1
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Shaliutina-Loginova A, Loginov DS. Transferrin maintains the motility rate, ATP content, and DNA integrity of common carp spermatozoa during short-term storage. Anim Reprod Sci 2024; 263:107437. [PMID: 38395011 DOI: 10.1016/j.anireprosci.2024.107437] [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] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024]
Abstract
Short-term sperm storage is a straightforward and cost-effective method of managing logistics in large scale fish hatchery operations but may result in decline in sperm quality. For effective artificial reproduction of fish, use of an appropriate additive to optimize sperm storage conditions is essential. In this study, it was investigated the effect of purified seminal plasma transferrin (Tf) at 10 μg/ml on relevant parameters in common carp Cyprinus carpio sperm during short-term storage. We compared sperm motility and curvilinear velocity, adenosine triphosphate (ATP) content and DNA fragmentation of fresh spermatozoa to that stored for 24, 48, 72, and 144 h with or without Tf. The percentage of motile cells and the curvilinear velocity of spermatozoa in stored samples for 72 h with transferrin supplementation were greater compared to samples with no added protein. The ATP content in samples without added transferrin was reduced (P < 0.05) after 72 h of storage, in contrast to the levels observed in transferrin-supplemented sperm. A time-dependent increase in DNA fragmentation was observed. Significantly lower DNA damage, expressed as percent tail DNA (10.99 ± 1.28) and olive tail moment (0.54 ± 0.12), was recorded in Tf-supplemented samples stored for 48 h compared to that with no Tf. Hence, it is concluded that the beneficial effects of transferrin on common carp sperm could serve as an additional tool for developing and enhancing short-term sperm preservation procedures commonly used in aquaculture.
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Affiliation(s)
- Anna Shaliutina-Loginova
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Zátiší 728/II, Vodňany 389 25, Czech Republic; Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic.
| | - Dmitry S Loginov
- BioCeV - Institute of Microbiology of the CAS, Průmyslová 595, Vestec 252 50, Czech Republic
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2
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Felčíková K, Hovan A, Polák M, Loginov DS, Holotová V, Díaz C, Kožár T, Lee O, Varhač R, Novák P, Bánó G, Sedlák E. Design of AsLOV2 domain as a carrier of light-induced dissociable FMN photosensitizer. Protein Sci 2024; 33:e4921. [PMID: 38501448 PMCID: PMC10949324 DOI: 10.1002/pro.4921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 03/20/2024]
Abstract
Flavin mononucleotide (FMN) is a highly efficient photosensitizer (PS) yielding singlet oxygen (1 O2 ). However, its 1 O2 production efficiency significantly decreases upon isoalloxazine ring encapsulation into the protein matrix in genetically encoded photosensitizers (GEPS). Reducing isoalloxazine ring interactions with surrounding amino acids by protein engineering may increase 1 O2 production efficiency GEPS, but at the same time weakened native FMN-protein interactions may cause undesirable FMN dissociation. Here, in contrast, we intentionally induce the FMN release by light-triggered sulfur oxidation of strategically placed cysteines (oxidation-prone amino acids) in the isoalloxazine-binding site due to significantly increased volume of the cysteinyl side residue(s). As a proof of concept, in three variants of the LOV2 domain of Avena sativa (AsLOV2), namely V416C, T418C, and V416C/T418C, the effective 1 O2 production strongly correlated with the efficiency of irradiation-induced FMN dissociation (wild type (WT) < V416C < T418C < V416C/T418C). This alternative approach enables us: (i) to overcome the low 1 O2 production efficiency of flavin-based GEPSs without affecting native isoalloxazine ring-protein interactions and (ii) to utilize AsLOV2, due to its inherent binding propensity to FMN, as a PS vehicle, which is released at a target by light irradiation.
