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Galzitskaya OV, Grishin SY, Glyakina AV, Dovidchenko NV, Konstantinova AV, Kravchenko SV, Surin AK. The Strategies of Development of New Non-Toxic Inhibitors of Amyloid Formation. Int J Mol Sci 2023; 24:ijms24043781. [PMID: 36835194 PMCID: PMC9964835 DOI: 10.3390/ijms24043781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
In recent years, due to the aging of the population and the development of diagnostic medicine, the number of identified diseases associated with the accumulation of amyloid proteins has increased. Some of these proteins are known to cause a number of degenerative diseases in humans, such as amyloid-beta (Aβ) in Alzheimer's disease (AD), α-synuclein in Parkinson's disease (PD), and insulin and its analogues in insulin-derived amyloidosis. In this regard, it is important to develop strategies for the search and development of effective inhibitors of amyloid formation. Many studies have been carried out aimed at elucidating the mechanisms of amyloid aggregation of proteins and peptides. This review focuses on three amyloidogenic peptides and proteins-Aβ, α-synuclein, and insulin-for which we will consider amyloid fibril formation mechanisms and analyze existing and prospective strategies for the development of effective and non-toxic inhibitors of amyloid formation. The development of non-toxic inhibitors of amyloid will allow them to be used more effectively for the treatment of diseases associated with amyloid.
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Affiliation(s)
- Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
- Correspondence:
| | - Sergei Y. Grishin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Anna V. Glyakina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Mathematical Problems of Biology RAS, The Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Nikita V. Dovidchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Anastasiia V. Konstantinova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Faculty of Biotechnology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sergey V. Kravchenko
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
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Glyakina AV, Galzitskaya OV. Structural and functional analysis of actin point mutations leading to nemaline myopathy to elucidate their role in actin function. Biophys Rev 2022; 14:1527-1538. [PMID: 36659996 PMCID: PMC9842827 DOI: 10.1007/s12551-022-01027-4] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2022] [Indexed: 12/15/2022] Open
Abstract
In this work, we analyzed 78 mutations in the actin protein that cause the disease nemaline myopathy. We analyzed how these mutations are distributed in important regions of the actin molecule (folding nucleus, core of the filament, amyloidogenic regions, disordered regions, regions involved in interaction with other proteins). It was found that 54 mutations (43 residues) fall into the folding nucleus (Ф ≥ 0.5), 11 mutations (10 residues) into the filament core, 14 mutations into the amyloidogenic regions (11 residues), 14 mutations (9 residues) in the unstructured regions, and 24 mutations (22 residues) in regions involved in interaction with other proteins. It was also found that the occurrence of single mutations G44V, V45F, T68I, P72R, K338I and S350L leads to the appearance of new amyloidogenic regions that are not present in native actin. The largest number of mutations (54 out of 78) occurs in the folding nucleus; these mutations are important for folding and therefore can affect the protein folding rate. We have shown that almost all of the considered mutations are associated with the structural characteristics of the actin molecule, and some of the residues we have considered have several important characteristics.
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Affiliation(s)
- Anna V. Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia ,Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Russia
| | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia ,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
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Glyakina AV, Balabaev NK, Galzitskaya OV. Determination of the Most Stable Packing of Peptides from Ribosomal S1 Protein, Protein Bgl2p, and Aβ peptide in β-layers During Molecular Dynamics Simulations. Methods Mol Biol 2022; 2340:221-233. [PMID: 35167077 DOI: 10.1007/978-1-0716-1546-1_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Our task was to determine the most stable packing of peptides in β-layers to construct an oligomer structure for fibril growth. The β-layers consisting of eight short peptides with the amino acid sequences IVRGVVVAID, VDSWNVLVAG (VESWNVLVAG), KLVFFAEDVG, and IIGLMVGGVV were built. These sequences correspond to the amyloidogenic regions of ribosomal S1 protein from E. coli, protein glucantransferase Bgl2p from the yeast cell wall, and Aβ peptide. First, the amyloidogenic regions were predicted theoretically, and then were confirmed experimentally. Four β-layers with different orientation of the peptides in the layers and the layers relative to each other were constructed. To determine the most stable packing of β-strands, the molecular dynamic (MD) simulations in explicit water were carried out. Two charge states (pH3 and pH5) for each β-layer were considered. The fraction of the secondary structure was a measure of stability for β-layers. β-Layers, in which β-strands are antiparallel relative to each other, were the most stable. Using this packing for β-strands, we constructed the oligomer structures and also checked their stability by using MD simulations.
