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Starkova TY, Polyanichko AM, Artamonova TO, Tsimokha AS, Tomilin AN, Chikhirzhina EV. Structural Characteristics of High-Mobility Group Proteins HMGB1 and HMGB2 and Their Interaction with DNA. Int J Mol Sci 2023; 24:ijms24043577. [PMID: 36834988 PMCID: PMC9962726 DOI: 10.3390/ijms24043577] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/27/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Non-histone nuclear proteins HMGB1 and HMGB2 (High Mobility Group) are involved in many biological processes, such as replication, transcription, and repair. The HMGB1 and HMGB2 proteins consist of a short N-terminal region, two DNA-binding domains, A and B, and a C-terminal sequence of glutamic and aspartic acids. In this work, the structural organization of calf thymus HMGB1 and HMGB2 proteins and their complexes with DNA were studied using UV circular dichroism (CD) spectroscopy. Post-translational modifications (PTM) of HMGB1 and HMGB2 proteins were determined with MALDI mass spectrometry. We have shown that despite the similar primary structures of the HMGB1 and HMGB2 proteins, their post-translational modifications (PTMs) demonstrate quite different patterns. The HMGB1 PTMs are located predominantly in the DNA-binding A-domain and linker region connecting the A and B domains. On the contrary, HMGB2 PTMs are found mostly in the B-domain and within the linker region. It was also shown that, despite the high degree of homology between HMGB1 and HMGB2, the secondary structure of these proteins is also slightly different. We believe that the revealed structural properties might determine the difference in the functioning of the HMGB1 and HMGB2 as well as their protein partners.
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Chikhirzhina EV, Starkova TY, Polyanichko AM. The Structural Organization of the HMGB1 Nuclear Protein and Its Effect on the Formation of Ordered Supramolecular Complexes. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921030039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Paston SV, Polyanichko AM, Shulenina OV, Osinnikova DN. A Study of the DNA Structure in Films Using FTIR Spectroscopy. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920060159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Chikhirzhina E, Starkova T, Beljajev A, Polyanichko A, Tomilin A. Functional Diversity of Non-Histone Chromosomal Protein HmgB1. Int J Mol Sci 2020; 21:E7948. [PMID: 33114717 PMCID: PMC7662367 DOI: 10.3390/ijms21217948] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/27/2022] Open
Abstract
The functioning of DNA in the cell nucleus is ensured by a multitude of proteins, whose interactions with DNA as well as with other proteins lead to the formation of a complicated, organized, and quite dynamic system known as chromatin. This review is devoted to the description of properties and structure of the progenitors of the most abundant non-histone protein of the HMGB family-the HmgB1 protein. The proteins of the HMGB family are also known as "architectural factors" of chromatin, which play an important role in gene expression, transcription, DNA replication, and repair. However, as soon as HmgB1 goes outside the nucleus, it acquires completely different functions, post-translational modifications, and change of its redox state. Despite a lot of evidence of the functional activity of HmgB1, there are still many issues to be solved related to the mechanisms of the influence of HmgB1 on the development and treatment of different diseases-from oncological and cardiovascular diseases to pathologies during pregnancy and childbirth. Here, we describe molecular structure of the HmgB1 protein and discuss general mechanisms of its interactions with other proteins and DNA in cell.
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Affiliation(s)
| | | | | | - Alexander Polyanichko
- Laboratory of Molecular Biology of Stem Cells, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Tikhoretsky Av. 4, Russia; (T.S.); (A.B.); (A.T.)
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Chikhirzhina EV, Starkova TY, Polyanichko AM. The Role of Linker Histones in Chromatin Structural Organization. 2. Interaction with DNA and Nuclear Proteins. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920020049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Folding of poly-amino acids and intrinsically disordered proteins in overcrowded milieu induced by pH change. Int J Biol Macromol 2018; 125:244-255. [PMID: 30529354 DOI: 10.1016/j.ijbiomac.2018.12.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/27/2018] [Accepted: 12/02/2018] [Indexed: 12/24/2022]
Abstract
pH-induced structural changes of the synthetic homopolypeptides poly-E, poly-K, poly-R, and intrinsically disordered proteins (IDPs) prothymosin α (ProTα) and linker histone H1, in concentrated PEG solutions simulating macromolecular crowding conditions within the membrane-less organelles, were characterized. The conformational transitions of the studied poly-amino acids in the concentrated PEG solutions depend on the polymerization degree of these homopolypeptides, the size of their side chains, the charge distribution of the side chains, and the crowding agent concentration. The results obtained for poly-amino acids are valid for IDPs having a significant total charge. The overcrowded conditions promote a significant increase in the cooperativity of the pH-induced coil-α-helix transition of ProTα and provoke histone H1 aggregation. The most favorable conditions for the pH-induced structural transitions in concentrated PEG solutions are realized when the charged residues are grouped in blocks, and when the distance between the end of the side group carrying charge and the backbone is small. Therefore, the block-wise distribution of charged residues within the IDPs not only plays an important role in the liquid-liquid phase transitions, but may also define the expressivity of structural transitions of these proteins in the overcrowded conditions of the membrane-less organelles.
