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Nováková M, Škerlová J, Brynda J, Sieglová I, Fábry M, Řezáčová P. SorC protein family: the structural insight into their DNA recognition. Acta Cryst Sect A 2022. [DOI: 10.1107/s205327332209386x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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2
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Kalousková B, Skořepa O, Cmunt D, Abreu C, Krejčová K, Bláha J, Sieglová I, Král V, Fábry M, Pola R, Pechar M, Vaněk O. Tumor Marker B7-H6 Bound to the Coiled Coil Peptide-Polymer Conjugate Enables Targeted Therapy by Activating Human Natural Killer Cells. Biomedicines 2021; 9:biomedicines9111597. [PMID: 34829829 PMCID: PMC8615638 DOI: 10.3390/biomedicines9111597] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 01/02/2023] Open
Abstract
Targeted cancer immunotherapy is a promising tool for restoring immune surveillance and eradicating cancer cells. Hydrophilic polymers modified with coiled coil peptide tags can be used as universal carriers designed for cell-specific delivery of such biologically active proteins. Here, we describe the preparation of pHPMA-based copolymer conjugated with immunologically active protein B7-H6 via complementary coiled coil VAALEKE (peptide E) and VAALKEK (peptide K) sequences. Receptor B7-H6 was described as a binding partner of NKp30, and its expression has been proven for various tumor cell lines. The binding of B7-H6 to NKp30 activates NK cells and results in Fas ligand or granzyme-mediated apoptosis of target tumor cells. In this work, we optimized the expression of coiled coil tagged B7-H6, its ability to bind activating receptor NKp30 has been confirmed by isothermal titration calorimetry, and the binding stoichiometry of prepared chimeric biopolymer has been characterized by analytical ultracentrifugation. Furthermore, this coiled coil B7-H6-loaded polymer conjugate activates NK cells in vitro and, in combination with coiled coil scFv, enables their targeting towards a model tumor cell line. Prepared chimeric biopolymer represents a promising precursor for targeted cancer immunotherapy by activating the cytotoxic activity of natural killer cells.
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Affiliation(s)
- Barbora Kalousková
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
| | - Denis Cmunt
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
| | - Celeste Abreu
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
| | - Kateřina Krejčová
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
| | - Jan Bláha
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
| | - Irena Sieglová
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; (I.S.); (V.K.); (M.F.)
| | - Vlastimil Král
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; (I.S.); (V.K.); (M.F.)
| | - Milan Fábry
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; (I.S.); (V.K.); (M.F.)
| | - Robert Pola
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 16206 Prague, Czech Republic; (R.P.); (M.P.)
| | - Michal Pechar
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 16206 Prague, Czech Republic; (R.P.); (M.P.)
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
- Correspondence:
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3
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Šoltysová M, Sieglová I, Fábry M, Brynda J, Škerlová J, Řezáčová P. Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family. Acta Crystallogr D Struct Biol 2021; 77:1411-1424. [PMID: 34726169 DOI: 10.1107/s2059798321009633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/16/2021] [Indexed: 11/11/2022]
Abstract
The SorC/DeoR family is a large family of bacterial transcription regulators that are involved in the control of carbohydrate metabolism and quorum sensing. To understand the structural basis of DNA recognition, structural studies of two functionally characterized SorC/DeoR family members from Bacillus subtilis were performed: the deoxyribonucleoside regulator bsDeoR and the central glycolytic genes regulator bsCggR. Each selected protein represents one of the subgroups that are recognized within the family. Crystal structures were determined of the N-terminal DNA-binding domains of bsDeoR and bsCggR in complex with DNA duplexes representing the minimal operator sequence at resolutions of 2.3 and 2.1 Å, respectively. While bsDeoRDBD contains a homeodomain-like HTH-type domain, bsCggRDBD contains a winged helix-turn-helix-type motif. Both proteins form C2-symmetric dimers that recognize two consecutive major grooves, and the protein-DNA interactions have been analyzed in detail. The crystal structures were used to model the interactions of the proteins with the full DNA operators, and a common mode of DNA recognition is proposed that is most likely to be shared by other members of the SorC/DeoR family.
