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Hadži S, Živič Z, Kovačič M, Zavrtanik U, Haesaerts S, Charlier D, Plavec J, Volkov AN, Lah J, Loris R. Author Correction: Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae. Nat Commun 2024; 15:3484. [PMID: 38664458 PMCID: PMC11045843 DOI: 10.1038/s41467-024-47946-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2024] Open
Affiliation(s)
- San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Zala Živič
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Matic Kovačič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Sarah Haesaerts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Daniel Charlier
- Research group of Microbiology, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
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Hadži S, Živič Z, Kovačič M, Zavrtanik U, Haesaerts S, Charlier D, Plavec J, Volkov AN, Lah J, Loris R. Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae. Nat Commun 2024; 15:3105. [PMID: 38600130 PMCID: PMC11006873 DOI: 10.1038/s41467-024-47296-3] [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: 05/21/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disordered protein sequences can exhibit different binding modes, ranging from well-ordered folding-upon-binding to highly dynamic fuzzy binding. The primary function of the intrinsically disordered region of the antitoxin HigA2 from Vibrio cholerae is to neutralize HigB2 toxin through ultra-high-affinity folding-upon-binding interaction. Here, we show that the same intrinsically disordered region can also mediate fuzzy interactions with its operator DNA and, through interplay with the folded helix-turn-helix domain, regulates transcription from the higBA2 operon. NMR, SAXS, ITC and in vivo experiments converge towards a consistent picture where a specific set of residues in the intrinsically disordered region mediate electrostatic and hydrophobic interactions while "hovering" over the DNA operator. Sensitivity of the intrinsically disordered region to scrambling the sequence, position-specific contacts and absence of redundant, multivalent interactions, point towards a more specific type of fuzzy binding. Our work demonstrates how a bacterial regulator achieves dual functionality by utilizing two distinct interaction modes within the same disordered sequence.
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Affiliation(s)
- San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Zala Živič
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Matic Kovačič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Sarah Haesaerts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Daniel Charlier
- Research group of Microbiology, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
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Sülzen H, Volkov AN, Geens R, Zahedifard F, Stijlemans B, Zoltner M, Magez S, Sterckx YGJ, Zoll S. Beyond the VSG layer: Exploring the role of intrinsic disorder in the invariant surface glycoproteins of African trypanosomes. PLoS Pathog 2024; 20:e1012186. [PMID: 38648216 PMCID: PMC11065263 DOI: 10.1371/journal.ppat.1012186] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/02/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
In the bloodstream of mammalian hosts, African trypanosomes face the challenge of protecting their invariant surface receptors from immune detection. This crucial role is fulfilled by a dense, glycosylated protein layer composed of variant surface glycoproteins (VSGs), which undergo antigenic variation and provide a physical barrier that shields the underlying invariant surface glycoproteins (ISGs). The protective shield's limited permeability comes at the cost of restricted access to the extracellular host environment, raising questions regarding the specific function of the ISG repertoire. In this study, we employ an integrative structural biology approach to show that intrinsically disordered membrane-proximal regions are a common feature of members of the ISG super-family, conferring the ability to switch between compact and elongated conformers. While the folded, membrane-distal ectodomain is buried within the VSG layer for compact conformers, their elongated counterparts would enable the extension beyond it. This dynamic behavior enables ISGs to maintain a low immunogenic footprint while still allowing them to engage with the host environment when necessary. Our findings add further evidence to a dynamic molecular organization of trypanosome surface antigens wherein intrinsic disorder underpins the characteristics of a highly flexible ISG proteome to circumvent the constraints imposed by the VSG coat.
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Affiliation(s)
- Hagen Sülzen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Rob Geens
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Center of Excellence, Department of Pharmaceutical Sciences, Universiteit of Antwerp, Wilrijk, Belgium
| | - Farnaz Zahedifard
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | - Benoit Stijlemans
- Brussels Center for Immunology (BCIM), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium
| | - Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | - Stefan Magez
- Brussels Center for Immunology (BCIM), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- Laboratory for Biomedical Research, Department of Molecular Biotechnology, Environment Technology and Food Technology, Ghent University Global Campus, Incheon, South Korea
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Center of Excellence, Department of Pharmaceutical Sciences, Universiteit of Antwerp, Wilrijk, Belgium
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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Dhillon A, Persson BD, Volkov AN, Sülzen H, Kádek A, Pompach P, Kereïche S, Lepšík M, Danskog K, Uetrecht C, Arnberg N, Zoll S. Structural insights into the interaction between adenovirus C5 hexon and human lactoferrin. J Virol 2024; 98:e0157623. [PMID: 38323814 PMCID: PMC10949841 DOI: 10.1128/jvi.01576-23] [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: 10/10/2023] [Accepted: 01/13/2024] [Indexed: 02/08/2024] Open
Abstract
Adenovirus (AdV) infection of the respiratory epithelium is common but poorly understood. Human AdV species C types, such as HAdV-C5, utilize the Coxsackie-adenovirus receptor (CAR) for attachment and subsequently integrins for entry. CAR and integrins are however located deep within the tight junctions in the mucosa where they would not be easily accessible. Recently, a model for CAR-independent AdV entry was proposed. In this model, human lactoferrin (hLF), an innate immune protein, aids the viral uptake into epithelial cells by mediating interactions between the major capsid protein, hexon, and yet unknown host cellular receptor(s). However, a detailed understanding of the molecular interactions driving this mechanism is lacking. Here, we present a new cryo-EM structure of HAdV-5C hexon at high resolution alongside a hybrid structure of HAdV-5C hexon complexed with human lactoferrin (hLF). These structures reveal the molecular determinants of the interaction between hLF and HAdV-C5 hexon. hLF engages hexon primarily via its N-terminal lactoferricin (Lfcin) region, interacting with hexon's hypervariable region 1 (HVR-1). Mutational analyses pinpoint critical Lfcin contacts and also identify additional regions within hLF that critically contribute to hexon binding. Our study sheds more light on the intricate mechanism by which HAdV-C5 utilizes soluble hLF/Lfcin for cellular entry. These findings hold promise for advancing gene therapy applications and inform vaccine development. IMPORTANCE Our study delves into the structural aspects of adenovirus (AdV) infections, specifically HAdV-C5 in the respiratory epithelium. It uncovers the molecular details of a novel pathway where human lactoferrin (hLF) interacts with the major capsid protein, hexon, facilitating viral entry, and bypassing traditional receptors such as CAR and integrins. The study's cryo-EM structures reveal how hLF engages hexon, primarily through its N-terminal lactoferricin (Lfcin) region and hexon's hypervariable region 1 (HVR-1). Mutational analyses identify critical Lfcin contacts and other regions within hLF vital for hexon binding. This structural insight sheds light on HAdV-C5's mechanism of utilizing soluble hLF/Lfcin for cellular entry, holding promise for gene therapy and vaccine development advancements in adenovirus research.