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Affiliation(s)
- Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
| | - Nikolai K Balabaev
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia. .,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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4
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Glyakina AV, Pavlov CD, Sopova JV, Gainetdinov RR, Leonova EI, Galzitskaya OV. Search for Structural Basis of Interactions of Biogenic Amines with Human TAAR1 and TAAR6 Receptors. Int J Mol Sci 2021; 23:ijms23010209. [PMID: 35008636 PMCID: PMC8745718 DOI: 10.3390/ijms23010209] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022] Open
Abstract
The identification and characterization of ligand-receptor binding sites are important for drug development. Trace amine-associated receptors (TAARs, members of the class A GPCR family) can interact with different biogenic amines and their metabolites, but the structural basis for their recognition by the TAARs is not well understood. In this work, we have revealed for the first time a group of conserved motifs (fingerprints) characterizing TAARs and studied the docking of aromatic (β-phenylethylamine, tyramine) and aliphatic (putrescine and cadaverine) ligands, including gamma-aminobutyric acid, with human TAAR1 and TAAR6 receptors. We have identified orthosteric binding sites for TAAR1 (Asp68, Asp102, Asp284) and TAAR6 (Asp78, Asp112, Asp202). By analyzing the binding results of 7500 structures, we determined that putrescine and cadaverine bind to TAAR1 at one site, Asp68 + Asp102, and to TAAR6 at two sites, Asp78 + Asp112 and Asp112 + Asp202. Tyramine binds to TAAR6 at the same two sites as putrescine and cadaverine and does not bind to TAAR1 at the selected Asp residues. β-Phenylethylamine and gamma-aminobutyric acid do not bind to the TAAR1 and TAAR6 receptors at the selected Asp residues. The search for ligands targeting allosteric and orthosteric sites of TAARs has excellent pharmaceutical potential.
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Affiliation(s)
- Anna V. Glyakina
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia;
| | - Constantine D. Pavlov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia;
| | - Julia V. Sopova
- Institute of Translational Biomedicine, St. Petersburg State University, 199034 St. Petersburg, Russia; (J.V.S.); (R.R.G.)
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Raul R. Gainetdinov
- Institute of Translational Biomedicine, St. Petersburg State University, 199034 St. Petersburg, Russia; (J.V.S.); (R.R.G.)
| | - Elena I. Leonova
- Institute of Translational Biomedicine, St. Petersburg State University, 199034 St. Petersburg, Russia; (J.V.S.); (R.R.G.)
- Animal Genetic Technologies Department, University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Correspondence: (E.I.L.); (O.V.G.)
| | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia;
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Correspondence: (E.I.L.); (O.V.G.)
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Kurpe SR, Grishin SY, Glyakina AV, Slizen MV, Panfilov AV, Kochetov AP, Surin AK, Kobyakova MI, Fadeev RS, Galzitskaya OV. [Antibacterial effects of peptides synthesized based on the sequence of ribosome protein S1]. Biomed Khim 2021; 67:231-243. [PMID: 34142530 DOI: 10.18097/pbmc20216703231] [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] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Antibiotic resistance of bacteria is a topical problem on a global scale. Sometimes vigorous human activity leads to an increase in the number of bacteria carrying resistance genes in the environment. Antimicrobial peptides (AMPs) and similar compounds are potential candidates for combating antibiotic-resistant bacteria. Previously, we proposed and successfully tested on Thermus thermophilus a new mechanism of AMP action. This mechanism of directed coaggregation is based on the interaction of a peptide capable of forming fibrils with a target protein. In this work, we discuss the criteria for choosing a target for the targeted action of AMP, describe the features of the "parental" S1 ribosomal proteins T. thermophilus and Escherichia coli and the studied peptides using bioinformatic analysis methods, assess the antimicrobial effect of the synthesized peptides on a model organism of E. coli and cytotoxicity on cells of human fibroblasts. The obtained results will be important for the creation of new AMPs for pathogenic organisms.
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Affiliation(s)
- S R Kurpe
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - S Yu Grishin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - A V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Russia
| | - M V Slizen
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - A V Panfilov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - A P Kochetov
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
| | - A K Surin
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia; State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - M I Kobyakova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - R S Fadeev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - O V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
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Glyakina AV, Galzitskaya OV. Bioinformatics Analysis of Actin Molecules: Why Quantity Does Not Translate Into Quality? Front Genet 2020; 11:617763. [PMID: 33362870 PMCID: PMC7758494 DOI: 10.3389/fgene.2020.617763] [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: 10/15/2020] [Accepted: 11/20/2020] [Indexed: 11/13/2022] Open
Abstract
It is time to review all the available data and find the distinctive characteristics of actin that make it such an important cell molecule. The presented double-stranded organization of filamentous actin cannot explain the strong polymorphism of actin fibrils. In this work, we performed bioinformatics analysis of a set of 296 amino acid actin sequences from representatives of different classes of the Chordate type. Based on the results of the analysis, the degree of conservatism of the primary structure of this protein in representatives of the Chordate type was determined. In addition, 155 structures of rabbit actin obtained using X-ray diffraction analysis and electron microscopy have been analyzed over the past 30 years. From pairwise alignments and the calculation of root-mean-square deviations (RMSDs) for these structures, it follows that they are very similar to each other without correlation with the structure resolution and the reconstruction method: the RMSDs for 11,781 pairs did not exceed 3 Å. It turned out that in rabbit actin most of the charged amino acid residues are located inside the protein, which is not typical for the protein structure. We found that two of six exon regions correspond to structural subdomains. To test the double-stranded organization of the actin structure, it is necessary to use new approaches and new techniques, taking into account our new data obtained from the structural analysis of actin.
