 3-hydroxyvalerate content in produced PHB-HV-PEG copolymer, and change in bacterial cells morphology that were depended on the nature of the precursors (carboxylic acids or EG derivatives) and the timing of its addition to the growth medium.
Collapse
Affiliation(s)
- A P Bonartsev
- a A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences , Moscow , Russia.,b Faculty of Biology , Moscow State University , Moscow , Russia.,c Department of Maxillofacial and Oral Surgery , Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - I I Zharkova
- b Faculty of Biology , Moscow State University , Moscow , Russia
| | - S G Yakovlev
- a A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences , Moscow , Russia.,c Department of Maxillofacial and Oral Surgery , Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - V L Myshkina
- a A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences , Moscow , Russia
| | - T K Mahina
- a A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences , Moscow , Russia
| | - V V Voinova
- b Faculty of Biology , Moscow State University , Moscow , Russia.,c Department of Maxillofacial and Oral Surgery , Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - A L Zernov
- a A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences , Moscow , Russia.,c Department of Maxillofacial and Oral Surgery , Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - V A Zhuikov
- a A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences , Moscow , Russia.,c Department of Maxillofacial and Oral Surgery , Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - E A Akoulina
- a A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences , Moscow , Russia
| | - E V Ivanova
- b Faculty of Biology , Moscow State University , Moscow , Russia
| | - E S Kuznetsova
- b Faculty of Biology , Moscow State University , Moscow , Russia
| | - K V Shaitan
- b Faculty of Biology , Moscow State University , Moscow , Russia
| | - G A Bonartseva
- a A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences , Moscow , Russia
| |
Collapse
|
30
|
Ivanov SY, Bonartsev AP, Gazhva YV, Zharkova II, Mukhametshin RF, Mahina TK, Myshkina VL, Bonartseva GA, Voinova VV, Andreeva NV, Akulina EA, Kharitonova ES, Shaitan KV, Muraev AA. [Development and preclinical studies of insulating membranes based on poly-3-hydroxybutyrate-co-3-hydroxyvalerate for guided bone regeneration]. Biomed Khim 2016; 61:717-23. [PMID: 26716743 DOI: 10.18097/pbmc20156106717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bone tissue damages are one of the dominant causes of temporary disability and developmental disability. Currently, there are some methods of guided bone regeneration employing different osteoplastic materials and insulation membranes used in surgery. In this study, we have developed a method of preparation of porous membranes from the biopolymer poly-3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV), produced by a strain of Azotobacter chroococcum 7B. The biocompatibility of the porous membranes was investigated in vitro using mesenchymal stem cells (MSCs) and in vivo on laboratory animals. The cytotoxicity test showed the possibility of cell attachment on membrane and histological studies confirmed good insulating properties the material. The data obtained demonstrate the high biocompatibility and the potential application of insulating membranes based on PHBV in bone tissue engineering.
Collapse
Affiliation(s)
- S Yu Ivanov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - A P Bonartsev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia; Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yu V Gazhva
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - I I Zharkova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - T K Mahina
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
| | - V L Myshkina
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
| | - G A Bonartseva
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
| | - V V Voinova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - N V Andreeva
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
| | - E A Akulina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - E S Kharitonova
- Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - K V Shaitan
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - A A Muraev
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| |
Collapse
|
31
|
Shaitan KV, Armeev GA, Shaytan AK. [Dynamics of Irreversible Evaporation of a Water-Protein Droplet and a Problem of Structural and Dynamical Experiments with Single Molecules]. Biofizika 2016; 61:213-221. [PMID: 27192821] [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: 06/05/2023]
Abstract
We discuss the effect of isothermal and adiabatic evaporation of water on the state of a water-protein droplet. The discussed problem is of current importance due to development of techniques to perform single molecule experiments using free electron lasers. In such structure-dynamic experiments the delivery of a sample into the X-ray beam is performed using the microdroplet injector. The time between the injection and delivery is in the order of microseconds. In this paper we developed a specialized variant of all-atom molecular dynamics simulations for the study of irreversible isothermal evaporation of the droplet. Using in silico experiments we determined the parameters of isothermal evaporation of the water-protein droplet with the sodium and chloride ions in the concentration range of 0.3 M at different temperatures. The energy of irreversible evaporation determined from in silico experiments at the initial stages of evaporation virtually coincides with the specific heat of evaporation for water. For the kinetics of irreversible adiabatic evaporation an exact analytical solution was obtained in the limit of high thermal conductivity of the droplet (or up to the droplet size of -100 Å). This analytical solution incorporates parameters that are determined using in silico. experiments on isothermal droplet evaporation. We show that the kinetics of adiabatic evaporation and cooling of the droplet scales with the droplet size. Our estimates of the water-protemi droplet. freezing rate in the adiabatic regime in a vacuum chamber show that additional techniques for stabilizing the temperature inside the droplet should be used in order to study the conformational transitions of the protein in single molecules. Isothermal and quasi-isothermal conditions are most suitable for studying the conformational transitions upon object functioning. However, in this case it is necessary to take into account the effects of dehydration and rapid increase of ionic strength in an aqueous microenvironment surrounding the protein.