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Affiliation(s)
- Arun Dhillon
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Hagen Sülzen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Alan Kádek
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Petr Pompach
- Biotechnology and Biomedical Center of the Academy of Sciences and Charles University in Vestec, Vestec, Czech Republic
| | - Sami Kereïche
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katarina Danskog
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Charlotte Uetrecht
- Department of Health Sciences and Biomedicine, Faculty V: School of Life Sciences, CSSB Centre for Structural Systems Biology, Deutsches Elektronen Synchrotron DESY and Leibniz Institute of Virology, Hamburg, University of Siegen, Siegen, Germany
| | - Niklas Arnberg
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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Garcia-Rodriguez G, Girardin Y, Kumar Singh R, Volkov AN, Van Dyck J, Muruganandam G, Sobott F, Charlier D, Loris R. Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module. Sci Adv 2024; 10:eadj2403. [PMID: 38181072 PMCID: PMC10776004 DOI: 10.1126/sciadv.adj2403] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024]
Abstract
The parDE family of toxin-antitoxin (TA) operons is ubiquitous in bacterial genomes and, in Vibrio cholerae, is an essential component to maintain the presence of chromosome II. Here, we show that transcription of the V. cholerae parDE2 (VcparDE) operon is regulated in a toxin:antitoxin ratio-dependent manner using a molecular mechanism distinct from other type II TA systems. The repressor of the operon is identified as an assembly with a 6:2 stoichiometry with three interacting ParD2 dimers bridged by two ParE2 monomers. This assembly docks to a three-site operator containing 5'- GGTA-3' motifs. Saturation of this TA complex with ParE2 toxin results in disruption of the interface between ParD2 dimers and the formation of a TA complex of 2:2 stoichiometry. The latter is operator binding-incompetent as it is incompatible with the required spacing of the ParD2 dimers on the operator.
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Affiliation(s)
- Gabriela Garcia-Rodriguez
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Yana Girardin
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Ranjan Kumar Singh
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Alexander N. Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussel, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Jeroen Van Dyck
- Department of Chemistry, Universiteit Antwerpen, Groenenborgerlaan 171, Antwerpen 2020, Belgium
| | - Gopinath Muruganandam
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussel, Belgium
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6
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Geens R, Stanisich J, Beyens O, D'Hondt S, Thiberge J, Ryckebosch A, De Groot A, Magez S, Vertommen D, Amino R, De Winter H, Volkov AN, Tompa P, Sterckx YG. Biophysical characterization of the Plasmodium falciparum circumsporozoite protein's N-terminal domain. Protein Sci 2024; 33:e4852. [PMID: 38059674 PMCID: PMC10749493 DOI: 10.1002/pro.4852] [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: 04/26/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/08/2023]
Abstract
The circumsporozoite protein (CSP) is the main surface antigen of the Plasmodium sporozoite (SPZ) and forms the basis of the currently only licensed anti-malarial vaccine (RTS,S/AS01). CSP uniformly coats the SPZ and plays a pivotal role in its immunobiology, in both the insect and the vertebrate hosts. Although CSP's N-terminal domain (CSPN ) has been reported to play an important role in multiple CSP functions, a thorough biophysical and structural characterization of CSPN is currently lacking. Here, we present an alternative method for the recombinant production and purification of CSPN from Plasmodium falciparum (PfCSPN ), which provides pure, high-quality protein preparations with high yields. Through an interdisciplinary approach combining in-solution experimental methods and in silico analyses, we provide strong evidence that PfCSPN is an intrinsically disordered region displaying some degree of compaction.