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Affiliation(s)
- Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
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Glyakina AV, Surin AK, Grishin SY, Selivanova OM, Suvorina MY, Bobyleva LG, Vikhlyantsev IM, Galzitskaya OV. New Model for Stacking Monomers in Filamentous Actin from Skeletal Muscles of Oryctolagus cuniculus. Int J Mol Sci 2020; 21:ijms21218319. [PMID: 33171915 PMCID: PMC7664232 DOI: 10.3390/ijms21218319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/23/2020] [Accepted: 11/03/2020] [Indexed: 12/27/2022] Open
Abstract
To date, some scientific evidence (limited proteolysis, mass spectrometry analysis, electron microscopy (EM)) has accumulated, which indicates that the generally accepted model of double-stranded of filamentous actin (F-actin) organization in eukaryotic cells is not the only one. This entails an ambiguous understanding of many of the key cellular processes in which F-actin is involved. For a detailed understanding of the mechanism of F-actin assembly and actin interaction with its partners, it is necessary to take into account the polymorphism of the structural organization of F-actin at the molecular level. Using electron microscopy, limited proteolysis, mass spectrometry, X-ray diffraction, and structural modeling we demonstrated that F-actin presented in the EM images has no double-stranded organization, the regions of protease resistance are accessible for action of proteases in F-actin models. Based on all data, a new spatial model of filamentous actin is proposed, and the F-actin polymorphism is discussed.
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Affiliation(s)
- Anna V. Glyakina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (A.V.G.); (A.K.S.); (S.Y.G.); (O.M.S.); (M.Y.S.)
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (A.V.G.); (A.K.S.); (S.Y.G.); (O.M.S.); (M.Y.S.)
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Sergei Yu. Grishin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (A.V.G.); (A.K.S.); (S.Y.G.); (O.M.S.); (M.Y.S.)
| | - Olga M. Selivanova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (A.V.G.); (A.K.S.); (S.Y.G.); (O.M.S.); (M.Y.S.)
| | - Mariya Yu. Suvorina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (A.V.G.); (A.K.S.); (S.Y.G.); (O.M.S.); (M.Y.S.)
| | - Liya G. Bobyleva
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (L.G.B.); (I.M.V.)
| | - Ivan M. Vikhlyantsev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (L.G.B.); (I.M.V.)
| | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (A.V.G.); (A.K.S.); (S.Y.G.); (O.M.S.); (M.Y.S.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (L.G.B.); (I.M.V.)
- Correspondence: ; Tel.: +7-903-675-0156
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Grishin SY, Deryusheva EI, Machulin AV, Selivanova OM, Glyakina AV, Gorbunova EY, Mustaeva LG, Azev VN, Rekstina VV, Kalebina TS, Surin AK, Galzitskaya OV. Amyloidogenic Propensities of Ribosomal S1 Proteins: Bioinformatics Screening and Experimental Checking. Int J Mol Sci 2020; 21:E5199. [PMID: 32707977 PMCID: PMC7432502 DOI: 10.3390/ijms21155199] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
Structural S1 domains belong to the superfamily of oligosaccharide/oligonucleotide-binding fold domains, which are highly conserved from prokaryotes to higher eukaryotes and able to function in RNA binding. An important feature of this family is the presence of several copies of the structural domain, the number of which is determined in a strictly limited range from one to six. Despite the strong tendency for the aggregation of several amyloidogenic regions in the family of the ribosomal S1 proteins, their fibril formation process is still poorly understood. Here, we combined computational and experimental approaches for studying some features of the amyloidogenic regions in this protein family. The FoldAmyloid, Waltz, PASTA 2.0 and Aggrescan programs were used to assess the amyloidogenic propensities in the ribosomal S1 proteins and to identify such regions in various structural domains. The thioflavin T fluorescence assay and electron microscopy were used to check the chosen amyloidogenic peptides' ability to form fibrils. The bioinformatics tools were used to study the amyloidogenic propensities in 1331 ribosomal S1 proteins. We found that amyloidogenicity decreases with increasing sizes of proteins. Inside one domain, the amyloidogenicity is higher in the terminal parts. We selected and synthesized 11 amyloidogenic peptides from the Escherichia coli and Thermus thermophilus ribosomal S1 proteins and checked their ability to form amyloids using the thioflavin T fluorescence assay and electron microscopy. All 11 amyloidogenic peptides form amyloid-like fibrils. The described specific amyloidogenic regions are actually responsible for the fibrillogenesis process and may be potential targets for modulating the amyloid properties of bacterial ribosomal S1 proteins.