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Affiliation(s)
- Kristína Felčíková
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Andrej Hovan
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Marek Polák
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
- Department of Biochemistry, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Dmitry S. Loginov
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Veronika Holotová
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Carlos Díaz
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Tibor Kožár
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - One‐Sun Lee
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Rastislav Varhač
- Department of Biochemistry, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Petr Novák
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Gregor Bánó
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
- Department of Biochemistry, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
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3
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Zakopcanik M, Kavan D, Novak P, Loginov DS. Quantifying the Impact of the Peptide Identification Framework on the Results of Fast Photochemical Oxidation of Protein Analysis. J Proteome Res 2024; 23:609-617. [PMID: 38158558 PMCID: PMC10845142 DOI: 10.1021/acs.jproteome.3c00390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/17/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
Fast Photochemical Oxidation of Proteins (FPOP) is a promising technique for studying protein structure and dynamics. The quality of insight provided by FPOP depends on the reliability of the determination of the modification site. This study investigates the performance of two search engines, Mascot and PEAKS, for the data processing of FPOP analyses. Comparison of Mascot and PEAKS of the hemoglobin--haptoglobin Bruker timsTOF data set (PXD021621) revealed greater consistency in the Mascot identification of modified peptides, with around 26% of the IDs being mutual for all three replicates, compared to approximately 22% for PEAKS. The intersection between Mascot and PEAKS results revealed a limited number (31%) of shared modified peptides. Principal Component Analysis (PCA) using the peptide-spectrum match (PSM) score, site probability, and peptide intensity was applied to evaluate the results, and the analyses revealed distinct clusters of modified peptides. Mascot showed the ability to assess confident site determination, even with lower PSM scores. However, high PSM scores from PEAKS did not guarantee a reliable determination of the modification site. Fragmentation coverage of the modification position played a crucial role in Mascot assignments, while the AScore localizations from PEAKS often become ambiguous because the software employs MS/MS merging.
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Affiliation(s)
- Marek Zakopcanik
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, 12820 Prague, Czech Republic
| | - Daniel Kavan
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Petr Novak
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Dmitry S. Loginov
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
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4
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Vankova P, Pacheco-Garcia JL, Loginov DS, Gómez-Mulas A, Kádek A, Martín-Garcia JM, Salido E, Man P, Pey AL. Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants. FEBS Lett 2024; 598:485-499. [PMID: 38243391 DOI: 10.1002/1873-3468.14800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Primary hyperoxaluria type I (PH1) is caused by deficient alanine:glyoxylate aminotransferase (AGT) activity. PH1-causing mutations in AGT lead to protein mistargeting and aggregation. Here, we use hydrogen-deuterium exchange (HDX) to characterize the wild-type (WT), the LM (a polymorphism frequent in PH1 patients) and the LM G170R (the most common mutation in PH1) variants of AGT. We provide the first experimental analysis of AGT structural dynamics, showing that stability is heterogeneous in the native state and providing a blueprint for frustrated regions with potentially functional relevance. The LM and LM G170R variants only show local destabilization. Enzymatic transamination of the pyridoxal 5-phosphate cofactor bound to AGT hardly affects stability. Our study, thus, supports that AGT misfolding is not caused by dramatic effects on structural dynamics.
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Affiliation(s)
- Pavla Vankova
- Institute of Biotechnology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | | | - Dmitry S Loginov
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | | | - Alan Kádek
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - José Manuel Martín-Garcia
- Department of Crystallography & Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
| | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de la Laguna, Tenerife, Spain
| | - Petr Man
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Spain
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5
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Shaliutina-Loginova A, Loginov DS. Oxidative Stress and DNA Fragmentation in Frozen/Thawed Common Carp Cyprinus carpio Sperm With and Without Supplemental Proteins. Anim Reprod Sci 2023; 251:107213. [PMID: 36966610 DOI: 10.1016/j.anireprosci.2023.107213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/09/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023]
Abstract
Using cryopreservation techniques can increase the effectiveness of reproducing cultured fish species by ensuring a dependable supply of sperm, although the quality of the sperm could be impacted by the procedures involved. The goal of this study was to investigate the effect of purified seminal plasma transferrin (Tf), bovine serum albumin (BSA), and antifreeze protein (AFP) types I and III at 1 µg mL-1 on relevant characteristics of cryopreserved sperm from common carp Cyprinus carpio. We compared oxidative stress indices, antioxidant activity, and DNA fragmentation of fresh sperm to that frozen with extender only or with Tf, BSA, or AFP types I and III. Fresh sperm had significantly lower levels of thiobarbituric acid reactive substances (TBARS) compared to samples that underwent cryopreservation without protein treatment, which resulted in 0.54 ± 0.06 nmol/108 cells of TBARS. Carbonyl derivatives of proteins (CP) decreased significantly (ANOVA; P > 0.05) in carp sperm with addition of Tf, AFPI, and AFPIII. Significant differences in superoxide dismutase (SOD), glutathione reductase (GR), and glutathione peroxidase (GPx) activity were seen in sperm supplemented with Tf, BSA, AFPI, and AFPIII from those without. Significantly less DNA damage, expressed as percent tail DNA (11.56 ± 1.34) and olive tail moment (0.59 ± 0.13), was recorded in samples cryopreserved with Tf. The findings indicated that addition of Tf, BSA, AFPI, or AFPIII to cryopreservation medium is beneficial to sperm preservation. The mechanisms through which these proteins act positively on sperm need to be further investigated.