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Affiliation(s)
- Rob Geens
- Laboratory of Medical Biochemistry (LMB)University of AntwerpAntwerpBelgium
- Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
| | - Jessica Stanisich
- Cellular and Molecular ImmunologyVrije Universiteit BrusselBrusselsBelgium
| | - Olivier Beyens
- Laboratory of Medicinal Chemistry (UAMC)University of AntwerpAntwerpBelgium
| | - Stijn D'Hondt
- Laboratory of Medicinal Chemistry (UAMC)University of AntwerpAntwerpBelgium
| | | | - Amber Ryckebosch
- Laboratory of Medical Biochemistry (LMB)University of AntwerpAntwerpBelgium
| | - Anke De Groot
- Laboratory of Medical Biochemistry (LMB)University of AntwerpAntwerpBelgium
| | - Stefan Magez
- Cellular and Molecular ImmunologyVrije Universiteit BrusselBrusselsBelgium
- Ghent University Global CampusIncheonSouth Korea
| | - Didier Vertommen
- de Duve Institute and MASSPROT Platform, UCLouvainBrusselsBelgium
| | - Rogerio Amino
- Unit of Malaria Infection & ImmunityInstitut PasteurParisFrance
| | - Hans De Winter
- Laboratory of Medicinal Chemistry (UAMC)University of AntwerpAntwerpBelgium
| | - Alexander N. Volkov
- Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
- VIB‐VUB Center for Structural BiologyVlaams Instituut voor Biotechnologie (VIB)BrusselsBelgium
- Jean Jeener NMR CentreVrije Universiteit BrusselBrusselsBelgium
| | - Peter Tompa
- Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
- VIB‐VUB Center for Structural BiologyVlaams Instituut voor Biotechnologie (VIB)BrusselsBelgium
- Institute of Enzymology, Biological Research CenterHungarian Academy of SciencesBudapestHungary
| | - Yann G.‐J. Sterckx
- Laboratory of Medical Biochemistry (LMB)University of AntwerpAntwerpBelgium
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Caccamo A, Vega de Luna F, Wahni K, Volkov AN, Przybyla-Toscano J, Amelii A, Kriznik A, Rouhier N, Messens J, Remacle C. Ascorbate Peroxidase 2 (APX2) of Chlamydomonas Binds Copper and Modulates the Copper Insertion into Plastocyanin. Antioxidants (Basel) 2023; 12:1946. [PMID: 38001799 PMCID: PMC10669542 DOI: 10.3390/antiox12111946] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Recent phylogenetic studies have unveiled a novel class of ascorbate peroxidases called "ascorbate peroxidase-related" (APX-R). These enzymes, found in green photosynthetic eukaryotes, lack the amino acids necessary for ascorbate binding. This study focuses on the sole APX-R from Chlamydomonas reinhardtii referred to as ascorbate peroxidase 2 (APX2). We used immunoblotting to locate APX2 within the chloroplasts and in silico analysis to identify key structural motifs, such as the twin-arginine transport (TAT) motif for lumen translocation and the metal-binding MxxM motif. We also successfully expressed recombinant APX2 in Escherichia coli. Our in vitro results showed that the peroxidase activity of APX2 was detected with guaiacol but not with ascorbate as an electron donor. Furthermore, APX2 can bind both copper and heme, as evidenced by spectroscopic, and fluorescence experiments. These findings suggest a potential interaction between APX2 and plastocyanin, the primary copper-containing enzyme within the thylakoid lumen of the chloroplasts. Predictions from structural models and evidence from 1H-NMR experiments suggest a potential interaction between APX2 and plastocyanin, emphasizing the influence of APX2 on the copper-binding abilities of plastocyanin. In summary, our results propose a significant role for APX2 as a regulator in copper transfer to plastocyanin. This study sheds light on the unique properties of APX-R enzymes and their potential contributions to the complex processes of photosynthesis in green algae.
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Affiliation(s)
- Anna Caccamo
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium; (A.C.); (F.V.d.L.); (J.P.-T.); (A.A.)
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium; (K.W.); (A.N.V.)
- Brussels Center for Redox Biology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Félix Vega de Luna
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium; (A.C.); (F.V.d.L.); (J.P.-T.); (A.A.)
| | - Khadija Wahni
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium; (K.W.); (A.N.V.)
- Brussels Center for Redox Biology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium; (K.W.); (A.N.V.)
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Jonathan Przybyla-Toscano
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium; (A.C.); (F.V.d.L.); (J.P.-T.); (A.A.)
| | - Antonello Amelii
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium; (A.C.); (F.V.d.L.); (J.P.-T.); (A.A.)
| | - Alexandre Kriznik
- CNRS, IMoPA and IBSLor, Université de Lorraine, F-54000 Nancy, France;
| | | | - Joris Messens
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium; (K.W.); (A.N.V.)
- Brussels Center for Redox Biology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Claire Remacle
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium; (A.C.); (F.V.d.L.); (J.P.-T.); (A.A.)