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Affiliation(s)
- Sergei Y Grishin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Evgeniya I Deryusheva
- Institute for Biological Instrumentation, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Andrey V Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Olga M Selivanova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Elena Y Gorbunova
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Leila G Mustaeva
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Vyacheslav N Azev
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Valentina V Rekstina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Tatyana S Kalebina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, Obolensk 142279, Moscow Region, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
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9
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Glyakina AV, Strizhov NI, Karpov MV, Dovidchenko NV, Matkarimov BT, Isaeva LV, Efimova VS, Rubtsov MA, Novikova LA, Donova MV, Galzitskaya OV. Ile351, Leu355 and Ile461 residues are essential for catalytic activity of bovine cytochrome P450scc (CYP11A1). Steroids 2019; 143:80-90. [PMID: 30641046 DOI: 10.1016/j.steroids.2019.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/28/2018] [Accepted: 01/07/2019] [Indexed: 11/23/2022]
Abstract
Cytochrome P450scc (CYP11A1) is a mammalian mitochondrial enzyme which catalyzes cholesterol side chain cleavage to form pregnenolone. Along with cholesterol, some other steroids including sterols with a branched side chain like β-sitosterol are the substrates for the enzyme, but the activity towards β-sitosterol is rather low. Modification of the catalytic site conformation could provide more effective β-sitosterol bioconversion by the enzyme. This study was aimed to find out the amino acid residues substitution of which could modify the conformation of the active site providing possible higher enzyme activity towards β-sitosterol. After structural and bioinformatics analysis three amino acid residues I351, L355, I461 were chosen. Molecular dynamics simulations of P450scc evidenced the stability of the wild type, double (I351A/L355A) and triple (I351A/L355A/I461A) mutants. Mutant variants of cDNA encoding P450scc with the single, double and triple mutations were obtained by site-directed mutagenesis. However, the experimental data indicate that the introduced single mutations Ile351A, Leu355A and Ile461A dramatically decrease the target catalytic activity of CYP11A1, and no activity was observed for double and triple mutants obtained. Therefore, isoleucine residues 351 and 461, and leucine residue 355 are important for the cytochrome P450scc functioning towards sterols both with unbranched (cholesterol) and branched (sitosterol) side chains.
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Affiliation(s)
- Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Nicolai I Strizhov
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; Pharmins, Ltd., R&D, 142290 Pushchino, Moscow Region, Russia
| | - Mikhail V Karpov
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; Pharmins, Ltd., R&D, 142290 Pushchino, Moscow Region, Russia
| | - Nikita V Dovidchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | | | - Ludmila V Isaeva
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia
| | - Vera S Efimova
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia
| | - Mikhail A Rubtsov
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia; Department of Biochemistry, Institute of Translational Medicine and Biotechnology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Ludmila A Novikova
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia
| | - Marina V Donova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; Pharmins, Ltd., R&D, 142290 Pushchino, Moscow Region, Russia.
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
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10
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Galzitskaya OV, Surin AK, Glyakina AV, Rogachevsky VV, Selivanova OM. Should the Treatment of Amyloidosis Be Personified? Molecular Mechanism of Amyloid Formation by Aβ Peptide and Its Fragments. J Alzheimers Dis Rep 2018; 2:181-199. [PMID: 30480261 PMCID: PMC6218156 DOI: 10.3233/adr-180063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Aβ40 and Aβ42 peptides are believed to be associated with Alzheimer's disease. Aggregates (plaques) of Aβ fibrils are found in the brains of humans affected with this disease. The mechanism of formation of Aβ fibrils has not been studied completely, which hinders the development of a correct strategy for therapeutic prevention of this neurodegenerative disorder. It has been found that the most toxic samples upon generation of fibrils are different oligomeric formations. Based on different research methods used for studying amyloidogenesis of Aβ40 and Aβ42 peptides and its amyloidogenic fragments, we have proposed a new mechanism of formation of amyloid fibrils. In accord with this mechanism, the main building unit for fibril generation is a ring-like oligomer. Association of ring-like oligomers results in the formation of fibrils of different morphologies. Our model implies that to prevent development of Alzheimer's disease a therapeutic intervention is required at the earliest stages of amyloidogenesis-at the stage of formation of ring-like oligomers. Therefore, the possibility of a personified approach for prevention not only of Alzheimer's disease development but also of other neurodegenerative diseases associated with the formation of fibrils is argued.