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Affiliation(s)
- Anna Shaliutina-Loginova
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Zátiší 728/II, 389 25 Vodňany, Czech Republic; Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic.
| | - Dmitry S Loginov
- BioCeV - Institute of Microbiology of the CAS, Průmyslová 595, 252 50 Vestec, Czech Republic; University of South Bohemia in Ceske Budejovice, Faculty of Science, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic; Orekhovich Institute of Biomedical Chemistry, Pogodinskaja str. 10, 119191, Moscow, Russia
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6
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Pacheco‐García JL, Anoz‐Carbonell E, Loginov DS, Kavan D, Salido E, Man P, Medina M, Pey AL. Counterintuitive structural and functional effects due to naturally‐occurring mutations targeting the active site of the disease‐associated
NQO1
enzyme. FEBS J 2022; 290:1855-1873. [PMID: 36378023 DOI: 10.1111/febs.16677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/29/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022]
Abstract
Our knowledge on the genetic diversity of the human genome is exponentially growing. However, our capacity to establish genotype-phenotype correlations on a large scale requires a combination of detailed experimental and computational work. This is a remarkable task in human proteins which are typically multifunctional and structurally complex. In addition, mutations often prevent the determination of mutant high-resolution structures by X-ray crystallography. We have characterized here the effects of five mutations in the active site of the disease-associated NQO1 protein, which are found either in cancer cell lines or in massive exome sequencing analysis in human population. Using a combination of H/D exchange, rapid-flow enzyme kinetics, binding energetics and conformational stability, we show that mutations in both sets may cause counterintuitive functional effects that are explained well by their effects on local stability regarding different functional features. Importantly, mutations predicted to be highly deleterious (even those affecting the same protein residue) may cause mild to catastrophic effects on protein function. These functional effects are not well explained by current predictive bioinformatic tools and evolutionary models that account for site conservation and physicochemical changes upon mutation. Our study also reinforces the notion that naturally occurring mutations not identified as disease-associated can be highly deleterious. Our approach, combining protein biophysics and structural biology tools, is readily accessible to broadly increase our understanding of genotype-phenotype correlations and to improve predictive computational tools aimed at distinguishing disease-prone against neutral missense variants in the human genome.
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Affiliation(s)
- Juan Luis Pacheco‐García
- Departamento de Química Física, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada Spain
| | - Ernesto Anoz‐Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC‐CSIC Joint Unit), Universidad de Zaragoza, 50009 Zaragoza Spain
| | - Dmitry S. Loginov
- Institute of Microbiology ‐ BioCeV Academy of Sciences of the Czech Republic, Prumyslova 595, Vestec 252 50 Czech Republic
| | - Daniel Kavan
- Institute of Microbiology ‐ BioCeV Academy of Sciences of the Czech Republic, Prumyslova 595, Vestec 252 50 Czech Republic
| | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de la Laguna, 38320 Tenerife Spain
| | - Petr Man
- Institute of Microbiology ‐ BioCeV Academy of Sciences of the Czech Republic, Prumyslova 595, Vestec 252 50 Czech Republic
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC‐CSIC Joint Unit), Universidad de Zaragoza, 50009 Zaragoza Spain
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada Spain
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7
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Pacheco-Garcia JL, Anoz-Carbonell E, Loginov DS, Vankova P, Salido E, Man P, Medina M, Palomino-Morales R, Pey AL. Different phenotypic outcome due to site-specific phosphorylation in the cancer-associated NQO1 enzyme studied by phosphomimetic mutations. Arch Biochem Biophys 2022; 729:109392. [PMID: 36096178 DOI: 10.1016/j.abb.2022.109392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/02/2022]
Abstract
Protein phosphorylation is a common phenomenon in human flavoproteins although the functional consequences of this site-specific modification are largely unknown. Here, we evaluated the effects of site-specific phosphorylation (using phosphomimetic mutations at sites S40, S82 and T128) on multiple functional aspects as well as in the structural stability of the antioxidant and disease-associated human flavoprotein NQO1 using biophysical and biochemical methods. In vitro biophysical studies revealed effects of phosphorylation at different sites such as decreased binding affinity for FAD and structural stability of its binding site (S82), conformational stability (S40 and S82) and reduced catalytic efficiency and functional cooperativity (T128). Local stability measurements by H/D exchange in different ligation states provided structural insight into these effects. Transfection of eukaryotic cells showed that phosphorylation at sites S40 and S82 may reduce steady-levels of NQO1 protein by enhanced proteasome-induced degradation. We show that site-specific phosphorylation of human NQO1 may cause pleiotropic and counterintuitive effects on this multifunctional protein with potential implications for its relationships with human disease. Our approach allows to establish relationships between site-specific phosphorylation, functional and structural stability effects in vitro and inside cells paving the way for more detailed analyses of phosphorylation at the flavoproteome scale.