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8
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Maseko SB, Brammerloo Y, Van Molle I, Sogues A, Martin C, Gorgulla C, Plant E, Olivet J, Blavier J, Ntombela T, Delvigne F, Arthanari H, El Hajj H, Bazarbachi A, Van Lint C, Salehi-Ashtiani K, Remaut H, Ballet S, Volkov AN, Twizere JC. Identification of small molecule antivirals against HTLV-1 by targeting the hDLG1-Tax-1 protein-protein interaction. Antiviral Res 2023; 217:105675. [PMID: 37481039 DOI: 10.1016/j.antiviral.2023.105675] [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: 06/24/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
Human T-cell leukemia virus type-1 (HTLV-1) is the first pathogenic retrovirus discovered in human. Although HTLV-1-induced diseases are well-characterized and linked to the encoded Tax-1 oncoprotein, there is currently no strategy to target Tax-1 functions with small molecules. Here, we analyzed the binding of Tax-1 to the human homolog of the drosophila discs large tumor suppressor (hDLG1/SAP97), a multi-domain scaffolding protein involved in Tax-1-transformation ability. We have solved the structures of the PDZ binding motif (PBM) of Tax-1 in complex with the PDZ1 and PDZ2 domains of hDLG1 and assessed the binding of 10 million molecules by virtual screening. Among the 19 experimentally confirmed compounds, one systematically inhibited the Tax-1-hDLG1 interaction in different biophysical and cellular assays, as well as HTLV-1 cell-to-cell transmission in a T-cell model. Thus, our work demonstrates that interactions involving Tax-1 PDZ-domains are amenable to small-molecule inhibition, which provides a framework for the design of targeted therapies for HTLV-1-induced diseases.
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Affiliation(s)
- Sibusiso B Maseko
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | - Yasmine Brammerloo
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | - Inge Van Molle
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Adrià Sogues
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Estelle Plant
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Julien Olivet
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium; Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research and Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Jeremy Blavier
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | | | - Frank Delvigne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liege Belgium
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hiba El Hajj
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ali Bazarbachi
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University of Abu Dhabi, Abu Dhabi United Arab Emirates
| | - Han Remaut
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Alexander N Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium; Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels Belgium.
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium; TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liege Belgium; Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University of Abu Dhabi, Abu Dhabi United Arab Emirates.
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9
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Daccache D, De Jonge E, Liloku P, Mechleb K, Haddad M, Corthaut S, Sterckx YGJ, Volkov AN, Claeys Bouuaert C. Evolutionary conservation of the structure and function of meiotic Rec114-Mei4 and Mer2 complexes. Genes Dev 2023; 37:535-553. [PMID: 37442581 PMCID: PMC10393190 DOI: 10.1101/gad.350462.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 01/22/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023]
Abstract
Meiosis-specific Rec114-Mei4 and Mer2 complexes are thought to enable Spo11-mediated DNA double-strand break (DSB) formation through a mechanism that involves DNA-dependent condensation. However, the structure, molecular properties, and evolutionary conservation of Rec114-Mei4 and Mer2 are unclear. Here, we present AlphaFold models of Rec114-Mei4 and Mer2 complexes supported by nuclear magnetic resonance (NMR) spectroscopy, small-angle X-ray scattering (SAXS), and mutagenesis. We show that dimers composed of the Rec114 C terminus form α-helical chains that cup an N-terminal Mei4 α helix, and that Mer2 forms a parallel homotetrameric coiled coil. Both Rec114-Mei4 and Mer2 bind preferentially to branched DNA substrates, indicative of multivalent protein-DNA interactions. Indeed, the Rec114-Mei4 interaction domain contains two DNA-binding sites that point in opposite directions and drive condensation. The Mer2 coiled-coil domain bridges coaligned DNA duplexes, likely through extensive electrostatic interactions along the length of the coiled coil. Finally, we show that the structures of Rec114-Mei4 and Mer2 are conserved across eukaryotes, while DNA-binding properties vary significantly. This work provides insights into the mechanism whereby Rec114-Mei4 and Mer2 complexes promote the assembly of the meiotic DSB machinery and suggests a model in which Mer2 condensation is the essential driver of assembly, with the DNA-binding activity of Rec114-Mei4 playing a supportive role.
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Affiliation(s)
- Dima Daccache
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-La-Neuve, Belgium
| | - Emma De Jonge
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-La-Neuve, Belgium
| | - Pascaline Liloku
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-La-Neuve, Belgium
| | - Karen Mechleb
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-La-Neuve, Belgium
| | - Marita Haddad
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-La-Neuve, Belgium
| | - Sam Corthaut
- Laboratory of Medical Biochemistry (LMB), the Infla-Med Centre of Excellence, University of Antwerp, 2610 Wilrijk, Belgium
| | - Yann G-J Sterckx
- Laboratory of Medical Biochemistry (LMB), the Infla-Med Centre of Excellence, University of Antwerp, 2610 Wilrijk, Belgium
| | - Alexander N Volkov
- Vlaams Instituut voor Biotechnologie (VIB)-Vrije Universiteit Brussel (VUB) Center for Structural Biology, VIB, 1050 Brussels, Belgium;
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Corentin Claeys Bouuaert
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-La-Neuve, Belgium;
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10
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Sleutel M, Pradhan B, Volkov AN, Remaut H. Structural analysis and architectural principles of the bacterial amyloid curli. Nat Commun 2023; 14:2822. [PMID: 37198180 DOI: 10.1038/s41467-023-38204-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 04/20/2023] [Indexed: 05/19/2023] Open
Abstract
Two decades have passed since the initial proposition that amyloids are not only (toxic) byproducts of an unintended aggregation cascade, but that they can also be produced by an organism to serve a defined biological function. That revolutionary idea was borne out of the realization that a large fraction of the extracellular matrix that holds Gram-negative cells into a persistent biofilm is composed of protein fibers (curli; tafi) with cross-β architecture, nucleation-dependent polymerization kinetics and classic amyloid tinctorial properties. The list of proteins shown to form so-called functional amyloid fibers in vivo has greatly expanded over the years, but detailed structural insights have not followed at a similar pace in part due to the associated experimental barriers. Here we combine extensive AlphaFold2 modelling and cryo-electron transmission microscopy to propose an atomic model of curli protofibrils, and their higher modes of organization. We uncover an unexpected structural diversity of curli building blocks and fibril architectures. Our results allow for a rationalization of the extreme physico-chemical robustness of curli, as well as earlier observations of inter-species curli promiscuity, and should facilitate further engineering efforts to expand the repertoire of curli-based functional materials.