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Ferrandi A, Castani F, Pitaro M, Tagliaferri S, de la Tour CB, Alduina R, Sommer S, Fasano M, Barbieri P, Mancini M, Bonapace IM. Deinococcus radiodurans' SRA-HNH domain containing protein Shp (Dr1533) is involved in faithful genome inheritance maintenance following DNA damage. Biochim Biophys Acta Gen Subj 2018; 1863:118-129. [PMID: 30308220 DOI: 10.1016/j.bbagen.2018.09.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/18/2018] [Accepted: 09/25/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Deinococcus radiodurans R1 (DR) survives conditions of extreme desiccation, irradiation and exposure to genotoxic chemicals, due to efficient DNA breaks repair, also through Mn2+ protection of DNA repair enzymes. METHODS Possible annotated domains of the DR1533 locus protein (Shp) were searched by bioinformatic analysis. The gene was cloned and expressed as fusion protein. Band-shift assays of Shp or the SRA and HNH domains were performed on oligonucleotides, genomic DNA from E. coli and DR. shp knock-out mutant was generated by homologous recombination with a kanamycin resistance cassette. RESULTS DR1533 contains an N-terminal SRA domain and a C-terminal HNH motif (SRA-HNH Protein, Shp). Through its SRA domain, Shp binds double-strand oligonucleotides containing 5mC and 5hmC, but also unmethylated and mismatched cytosines in presence of Mn2+. Shp also binds to Escherichia coli dcm+ genomic DNA, and to cytosine unmethylated DR and E. coli dcm- genomic DNAs, but only in presence of Mn2+. Under these binding conditions, Shp displays DNAse activity through its HNH domain. Shp KO enhanced >100 fold the number of spontaneous mutants, whilst the treatment with DNA double strand break inducing agents enhanced up to 3-log the number of survivors. CONCLUSIONS The SRA-HNH containing protein Shp binds to and cuts 5mC DNA, and unmethylated DNA in a Mn2+ dependent manner, and might be involved in faithful genome inheritance maintenance following DNA damage. GENERAL SIGNIFICANCE Our results provide evidence for a potential role of DR Shp protein for genome integrity maintenance, following DNA double strand breaks induced by genotoxic agents.
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Affiliation(s)
- Alex Ferrandi
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Federica Castani
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Mauro Pitaro
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Sara Tagliaferri
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Claire Bouthier de la Tour
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, France and Institut de Génétique et Microbiologie - Université Paris-Sud, Paris, France
| | - Rosa Alduina
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Palermo, Italy
| | - Suzanne Sommer
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, France and Institut de Génétique et Microbiologie - Université Paris-Sud, Paris, France
| | - Mauro Fasano
- Department of Sciences and High technology, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Paola Barbieri
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Monica Mancini
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy.
| | - Ian Marc Bonapace
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy.
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Tankovskaia SA, Kotb OM, Dommes OA, Paston SV. Application of spectral methods for studying DNA damage induced by gamma-radiation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 200:85-92. [PMID: 29674243 DOI: 10.1016/j.saa.2018.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
Spectral methods can provide a variety of possibilities to determine several types of radiation-induced DNA damage, such as nucleobase destruction and local denaturation. DNA UV absorption and CD spectra measured at room temperature undergo noticeable alteration under the action of γ-radiation. We have applied the Spirin method of total nucleobases determination, and have measured the molar extinction coefficient of DNA and DNA CD spectra for solutions with different NaCl concentrations (3mM-3.2M) and containing MgCl2, exposed to γ-radiation with the doses of 0-103Gy. The melting temperatures of DNA in irradiated solutions at the doses of 0-50Gy were obtained with the help of spectrophotometric melting. It was found that the amount of destructed nucleobases and radiation-induced loss of DNA helicity significantly decreases with the rise of the ionic strength of the irradiated solution. Substitution of a portion of Na+ ions on Mg2+ while keeping the total ionic strength constant (μ=5mM) does not affect the considered radiation effects. The role of the structure and composition of the DNA secondary hydration layer in the radiation-induced damages is discussed.
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Affiliation(s)
- Svetlana A Tankovskaia
- Department of Molecular Biophysics and Polymer Physics, Faculty of Physics, Saint-Petersburg State University, Ulyanovskaya, 3, St. Petersburg 198504, Russia
| | - Omar M Kotb
- Department of Molecular Biophysics and Polymer Physics, Faculty of Physics, Saint-Petersburg State University, Ulyanovskaya, 3, St. Petersburg 198504, Russia; Department of Physics, Faculty of Science, Zagazig University, Sharkia Gov, Zagazig 44519, Egypt
| | - Olga A Dommes
- Institute of Macromolecular Compounds, Bolshoy pr. 31, 199004 Saint-Petersburg, Russia
| | - Sofia V Paston
- Department of Molecular Biophysics and Polymer Physics, Faculty of Physics, Saint-Petersburg State University, Ulyanovskaya, 3, St. Petersburg 198504, Russia.