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Affiliation(s)
- Juan Luis Pacheco-Garcia
- Departamento de Química Física, Universidad de Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Cellular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50009, Zaragoza, Spain
| | - Dmitry S Loginov
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Pavla Vankova
- Institute of Biotechnology - BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de la Laguna, 38320, Tenerife, Spain
| | - Petr Man
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Cellular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50009, Zaragoza, Spain
| | - Rogelio Palomino-Morales
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences and Biomedical Research Center (CIBM), University of Granada, Granada, Spain
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Av. Fuentenueva s/n, 18071, Granada, Spain.
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8
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Pacheco-Garcia JL, Loginov DS, Anoz-Carbonell E, Vankova P, Palomino-Morales R, Salido E, Man P, Medina M, Naganathan AN, Pey AL. Allosteric Communication in the Multifunctional and Redox NQO1 Protein Studied by Cavity-Making Mutations. Antioxidants (Basel) 2022; 11:antiox11061110. [PMID: 35740007 PMCID: PMC9219786 DOI: 10.3390/antiox11061110] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 02/01/2023] Open
Abstract
Allosterism is a common phenomenon in protein biochemistry that allows rapid regulation of protein stability; dynamics and function. However, the mechanisms by which allosterism occurs (by mutations or post-translational modifications (PTMs)) may be complex, particularly due to long-range propagation of the perturbation across protein structures. In this work, we have investigated allosteric communication in the multifunctional, cancer-related and antioxidant protein NQO1 by mutating several fully buried leucine residues (L7, L10 and L30) to smaller residues (V, A and G) at sites in the N-terminal domain. In almost all cases, mutated residues were not close to the FAD or the active site. Mutations L→G strongly compromised conformational stability and solubility, and L30A and L30V also notably decreased solubility. The mutation L10A, closer to the FAD binding site, severely decreased FAD binding affinity (≈20 fold vs. WT) through long-range and context-dependent effects. Using a combination of experimental and computational analyses, we show that most of the effects are found in the apo state of the protein, in contrast to other common polymorphisms and PTMs previously characterized in NQO1. The integrated study presented here is a first step towards a detailed structural–functional mapping of the mutational landscape of NQO1, a multifunctional and redox signaling protein of high biomedical relevance.
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Affiliation(s)
- Juan Luis Pacheco-Garcia
- Departamento de Química Física, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada, Spain
- Correspondence: (J.L.P.-G.); (A.L.P.); Tel.: +34-958243173 (A.L.P.)
| | - Dmitry S. Loginov
- Institute of Microbiology—BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, 252 50 Vestec, Czech Republic; (D.S.L.); (P.M.)
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50009 Zaragoza, Spain; (E.A.-C.); (M.M.)
| | - Pavla Vankova
- Institute of Biotechnology—BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, 252 50 Vestec, Czech Republic;
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 128 43 Prague, Czech Republic
| | - Rogelio Palomino-Morales
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias y Centro de Investigaciones Biomédicas (CIBM), Universidad de Granada, 18016 Granada, Spain;
| | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de la Laguna, 38320 Tenerife, Spain;
| | - Petr Man
- Institute of Microbiology—BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, 252 50 Vestec, Czech Republic; (D.S.L.); (P.M.)
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50009 Zaragoza, Spain; (E.A.-C.); (M.M.)
| | - Athi N. Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai 600036, India;
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada, Spain
- Correspondence: (J.L.P.-G.); (A.L.P.); Tel.: +34-958243173 (A.L.P.)
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9
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Polák M, Yassaghi G, Kavan D, Filandr F, Fiala J, Kukačka Z, Halada P, Loginov DS, Novák P. Utilization of Fast Photochemical Oxidation of Proteins and Both Bottom-up and Top-down Mass Spectrometry for Structural Characterization of a Transcription Factor-dsDNA Complex. Anal Chem 2022; 94:3203-3210. [PMID: 35134296 DOI: 10.1021/acs.analchem.1c04746] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A combination of covalent labeling techniques and mass spectrometry (MS) is currently a progressive approach for deriving insights related to the mapping of protein surfaces or protein-ligand interactions. In this study, we mapped an interaction interface between the DNA binding domain (DBD) of FOXO4 protein and the DNA binding element (DAF16) using fast photochemical oxidation of proteins (FPOP). Residues involved in protein-DNA interaction were identified using the bottom-up approach. To confirm the findings and avoid a misinterpretation of the obtained data, caused by possible multiple radical oxidations leading to the protein surface alteration and oxidation of deeply buried amino acid residues, a top-down approach was employed for the first time in FPOP analysis. An isolation of singly oxidized ions enabled their gas-phase separation from multiply oxidized species followed by CID and ECD fragmentation. Application of both fragmentation techniques allowed generation of complementary fragment sets, out of which the regions shielded in the presence of DNA were deduced. The findings obtained by bottom-up and top-down approaches were highly consistent. Finally, FPOP results were compared with those of the HDX study of the FOXO4-DBD·DAF16 complex. No contradictions were found between the methods. Moreover, their combination provides complementary information related to the structure and dynamics of the protein-DNA complex. Data are available via ProteomeXchange with identifier PXD027624.