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Affiliation(s)
- Mike Sleutel
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, Brussels, Belgium.
| | - Brajabandhu Pradhan
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Alexander N Volkov
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Jean Jeener NMR Center, Brussel, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, Brussels, Belgium.
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11
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Prolič-Kalinšek M, Volkov AN, Hadži S, Van Dyck J, Bervoets I, Charlier D, Loris R. Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7. Acta Crystallogr D Struct Biol 2023; 79:245-258. [PMID: 36876434 PMCID: PMC9986795 DOI: 10.1107/s2059798323001249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 12/26/2022] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
YdaT is a functional equivalent of the CII repressor in certain lambdoid phages and prophages. YdaT from the cryptic prophage CP-933P in the genome of Escherichia coli O157:H7 is functional as a DNA-binding protein and recognizes a 5'-TTGATTN6AATCAA-3' inverted repeat. The DNA-binding domain is a helix-turn-helix (HTH)-containing POU domain and is followed by a long α-helix (α6) that forms an antiparallel four-helix bundle, creating a tetramer. The loop between helix α2 and the recognition helix α3 in the HTH motif is unusually long compared with typical HTH motifs, and is highly variable in sequence and length within the YdaT family. The POU domains have a large degree of freedom to move relative to the helix bundle in the free structure, but their orientation becomes fixed upon DNA binding.
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Affiliation(s)
- Maruša Prolič-Kalinšek
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Alexander N Volkov
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Jeroen Van Dyck
- Department of Chemistry, Universiteit Antwerpen, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
| | - Indra Bervoets
- Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
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12
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Kalyakin AS, Volkov AN. Electrochemical detection of simple alkanes by utilizing a solid-state zirconia-based gas sensor. Chim Tech Acta 2023. [DOI: 10.15826/chimtech.2023.10.1.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Solid-state gas sensors composed of complex oxide electrolytes offer great potential for analyzing various atmospheres at high temperatures. While relatively simple gas mixtures (H2O+N2, O2+N2) have been successfully studied by means of ZrO2-based sensors, the precise detection of more complex compounds represents a challenging task. In this work, we present our findings regarding the analysis of lower alkanes (CH4, C2H6, and C3H8) mixed with nitrogen as an inert gas, utilizing an amperometric ZrO2-based sensor. This sensor, serving as an electrochemical cell with a diffusion barrier, was tested at 500–600 °C to measure the limiting current, which depends on the gas composition and can be further used as a basis for calibration curves. In addition, the diffusion coefficients of the specified gas mixtures were successfully found and compared with references, confirming the applicability of the fabricated sensor for studying diffusion processes in wide concentration and temperature ranges.
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13
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Bhattacharya S, Margheritis EG, Takahashi K, Kulesha A, D'Souza A, Kim I, Yoon JH, Tame JRH, Volkov AN, Makhlynets OV, Korendovych IV. NMR-guided directed evolution. Nature 2022; 610:389-393. [PMID: 36198791 PMCID: PMC10116341 DOI: 10.1038/s41586-022-05278-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/25/2022] [Indexed: 11/09/2022]
Abstract
Directed evolution is a powerful tool for improving existing properties and imparting completely new functionalities to proteins1-4. Nonetheless, its potential in even small proteins is inherently limited by the astronomical number of possible amino acid sequences. Sampling the complete sequence space of a 100-residue protein would require testing of 20100 combinations, which is beyond any existing experimental approach. In practice, selective modification of relatively few residues is sufficient for efficient improvement, functional enhancement and repurposing of existing proteins5. Moreover, computational methods have been developed to predict the locations and, in certain cases, identities of potentially productive mutations6-9. Importantly, all current approaches for prediction of hot spots and productive mutations rely heavily on structural information and/or bioinformatics, which is not always available for proteins of interest. Moreover, they offer a limited ability to identify beneficial mutations far from the active site, even though such changes may markedly improve the catalytic properties of an enzyme10. Machine learning methods have recently showed promise in predicting productive mutations11, but they frequently require large, high-quality training datasets, which are difficult to obtain in directed evolution experiments. Here we show that mutagenic hot spots in enzymes can be identified using NMR spectroscopy. In a proof-of-concept study, we converted myoglobin, a non-enzymatic oxygen storage protein, into a highly efficient Kemp eliminase using only three mutations. The observed levels of catalytic efficiency exceed those of proteins designed using current approaches and are similar with those of natural enzymes for the reactions that they are evolved to catalyse. Given the simplicity of this experimental approach, which requires no a priori structural or bioinformatic knowledge, we expect it to be widely applicable and to enable the full potential of directed enzyme evolution.
