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Yurina L, Vasilyeva A, Indeykina M, Bugrova A, Biryukova M, Kononikhin A, Nikolaev E, Rosenfeld M. Ozone-induced damage of fibrinogen molecules: identification of oxidation sites by high-resolution mass spectrometry. Free Radic Res 2019; 53:430-455. [DOI: 10.1080/10715762.2019.1600686] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lyubov Yurina
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexandra Vasilyeva
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria Indeykina
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Anna Bugrova
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Marina Biryukova
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey Kononikhin
- Moskovskij Fiziko-Tehniceskij Institut, Dolgoprudnyi, Russian Federation
| | - Evgene Nikolaev
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Moscow, Russian Federation
| | - Mark Rosenfeld
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
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Oxidation-induced modifications of the catalytic subunits of plasma fibrin-stabilizing factor at the different stages of its activation identified by mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:875-884. [PMID: 29738861 DOI: 10.1016/j.bbapap.2018.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 04/13/2018] [Accepted: 05/02/2018] [Indexed: 12/24/2022]
Abstract
Plasma fibrin-stabilizing factor (pFXIII) is a heterotetrameric proenzyme composed of two catalytic A subunits (FXIII-A2) and two inhibitory/carrier B subunits (FXIII-B2). The main function of the protein is the formation of cross-links between the polypeptide chains of the fibrin clot. The conversion of pFXIII into the enzymatic form FXIII-A2* is a multistage process. Like many other blood plasma proteins, pFXIII is an oxidant-susceptible target. The influence of distinct sites susceptible to oxidation-mediated modifications on the changes in the structural-functional characteristics of the protein remains fully unexplored. For the first time, a set of the oxidation sites within FXIII-A2 under ozone-induced oxidation of pFXIII at different stages of its activation have been identified by mass spectrometry, and the extent as well as the chemical nature of these modifications have been explored. It was shown that the set of amino acid residues susceptible to oxidative attack and the degree of oxidation of these residues in FXIII-A2 of non-activated pFXIII, pFXIII activated by Ca2+ and fully activated pFXIII treated with thrombin and Ca2+ significantly differ. The obtained data enable one to postulate that in the process of the proenzyme conversion into FXIII-A2*, new earlier-unexposed amino acid residues become available for the oxidizer while some of the initially surface-exhibited residues are buried within the protein globule.
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Rosenfeld MA, Vasilyeva AD, Yurina LV, Bychkova AV. Oxidation of proteins: is it a programmed process? Free Radic Res 2017; 52:14-38. [DOI: 10.1080/10715762.2017.1402305] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mark A. Rosenfeld
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra D. Vasilyeva
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Lyubov V. Yurina
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Bychkova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
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Vasilyeva AD, Bychkova AV, Bugrova AE, Indeykina MI, Chikunova AP, Leonova VB, Kostanova EA, Biryukova MI, Konstantinova ML, Kononikhin AS, Nikolaev EN, Rosenfeld MA. Modification of the catalytic subunit of plasma fibrin-stabilizing factor under induced oxidation. DOKL BIOCHEM BIOPHYS 2017; 472:40-43. [PMID: 28421433 DOI: 10.1134/s160767291701015x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Indexed: 11/23/2022]
Abstract
For the first time, by using mass-spectrometry method, the oxidation-mediated modification of the catalytic FXIII-A subunit of plasma fibrin-stabilizing factor, pFXIII, has been studied. The oxidative sites were identified to belong to all structural elements of the catalytic subunit: the β-sandwich (Tyr104, Tyr117, and Cys153), the catalytic core domain (Met160, Trp165, Met266, Cys328, Asp352, Pro387, Arg409, Cys410, Tyr442, Met475, Met476, Tyr482, and Met500), the β-barrel 1 (Met596), and the β-barrel 2 (Met647, Pro676, Trp692, Cys696, and Met710), which correspond to 3.9%, 1.11%, 0.7%, and 3.2%, respectively, of oxidative modifications as compared to the detectable amounts of amino acid residues in each of the structural domains. Lack of information on some parts of the molecule may be associated with the spatial unavailability of residues, complicating analysis of the molecule. The absence of oxidative sites localized within crucial areas of the structural domains may be brought about by both the spatial inaccessibility of the oxidant to amino acid residues in the zymogen and the screening effect of the regulatory FXIII-B subunit.