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Affiliation(s)
- Marek Polák
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic.,Faculty of Science, Charles University, Prague, 12843, Czech Republic
| | - Ghazaleh Yassaghi
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic.,Faculty of Science, Charles University, Prague, 12843, Czech Republic
| | - František Filandr
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic.,Faculty of Science, Charles University, Prague, 12843, Czech Republic
| | - Jan Fiala
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic.,Faculty of Science, Charles University, Prague, 12843, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic
| | - Petr Halada
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic
| | - Dmitry S Loginov
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic.,Orekhovich Institute of Biomedical Chemistry, Moscow, 119191, Russia
| | - Petr Novák
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic
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10
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Loginov DS, Fiala J, Brechlin P, Kruppa G, Novak P. Hydroxyl radical footprinting analysis of a human haptoglobin-hemoglobin complex. Biochim Biophys Acta Proteins Proteom 2022; 1870:140735. [PMID: 34742912 DOI: 10.1016/j.bbapap.2021.140735] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 09/22/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022]
Abstract
Methods of structural mass spectrometry have become more popular to study protein structure and dynamics. Among them, fast photochemical oxidation of proteins (FPOP) has several advantages such as irreversibility of modifications and more facile determination of the site of modification with single residue resolution. In the present study, FPOP analysis was applied to study the hemoglobin (Hb) - haptoglobin (Hp) complex allowing identification of respective regions altered upon the complex formation. FPOP footprinting using a timsTOF Pro mass spectrometer revealed structural information for 84 and 76 residues in Hp and Hb, respectively, including statistically significant differences in the modification extent below 0.3%. The most affected residues upon complex formation were Met76 and Tyr140 in Hbα, and Tyr280 and Trp284 in Hpβ. The data allowed determination of amino acids directly involved in Hb - Hp interactions and those located outside of the interaction interface yet affected by the complex formation. Also, previously modeled interaction between Hb βTrp37 and Hp βPhe292 was not confirmed by our data. Data are available via ProteomeXchange with identifier PXD021621.
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Affiliation(s)
- Dmitry S Loginov
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic; Orekhovich Institute of Biomedical Chemistry, Pogodinskaja str. 10, 119191 Moscow, Russia.
| | - Jan Fiala
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic; Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Peter Brechlin
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Gary Kruppa
- Bruker s.r.o., Prazakova 60, 619 00, Brno, Czech Republic
| | - Petr Novak
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic.
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11
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Rusanov AL, Kozhin PM, Tikhonova OV, Zgoda VG, Loginov DS, Chlastáková A, Selinger M, Sterba J, Grubhoffer L, Luzgina NG. Proteome Profiling of PMJ2-R and Primary Peritoneal Macrophages. Int J Mol Sci 2021; 22:6323. [PMID: 34204832 PMCID: PMC8231560 DOI: 10.3390/ijms22126323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 05/30/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022] Open
Abstract
In vitro models are often used for studying macrophage functions, including the process of phagocytosis. The application of primary macrophages has limitations associated with the individual characteristics of animals, which can lead to insufficient standardization and higher variability of the obtained results. Immortalized cell lines do not have these disadvantages, but their responses to various signals can differ from those of the living organism. In the present study, a comparative proteomic analysis of immortalized PMJ2-R cell line and primary peritoneal macrophages isolated from C57BL/6 mice was performed. A total of 4005 proteins were identified, of which 797 were quantified. Obtained results indicate significant differences in the abundances of many proteins, including essential proteins associated with the process of phagocytosis, such as Elmo1, Gsn, Hspa8, Itgb1, Ncf2, Rac2, Rack1, Sirpa, Sod1, C3, and Msr1. These findings indicate that outcomes of studies utilizing PMJ2-R cells as a model of peritoneal macrophages should be carefully validated. All MS data are deposited in ProteomeXchange with the identifier PXD022133.