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Affiliation(s)
- Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Science, Pushchino, Moscow Region, Russia
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Science, Pushchino, Moscow Region, Russia.,State Scientific Center of Applied Microbiology and Biotechnology, Moscow Region, Serpukhov District, Obolensk, Russia.,Gamaleya Research Center of Epidemiology and Microbiology, Moscow, Russia
| | - Anna V Glyakina
- Institute of Protein Research, Russian Academy of Science, Pushchino, Moscow Region, Russia.,Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
| | - Vadim V Rogachevsky
- Institute of Cell Biophysics, Russian Academy of Science, Pushchino, Moscow Region, Russia
| | - Olga M Selivanova
- Institute of Protein Research, Russian Academy of Science, Pushchino, Moscow Region, Russia
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11
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Selivanova OM, Surin AK, Ryzhykau YL, Glyakina AV, Suvorina MY, Kuklin AI, Rogachevsky VV, Galzitskaya OV. To Be Fibrils or To Be Nanofilms? Oligomers Are Building Blocks for Fibril and Nanofilm Formation of Fragments of Aβ Peptide. Langmuir 2018; 34:2332-2343. [PMID: 29338255 DOI: 10.1021/acs.langmuir.7b03393] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
To identify the key stages in the amyloid fibril formation we studied the aggregation of amyloidogenic fragments of Aβ peptide, Aβ(16-25), Aβ(31-40), and Aβ(33-42), using the methods of electron microscopy, X-ray analysis, mass spectrometry, and structural modeling. We have found that fragments Aβ(31-40) and Aβ(33-42) form amyloid fibrils in the shape of bundles and ribbons, while fragment Aβ(16-25) forms only nanofilms. We are the first who performed 2D reconstruction of amyloid fibrils by the Markham rotation technique on electron micrographs of negatively stained fragments of Aβ peptide. Combined analysis of the data allows us to speculate that both the fibrils and the films are formed via association of ring-shaped oligomers with the external diameter of about 6 to 7 nm, the internal diameter of 2 to 3 nm, and the height of ∼3 nm. We conclude that such oligomers are the main building blocks in fibrils of any morphology. The interaction of ring oligomers with each other in different ways makes it possible to explain their polymorphism. The new mechanism of polymerization of amyloidogenic proteins and peptides, described here, could stimulate new approaches in the development of future therapeutics for the treatment of amyloid-related diseases.
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Affiliation(s)
- Olga M Selivanova
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
- State Research Center for Applied Microbiology & Biotechnology , Obolensk 142279, Russia
| | - Yury L Ryzhykau
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russian Federation
| | - Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences , Pushchino 142290, Russia
| | - Mariya Yu Suvorina
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
| | - Alexander I Kuklin
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russian Federation
- Joint Institute for Nuclear Research , Dubna 141980, Russian Federation
| | - Vadim V Rogachevsky
- Institute of Cell Biophysics, Russian Academy of Sciences , Pushchino 142290, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
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12
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Selivanova OM, Surin AK, Marchenkov VV, Dzhus UF, Grigorashvili EI, Suvorina MY, Glyakina AV, Dovidchenko NV, Galzitskaya OV. The Mechanism Underlying Amyloid Polymorphism is Opened for Alzheimer's Disease Amyloid-β Peptide. J Alzheimers Dis 2018; 54:821-30. [PMID: 27567850 DOI: 10.3233/jad-160405] [Citation(s) in RCA: 24] [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: 11/15/2022]
Abstract
It has been demonstrated using Aβ40 and Aβ42 recombinant and synthetic peptides that their fibrils are formed of complete oligomer ring structures. Such ring structures have a diameter of about 8-9 nm, an oligomer height of about 2- 4 nm, and an internal diameter of the ring of about 3-4 nm. Oligomers associate in a fibril in such a way that they interact with each other, overlapping slightly. There are differences in the packing of oligomers in fibrils of recombinant and synthetic Aβ peptides. The principal difference is in the degree of orderliness of ring-like oligomers that leads to generation of morphologically different fibrils. Most ordered association of ring-like structured oligomers is observed for a recombinant Aβ40 peptide. Less ordered fibrils are observed with the synthetic Aβ42 peptide. Fragments of fibrils the most protected from the action of proteases have been determined by tandem mass spectrometry. It was shown that unlike Aβ40, fibrils of Aβ42 are more protected, showing less ordered organization compared to that of Aβ40 fibrils. Thus, the mass spectrometry data agree with the electron microscopy data and structural models presented here.
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Affiliation(s)
- Olga M Selivanova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,State Research Center for Applied Microbiology & Biotechnology, Obolensk, Serpukhov District, Moscow Region, Russia
| | - Victor V Marchenkov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Ulyana F Dzhus
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | | | - Mariya Yu Suvorina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,Institute of Mathematical Problems of Biology, Pushchino, Moscow Region, Russia
| | - Nikita V Dovidchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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13
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Pereyaslavets LB, Glyakina AV, Dovidchenko NV, Sokolovskiy IV, Galzitskaya OV. What handedness and angles between helices has the studied three-helical protein domain? Bioinformatics 2015; 31:963-5. [PMID: 25388147 DOI: 10.1093/bioinformatics/btu737] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have created a new server FoldHandedness. Using this server it is possible: (i) to define the regions of helices from two issues (from the PDB file and using the last version of the DSSP program), (ii) to determine the handedness for any chosen three helices and (iii) to calculate the angle and sign between the chosen pairs of the helices for large proteins and complexes of proteins with DNA or RNA.