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Affiliation(s)
- A D Vasilyeva
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
| | - A V Bychkova
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
| | - A E Bugrova
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
| | - M I Indeykina
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
| | - A P Chikunova
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
| | - V B Leonova
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
| | - E A Kostanova
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
| | - M I Biryukova
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
| | - M L Konstantinova
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
| | - A S Kononikhin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia.,N.M. Emanuel Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 117334, Russia.,Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow region, 141700, Russia
| | - E N Nikolaev
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia.,N.M. Emanuel Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 117334, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow oblast, 143025, Russia
| | - M A Rosenfeld
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia.
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Rosenfeld MA, Bychkova AV, Shchegolikhin AN, Leonova VB, Kostanova EA, Biryukova MI, Sultimova NB, Konstantinova ML. Fibrin self-assembly is adapted to oxidation. Free Radic Biol Med 2016; 95:55-64. [PMID: 26969792 DOI: 10.1016/j.freeradbiomed.2016.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/29/2016] [Accepted: 03/07/2016] [Indexed: 10/22/2022]
Abstract
Fibrinogen is extremely susceptible to attack by reactive oxygen species (ROS). Having been suffered an oxidative modification, the fibrinogen molecules, now with altered spatial structure and function of fibrin network, affect hemostasis differently. However, the potential effects of the oxidative stress on the early stages of the fibrin self-assembly process remain unexplored. To clarify the damaging influence of ROS on the knob 'A': hole 'a' and the D:D interactions, the both are operating on the early stages of the fibrin polymerization, we have used a novel approach based on exploration of FXIIIa-mediated self-assembly of the cross-linked fibrin oligomers dissolved in the moderately concentrated urea solutions. The oligomers were composed of monomeric desA fibrin molecules created by cleaving the fibrinopeptides A off the fibrinogen molecules with a thrombin-like enzyme, reptilase. According to the UV-absorbance and fluorescence measurements data, the employed low ozone/fibrinogen ratios have induced only a slight fibrinogen oxidative modification that was accompanied by modest chemical transformations of the aromatic amino acid residues of the protein. Else, a slight consumption of the accessible tyrosine residues has been observed due to intermolecular dityrosine cross-links formation. The set of experimental data gathered with the aid of electrophoresis, elastic light scattering and analytical centrifugation has clearly witnessed that the oxidation can serve as an effective promoter for the observed enhanced self-assembly of the covalently cross-linked oligomers. At urea concentration of 1.20M, the pristine and oxidized fibrin oligomers were found to comprise a heterogeneous set of the double-stranded protofibrils that are cross-linked only by γ-γ dimers and the fibers consisting on average of four strands that are additionally linked by α polymers. The amounts of the oxidized protofibrils and the fibers accumulated in the system were higher than those of the non-oxidized counterparts. Moreover, the γ and α polypeptide chains of the oxidized molecules were more readily crosslinked by the FXIIIa. Upon increasing the urea solution concentration to 4.20M, the cross-linked double-stranded desA fibrin protofibrils have dissociated into the single-stranded fibrin oligomers, whereas the fibers dissociated into both the double-stranded desA fibrin oligomers, the structural integrity of the latter being maintained by means of the intermolecular α polymers, and the single-stranded fibrin oligomers cross-linked only by γ-γ dimers. The data we have obtained in this study indicate that the FXIIIa-mediated process of assembling the cross-linked protofibrils and the fibers constructed from the oxidized monomeric fibrin molecules was facilitated due to the strengthening of D:D interactions. The findings infer that the enhanced longitudinal D:D interactions become more essential in the assembly of soluble protofibrils when the interactions knobs 'A': holes 'a' are injured by oxidation. The new experimental findings presented here could be of help for elucidating the essential adaptive molecular mechanisms capable of mitigating the detrimental action of ROS in the oxidatively damaged fibrin self-assemblage processes.
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Affiliation(s)
- Mark A Rosenfeld
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia.
| | - Anna V Bychkova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
| | - Alexander N Shchegolikhin
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
| | - Vera B Leonova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
| | - Elizaveta A Kostanova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
| | - Marina I Biryukova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
| | - Natalia B Sultimova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
| | - Marina L Konstantinova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
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