Collapse
|
32
|
Volokh OI, Bozdaganyan ME, Shaitan KV. [Assessment of Binding Properties of Actinomycin and Its Derivatives with DNA Molecule Using Molecular Dynamics Simulation Method]. Biofizika 2015; 60:1077-1084. [PMID: 26841500] [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: 06/05/2023]
Abstract
Molecular dynamics simulation method was used to assess an influence of actinomycins (antibiotics used in chemotherapy for treatment of some oncology diseases) on DNA fragment elasticity. Also the efficiency of binding of actinomycin to DNA fragment was estimated. Energetic contributions of different substitutions of hydroxyl and amino-group to the phenoxazine ring of actinomycin were studied to analyze dynamic behavior and stability of antibiotic-DNA fragment complexes. Young modulus values were calculated for structures: DNA/DNA-actinomycin/DNA-7-hydroxyactinomycin/DNA-7-aminoactinomycin. Free energy calculations were performed for the formation of actinomycin- and two actinomycin analogues-DNA fragment complexes. Our results suggest that the inserted substitutions stabilize the structure of a DNA fragment via the formation of additional hydrogen bonds.
Collapse
|
33
|
Shumyantseva VV, Shebanova AS, Chalenko YM, Voeikova TA, Kirpichnikov MP, Shaitan KV, Debabov VG. Electroanalysis of Shewanella oneidensis MR-1. DOKL BIOCHEM BIOPHYS 2015; 464:325-8. [PMID: 26518560 DOI: 10.1134/s1607672915050154] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Indexed: 11/22/2022]
Abstract
Electrochemical parameters of bacterial cells Shewanella oneidensis MR-1 were investigated. For registration of the direct electron transfer between S. oneidensis MR-1 and electrode, bacterial cells were pretreated with didodecyldimethylammonium bromide (DDAB), a synthetic membrane-like substance of polycationic nature that exhibits membrane-loosening properties. Such pretreatment of S. oneidensis MR-1 allowed increasing the efficiency of extracellular electron transfer by the proteobacterium due to better availability of electroactive proteins for registration of electron transfer processes. The electroanalysis of bacterial cells S. oneidensis MR-1 under anaerobic conditions allows registering redox-active proteins and biomolecules in the range of potentials of-0.40,-0.16, and-0 V, which corresponds to flavohemoproteins, quinone derivatives, and c-type cytochromes of the external membrane of S. oneidensis MR-1 cells.