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Affiliation(s)
| | - Eleonora G Margheritis
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Katsuya Takahashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Alona Kulesha
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Areetha D'Souza
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Inhye Kim
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Jennifer H Yoon
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Alexander N Volkov
- VIB Centre for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium.
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
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14
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Olivet J, Maseko SB, Volkov AN, Salehi-Ashtiani K, Das K, Calderwood MA, Twizere JC, Gorgulla C. A systematic approach to identify host targets and rapidly deliver broad-spectrum antivirals. Mol Ther 2022; 30:1797-1800. [PMID: 35231394 PMCID: PMC8884476 DOI: 10.1016/j.ymthe.2022.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/10/2021] [Accepted: 02/11/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Julien Olivet
- Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research and Department of Microbiology, Immunology and Transplantation, Catholic University of Leuven (KU Leuven), Leuven, Belgium; Laboratory of Viral Interactomes Networks, Unit of Molecular Biology of Diseases, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, Liège, Belgium
| | - Sibusiso B Maseko
- Laboratory of Viral Interactomes Networks, Unit of Molecular Biology of Diseases, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, Liège, Belgium
| | - Alexander N Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium; Jean Jeener NMR Centre, Free University of Brussels (VUB), Brussels, Belgium
| | | | - Kalyan Das
- Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research and Department of Microbiology, Immunology and Transplantation, Catholic University of Leuven (KU Leuven), Leuven, Belgium
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes Networks, Unit of Molecular Biology of Diseases, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, Liège, Belgium; Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liège, Gembloux, Belgium.
| | - Christoph Gorgulla
- Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA.
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15
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Ernst S, Volkov AN, Stark M, Hölscher L, Steinert K, Fetzner S, Hennecke U, Drees SL. Azetidomonamide and Diazetidomonapyridone Metabolites Control Biofilm Formation and Pigment Synthesis in Pseudomonas aeruginosa. J Am Chem Soc 2022; 144:7676-7685. [PMID: 35451837 DOI: 10.1021/jacs.1c13653] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Synthesis of azetidine-derived natural products by the opportunistic pathogen Pseudomonas aeruginosa is controlled by quorum sensing, a process involving the production and sensing of diffusible signal molecules that is decisive for virulence regulation. In this study, we engineered P. aeruginosa for the titratable expression of the biosynthetic aze gene cluster, which allowed the purification and identification of two new products, azetidomonamide C and diazetidomonapyridone. Diazetidomonapyridone was shown to have a highly unusual structure with two azetidine rings and an open-chain diimide moiety. Expression of aze genes strongly increased biofilm formation and production of phenazine and alkyl quinolone virulence factors. Further physiological studies revealed that all effects were mainly mediated by azetidomonamide A and diazetidomonapyridone, whereas azetidomonamides B and C had little or no phenotypic impact. The P450 monooxygenase AzeF which catalyzes a challenging, stereoselective hydroxylation of the azetidine ring converting azetidomonamide C into azetidomonamide A is therefore crucial for biological activity. Based on our findings, we propose this group of metabolites to constitute a new class of diffusible regulatory molecules with community-related effects in P. aeruginosa.
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Affiliation(s)
- Simon Ernst
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, Münster 48149, Germany
| | - Alexander N Volkov
- VIB Centre for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Pleinlaan 2, Brussels 1050, Belgium.,Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels 1050 Belgium
| | - Melina Stark
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, Münster 48149, Germany
| | - Lea Hölscher
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, Münster 48149, Germany
| | - Katharina Steinert
- Institute for Food Chemistry, University of Münster, Corrensstr. 45, Münster 48149, Germany
| | - Susanne Fetzner
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, Münster 48149, Germany
| | - Ulrich Hennecke
- Organic Chemistry Research Group, Department of Chemistry and Department of Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels 1050, Belgium
| | - Steffen Lorenz Drees
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, Münster 48149, Germany
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16
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Bdira FB, Erkelens AM, Qin L, Volkov AN, Lippa A, Bowring N, Boyle A, Ubbink M, Dove S, Dame R. Novel anti-repression mechanism of H-NS proteins by a phage protein. Nucleic Acids Res 2021; 49:10770-10784. [PMID: 34520554 PMCID: PMC8501957 DOI: 10.1093/nar/gkab793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/16/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
H-NS family proteins, bacterial xenogeneic silencers, play central roles in genome organization and in the regulation of foreign genes. It is thought that gene repression is directly dependent on the DNA binding modes of H-NS family proteins. These proteins form lateral protofilaments along DNA. Under specific environmental conditions they switch to bridging two DNA duplexes. This switching is a direct effect of environmental conditions on electrostatic interactions between the oppositely charged DNA binding and N-terminal domains of H-NS proteins. The Pseudomonas lytic phage LUZ24 encodes the protein gp4, which modulates the DNA binding and function of the H-NS family protein MvaT of Pseudomonas aeruginosa. However, the mechanism by which gp4 affects MvaT activity remains elusive. In this study, we show that gp4 specifically interferes with the formation and stability of the bridged MvaT-DNA complex. Structural investigations suggest that gp4 acts as an 'electrostatic zipper' between the oppositely charged domains of MvaT protomers, and stabilizes a structure resembling their 'half-open' conformation, resulting in relief of gene silencing and adverse effects on P. aeruginosa growth. The ability to control H-NS conformation and thereby its impact on global gene regulation and growth might open new avenues to fight Pseudomonas multidrug resistance.
