1
|
Wójcik P, Glanowski M, Mrugała B, Procner M, Zastawny O, Flejszar M, Kurpiewska K, Niedziałkowska E, Minor W, Oszajca M, Bojarski AJ, Wojtkiewicz AM, Szaleniec M. Structure, Mutagenesis, and QM:MM Modeling of 3-Ketosteroid Δ 1-Dehydrogenase from Sterolibacterium denitrificans─The Role of a New Putative Membrane-Associated Domain and Proton-Relay System in Catalysis. Biochemistry 2023; 62:808-823. [PMID: 36625854 PMCID: PMC9960185 DOI: 10.1021/acs.biochem.2c00576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
3-Ketosteroid Δ1-dehydrogenases (KstD) are important microbial flavin enzymes that initiate the metabolism of steroid ring A and find application in the synthesis of steroid drugs. We present a structure of the KstD from Sterolibacterium denitrificans (AcmB), which contains a previously uncharacterized putative membrane-associated domain and extended proton-relay system. The experimental and theoretical studies show that the steroid Δ1-dehydrogenation proceeds according to the Ping-Pong bi-bi kinetics and a two-step base-assisted elimination (E2cB) mechanism. The mechanism is validated by evaluating the experimental and theoretical kinetic isotope effect for deuterium-substituted substrates. The role of the active-site residues is quantitatively assessed by point mutations, experimental activity assays, and QM/MM MD modeling of the reductive half-reaction (RHR). The pre-steady-state kinetics also reveals that the low pH (6.5) optimum of AcmB is dictated by the oxidative half-reaction (OHR), while the RHR exhibits a slight optimum at the pH usual for the KstD family of 8.5. The modeling confirms the origin of the enantioselectivity of C2-H activation and substrate specificity for Δ4-3-ketosteroids. Finally, the cholest-4-en-3-one turns out to be the best substrate of AcmB in terms of ΔG of binding and predicted rate of dehydrogenation.
Collapse
Affiliation(s)
- Patrycja Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Michał Glanowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Beata Mrugała
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Magdalena Procner
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland; Jerzy Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Kraków, Poland
| | - Olga Zastawny
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Monika Flejszar
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland; Department of Physical Chemistry, Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland
| | | | - Ewa Niedziałkowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Maria Oszajca
- Faculty of Chemistry, Jagiellonian University,30-387 Kraków, Poland
| | - Andrzej J. Bojarski
- Jerzy Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Kraków, Poland
| | - Agnieszka M. Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| |
Collapse
|
2
|
1,2-Hydrogenation and Transhydrogenation Catalyzed by 3-Ketosteroid Δ 1-Dehydrogenase from Sterolibacterium denitrificans-Kinetics, Isotope Labelling and QM:MM Modelling Studies. Int J Mol Sci 2022; 23:ijms232314660. [PMID: 36498984 PMCID: PMC9736390 DOI: 10.3390/ijms232314660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
Bacteria and fungi that are able to metabolize steroids express 3-ketosteroid-Δ1-dehydrogenases (KstDs). KstDs such as AcmB form Sterolibacterium denitrificans Chol-1 catalyze the enantioselective 1α,2β-dehydrogenation of steroids to their desaturated analogues, e.g., the formation of 1,4-androstadiene-3,17-dione (ADD) from 4-androsten-3,17-dione (AD). The reaction catalyzed by KstD can be reversed if the appropriate electron donor, such as benzyl viologen radical cation, is present. Furthermore, KstDs can also catalyze transhydrogenation, which is the transfer of H atoms between 3-ketosteroids and 1-dehydrosteroids. In this paper, we showed that AcmB exhibits lower pH optima for hydrogenation and dehydrogenation by 3.5-4 pH units than those observed for KstD from Nocardia corallina. We confirmed the enantiospecificity of 1α,2β-hydrogenation and 1α,2β-transhydrogenation catalyzed by AcmB and showed that, under acidic pH conditions, deuterons are introduced not only at 2β but also at the 1α position. We observed a higher degree of H/D exchange at Y363, which activates the C2-H bond, compared to that at FAD, which is responsible for redox at the C1 position. Furthermore, for the first time, we observed the introduction of the third deuteron into the steroid core. This effect was explained through a combination of LC-MS experiments and QM:MM modelling, and we attribute it to a decrease in the enantioselectivity of C2-H activation upon the deuteration of the 2β position. The increase in the activation barrier resulting from isotopic substitution increases the chance of the formation of d3-substituted 3-ketosteroids. Finally, we demonstrate a method for the synthesis of 3-ketosteroids chirally deuterated at 1α,2β positions, obtaining 1α,2β-d2-4-androsten-3,17-dione with a 51% yield (8.61 mg).