Collapse
Affiliation(s)
- V V Shumyantseva
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, ul. Pogodinskaya 10/8, Moscow, 119121, Russia.
| | | | - Ya M Chalenko
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, ul. Pogodinskaya 10/8, Moscow, 119121, Russia
| | - T A Voeikova
- State Research Institute for Genetics and Selection of Industrial Microorganisms, 1 Dorozhnyi pr. 1, Moscow, 117545, Russia
| | | | - K V Shaitan
- Moscow State University, Moscow, 119991, Russia.,Semenov Institute of Chemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow, 119991, Russia
| | - V G Debabov
- State Research Institute for Genetics and Selection of Industrial Microorganisms, 1 Dorozhnyi pr. 1, Moscow, 117545, Russia
| |
Collapse
|
34
|
Orekhov PS, Klose D, Mulkidjanian AY, Shaitan KV, Engelhard M, Klare JP, Steinhoff HJ. Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis. PLoS Comput Biol 2015; 11:e1004561. [PMID: 26496122 PMCID: PMC4651059 DOI: 10.1371/journal.pcbi.1004561] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 09/18/2015] [Indexed: 11/19/2022] Open
Abstract
Motile bacteria and archaea respond to chemical and physical stimuli seeking optimal conditions for survival. To this end transmembrane chemo- and photoreceptors organized in large arrays initiate signaling cascades and ultimately regulate the rotation of flagellar motors. To unravel the molecular mechanism of signaling in an archaeal phototaxis complex we performed coarse-grained molecular dynamics simulations of a trimer of receptor/transducer dimers, namely NpSRII/NpHtrII from Natronomonas pharaonis. Signaling is regulated by a reversible methylation mechanism called adaptation, which also influences the level of basal receptor activation. Mimicking two extreme methylation states in our simulations we found conformational changes for the transmembrane region of NpSRII/NpHtrII which resemble experimentally observed light-induced changes. Further downstream in the cytoplasmic domain of the transducer the signal propagates via distinct changes in the dynamics of HAMP1, HAMP2, the adaptation domain and the binding region for the kinase CheA, where conformational rearrangements were found to be subtle. Overall these observations suggest a signaling mechanism based on dynamic allostery resembling models previously proposed for E. coli chemoreceptors, indicating similar properties of signal transduction for archaeal photoreceptors and bacterial chemoreceptors. Achaea and bacteria can “see” and “sniffle”, they have photo- and chemosensors that measure the environment. On the cell poles, these sensor proteins form large arrays built of several thousands of different receptors. The receptors comprise extracellular or transmembrane sensory domains and elongated homodimeric coiled-coil bundles, which transduce the signals from the membrane across ~20 nm to a conserved cytoplasmic signaling subdomain in an unknown manner. In our study we performed coarse-grained molecular dynamics simulations of the phototactic receptor/transducer complex from Natronomonas pharaonis. Comparing fully methylated and demethylated complexes reveals an interconversion between states of different dynamics along the coiled-coil bundle, which might represent the essential characteristics of the signal transfer from the membrane to the binding sites of the downstream kinase CheA.
Collapse
Affiliation(s)
- Philipp S. Orekhov
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Daniel Klose
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
- Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Martin Engelhard
- Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
| | - Johann P. Klare
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
| | | |
Collapse
|
35
|
Shaitan KV. [The Relaxation Model of Ideal Folding in a Homogeneous Viscous Medium]. Biofizika 2015; 60:843-852. [PMID: 26591594] [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: 06/05/2023]
Abstract
The problem of 3D biopolymer structure formation is investigated by the methods of a theory of stochastic dynamics. The variational principle for. elementary displacement and velocity of conformational movements and its implications for the folding process of the polymer chain in a viscous medium are formulated. The result is a most smooth decrease in potential energy during conformational relaxation of the system (a timid mountain-skier principle), which is in consistence with the Onsager principle for kinetics in weakly nonequilibrium systems. The model is in accordance with the results of molecular simulations of the similar systems. The relationship between the structure of the multidimensional potential energy surface and folding kinetics is discussed. The model of a parabolic energy funnel formed by non-bonded interactions is developed. The folding kinetics in the parabolic model of energy funnel is almost close to exponential law.