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Affiliation(s)
- Markéta Šoltysová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Irena Sieglová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jiří Brynda
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jana Škerlová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Pavlína Řezáčová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
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Man P, Fábry M, Sieglová I, Kavan D, Novák P, Hnízda A. Thiopurine intolerance-causing mutations in NUDT15 induce temperature-dependent destabilization of the catalytic site. Biochim Biophys Acta Proteins Proteom 2019; 1867:376-381. [PMID: 30639426 DOI: 10.1016/j.bbapap.2019.01.006] [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] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/16/2018] [Accepted: 01/06/2019] [Indexed: 01/18/2023]
Abstract
Germline mutations in NUDT15 cause thiopurine intolerance during treatment of leukemia or autoimmune diseases. Previously, it has been shown that the mutations affect the enzymatic activity of the NUDT15 hydrolase due to decreased protein stability in vivo. Here we provide structural insights into protein destabilization in R139C and V18I mutants using thermolysin-based proteolysis and H/D exchange followed by mass spectrometry. Both mutants exhibited destabilization of the catalytic site, which was more pronounced at higher temperature. This structural perturbation is shared by the mutations despite their different positions within the protein structure. Reaction products of NUDT15 reverted these conformational abnormalities, demonstrating the importance of ligands for stabilization of a native state of the mutants. This study shows the action of pharmacogenetic variants in NUDT15 in a context of protein structure, which might open novel directions in personalized chemotherapy.
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Affiliation(s)
- Petr Man
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic; Faculty of Science, Charles University, Hlavova 2030/8, Prague 2 128 43, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Irena Sieglová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic; Faculty of Science, Charles University, Hlavova 2030/8, Prague 2 128 43, Czech Republic
| | - Petr Novák
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic; Faculty of Science, Charles University, Hlavova 2030/8, Prague 2 128 43, Czech Republic
| | - Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10, Czech Republic.
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Čepa A, Ráliš J, Marešová L, Kleinová M, Seifert D, Sieglová I, Král V, Polášek M, Paurová M, Lázníček M, Lebeda O. Radiolabeling of the antibody IgG M75 for epitope of human carbonic anhydrase IX by 61Cu and 64Cu and its biological testing. Appl Radiat Isot 2019; 143:87-97. [DOI: 10.1016/j.apradiso.2018.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 10/16/2018] [Accepted: 10/23/2018] [Indexed: 10/28/2022]
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Pola R, Král V, Filippov SK, Kaberov L, Etrych T, Sieglová I, Sedláček J, Fábry M, Pechar M. Polymer Cancerostatics Targeted by Recombinant Antibody Fragments to GD2-Positive Tumor Cells. Biomacromolecules 2018; 20:412-421. [PMID: 30485077 DOI: 10.1021/acs.biomac.8b01616] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A water-soluble polymer cancerostatic actively targeted against cancer cells expressing a disialoganglioside antigen GD2 was designed, synthesized and characterized. A polymer conjugate of an antitumor drug doxorubicin with a N-(2-hydroxypropyl)methacrylamide-based copolymer was specifically targeted against GD2 antigen-positive tumor cells using a recombinant single chain fragment (scFv) of an anti-GD2 monoclonal antibody. The targeting protein ligand was attached to the polymer-drug conjugate either via a covalent bond between the amino groups of the protein using a traditional nonspecific aminolytic reaction with a reactive polymer precursor or via a noncovalent but highly specific interaction between bungarotoxin covalently linked to the polymer and the recombinant scFv modified with a C-terminal bungarotoxin-binding peptide. The GD2 antigen binding activity and GD2-specific cytotoxicity of the targeted noncovalent polymer-scFv complex proved to be superior to the covalent polymer-scFv conjugate.