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Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Amanda M Erkelens
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Liang Qin
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexander N Volkov
- VIB-VUB Structural Biology Research Center, Pleinlaan 2, 1050 Brussels, Belgium
- Jean Jeener NMR Centre, VUB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Andrew M Lippa
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas Bowring
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Aimee L Boyle
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Simon L Dove
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Remus T Dame
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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17
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Kalyakin AS, Danilov NA, Volkov AN. Determining humidity of nitrogen and air atmospheres by means of a protonic ceramic sensor. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Garcia-Rodriguez G, Girardin Y, Volkov AN, Singh RK, Muruganandam G, Van Dyck J, Sobott F, Versées W, Charlier D, Loris R. Entropic pressure controls the oligomerization of the Vibrio cholerae ParD2 antitoxin. Acta Crystallogr D Struct Biol 2021; 77:904-920. [PMID: 34196617 PMCID: PMC8251345 DOI: 10.1107/s2059798321004873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/04/2021] [Accepted: 05/07/2021] [Indexed: 11/22/2022] Open
Abstract
ParD2 is the antitoxin component of the parDE2 toxin-antitoxin module from Vibrio cholerae and consists of an ordered DNA-binding domain followed by an intrinsically disordered ParE-neutralizing domain. In the absence of the C-terminal intrinsically disordered protein (IDP) domain, V. cholerae ParD2 (VcParD2) crystallizes as a doughnut-shaped hexadecamer formed by the association of eight dimers. This assembly is stabilized via hydrogen bonds and salt bridges rather than by hydrophobic contacts. In solution, oligomerization of the full-length protein is restricted to a stable, open decamer or dodecamer, which is likely to be a consequence of entropic pressure from the IDP tails. The relative positioning of successive VcParD2 dimers mimics the arrangement of Streptococcus agalactiae CopG dimers on their operator and allows an extended operator to wrap around the VcParD2 oligomer.
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Affiliation(s)
- Gabriela Garcia-Rodriguez
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
| | - Yana Girardin
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
| | - Alexander N. Volkov
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
- Jean Jeener NMR Center, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Ranjan Kumar Singh
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
| | - Gopinath Muruganandam
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jeroen Van Dyck
- Department of Chemistry, Universiteit Antwerpen, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Frank Sobott
- Department of Chemistry, Universiteit Antwerpen, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
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19
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Kalyakin AS, Medvedev DA, Volkov AN. Electrochemical sensors based on proton-conducting electrolytes for determination of concentration and diffusion coefficient of CO2 in inert gases. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2020.116046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Ben Bdira F, Waudby CA, Volkov AN, Schröder SP, AB E, Codée JDC, Overkleeft HS, Aerts JMFG, Ingen H, Ubbink M. Dynamics of Ligand Binding to a Rigid Glycosidase**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003236] [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: 11/06/2022]
Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Christopher A. Waudby
- Institute of Structural and Molecular Biology University College London and Birkbeck College London WC1E 6BT UK
| | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology Pleinlaan 2 1050 Brussels Belgium
- Jean Jeener NMR Centre VUB Pleinlaan 2 1050 Brussels Belgium
| | - Sybrin P. Schröder
- Department of Bio-organic Synthesis Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Eiso AB
- ZoBio BV BioPartner 2 building J.H. Oortweg 19 2333 CH Leiden The Netherlands
| | - Jeroen D. C. Codée
- Department of Bio-organic Synthesis Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Department of Bio-organic Synthesis Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hugo Ingen
- Department of Macromolecular Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
- Present address: NMR Spectroscopy Research Group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
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21
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Ben Bdira F, Waudby CA, Volkov AN, Schröder SP, AB E, Codée JDC, Overkleeft HS, Aerts JMFG, van Ingen H, Ubbink M. Dynamics of Ligand Binding to a Rigid Glycosidase*. Angew Chem Int Ed Engl 2020; 59:20508-20514. [PMID: 32533782 PMCID: PMC7693232 DOI: 10.1002/anie.202003236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/29/2020] [Indexed: 11/09/2022]
Abstract
The single-domain GH11 glycosidase from Bacillus circulans (BCX) is involved in the degradation of hemicellulose, which is one of the most abundant renewable biomaterials in nature. We demonstrate that BCX in solution undergoes minimal structural changes during turnover. NMR spectroscopy results show that the rigid protein matrix provides a frame for fast substrate binding in multiple conformations, accompanied by slow conversion, which is attributed to an enzyme-induced substrate distortion. A model is proposed in which the rigid enzyme takes advantage of substrate flexibility to induce a conformation that facilitates the acyl formation step of the hydrolysis reaction.