Collapse
|
36
|
Shaitan KV, Orshanskiy IA. [Molecular Dynamics of Self-assembling and Rheology of Superhelical Structure of Protofiber of Spider Web]. Biofizika 2015; 60:656-660. [PMID: 26394464] [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: 06/05/2023]
Abstract
In this study we suggested a dynamics simulation for the formation of protofiber of spider web nanofiber. It was shown that a bundle of parallel polyalanine β-strands of sufficient length is arranged through self-assembly into a stable right-handed super helix. By numerical analysis we investigated the rheological properties and provided in nonlinear regime a generalization of the model of Singer for description of the rheological behaviour of super helix.
Collapse
|
37
|
Shaitan KV, Fedik IV. [Molecular Dynamics Simulations of Self-organization of the Structure of Model Biomimetic Polymers]. Biofizika 2015; 60:421-427. [PMID: 26349205] [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: 06/05/2023]
Abstract
By using the molecular dynamics method the problem of macromolecules' folding into spatial structures is examined. The freely jointed polymer chain with strong covalent bonds where van-der-Waals forces act between the units of the chain is considered. Conditions for the formation of different spatial structures resembling the structures called alpha-helices, beta-sheets and double helices found in biomolecular systems are determined.
Collapse
|
38
|
Orshanskiy IA, Popinako AV, Volokh OI, Shaitan KV, Sokolova OS. [Molecular Dynamics of N- and C-terminal Interactions during Autoinhibition and Activation of Formin mDial]. Biofizika 2015; 60:451-456. [PMID: 26349208] [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: 06/05/2023]
Abstract
With the method of molecular dynamics, pairs of amino acid residues have been identified on the surface of the interacting formin mDial domains: DID-DAD, which are responsible for the autoinhibition of formin, and the GTPase Rho-DID domain, and control activation. It was found that the most stable interactions are ionic interactions between Glu178 residue and Arg248 residue, as well as hydrophobic interactions between Thr175 and Phe247. The strongest interactions proved to be between the DID domain with Rho-GTPase. These interactions are mediated by specific triple ionic interactions between positively charged amino acid in Rho, and a triplet of amino acids in DID, consisting of two negatively charged amino acids, separated by one uncharged. Binding sites for Rho-GTPase and DAD partially overlap, but various amino acids on the DID participate in interactions with different domains. We discuss the possible conformational changes in formin domains during activation and inactivation.
Collapse
|
39
|
Zharkova II, Staroverova OV, Voinova VV, Andreeva NV, Shushckevich AM, Sklyanchuk ED, Kuzmicheva GM, Bespalova AE, Akulina EA, Shaitan KV, Okhlov AA. [Biocompatibility of electrospun poly(3-hydroxybutyrate) and its composites scaffolds for tissue engineering]. Biomed Khim 2014; 60:553-60. [PMID: 25386884 DOI: 10.18097/pbmc20146005553] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Development of biodegradable polymers-based scaffolds for tissue engineering is a promising trend in bioengineering. The electrospun scaffolds from poly(3-hydroxybutyrate) (PHB) were produced using different additives that changed the physical and chemical characteristics of the products. As a result, the construct consisting of interwoven threads of different diameter (0.8-3.4 mm) were obtained, the smallest diameter was observed in the threads from the PHB using tetrabutilammonium iodide (TBAI) and titanium oxide II (TiO2) as additives. Mesenchymal stem cells (MSC) were cultivated on the scaffolds for the biocompatibility evaluation of obtained materials. Cells viability was determined by the XTT assay test. It was shown that the scaffold from the interwoven threads of lowest diameter is most favorable for MSC growth in comparison with the polymer film and scaffolds from the threads of larger diameter. Thus, it was shown that the biocompatibility of electrospun PHB scaffolds depended on their microstructure. The obtained data can be used for development of scaffolds for tissue engineering.