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Affiliation(s)
- Alexander L. Rusanov
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Pogodinskaja Str. 10, 119121 Moscow, Russia; (P.M.K.); (O.V.T.); (V.G.Z.); (D.S.L.); (N.G.L.)
| | - Peter M. Kozhin
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Pogodinskaja Str. 10, 119121 Moscow, Russia; (P.M.K.); (O.V.T.); (V.G.Z.); (D.S.L.); (N.G.L.)
| | - Olga V. Tikhonova
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Pogodinskaja Str. 10, 119121 Moscow, Russia; (P.M.K.); (O.V.T.); (V.G.Z.); (D.S.L.); (N.G.L.)
| | - Victor G. Zgoda
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Pogodinskaja Str. 10, 119121 Moscow, Russia; (P.M.K.); (O.V.T.); (V.G.Z.); (D.S.L.); (N.G.L.)
| | - Dmitry S. Loginov
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Pogodinskaja Str. 10, 119121 Moscow, Russia; (P.M.K.); (O.V.T.); (V.G.Z.); (D.S.L.); (N.G.L.)
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (A.C.); (M.S.); (J.S.); (L.G.)
- BioCeV—Institute of Microbiology of the CAS, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Adéla Chlastáková
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (A.C.); (M.S.); (J.S.); (L.G.)
| | - Martin Selinger
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (A.C.); (M.S.); (J.S.); (L.G.)
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Jan Sterba
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (A.C.); (M.S.); (J.S.); (L.G.)
| | - Libor Grubhoffer
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (A.C.); (M.S.); (J.S.); (L.G.)
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Nataliya G. Luzgina
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Pogodinskaja Str. 10, 119121 Moscow, Russia; (P.M.K.); (O.V.T.); (V.G.Z.); (D.S.L.); (N.G.L.)
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12
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Loginov DS, Fiala J, Chmelik J, Brechlin P, Kruppa G, Novak P. Correction to "Benefits of Ion Mobility Separation and Parallel Accumulation-Serial Fragmentation Technology on timsTOF Pro for the Needs of Fast Photochemical Oxidation of Protein Analysis". ACS Omega 2021; 6:14726. [PMID: 34124494 PMCID: PMC8190877 DOI: 10.1021/acsomega.1c02648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 06/12/2023]
Abstract
[This corrects the article DOI: 10.1021/acsomega.1c00732.].
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Affiliation(s)
- Dmitry S Loginov
- Institute of Microbiology, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
- Orekhovich Institute of Biomedical Chemistry, Pogodinskaja str. 10, 119191 Moscow, Russia
| | - Jan Fiala
- Faculty of Science, Charles University, Hlavova 8, 128 20 Prague, Czech Republic
| | - Josef Chmelik
- Institute of Microbiology, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
| | - Peter Brechlin
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Gary Kruppa
- Bruker s.r.o., Prazakova 60, 619 00 Brno, Czech Republic
| | - Petr Novak
- Institute of Microbiology, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
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13
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Loginov DS, Fiala J, Chmelik J, Brechlin P, Kruppa G, Novak P. Benefits of Ion Mobility Separation and Parallel Accumulation-Serial Fragmentation Technology on timsTOF Pro for the Needs of Fast Photochemical Oxidation of Protein Analysis. ACS Omega 2021; 6:10352-10361. [PMID: 34056188 PMCID: PMC8153767 DOI: 10.1021/acsomega.1c00732] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/29/2021] [Indexed: 05/07/2023]
Abstract
Fast photochemical oxidation of proteins (FPOP) is a recently developed technique for studying protein folding, conformations, interactions, etc. In this method, hydroxyl radicals, usually generated by KrF laser photolysis of H2O2, are used for irreversible labeling of solvent-exposed side chains of amino acids. Mapping of the oxidized residues to the protein's structure requires pinpointing of modifications using a bottom-up proteomic approach. In this work, a quadrupole time-of-flight (QTOF) mass spectrometer coupled with trapped ion mobility spectrometry (timsTOF Pro) was used for identification of oxidative modifications in a model protein. Multiple modifications on the same residues, including six modifications of histidine, were successfully resolved. Moreover, parallel accumulation-serial fragmentation (PASEF) technology allows successful sequencing of even minor populations of modified peptides. The data obtained indicate a clear improvement of the quality of the FPOP analysis from the viewpoint of the number of identified peptides bearing oxidative modifications and their precise localization. Data are available via ProteomeXchange with identifier PXD020509.