Collapse
|
3
|
Plasmonic hot spots reveal local conformational transitions induced by DNA double-strand breaks. Sci Rep 2022; 12:12158. [PMID: 35840615 PMCID: PMC9287445 DOI: 10.1038/s41598-022-15313-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/22/2022] [Indexed: 11/08/2022] Open
Abstract
DNA double-strand breaks (DSBs) are typical DNA lesions that can lead to cell death, translocations, and cancer-driving mutations. The repair process of DSBs is crucial to the maintenance of genomic integrity in all forms of life. However, the limitations of sensitivity and special resolution of analytical techniques make it difficult to investigate the local effects of chemotherapeutic drugs on DNA molecular structure. In this work, we exposed DNA to the anticancer antibiotic bleomycin (BLM), a damaging factor known to induce DSBs. We applied a multimodal approach combining (i) atomic force microscopy (AFM) for direct visualization of DSBs, (ii) surface-enhanced Raman spectroscopy (SERS) to monitor local conformational transitions induced by DSBs, and (iii) multivariate statistical analysis to correlate the AFM and SERS results. On the basis of SERS results, we identified that bands at 1050 cm-1 and 730 cm-1 associated with backbone and nucleobase vibrations shifted and changed their intensities, indicating conformational modifications and strand ruptures. Based on averaged SERS spectra, the PLS regressions for the number of DSBs caused by corresponding molar concentrations of bleomycin were calculated. The strong correlation (R2 = 0.92 for LV = 2) between the predicted and observed number of DSBs indicates, that the model can not only predict the number of DSBs from the spectra but also detect the spectroscopic markers of DNA damage and the associated conformational changes.
Collapse
|
4
|
Wójcik P, Glanowski M, Wojtkiewicz AM, Rohman A, Szaleniec M. Universal capability of 3-ketosteroid Δ 1-dehydrogenases to catalyze Δ 1-dehydrogenation of C17-substituted steroids. Microb Cell Fact 2021; 20:119. [PMID: 34162386 PMCID: PMC8220720 DOI: 10.1186/s12934-021-01611-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 3-Ketosteroid Δ1-dehydrogenases (KSTDs) are the enzymes involved in microbial cholesterol degradation and modification of steroids. They catalyze dehydrogenation between C1 and C2 atoms in ring A of the polycyclic structure of 3-ketosteroids. KSTDs substrate spectrum is broad, even though most of them prefer steroids with small substituents at the C17 atom. The investigation of the KSTD's substrate specificity is hindered by the poor solubility of the hydrophobic steroids in aqueous solutions. In this paper, we used 2-hydroxpropyl-β-cyclodextrin (HBC) as a solubilizing agent in a study of the KSTDs steady-state kinetics and demonstrated that substrate bioavailability has a pivotal impact on enzyme specificity. RESULTS Molecular dynamics simulations on KSTD1 from Rhodococcus erythropolis indicated no difference in ΔGbind between the native substrate, androst-4-en-3,17-dione (AD; - 8.02 kcal/mol), and more complex steroids such as cholest-4-en-3-one (- 8.40 kcal/mol) or diosgenone (- 6.17 kcal/mol). No structural obstacle for binding of the extended substrates was also observed. Following this observation, our kinetic studies conducted in the presence of HBC confirmed KSTD1 activity towards both types of steroids. We have compared the substrate specificity of KSTD1 to the other enzyme known for its activity with cholest-4-en-3-one, KSTD from Sterolibacterium denitrificans (AcmB). The addition of solubilizing agent caused AcmB to exhibit a higher affinity to cholest-4-en-3-one (Ping-Pong bi bi KmA = 23.7 μM) than to AD (KmA = 529.2 μM), a supposedly native substrate of the enzyme. Moreover, we have isolated AcmB isoenzyme (AcmB2) and showed that conversion of AD and cholest-4-en-3-one proceeds at a similar rate. We demonstrated also that the apparent specificity constant of AcmB for cholest-4-en-3-one (kcat/KmA = 9.25∙106 M-1 s-1) is almost 20 times higher than measured for KSTD1 (kcat/KmA = 4.71∙105 M-1 s-1). CONCLUSIONS We confirmed the existence of AcmB preference for a substrate with an undegraded isooctyl chain. However, we showed that KSTD1 which was reported to be inactive with such substrates can catalyze the reaction if the solubility problem is addressed.