Collapse
|
40
|
Bozdaganyan ME, Orekhov PS, Shaytan AK, Shaitan KV. Comparative computational study of interaction of C60-fullerene and tris-malonyl-C60-fullerene isomers with lipid bilayer: relation to their antioxidant effect. PLoS One 2014; 9:e102487. [PMID: 25019215 PMCID: PMC4097404 DOI: 10.1371/journal.pone.0102487] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/19/2014] [Indexed: 11/28/2022] Open
Abstract
Oxidative stress induced by excessive production of reactive oxygen species (ROS) has been implicated in the etiology of many human diseases. It has been reported that fullerenes and some of their derivatives–carboxyfullerenes–exhibits a strong free radical scavenging capacity. The permeation of C60-fullerene and its amphiphilic derivatives–C3-tris-malonic-C60-fullerene (C3) and D3-tris-malonyl-C60-fullerene (D3)–through a lipid bilayer mimicking the eukaryotic cell membrane was studied using molecular dynamics (MD) simulations. The free energy profiles along the normal to the bilayer composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) for C60, C3 and D3 were calculated. We found that C60 molecules alone or in clusters spontaneously translocate to the hydrophobic core of the membrane and stay inside the bilayer during the whole period of simulation time. The incorporation of cluster of fullerenes inside the bilayer changes properties of the bilayer and leads to its deformation. In simulations of the tris-malonic fullerenes we discovered that both isomers, C3 and D3, adsorb at the surface of the bilayer but only C3 tends to be buried in the area of the lipid headgroups forming hydrophobic contacts with the lipid tails. We hypothesize that such position has implications for ROS scavenging mechanism in the specific cell compartments.
Collapse
Affiliation(s)
| | - Philipp S. Orekhov
- Biological department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey K. Shaytan
- Biological department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin V. Shaitan
- Biological department, M.V. Lomonosov Moscow State University, Moscow, Russia
- * E-mail:
| |
Collapse
|
41
|
Novikov GV, Sivozhelezov VS, Shaitan KV. [Influence of the orthosteric ligands binding on the conformational dynamics of the B-2-adrenergic receptor by means of essential dynamics sampling simulation]. Mol Biol (Mosk) 2014; 48:463-479. [PMID: 25831896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The influence of binding of the orthosteric ligands on the conformational dynamics of the beta-2-adrenoreceptor was identified using the molecular dynamics method. It was found that there was alittle fraction of the active states of the receptor in its apo (ligand free) ensemble. Analysis of the MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion of its VI helix. Thus receptor's constitutive activity is the direct result of its conformational dynamics. On other hand binding of the full agonist resulted in the significant shift of the initial equilibrium towards its active state. Finally binding of the inverse agonist stabilized receptor in its inactive state. Its likely that the binding of the inverse agonists might be the universal way of the constitutive activity inhibition. Our results indicate that ligand binding rather redistribute prexisting conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) than cause induced fit in it. Therefore ensemble of the biological-relevant receptor conformations have been encoded in its spatial structure and individual conformations from that ensemble might be used by the cell according to the physiological behavior.
Collapse
|
42
|
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.
Collapse
|
43
|
Novikov GV, Sivozhelezov VS, Kolesnikov SS, Shaitan KV. Investigation of the influence of external factors on the conformational dynamics of rhodopsin-like receptors by means of molecular dynamics simulation. J Recept Signal Transduct Res 2014; 34:104-18. [PMID: 24495290 DOI: 10.3109/10799893.2013.863918] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The study reports about the influence of binding of orthosteric ligands on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics (MD) simulation, we found that there was a little fraction of active states of the receptor in its apo (ligand-free) ensemble. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus, receptor's constitutive activity directly results from its conformational dynamics. On the other hand, the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behavior.