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Affiliation(s)
- Robert Pola
- Institute of Macromolecular Chemistry , Czech Academy of Sciences , Heyrovského nám. 2 , 162 06 Prague 6 , Czech Republic
| | - Vlastimil Král
- Institute of Molecular Genetics , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
| | - Sergey K Filippov
- Institute of Macromolecular Chemistry , Czech Academy of Sciences , Heyrovského nám. 2 , 162 06 Prague 6 , Czech Republic
| | - Leonid Kaberov
- Institute of Macromolecular Chemistry , Czech Academy of Sciences , Heyrovského nám. 2 , 162 06 Prague 6 , Czech Republic
| | - Tomáš Etrych
- Institute of Macromolecular Chemistry , Czech Academy of Sciences , Heyrovského nám. 2 , 162 06 Prague 6 , Czech Republic
| | - Irena Sieglová
- Institute of Molecular Genetics , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
| | - Juraj Sedláček
- Institute of Molecular Genetics , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
| | - Michal Pechar
- Institute of Macromolecular Chemistry , Czech Academy of Sciences , Heyrovského nám. 2 , 162 06 Prague 6 , Czech Republic
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7
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Pechar M, Pola R, Janoušková O, Sieglová I, Král V, Fábry M, Tomalová B, Kovář M. Polymer Cancerostatics Targeted with an Antibody Fragment Bound via a Coiled Coil Motif: In Vivo Therapeutic Efficacy against Murine BCL1 Leukemia. Macromol Biosci 2017; 18. [DOI: 10.1002/mabi.201700173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/17/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Michal Pechar
- Institute of Macromolecular Chemistry; Czech Academy of Sciences; Heyrovského nám. 2 162 06 Prague 6 Czech Republic
| | - Robert Pola
- Institute of Macromolecular Chemistry; Czech Academy of Sciences; Heyrovského nám. 2 162 06 Prague 6 Czech Republic
| | - Olga Janoušková
- Institute of Macromolecular Chemistry; Czech Academy of Sciences; Heyrovského nám. 2 162 06 Prague 6 Czech Republic
| | - Irena Sieglová
- Institute of Molecular Genetics; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Vlastimil Král
- Institute of Molecular Genetics; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Barbora Tomalová
- Institute of Microbiology; Czech Academy of Sciences; Vídeňská 1083 142 20 Prague 4 Czech Republic
| | - Marek Kovář
- Institute of Microbiology; Czech Academy of Sciences; Vídeňská 1083 142 20 Prague 4 Czech Republic
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Hexnerová R, Křížková K, Fábry M, Sieglová I, Kedrová K, Collinsová M, Ullrichová P, Srb P, Williams C, Crump MP, Tošner Z, Jiráček J, Veverka V, Žáková L. Probing Receptor Specificity by Sampling the Conformational Space of the Insulin-like Growth Factor II C-domain. J Biol Chem 2016; 291:21234-21245. [PMID: 27510031 PMCID: PMC5076530 DOI: 10.1074/jbc.m116.741041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Indexed: 01/22/2023] Open
Abstract
Insulin and insulin-like growth factors I and II are closely related protein hormones. Their distinct evolution has resulted in different yet overlapping biological functions with insulin becoming a key regulator of metabolism, whereas insulin-like growth factors (IGF)-I/II are major growth factors. Insulin and IGFs cross-bind with different affinities to closely related insulin receptor isoforms A and B (IR-A and IR-B) and insulin-like growth factor type I receptor (IGF-1R). Identification of structural determinants in IGFs and insulin that trigger their specific signaling pathways is of increasing importance in designing receptor-specific analogs with potential therapeutic applications. Here, we developed a straightforward protocol for production of recombinant IGF-II and prepared six IGF-II analogs with IGF-I-like mutations. All modified molecules exhibit significantly reduced affinity toward IR-A, particularly the analogs with a Pro-Gln insertion in the C-domain. Moreover, one of the analogs has enhanced binding affinity for IGF-1R due to a synergistic effect of the Pro-Gln insertion and S29N point mutation. Consequently, this analog has almost a 10-fold higher IGF-1R/IR-A binding specificity in comparison with native IGF-II. The established IGF-II purification protocol allowed for cost-effective isotope labeling required for a detailed NMR structural characterization of IGF-II analogs that revealed a link between the altered binding behavior of selected analogs and conformational rearrangement of their C-domains.