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Affiliation(s)
- Leonid B Pereyaslavets
- Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Anna V Glyakina
- Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Nikita V Dovidchenko
- Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Igor V Sokolovskiy
- Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
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14
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Glyakina AV, Likhachev IV, Balabaev NK, Galzitskaya OV. Mechanical stability analysis of the protein L immunoglobulin-binding domain by full alanine screening using molecular dynamics simulations. Biotechnol J 2014; 10:386-94. [PMID: 25425165 DOI: 10.1002/biot.201400231] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/07/2014] [Accepted: 11/24/2014] [Indexed: 11/10/2022]
Abstract
This article is the first to study the mechanical properties of the immunoglobulin-binding domain of protein L (referred to as protein L) and its mutants at the atomic level. In the structure of protein L, each amino acid residue (except for alanines and glycines) was replaced sequentially by alanine. Thus, 49 mutants of protein L were obtained. The proteins were stretched at their termini at constant velocity using molecular dynamics simulations in water, i.e. by forced unfolding. 19 out of 49 mutations resulted in a large decrease of mechanical protein stability. These amino acids were affecting either the secondary structure (11 mutations) or loop structures (8 mutations) of protein L. Analysis of mechanical unfolding of the generated protein that has the same topology as protein L but consists of only alanines and glycines allows us to suggest that the mechanical stability of proteins, and specifically protein L, is determined by interactions between certain amino acid residues, although the unfolding pathway depends on the protein topology. This insight can now be used to modulate the mechanical properties of proteins and their unfolding pathways in the desired direction for using them in various biochips, biosensors and biomaterials for medicine, industry, and household purposes.
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Affiliation(s)
- Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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15
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16
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Glyakina AV, Balabaev NK, Galzitskaya OV. Experimental and theoretical studies of mechanical unfolding of different proteins. Biochemistry (Mosc) 2014; 78:1216-27. [PMID: 24460936 DOI: 10.1134/s0006297913110023] [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
Mechanical properties of proteins are important for a wide range of biological processes including cell adhesion, muscle contraction, and protein translocation across biological membranes. It is necessary to reveal how proteins achieve their required mechanical stability under natural conditions in order to understand the biological processes and also to use the knowledge for constructing new biomaterials for medical and industrial purposes. In this connection, it is important to know how a protein will behave in response to various impacts. Theoretical and experimental works on mechanical unfolding of globular proteins will be considered in detail in this review.
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Affiliation(s)
- A V Glyakina
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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17
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Glyakina AV, Likhachev IV, Balabaev NK, Galzitskaya OV. Right- and left-handed three-helix proteins. II. Similarity and differences in mechanical unfolding of proteins. Proteins 2013; 82:90-102. [PMID: 23873665 DOI: 10.1002/prot.24373] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/26/2013] [Accepted: 07/09/2013] [Indexed: 11/11/2022]
Abstract
Here, we study mechanical properties of eight 3-helix proteins (four right-handed and four left-handed ones), which are similar in size under stretching at a constant speed and at a constant force on the atomic level using molecular dynamics simulations. The analysis of 256 trajectories from molecular dynamics simulations with explicit water showed that the right-handed three-helix domains are more mechanically resistant than the left-handed domains. Such results are observed at different extension velocities studied (192 trajectories obtained at the following conditions: v = 0.1, 0.05, and 0.01 Å ps(-1) , T = 300 K) and under constant stretching force (64 trajectories, F = 800 pN, T = 300 K). We can explain this by the fact, at least in part, that the right-handed domains have a larger number of contacts per residue and the radius of cross section than the left-handed domains.
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Affiliation(s)
- Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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18
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Glyakina AV, Pereyaslavets LB, Galzitskaya OV. Right- and left-handed three-helix proteins. I. Experimental and simulation analysis of differences in folding and structure. Proteins 2013; 81:1527-41. [DOI: 10.1002/prot.24301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Anna V. Glyakina
- Institute of Protein Research; Russian Academy of Sciences; Pushchino, Moscow Region 142290 Russia
- Institute of Mathematical Problems of Biology; Russian Academy of Sciences; Pushchino, Moscow Region 142290 Russia
| | - Leonid B. Pereyaslavets
- Institute of Protein Research; Russian Academy of Sciences; Pushchino, Moscow Region 142290 Russia
| | - Oxana V. Galzitskaya
- Institute of Protein Research; Russian Academy of Sciences; Pushchino, Moscow Region 142290 Russia
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19
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Mamonova TB, Glyakina AV, Galzitskaya OV, Kurnikova MG. Stability and rigidity/flexibility-two sides of the same coin? Biochim Biophys Acta 2013; 1834:854-66. [PMID: 23416444 DOI: 10.1016/j.bbapap.2013.02.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 12/21/2012] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
Abstract