Collapse
Affiliation(s)
- Gleb V Novikov
- Institute of Cell Biophysics, Pushchino, Russian Academy of Sciences , Russian Federation and
| | | | | | | |
Collapse
|
44
|
Bozdaganyan M, Bragazzi NL, Pechkova E, Shaitan KV, Nicolini C. Identification of Best Protein Crystallization Methods by Molecular Dynamics (MD). Crit Rev Eukaryot Gene Expr 2014; 24:311-24. [DOI: 10.1615/critreveukaryotgeneexpr.2014010201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
45
|
Bonartsev AP, Yakovlev SG, Zharkova II, Boskhomdzhiev AP, Bagrov DV, Myshkina VL, Makhina TK, Kharitonova EP, Samsonova OV, Feofanov AV, Voinova VV, Zernov AL, Efremov YM, Bonartseva GA, Shaitan KV, Kirpichnikov MP. Cell attachment on poly(3-hydroxybutyrate)-poly(ethylene glycol) copolymer produced by Azotobacter chroococcum 7B. BMC Biochem 2013; 14:12. [PMID: 23692611 PMCID: PMC3724502 DOI: 10.1186/1471-2091-14-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 04/19/2013] [Indexed: 11/18/2022]
Abstract
BACKGROUND The improvement of biomedical properties, e.g. biocompatibility, of poly(3-hydroxyalkanoates) (PHAs) by copolymerization is a promising trend in bioengineering. We used strain Azotobacter chroococcum 7B, an effective producer of PHAs, for biosynthesis of not only poly(3-hydroxybutyrate) (PHB) and its main copolymer, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB-HV), but also alternative copolymer, poly(3-hydroxybutyrate)-poly(ethylene glycol) (PHB-PEG). RESULTS In biosynthesis we used sucrose as the primary carbon source and valeric acid or poly(ethylene glycol) 300 (PEG 300) as additional carbon sources. The chemical structure of PHB-PEG and PHB-HV was confirmed by 1H nuclear-magnetic resonance (1H NMR) analysis. The physico-chemical properties (molecular weight, crystallinity, hydrophilicity, surface energy) and surface morphology of films from PHB copolymers were studied. To study copolymers biocompatibility in vitro the protein adsorption and COS-1 fibroblasts growth on biopolymer films by XTT assay were analyzed. Both copolymers had changed physico-chemical properties compared to PHB homopolymer: PHB-HV and PHB-PEG had less crystallinity than PHB; PHB-HV was more hydrophobic than PHB in contrast to PHB-PEG appeared to have greater hydrophilicity than PHB; whereas the morphology of polymer films did not differ significantly. The protein adsorption to PHB-PEG was greater and more uniform than to PHB and PHB-PEG copolymer promoted better growth of COS-1 fibroblasts compared with PHB homopolymer. CONCLUSIONS Thus, despite low EG-monomers content in bacterial origin PHB-PEG copolymer, this polymer demonstrated significant improvement in biocompatibility in contrast to PHB and PHB-HV copolymers, which may be coupled with increased protein adsorption and hydrophilicity of PEG-containing copolymer.
Collapse
Affiliation(s)
- Anton P Bonartsev
- Faculty of Biology, M.V.Lomonosov Moscow State University, Leninskie gory, 1-12, Moscow, 119236, Russia
- A.N.Bach Institute of Biochemistry RAS, Leninskii av., 33-2, Moscow, 119071, Russia
| | - Sergey G Yakovlev
- Faculty of Biology, M.V.Lomonosov Moscow State University, Leninskie gory, 1-12, Moscow, 119236, Russia
- A.N.Bach Institute of Biochemistry RAS, Leninskii av., 33-2, Moscow, 119071, Russia
| | - Irina I Zharkova
- Faculty of Biology, M.V.Lomonosov Moscow State University, Leninskie gory, 1-12, Moscow, 119236, Russia
| | | | - Dmitrii V Bagrov
- Faculty of Biology, M.V.Lomonosov Moscow State University, Leninskie gory, 1-12, Moscow, 119236, Russia
| | - Vera L Myshkina
- A.N.Bach Institute of Biochemistry RAS, Leninskii av., 33-2, Moscow, 119071, Russia
| | - Tatiana K Makhina
- A.N.Bach Institute of Biochemistry RAS, Leninskii av., 33-2, Moscow, 119071, Russia
| | - Elena P Kharitonova
- Faculty of Physics, M.V.Lomonosov Moscow State University, Leninskie gory, 1-2, Moscow, 119991, Russia
| | - Olga V Samsonova
- Faculty of Biology, M.V.Lomonosov Moscow State University, Leninskie gory, 1-12, Moscow, 119236, Russia