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Affiliation(s)
- Dmitry S. Loginov
- Institute
of Microbiology, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
- Faculty
of Science, Charles University, Hlavova 8, 128 20 Prague, Czech Republic
| | - Jan Fiala
- Orekhovich
Institute of Biomedical Chemistry, Pogodinskaja str. 10, 119191 Moscow, Russia
| | - Josef Chmelik
- Institute
of Microbiology, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
| | - Peter Brechlin
- Bruker
Daltonik GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Gary Kruppa
- Bruker
s.r.o., Prazakova 60, 619 00 Brno, Czech
Republic
| | - Petr Novak
- Institute
of Microbiology, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
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14
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Loginov DS, Loginova YF, Dycka F, Böttinger K, Vechtova P, Sterba J. Tissue-specific signatures in tick cell line MS profiles. Parasit Vectors 2019; 12:212. [PMID: 31060584 PMCID: PMC6503378 DOI: 10.1186/s13071-019-3460-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/27/2019] [Indexed: 11/10/2022] Open
Abstract
Background The availability of tick in vitro cell culture systems has facilitated many aspects of tick research, including proteomics. However, certain cell lines have shown a tissue-specific response to infection. Thus, a more thorough characterization of tick cell lines is necessary. Proteomic comparative studies of various tick cell lines will contribute to more efficient application of tick cell lines as model systems for investigation of host-vector-pathogen interactions. Results Three cell lines obtained from a hard tick, Ixodes ricinus, and two from I. scapularis were investigated. A cell mass spectrometry approach (MALDI-TOF MS) was applied, as well as classical proteomic workflows. Using PCA, tick cell line MS profiles were grouped into three clusters comprising IRE/CTVM19 and ISE18, IRE11 and IRE/CTVM20, and ISE6 cell lines. Two other approaches confirmed the results of PCA: in-solution digestion followed by nanoLC-ESI-Q-TOF MS/MS and 2D electrophoresis. The comparison of MS spectra of the cell lines and I. ricinus tick organs revealed 29 shared peaks. Of these, five were specific for ovaries, three each for gut and salivary glands, and one for Malpighian tubules. For the first time, characteristic peaks in MS profiles of tick cell lines were assigned to proteins identified in acidic extracts of corresponding cell lines. Conclusions Several organ-specific MS signals were revealed in the profiles of tick cell lines. Electronic supplementary material The online version of this article (10.1186/s13071-019-3460-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dmitry S Loginov
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic. .,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic.
| | - Yana F Loginova
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic.,Orekhovich Institute of Biomedical Chemistry, Pogodinskaja str. 10, Moscow, 119191, Russia
| | - Filip Dycka
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic
| | - Katharina Böttinger
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic
| | - Pavlina Vechtova
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic
| | - Jan Sterba
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic
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15
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Loginov DS, Vavilova EA, Savinova ОS, Abyanova AR, Chulkin AM, Vasina DV, Zherdev AV, Koroleva OV. Immunoassays of fungal laccases for screening of natural enzymes and control of recombinant enzyme production. Biotechnol Appl Biochem 2013; 61:230-6. [PMID: 24112404 DOI: 10.1002/bab.1160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/23/2013] [Indexed: 11/07/2022]
Abstract
Because of the wide application of laccases in different biotechnological processes and intense studies of the enzymes from different sources, the development of efficient techniques for monitoring laccase level is a task of significant importance. Enzyme-linked immunosorbent assay (ELISA) and Western blotting techniques were developed to control total content and isoform composition of laccases, including their recombinant preparations. Because glycosylated and nonglycosylated forms have different structures and sets of epitopes, two kinds of polyclonal antibodies were obtained and applied. The first antibody recognized the native (glycosylated) laccase purified from Trametes hirsuta and the second one reacted with recombinant (nonglycosylated) laccase expressed in Escherichia coli. Titers of the antibodies were analyzed by indirect ELISA with laccases isolated from several strains of basidiomycetes. The obtained cross-reactivity data for both antibodies demonstrated a correspondence with sequence homology of the laccases. The antibodies raised against recombinant (nonglycosylated) laccase had higher titers and thus were preferable for screening of recombinant laccase in cultural media. Thus, optimal antibody preparations were selected for screening of laccase-producing strains, and the control of recombinant enzymes and the efficiency of their use in immunochemical control of laccase levels were confirmed.
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Affiliation(s)
- Dmitry S Loginov
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
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16
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Vasina DV, Loginov DS, Mustafaev ON, Goldenkova-Pavlova IV, Koroleva OV. [Range of Gene candidates involved in biosynthesis of laccase from basidiomycete Trametes hirsuta]. Genetika 2013; 49:1149-1154. [PMID: 25474891 DOI: 10.7868/s0016675813090129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A comparative analysis of transcripts from the basidiomycota T. hirsuta grown with and without an inducer of the laccase biosynthesis was carried out. Methods of subtraction hybridization and massive parallel sequencing were used for this purpose. Unique transcripts encoded by genes that have a relatively high level of expression and belong to different gene ontology categories were identified. Also, a large number of transcripts were found to encode for predicted proteins, as well as noncoding transcripts. The latter may represent regulatory RNA molecules. Transcripts that increase their abundance when the laccase synthesis is induced are selected as gene-candidates involved in the laccase biosynthetic pathway.