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Affiliation(s)
- Rozálie Hexnerová
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic, Faculty of Science, Charles University in Prague, Albertov 6, Prague 128 43, Czech Republic
| | - Květoslava Křížková
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic, Faculty of Science, Charles University in Prague, Albertov 6, Prague 128 43, Czech Republic
| | - Milan Fábry
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic, and
| | - Irena Sieglová
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic
| | - Kateřina Kedrová
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic, Faculty of Science, Charles University in Prague, Albertov 6, Prague 128 43, Czech Republic
| | - Michaela Collinsová
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic
| | - Pavlína Ullrichová
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 166 28 Prague 6, Czech Republic
| | - Pavel Srb
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic
| | - Christopher Williams
- Department of Organic and Biological Chemistry, School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Matthew P Crump
- Department of Organic and Biological Chemistry, School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Zdeněk Tošner
- Faculty of Science, Charles University in Prague, Albertov 6, Prague 128 43, Czech Republic
| | - Jiří Jiráček
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic
| | - Václav Veverka
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic,
| | - Lenka Žáková
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic,
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9
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Laga R, Pola R, Ulbrich K, Horřejší M, Sieglová I, Král V, Fábry M, Pechar M. Avidin-conjugated polymers with monobiotinylated antibody fragments: A new strategy for the noncovalent attachment of recombinant proteins for polymer therapeutics. J BIOACT COMPAT POL 2013. [DOI: 10.1177/0883911513486225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The high affinity and specificity between avidin and biotin were employed to bind a recombinant single-chain antibody fragment to synthetic hydrophilic polymer drug carriers. Two semitelechelic polymers, based on poly(ethylene glycol) and poly[ N-(2-hydroxypropyl)methacrylamide], each containing a single thiol end group, were conjugated to dithiopyridyl-modified avidin. The biotinylated recombinant single-chain antibody fragment of the M75 antibody was then noncovalently bound to the polymer-avidin conjugates. The recombinant protein was chosen as a targeting ligand against carbonic anhydrase IX, a marker overexpressed by tumor cells of various human carcinomas. The antigen-binding affinity of the polymer–single-chain antibody fragment complex was confirmed by enzyme-linked immuno sorbent assay (ELISA). This approach provides an original, nondestructive way of preparing supramolecular systems intended for targeted delivery of therapeutics utilizing modern chemical procedures, including reversible addition–fragmentation chain-transfer polymerization and recombinant DNA techniques.
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Affiliation(s)
- Richard Laga
- Institute of Macromolecular Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Robert Pola
- Institute of Macromolecular Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Karel Ulbrich
- Institute of Macromolecular Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Magda Horřejší
- Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Irena Sieglová
- Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Vlastimil Král
- Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Michal Pechar
- Institute of Macromolecular Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Pola R, Laga R, Ulbrich K, Sieglová I, Král V, Fábry M, Kabešová M, Kovář M, Pechar M. Polymer Therapeutics with a Coiled Coil Motif Targeted against Murine BCL1 Leukemia. Biomacromolecules 2013; 14:881-9. [DOI: 10.1021/bm3019592] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Robert Pola
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovského nám. 2, 162 06, Prague 6, Czech
Republic
| | - Richard Laga
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovského nám. 2, 162 06, Prague 6, Czech
Republic
| | - Karel Ulbrich
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovského nám. 2, 162 06, Prague 6, Czech
Republic
| | - Irena Sieglová
- Institute of Molecular
Genetics, Academy of Sciences of the Czech Republic, v.v.i.,
Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Vlastimil Král
- Institute of Molecular
Genetics, Academy of Sciences of the Czech Republic, v.v.i.,
Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Milan Fábry
- Institute of Molecular
Genetics, Academy of Sciences of the Czech Republic, v.v.i.,
Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Martina Kabešová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i.,
Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Marek Kovář
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i.,
Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Michal Pechar
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovského nám. 2, 162 06, Prague 6, Czech
Republic
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11
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Procházková K, Cermáková K, Pachl P, Sieglová I, Fábry M, Otwinowski Z, Rezáčová P. Structure of the effector-binding domain of the arabinose repressor AraR from Bacillus subtilis. Acta Crystallogr D Biol Crystallogr 2012; 68:176-85. [PMID: 22281747 DOI: 10.1107/s090744491105414x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 12/15/2011] [Indexed: 11/10/2022]
Abstract
In Bacillus subtilis, the arabinose repressor AraR negatively controls the expression of genes in the metabolic pathway of arabinose-containing polysaccharides. The protein is composed of two domains of different phylogenetic origin and function: an N-terminal DNA-binding domain belonging to the GntR family and a C-terminal effector-binding domain that shows similarity to members of the GalR/LacI family. The crystal structure of the C-terminal effector-binding domain of AraR in complex with the effector L-arabinose has been determined at 2.2 Å resolution. The L-arabinose binding affinity was characterized by isothermal titration calorimetry and differential scanning fluorimetry; the K(d) value was 8.4 ± 0.4 µM. The effect of L-arabinose on the protein oligomeric state was investigated in solution and detailed analysis of the crystal identified a dimer organization which is distinctive from that of other members of the GalR/LacI family.