| | - Alexey V Feofanov
- Faculty of Biology, M.V.Lomonosov Moscow State University, Leninskie gory, 1-12, Moscow, 119236, Russia
| | - Vera V Voinova
- Faculty of Biology, M.V.Lomonosov Moscow State University, Leninskie gory, 1-12, Moscow, 119236, Russia
- A.N.Bach Institute of Biochemistry RAS, Leninskii av., 33-2, Moscow, 119071, Russia
| | - Anton L Zernov
- Faculty of Biology, M.V.Lomonosov Moscow State University, Leninskie gory, 1-12, Moscow, 119236, Russia
- A.N.Bach Institute of Biochemistry RAS, Leninskii av., 33-2, Moscow, 119071, Russia
| | - Yurii M Efremov
- Faculty of Biology, M.V.Lomonosov Moscow State University, Leninskie gory, 1-12, Moscow, 119236, Russia
| | - Garina A Bonartseva
- A.N.Bach Institute of Biochemistry RAS, Leninskii av., 33-2, Moscow, 119071, Russia
| | - Konstantin V Shaitan
- Faculty of Biology, M.V.Lomonosov Moscow State University, Leninskie gory, 1-12, Moscow, 119236, Russia
| | - Michail P Kirpichnikov
- Faculty of Biology, M.V.Lomonosov Moscow State University, Leninskie gory, 1-12, Moscow, 119236, Russia
| |
Collapse
|
46
|
Novikov GV, Sivozhelezov VS, Shaitan KV. Study of structural dynamics of ligand-activated membrane receptors by means of principal component analysis. Biochemistry (Mosc) 2013; 78:403-11. [PMID: 23590443 DOI: 10.1134/s0006297913040093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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
The structural dynamics of three different ligand-activated G-protein coupled receptors (GPCRs) and the photoreactive receptor rhodopsin from mammals were comparatively studied. As a result, diagrams demonstrating the main structural differences between the studied membrane receptors were obtained. These diagrams represent the projection of the crystal structures of rhodopsin photointermediates and ligand-activated receptors onto the plane defined by the principal components. Thus, we were able to associate the activation process of the receptors with large-scale movements of their individual transmembrane (TM) domains. In addition, the dynamics of extracellular loops of ligand-activated receptors responsible for recognition and initial binding of ligands was studied. Based on these results, two parameters of functionally significant structural dynamics of membrane receptors can be thoroughly analyzed simultaneously - movements of individual TM helices and of extracellular loops.
Collapse
Affiliation(s)
- G V Novikov
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | | | | |
Collapse
|
47
|
Efremov YM, Dokrunova AA, Bagrov DV, Kudryashova KS, Sokolova OS, Shaitan KV. The effects of confluency on cell mechanical properties. J Biomech 2013; 46:1081-7. [PMID: 23453395 DOI: 10.1016/j.jbiomech.2013.01.022] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 12/27/2012] [Accepted: 01/21/2013] [Indexed: 11/17/2022]
Abstract
Mechanical properties of cells depend on various external and internal factors, like substrate stiffness and surface modifications, cell ageing and disease state. Some other currently unknown factors may exist. In this study we used force spectroscopy by AFM, confocal microscopy and flow cytometry to investigate the difference between single non-confluent and confluent (in monolayer) Vero cells. In all cases the stiffness values were fitted by log-normal rather than normal distribution. Log-normal distribution was also found for an amount of cortical actin in cells by flow cytometry. Cells in the monolayer were characterized by a significantly lower (1.4-1.7 times) Young's modulus and amount of cortical actin than in either of the single non-confluent cells or cells migrating in the experimental wound. Young's modulus as a function of indentation speed followed a weak power law for all the studied cell states, while the value of the exponent was higher for cells growing in monolayer. These results show that intercellular contacts and cell motile state significantly influence the cell mechanical properties.