Collapse
Affiliation(s)
- Patrycja Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30239, Krakow, Poland
| | - Michał Glanowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30239, Krakow, Poland
| | - Agnieszka M Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30239, Krakow, Poland
| | - Ali Rohman
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, 60115, Indonesia
- Laboratory of Proteomics, Research Center for Bio-Molecule Engineering (BIOME), Universitas Airlangga, Surabaya, 60115, Indonesia
- Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30239, Krakow, Poland.
| |
Collapse
|
5
|
Application of Immobilized Cholest-4-en-3-one Δ1-Dehydrogenase from Sterolibacterium Denitrificans for Dehydrogenation of Steroids. Catalysts 2020. [DOI: 10.3390/catal10121460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cholest-4-en-3-one Δ1-dehydrogenase (AcmB) from Sterolibacterium denitrificans was successfully immobilized on 3-aminopropyltrimethoysilane functionalized mesoporous cellular foam (MCF) and Santa Barbara Amorphous (SBA-15) silica supports using adsorption or covalently with glutaraldehyde or divinyl sulfone linkers. The best catalyst, AcmB on MCF linked covalently with glutaraldehyde, retained the specific activity of the homogenous enzyme while exhibiting a substantial increase of the operational stability. The immobilized enzyme was used continuously in the fed-batch reactor for 27 days, catalyzing 1,2-dehydrogenation of androst-4-en-3-one to androst-1,4-dien-3-one with a final yield of 29.9 mM (8.56 g/L) and 99% conversion. The possibility of reuse of the immobilized catalyst was also demonstrated and resulted in a doubling of the product amount compared to that in the reference homogenous reactor. Finally, it was shown that molecular oxygen from the air can efficiently be used as an electron acceptor either reoxidizing directly the enzyme or the reduced 2,4-dichlorophenolindophenol (DCPIPH2).
Collapse
|
6
|
Wojtkiewicz AM, Wójcik P, Procner M, Flejszar M, Oszajca M, Hochołowski M, Tataruch M, Mrugała B, Janeczko T, Szaleniec M. The efficient Δ 1-dehydrogenation of a wide spectrum of 3-ketosteroids in a broad pH range by 3-ketosteroid dehydrogenase from Sterolibacterium denitrificans. J Steroid Biochem Mol Biol 2020; 202:105731. [PMID: 32777354 DOI: 10.1016/j.jsbmb.2020.105731] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/20/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022]
Abstract
Cholest-4-en-3-one Δ1-dehydrogenase (AcmB) from Sterolibacterium denitrificans, a key enzyme of the central degradation pathway of cholesterol, is a protein catalyzing Δ1-dehydrogenation of a wide range of 3-ketosteroids. In this study, we demonstrate the application of AcmB in the synthesis of 1-dehydro-3-ketosteroids and investigate the influence of reaction conditions on the catalytic performance of the enzyme. The recombinant AcmB expressed in E. coli BL21(DE3)Magic exhibits a broad pH optimum and pH stability in the range of 6.5 to 9.0. The activity-based pH optimum of AcmB reaction depends on the type of electron acceptor (2,6-dichloroindophenol - DCPIP, phenazine methosulfate - PMS or potassium hexacyanoferrate - K3[Fe(CN)6]) used in the biocatalytic process yielding the best kinetic properties for the reaction with a DCPIP/PMS mixture (kcat/Km = 1.4·105 s-1·M-1 at pH 9.0) followed by DCPIP (kcat/Km = 1.0·105 s-1·M-1 at pH = 6.5) and K3[Fe(CN)6] (kcat/Km = 0.5·102 s-1·M-1 at pH = 8.0). The unique feature of AcmB is its capability to convert both testosterone derivatives (C20-C22) as well as steroids substituted at C17 (C27-C30) such as cholest-4-en-3-one or (25R)-spirost-4-en-3-one (diosgenone). Apparent steady-state kinetic parameters were determined for both groups of AcmB substrates. In a batch reactor synthesis, the solubility of water-insoluble steroids was facilitated by the addition of a solubilizer, 2-hydroxypropyl-β-cyclodextrin, and organic co-solvent, 2-methoxyethanol. Catalytic properties characterization of AcmB was tested in fed-batch reactor set-ups, using 0.81 μM of isolated enzyme, PMS and aerobic atmosphere resulting in >99% conversion of the C17-C20 3-ketosteroids within 2 h. Finally, the whole cell E. coli system with recombinant enzyme was demonstrated as an efficient biocatalyst in the synthesis of 1-dehydro-3-ketosteroids.