Protein molecules require both flexibility and rigidity for functioning. The fast and accurate prediction of protein rigidity/flexibility is one of the important problems in protein science. We have determined flexible regions for four homologous pairs from thermophilic and mesophilic organisms by two methods: the fast FoldUnfold which uses amino acid sequence and the time consuming MDFirst which uses three-dimensional structures. We demonstrate that both methods allow determining flexible regions in protein structure. For three of the four thermophile-mesophile pairs of proteins, FoldUnfold predicts practically the same flexible regions which have been found by the MD/First method. As expected, molecular dynamics simulations show that thermophilic proteins are more rigid in comparison to their mesophilic homologues. Analysis of rigid clusters and their decomposition provides new insights into protein stability. It has been found that the local networks of salt bridges and hydrogen bonds in thermophiles render their structure more stable with respect to fluctuations of individual contacts. Such network includes salt bridge triads Agr-Glu-Lys and Arg-Glu-Arg, or salt bridges (such as Arg-Glu) connected with hydrogen bonds. This ionic network connects alpha helices and rigidifies the structure. Mesophiles can be characterized by stand alone salt bridges and hydrogen bonds or small ionic clusters. Such difference in the network of salt bridges results in different flexibility of homologous proteins. Combining both approaches allows characterizing structural features in atomic detail that determine the rigidity/flexibility of a protein structure. This article is a part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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Affiliation(s)
- Tatyana B Mamonova
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
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20
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Galzitskaya OV, Glyakina AV. Nucleation-based prediction of the protein folding rate and its correlation with the folding nucleus size. Proteins 2012; 80:2711-27. [DOI: 10.1002/prot.24156] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 07/19/2012] [Accepted: 07/21/2012] [Indexed: 11/08/2022]
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21
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Kanev IL, Balabaev NK, Glyakina AV, Morozov VN. Computer Simulation of Gas-Phase Neutralization of Electrospray-Generated Protein Macroions. J Phys Chem B 2012; 116:5872-81. [DOI: 10.1021/jp300370r] [Citation(s) in RCA: 9] [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] [Indexed: 01/01/2023]
Affiliation(s)
- Igor L. Kanev
- Institute of Theoretical and
Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia 142290
| | - Nikolay K. Balabaev
- Institute of Mathematical Problems
of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia 142290
- Department of Bioengineering,
Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia 119991
| | - Anna V. Glyakina
- Institute of Mathematical Problems
of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia 142290
| | - Victor N. Morozov
- Institute of Theoretical and
Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia 142290
- The National Center for Biodefense
and Infectious Diseases, George Mason University, Manassas, Virginia 20110, United States
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22
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Glyakina AV, Bogatyreva NS, Galzitskaya OV. Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins. PLoS One 2011; 6:e28464. [PMID: 22145047 PMCID: PMC3228773 DOI: 10.1371/journal.pone.0028464] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [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: 06/05/2011] [Accepted: 11/08/2011] [Indexed: 11/19/2022] Open
Abstract
Here we present a systematic analysis of accessible surface areas and hydrogen bonds of 2554 globular proteins from four structural classes (all-α, all-β, α/β and α+β proteins) that is aimed to learn in which structural class the accessible surface area increases with increasing protein molecular mass more rapidly than in other classes, and what structural peculiarities are responsible for this effect. The beta structural class of proteins was found to be the leader, with the following possible explanations of this fact. First, in beta structural proteins, the fraction of residues not included in the regular secondary structure is the largest, and second, the accessible surface area of packaged elements of the beta-structure increases more rapidly with increasing molecular mass in comparison with the alpha-structure. Moreover, in the beta structure, the probability of formation of backbone hydrogen bonds is higher than that in the alpha helix for all residues of α+β proteins (the average probability is 0.73±0.01 for the beta-structure and 0.60±0.01 for the alpha-structure without proline) and α/β proteins, except for asparagine, aspartic acid, glycine, threonine, and serine (0.70±0.01 for the beta-structure and 0.60±0.01 for the alpha-structure without the proline residue). There is a linear relationship between the number of hydrogen bonds and the number of amino acid residues in the protein ().
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Affiliation(s)
- Anna V. Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Natalya S. Bogatyreva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- * E-mail:
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23
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Galzitskaya OV, Bogatyreva NS, Glyakina AV. Bacterial proteins fold faster than eukaryotic proteins with simple folding kinetics. Biochemistry (Mosc) 2011; 76:225-35. [PMID: 21568856 DOI: 10.1134/s000629791102009x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Protein domain frequency and distribution among kingdoms was statistically analyzed using the SCOP structural database. It appeared that among chosen protein domains with the best resolution, eukaryotic proteins more often belong to α-helical and β-structural proteins, while proteins of bacterial origin belong to α/β structural class. Statistical analysis of folding rates of 73 proteins with known experimental data revealed that bacterial proteins with simple kinetics (23 proteins) exhibit a higher folding rate compared to eukaryotic proteins with simple folding kinetics (27 proteins). Analysis of protein domain amino acid composition showed that the frequency of amino acid residues in proteins of eukaryotic and bacterial origin is different for proteins with simple and complex folding kinetics.