Collapse
Affiliation(s)
- Yu M Efremov
- M.V. Lomonosov Moscow State University, Faculty of Biology, Department of Bioengineering, Leninskie Gory, 1/73, 111991 Moscow, Russia.
| | | | | | | | | | | |
Collapse
|
48
|
Orekhov PS, Shaitan KV, Mulkidjanian AY. Inter- and Intra-Monomeric Communication in the Cytochrome Bc1 Complex: A Molecular Dynamics Study. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3653] [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: 10/27/2022] Open
|
49
|
Moldogazieva NT, Terentiev AA, Antonov MY, Kazimirsky AN, Shaitan KV. Correlation between biological activity and conformational dynamics properties of tetra- and pentapeptides derived from fetoplacental proteins. Biochemistry (Mosc) 2012; 77:469-84. [PMID: 22813588 DOI: 10.1134/s0006297912050070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [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
In this work, using molecular dynamics simulation, we study conformational and dynamic properties of biologically active penta- and tetrapeptides derived from fetoplacental proteins such as alpha-fetoprotein, pregnancy specific β1-glycoprotein, and carcinoembryonic antigen. Existence of correlation between flexibility of peptide backbone and biological activity of the investigated peptides was shown. It was also demonstrated that flexibility of peptide backbone depends not only on its length, but also on the presence of reactive functional groups in amino acid side chains that participate in intramolecular interactions. Peptides that demonstrate similar biological effects in regulation of proliferation of lymphocytes and expression of differentiation antigens on their surface (LDSYQCT, PYECE, YECE, and YVCE) are characterized by rigidity of their peptide backbone. Increased backbone flexibility in peptides PYQCE, YQCE, SYKCE, YQCT, YQCS, YVCS, YACS, and YACE is correlated with decreased biological activity. Conformational mobility of amino acid residues does not depend on physicochemical properties only, but also on intramolecular interactions. So, evolutionary restrictions should exist to maintain such interactions in the environment of functionally important sites.
Collapse
Affiliation(s)
- N T Moldogazieva
- Russian State Medical University, ul. Ostrovityanova 1, 117997 Moscow, Russia.
| | | | | | | | | |
Collapse
|
50
|
Terentiev AA, Moldogazieva NT, Levtsova OV, Maximenko DM, Borozdenko DA, Shaitan KV. Modeling of three dimensional structure of human alpha-fetoprotein complexed with diethylstilbestrol: docking and molecular dynamics simulation study. J Bioinform Comput Biol 2012; 10:1241012. [PMID: 22809347 DOI: 10.1142/s0219720012410120] [Citation(s) in RCA: 9] [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] [Indexed: 11/18/2022]
Abstract
It has been long experimentally demonstrated that human alpha-fetoprotein (HAFP) has an ability to bind immobilized estrogens with the most efficiency for synthetic estrogen analog - diethylstilbestrol (DES). However, the question remains why the human AFP (HAFP), unlike rodent AFP, cannot bind free estrogens. Moreover, despite the fact that AFP was first discovered more than 50 years ago and is presently recognized as a "golden standard" among onco-biomarkers, its three-dimensional (3D) structure has not been experimentally solved yet. In this work using MODELLER program, we generated 3D model of HAFP on the basis of homology with human serum albumin (HSA) and Vitamin D-binding protein (VTDB) with subsequent molecular docking of DES to the model structure and molecular dynamics (MD) simulation study of the complex obtained. The model constructed has U-shaped structure in which a cavity may be distinguished. In this cavity the putative estrogen-binding site is localized. Validation by RMSD calculation and with the use of PROCHECK program showed good quality of the model and stability of extended region of four alpha-helical structures that contains putative hormone-binding residues. Data extracted from MD simulation trajectory allow proposing two types of interactions between amino acid residues of HAFP and DES molecule: (1) hydrogen bonding with involvement of residues S445, R452, and E551; (2) hydrophobic interactions with participation of L138, M448, and M548 residues. A suggestion is made that immobilization of the hormone using a long spacer provides delivery of the estrogen molecule to the binding site and, thereby, facilitates interaction between HAFP and the hormone.
Collapse
Affiliation(s)
- Alexander A Terentiev
- Department of Biochemistry, Russian State Medical University, Moscow 117997, Russia.
| | | | | | | | | | | |
Collapse
|