Collapse
Affiliation(s)
- Agnieszka M Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland
| | - Patrycja Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland
| | - Magdalena Procner
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland
| | - Monika Flejszar
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland; Department of Physical Chemistry, Faculty of Chemistry, Rzeszow University of Technology, Al. Powstańców Warszawy 6, PL35959 Rzeszów, Poland; Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, PL30387 Kraków, Poland
| | - Maria Oszajca
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, PL30387 Kraków, Poland
| | - Mateusz Hochołowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland
| | - Mateusz Tataruch
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland
| | - Beata Mrugała
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland
| | - Tomasz Janeczko
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Norwida 25, PL50375 Wrocław, Poland
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL30239, Krakow, Poland.
| |
Collapse
|
7
|
Batys P, Nattich-Rak M, Adamczyk Z. Myoglobin molecule charging in electrolyte solutions. Phys Chem Chem Phys 2020; 22:26764-26775. [DOI: 10.1039/d0cp03771k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The compensated charge of myoglobin molecule in electrolyte solution is considerably smaller than the nominal charge.
Collapse
Affiliation(s)
- Piotr Batys
- Jerzy Haber Institute of Catalysis and Surface Chemistry
- Polish Academy of Sciences
- Niezapominajek 8
- PL-30239 Krakow
- Poland
| | - Małgorzata Nattich-Rak
- Jerzy Haber Institute of Catalysis and Surface Chemistry
- Polish Academy of Sciences
- Niezapominajek 8
- PL-30239 Krakow
- Poland
| | - Zbigniew Adamczyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry
- Polish Academy of Sciences
- Niezapominajek 8
- PL-30239 Krakow
- Poland
| |
Collapse
|
8
|
Hu J, Gao M, Wang Y, Liu M, Wang J, Li J, Song Z, Chen Y, Wang Z. Imaging the Substructures of Individual IgE Antibodies with Atomic Force Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14896-14901. [PMID: 31661619 DOI: 10.1021/acs.langmuir.9b02631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The interactions between antibodies and substrates directly affect their conformations and thus their immune functions. Therefore, it is desirable to study the structures of antibodies at the single molecule level. Herein, the substructures of Immunoglobulin E (IgE) on solid surfaces were investigated. For this purpose, tapping-mode atomic force microscopy (AFM) was applied to observe individual IgE substructures adsorbed onto Mg2+ and Na+ modified mica substrates in air. As expected, the AFM images revealed that the IgE antibodies exhibited different conformations on the surface of mica substrate consisting of the four basic orientations: three domain, two equivalent domain, two unequal domain, and single domain morphologies. Moreover, the differences in the different orientations in single IgE antibodies were also identified clearly.
Collapse
Affiliation(s)
- Jing Hu
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China
- International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Mingyan Gao
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China
- International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Ying Wang
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China
- International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Mengnan Liu
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China
- International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Jianfei Wang
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China
- International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Jiani Li
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China
- International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Zhengxun Song
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China
- International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Yujuan Chen
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China
- International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
- School of Life Sciences , Changchun University of Science and Technology , Changchun 130022 , China
| | - Zuobin Wang
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China
- International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
- JR3CN & IRAC , University of Bedfordshire , Luton LU1 3JU , U.K
| |
Collapse
|