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Affiliation(s)
- O V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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24
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Mamonova TB, Glyakina AV, Kurnikova MG, Galzitskaya OV. Flexibility and mobility in mesophilic and thermophilic homologous proteins from molecular dynamics and FoldUnfold method. J Bioinform Comput Biol 2010; 8:377-94. [PMID: 20556851 DOI: 10.1142/s0219720010004690] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 12/24/2009] [Accepted: 01/15/2010] [Indexed: 11/18/2022]
Abstract
To function properly protein molecules require both flexibility and rigidity, therefore fast and accurate prediction of protein rigidity/flexibility is one of the important problems in protein science. In this work we used two theoretical approaches to determine flexible regions in four homologous pairs of proteins from thermophilic and mesophilic organisms. Protein pairs chosen in this study were selected to represent four typical folding classes. Our first approach, FoldUnfold, uses amino acid sequence and statistical information on the density of contacts of amino acids in tertiary structures of known globular proteins. The main advantages of such knowledge-based methodology are its computational speed and ability to make predictions in the absence of three-dimensional (3D) structure of a protein. The second approach uses a graph theory-based rigid cluster decomposition termed FIRST, applied together with Molecular Dynamics (MD) simulations of proteins with known structure. While MD simulations are time-consuming, they are the most direct way of studying physical properties of proteins, including their rigidity/flexibility. Flexible regions predicted by both methods in this work were in good agreement with each other. We also showed that high mobility of a site is not necessarily indicative of its high flexibility and vice versa. In our simulations thermophile proteins were less flexible than their mesophilic homologues. Longer flexible loops were found in mesophilic proteins of all classes.
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Affiliation(s)
- Tatyana B Mamonova
- Chemistry Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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25
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Glyakina AV, Balabaev NK, Galzitskaya OV. Two-, three-, and four-state events occur in the mechanical unfolding of small protein L using molecular dynamics simulation. Protein Pept Lett 2010; 17:92-103. [PMID: 20214632 DOI: 10.2174/092986610789909449] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mechanical properties of (protein L)(5) have been recently investigated by single-molecule force spectroscopy. It has been demonstrated that the unfolding of individual domains proceeds through a two-state mechanism. Here, we study mechanical properties of protein L at the atomic level under stretching at constant velocity using molecular dynamics simulations. We have found that the unfolding process of protein L can occur either in a single step or through short living and quite native like intermediate states, which was not observed in previous studies. Analysis of the 24 trajectories from molecular dynamics simulations with explicit water showed that the mechanical unfolding of protein L occurs through at least two pathways. These pathways coincide in two- and multi-state events and at different extension velocities studied (0.125, 0.0625 and 0.005 A x ps(-1)).
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Affiliation(s)
- Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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26
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Glyakina AV, Balabaev NK, Galzitskaya OV. Multiple Unfolding Intermediates Obtained by Molecular Dynamic Simulations under Stretching for Immunoglobulin-Binding Domain of Protein G. Open Biochem J 2009; 3:66-77. [PMID: 20037652 PMCID: PMC2793399 DOI: 10.2174/1874091x00903010066] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 10/20/2009] [Accepted: 10/30/2009] [Indexed: 11/22/2022] Open
Abstract
We have studied the mechanical properties of the immunoglobulin-binding domain of protein G at the atomic level under stretching at constant velocity using molecular dynamics simulations. We have found that the unfolding process can occur either in a single step or through intermediate states. Analysis of the trajectories from the molecular dynamic simulations showed that the mechanical unfolding of the immunoglobulin-binding domain of protein G is triggered by the separation of the terminal beta-strands and the order in which the secondary-structure elements break is practically the same in two- and multi-state events and at the different extension velocities studied. It is seen from our analysis of 24 trajectories that the theoretical pathway of mechanical unfolding for the immunoglobulin-binding domain of protein G does not coincide with that proposed in denaturant studies in the absence of force.
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Affiliation(s)
- Anna V Glyakina
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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27
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Glyakina AV, Garbuzynskiy SO, Lobanov MY, Galzitskaya OV. Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms. Bioinformatics 2007; 23:2231-8. [PMID: 17599925 DOI: 10.1093/bioinformatics/btm345] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Understanding the basis of protein stability in thermophilic organisms raises a general question: what structural properties of proteins are responsible for the higher thermostability of proteins from thermophilic organisms compared to proteins from mesophilic organisms? RESULTS A unique database of 373 structurally well-aligned protein pairs from thermophilic and mesophilic organisms is constructed. Comparison of proteins from thermophilic and mesophilic organisms has shown that the external, water-accessible residues of the first group are more closely packed than those of the second. Packing of interior parts of proteins (residues inaccessible to water molecules) is the same in both cases. The analysis of amino acid composition of external residues of proteins from thermophilic organisms revealed an increased fraction of such amino acids as Lys, Arg and Glu, and a decreased fraction of Ala, Asp, Asn, Gln, Thr, Ser and His. Our theoretical investigation of folding/unfolding behavior confirms the experimental observations that the interactions that differ in thermophilic and mesophilic proteins form only after the passing of the transition state during folding. Thus, different packing of external residues can explain differences in thermostability of proteins from thermophilic and mesophilic organisms. AVAILABILITY The database of 373 structurally well-aligned protein pairs is available at http://phys.protres.ru/resources/termo_meso_base.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anna V Glyakina
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
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