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Belaya I, Chikhirzhina E, Polyanichko A. Interaction of DDP with bovine serum albumin facilitates formation of the protein dimers. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.12.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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The transcriptional repressor domain of Gli3 is intrinsically disordered. PLoS One 2013; 8:e76972. [PMID: 24146948 PMCID: PMC3798401 DOI: 10.1371/journal.pone.0076972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/26/2013] [Indexed: 01/03/2023] Open
Abstract
The transcription factor Gli3 is acting mainly as a transcriptional repressor in the Sonic hedgehog signal transduction pathway. Gli3 contains a repressor domain in its N-terminus from residue G106 to E236. In this study we have characterized the intracellular structure of the Gli3 repressor domain using a combined bioinformatics and experimental approach. According to our findings the Gli3 repressor domain while being intrinsically disordered contains predicted anchor sites for partner interactions. The obvious interaction partners to test were Ski and DNA; however, with both of these the structure of Gli3 repressor domain remained disordered. To locate residues important for the repressor function we mutated several residues within the Gli3 repressor domain. Two of these, H141A and H157N, targeting predicted helical regions, significantly decreased transcriptional repression and thus identify important functional parts of the domain.
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Polyanichko A, Chikhirzhina E. Interaction between DNA and chromosomal proteins HMGB1 and H1 studied by IR/VCD spectroscopy. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.01.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Urbanová M. Bioinspired interactions studied by vibrational circular dichroism. Chirality 2010; 21 Suppl 1:E215-30. [PMID: 19937957 DOI: 10.1002/chir.20803] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Vibrational circular dichroism (VCD) spectra are reliable indicators of the spatial structure of chiral molecules. The specific and characteristic feature of vibrational spectroscopy, and therefore also of VCD, where the energy of some vibrational modes is predominantly focused to a specific part of the molecule, enables monitoring both the structure of the molecule dissolved in different solvents and under different physicochemical conditions and molecular interactions. This minireview deals with recent contributions covering structural information on the bioinspired interactions obtained by means of VCD, especially in the following areas: interaction of DNA with biomolecules and biogenic metals, guanine tetramers and quadruplexes, biointeractions of bile pigments, and polypeptide and protein interactions with other biomolecules.
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Affiliation(s)
- Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Prague, Czech Republic.
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Walsh MJ, Fellous TG, Hammiche A, Lin WR, Fullwood NJ, Grude O, Bahrami F, Nicholson JM, Cotte M, Susini J, Pollock HM, Brittan M, Martin-Hirsch PL, Alison MR, Martin FL. Fourier transform infrared microspectroscopy identifies symmetric PO(2)(-) modifications as a marker of the putative stem cell region of human intestinal crypts. Stem Cells 2007; 26:108-18. [PMID: 17901405 DOI: 10.1634/stemcells.2007-0196] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Complex biomolecules absorb in the mid-infrared (lambda = 2-20 microm), giving vibrational spectra associated with structure and function. We used Fourier transform infrared (FTIR) microspectroscopy to "fingerprint" locations along the length of human small and large intestinal crypts. Paraffin-embedded slices of normal human gut were sectioned (10 microm thick) and mounted to facilitate infrared (IR) spectral analyses. IR spectra were collected using globar (15 microm x 15 microm aperture) FTIR microspectroscopy in reflection mode, synchrotron (<or=10 microm x 10 microm aperture) FTIR microspectroscopy in transmission mode or near-field photothermal microspectroscopy. Dependent on the location of crypt interrogation, clear differences in spectral characteristics were noted. Epithelial-cell IR spectra were subjected to principal component analysis to determine whether wavenumber-absorbance relationships expressed as single points in "hyperspace" might on the basis of multivariate distance reveal biophysical differences along the length of gut crypts. Following spectroscopic analysis, plotted clusters and their loadings plots pointed toward symmetric (nu(s))PO(2)(-) (1,080 cm(-1)) vibrations as a discriminating factor for the putative stem cell region; this proved to be a more robust marker than other phenotypic markers, such as beta-catenin or CD133. This pattern was subsequently confirmed by image mapping and points to a novel approach of nondestructively identifying a tissue's stem cell location. nu(s)PO(2)(-), probably associated with DNA conformational alterations, might facilitate a means of identifying stem cells, which may have utility in other tissues where the location of stem cells is unclear.
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Affiliation(s)
- Michael J Walsh
- Biomedical Sciences Unit, Department of Biological Sciences, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
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