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Abstract
Rate constants and activation parameters have been determined for the internal electron transfer from type 1 (T1) to type 3 (T3) copper ions in laccase from both the fungus Trametes hirsuta and the lacquer tree Rhus vernicifera, using the pulse radiolysis method. The rate constant at 298 K and the enthalpy and entropy of activation were 25 ± 1 s(-1), 39.7 ± 5.0 kJ·mol(-1) and -87 ± 9 J·mol(-1) ·K(-1) for the fungal enzyme and 1.1 ± 0.1 s(-1), 9.8 ± 0.2 kJ·mol(-1) and -211 ± 3 J·mol(-1) ·K(-1) for the tree enzyme. The initial reduction of the T1 site by pulse radiolytically produced radicals was direct in the case of T. hirsuta laccase, but occured indirectly via a disulfide radical in R. vernicifera. The equilibrium constant that characterizes the electron transfer from T1 to T3 copper ions was 0.4 for T. hirsuta laccase and 1.5 for R. vernicifera laccase, leading to full reduction of the T1 site occurring at 2.9 ± 0.2 electron equivalents for T. hirsuta and 4 electron equivalents for R. vernicifera laccase. These results were compared with each other and with those for the same process in other multicopper oxidases, ascorbate oxidase and Streptomyces coelicolor laccase, using available structural information and electron transfer theory.
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Affiliation(s)
- Ole Farver
- Institute of Analytical Chemistry, University of Copenhagen, Copenhagen, Denmark.
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18
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Abianova AR, Chulkin AM, Vavilova EA, Fedorova TV, Loginov DS, Koroleva OV, Benevolenskiĭ SV. [A heterologous production of the Trametes hirsuta laccase in the fungus Penicillium canescens]. Prikl Biokhim Mikrobiol 2010; 46:342-347. [PMID: 20586288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A heterologous protein expression in the fungus Penicillium canescens is described for the first time. The fungal strains producing Trametes hirsuta laccase under control of a highly efficient promoter of the P. canescens gene bgaS has been constructed. These strains efficiently transcribe the T. hirsuta 072 laccase gene with a correct intron splicing. Activity of the secreted heterologous laccase in the culture liquid reaches 3 U/ml, accounting for 98% of the total laccase activity, which demonstrates a high efficiency ofheterologous secretion. The synthesized P. canescens laccase has the same molecular weight as the enzyme produced by T. hirsuta 072.
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19
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Chulkin AM, Loginov DS, Vavilova EA, Abaianova AR, Zorov IN, Kurzeev SA, Koroleva OV, Benevolenskiĭ SV. [Cloning of the Penicillium canescens endo-1,4-beta-glucanase gene egl3 and the characterization of the recombinant enzyme]. Prikl Biokhim Mikrobiol 2009; 45:163-170. [PMID: 19382702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The gene egl3 of the filamentous fungus Penicillium canescens endo-1,4-beta-glucanase, belonging to family 12 glycosyl hydrolases, was cloned and sequenced. The gene was expressed in P. canescens under the control of the strong promoter of gene bgaS, coding for beta-galactosidase of this fungus, and efficient endoglucanase producer strains were obtained. The recombinant protein was isolated from the culture liquid of the producer strain EGL3-13 and purified to homogeneity; its specific activity was 31.7 IU; molecular weight, 26 kDa; and pH and temperature optimums, 3.2 and 54 degrees C, respectively. The Km and Vm values for CMC hydrolysis were determined; they amounted to 17.1 g/1 and 0.31 microM/(mg s), respectively.
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20
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Bodin ON, Loginov DS, Mitrokhina NI. [Improvement of ECG analysis in monitoring the electrical cardiac activity]. Med Tekh 2008:23-26. [PMID: 18688940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The goal of this work was to suggest a method for improving the efficiency of ECG analysis in measurements of the electrical cardiac activity. The suggested method is based on a solution of the inverse ECG problem. The algorithm for measuring the electrical cardiac activity includes storage of ECG signals from various sources in a database (the body and heart geometry are taken into account), determination of electrically active areas, and determination of the electrical activity at each point of the heart model surface. Test ECG signals available at a free-access web site were used to verify the results of monitoring of the electrical cardiac activity.
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