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Affiliation(s)
- Kateřina Procházková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, Czech Republic
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12
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Sedláček J, Fábry M, Sieglová I, Král V, Uhnáková B, Múdra M, Kronrád L, Sawicka A, Mikolajczak R, Řezáčová P. Recombinant fragment of an antibody tailored for direct radioiodination. J Labelled Comp Radiopharm 2011. [DOI: 10.1002/jlcr.1945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Juraj Sedláček
- Laboratory of Structural Biology, Institute of Molecular Genetics; Academy of Sciences of the Czech Republic; Flemingovo nam. 2 Praha 6; Praha 6 CZ; 16637; Czech Republic
| | - Milan Fábry
- Laboratory of Structural Biology, Institute of Molecular Genetics; Academy of Sciences of the Czech Republic; Flemingovo nam. 2 Praha 6; Praha 6 CZ; 16637; Czech Republic
| | - Irena Sieglová
- Laboratory of Structural Biology, Institute of Molecular Genetics; Academy of Sciences of the Czech Republic; Flemingovo nam. 2 Praha 6; Praha 6 CZ; 16637; Czech Republic
| | - Vlastimil Král
- Laboratory of Structural Biology, Institute of Molecular Genetics; Academy of Sciences of the Czech Republic; Flemingovo nam. 2 Praha 6; Praha 6 CZ; 16637; Czech Republic
| | - Bronislava Uhnáková
- Laboratory of Structural Biology, Institute of Molecular Genetics; Academy of Sciences of the Czech Republic; Flemingovo nam. 2 Praha 6; Praha 6 CZ; 16637; Czech Republic
| | - Marcela Múdra
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology; Slovak Academy of Sciences; Bratislava; Slovakia
| | - Leo Kronrád
- Division of Radiopharmaceuticals; Nuclear Research Institute Řež plc.; Řež near Prague; Czech Republic
| | | | | | - Pavlína Řezáčová
- Laboratory of Structural Biology, Institute of Molecular Genetics; Academy of Sciences of the Czech Republic; Flemingovo nam. 2 Praha 6; Praha 6 CZ; 16637; Czech Republic
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13
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Pechar M, Pola R, Laga R, Ulbrich K, Bednárová L, Maloň P, Sieglová I, Král V, Fábry M, Vaněk O. Coiled Coil Peptides as Universal Linkers for the Attachment of Recombinant Proteins to Polymer Therapeutics. Biomacromolecules 2011; 12:3645-55. [DOI: 10.1021/bm200897b] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Michal Pechar
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 162 06, Prague 6, Czech Republic
| | - Robert Pola
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 162 06, Prague 6, Czech Republic
| | - Richard Laga
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 162 06, Prague 6, Czech Republic
| | - Karel Ulbrich
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 162 06, Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Petr Maloň
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Irena Sieglová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague 6, Czech Republic
| | - Vlastimil Král
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague 6, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague 6, Czech Republic
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14
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Řezáčová P, Pokorná J, Brynda J, Kožíšek M, Cígler P, Lepšík M, Fanfrlík J, Řezáč J, Grantz Šašková K, Sieglová I, Plešek J, Šícha V, Grüner B, Oberwinkler H, Sedláček’ J, Kräusslich HG, Hobza P, Král V, Konvalinka J. Design of HIV Protease Inhibitors Based on Inorganic Polyhedral Metallacarboranes. J Med Chem 2009; 52:7132-41. [DOI: 10.1021/jm9011388] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic v.v.i., Flemingovo nam. 2, 166 10 Praha 6, Czech Republic
| | - Jana Pokorná
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 128 43 Praha 2, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic v.v.i., Flemingovo nam. 2, 166 10 Praha 6, Czech Republic
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 128 43 Praha 2, Czech Republic
| | - Petr Cígler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28 Praha 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Klára Grantz Šašková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 128 43 Praha 2, Czech Republic
| | - Irena Sieglová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic v.v.i., Flemingovo nam. 2, 166 10 Praha 6, Czech Republic
| | - Jaromír Plešek
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Area of Research Institutes 1001, 250 68 Husinec-Řež u Prahy, Czech Republic
| | - Václav Šícha
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Area of Research Institutes 1001, 250 68 Husinec-Řež u Prahy, Czech Republic
| | - Bohumír Grüner
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Area of Research Institutes 1001, 250 68 Husinec-Řež u Prahy, Czech Republic
| | - Heike Oberwinkler
- Department of Virology, University of Heidelberg, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany
| | - Juraj Sedláček’
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic v.v.i., Flemingovo nam. 2, 166 10 Praha 6, Czech Republic
| | - Hans-Georg Kräusslich
- Department of Virology, University of Heidelberg, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Vladimír Král
- Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28 Praha 6, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic v.v.i., Flemingovo nam. 2, 166 10 Praha 6, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 128 43 Praha 2, Czech Republic
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15
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Dostál J, Brynda J, Hrusková-Heidingsfeldová O, Sieglová I, Pichová I, Rezácová P. The crystal structure of the secreted aspartic protease 1 from Candida parapsilosis in complex with pepstatin A. J Struct Biol 2009; 167:145-52. [PMID: 19401235 DOI: 10.1016/j.jsb.2009.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 03/18/2009] [Accepted: 04/17/2009] [Indexed: 01/12/2023]
Abstract
Opportunistic pathogens of the genus Candida cause infections representing a major threat to long-term survival of immunocompromised patients. Virulence of the Candida pathogens is enhanced by production of extracellular proteolytic enzymes and secreted aspartic proteases (Saps) are therefore studied as potential virulence factors and possible targets for therapeutic drug design. Candida parapsilosis is less invasive than C. albicans, however, it is one of the leading causative agents of yeast infections. We report three-dimensional crystal structure of Sapp1p from C. parapsilosis in complex with pepstatin A, the classical inhibitor of aspartic proteases. The structure of Sapp1p was determined from protein isolated from its natural source and represents the first structure of Sap from C. parapsilosis. Overall fold and topology of Sapp1p is very similar to the archetypic fold of monomeric aspartic protease family and known structures of Sap isoenzymes from C. albicans and Sapt1p from C. tropicalis. Structural comparison revealed noticeable differences in the structure of loops surrounding the active site. This resulted in differential character, shape, and size of the substrate binding site explaining divergent substrate specificities and inhibitor affinities. Determination of structures of Sap isoenzymes from various species might contribute to the development of new Sap-specific inhibitors.
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Affiliation(s)
- Jirí Dostál
- Gilead Sciences and IOCB Research Centre, Prague, Czech Republic
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16
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Rezácová P, Kozísek M, Moy SF, Sieglová I, Joachimiak A, Machius M, Otwinowski Z. Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates. Mol Microbiol 2008; 69:895-910. [PMID: 18554327 DOI: 10.1111/j.1365-2958.2008.06318.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Expression of genes in the gapA operon encoding five enzymes for triose phosphate interconversion in Bacillus subtilis is negatively regulated by the Central glycolytic genes Regulator (CggR). CggR belongs to the large SorC/DeoR family of prokaryotic transcriptional regulators, characterized by an N-terminal DNA-binding domain and a large C-terminal effector-binding domain. When no glucose is present in growth media, CggR binds to its target DNA sequence and blocks the transcription of genes in the gapA operon. In the presence of glucose, binding of the known effector molecule fructose-1,6-bisphosphate abolishes this interaction. We have identified dihydroxyacetone phosphate, glucose-6-phosphate and fructose-6-phosphate as additional CggR ligands that can bind to the effector-binding site. Crystal structures of C-CggR, the C-terminal effector-binding domain of CggR, both unliganded as well as in complex with the four ligands at resolutions between 1.65 and 1.80 A reveal unique ligand-specific structural changes in the binding site that affect the dimer interface. Binding affinities of these ligands were determined by isothermal titration calorimetry. Chemical cross-linking shows that CggR oligomerization is mediated through its effector-binding domain, and that binding of the different ligands differentially affects the distribution of oligomers. Electrophoretic mobility shift assays (EMSAs) confirmed a destabilizing effect of fructose-1,6-bisphosphate on the CggR/DNA complex, and also showed similar effects for dihydroxyacetone phosphate. Our results suggest that CggR stability and function may be modulated by various effectors in a complex fashion.
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Affiliation(s)
- Pavlína Rezácová
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA.
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17
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Bartoňová V, Král V, Sieglová I, Brynda J, Fábry M, Hořejší M, Kožíšek M, Šašková KG, Konvalinka J, Sedláček J, Řezáčová P. Potent inhibition of drug-resistant HIV protease variants by monoclonal antibodies. Antiviral Res 2008; 78:275-7. [DOI: 10.1016/j.antiviral.2008.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 12/17/2007] [Accepted: 01/17/2008] [Indexed: 10/22/2022]
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