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Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Christopher A. Waudby
- Institute of Structural and Molecular BiologyUniversity College London and Birkbeck CollegeLondonWC1E 6BTUK
| | - Alexander N. Volkov
- VIB-VUB Center for Structural BiologyPleinlaan 21050BrusselsBelgium
- Jean Jeener NMR CentreVUBPleinlaan 21050BrusselsBelgium
| | - Sybrin P. Schröder
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Eiso AB
- ZoBio BVBioPartner 2 buildingJ.H. Oortweg 192333 CHLeidenThe Netherlands
| | - Jeroen D. C. Codée
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hermen S. Overkleeft
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hugo van Ingen
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
- Present address: NMR Spectroscopy Research GroupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
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22
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Zhegalik AG, Polyakov SL, Rolevich AI, Volkov AN, Minich AA, Vasilevich VJ, Mokhort AA, Krasny SA, Sukonko OG. Long-term results of a single-center prospective randomized trial assessing efficacy of a shortened course of adjuvant chemotherapy after radical cystectomy in patients with locally advanced bladder cancer. Cent European J Urol 2020; 73:26-32. [PMID: 32395319 PMCID: PMC7203780 DOI: 10.5173/ceju.2020.0032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 02/21/2020] [Revised: 02/23/2020] [Accepted: 02/23/2020] [Indexed: 12/24/2022] Open
Abstract
Introduction This study assesses the efficacy and tolerability of two cycles of adjuvant chemotherapy (AC) with gemcitabine and cisplatin after radical cystectomy in patients with a high risk of progression of muscle-invasive urothelial bladder cancer as compared to chemotherapy at relapse, in a prospective randomized study. Material and methods From 2008 to 2013, all patients after radical cystectomy at our institution for primary or recurrent urothelial bladder cancer with stage pT3-4 and/or pN+ on histopathology and without contraindications to combination cisplatin-based chemotherapy, were randomized either to two cycles of gemcitabine and cisplatin chemotherapy or to follow-up and chemotherapy at the time of relapse. The study endpoints were overall, cancer-specific, and disease-free survival. Results The study included 100 patients, of whom 53 received AC and the other 47 were assigned to the control arm. Out of 53 allocated to AC arm, 16 patients did not start chemotherapy or received only one cycle of AC. The median follow-up for patients in the AC and control arms was 88 and 86 months, respectively. In the AC arm the hazard ratio for death from any cause, death from bladder cancer, and disease relapse were 0.70 (95% CI 0.45-1.11; p = 0.13), 0.84 (95% CI 0.50-1.41; p = 0.51), and 0.77 (95% CI 0.46-1.28; p = 0.31), respectively. Conclusions Two cycles of AC with gemcitabine and cisplatin in patients with high-risk urothelial bladder cancer after radical cystectomy does not improve overall, cancer-specific, and disease-free survival. Only 53% of patients randomized to AC received the entire planned treatment.
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Affiliation(s)
- Alexander G Zhegalik
- Department of Urology, N.N. Alexandrov National Research Cancer Center, Minsk, Belarus
| | - Sergey L Polyakov
- Department of Urology, N.N. Alexandrov National Research Cancer Center, Minsk, Belarus
| | - Alexander I Rolevich
- Department of Urology, N.N. Alexandrov National Research Cancer Center, Minsk, Belarus
| | - Alexander N Volkov
- Department of Urology, N.N. Alexandrov National Research Cancer Center, Minsk, Belarus
| | - Alexander A Minich
- Department of Urology, N.N. Alexandrov National Research Cancer Center, Minsk, Belarus
| | | | - Andrey A Mokhort
- Department of Urology, N.N. Alexandrov National Research Cancer Center, Minsk, Belarus
| | - Sergey A Krasny
- Department of Urology, N.N. Alexandrov National Research Cancer Center, Minsk, Belarus
| | - Oleg G Sukonko
- Department of Urology, N.N. Alexandrov National Research Cancer Center, Minsk, Belarus
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23
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Prolič-Kalinšek M, De Bruyn P, Jurėnas D, Van Melderen L, Loris R, Volkov AN. 1H, 13C, and 15N backbone and side chain chemical shift assignment of YdaS, a monomeric member of the HigA family. Biomol NMR Assign 2020; 14:25-30. [PMID: 31625047 DOI: 10.1007/s12104-019-09915-9] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
The cryptic prophage CP-933P in Escherichia coli O157:H7 contains a parDE-like toxin-antitoxin module, the operator region of which is recognized by two flanking transcription regulators: PaaR2 (ParE associated Regulator), which forms part of the paaR2-paaA2-parE2 toxin-antitoxin operon and YdaS (COG4197), which is encoded in the opposite direction but shares the operator. Here we report the 1H, 15N and 13C backbone and side chain chemical shift assignments of YdaS from Escherichia coli O157:H7 in its free state. YdaS is a distinct relative to HigA antitoxins but behaves as a monomer in solution. The BMRB Accession Number is 27917.
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Affiliation(s)
- Maruša Prolič-Kalinšek
- Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Pieter De Bruyn
- Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Dukas Jurėnas
- Cellular and Molecular Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel, Brussels, Belgium.
- VIB-VUB Center for Structural Biology, Brussels, Belgium.
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Brussels, Belgium
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24
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Qin L, Bdira FB, Sterckx YGJ, Volkov AN, Vreede J, Giachin G, van Schaik P, Ubbink M, Dame RT. Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins. Nucleic Acids Res 2020; 48:2156-2172. [PMID: 31925429 PMCID: PMC7039000 DOI: 10.1093/nar/gkz1226] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 09/06/2019] [Revised: 11/29/2019] [Accepted: 12/19/2019] [Indexed: 01/07/2023] Open
Abstract
H-NS proteins act as osmotic sensors translating changes in osmolarity into altered DNA binding properties, thus, regulating enterobacterial genome organization and genes transcription. The molecular mechanism underlying the switching process and its conservation among H-NS family members remains elusive. Here, we focus on the H-NS family protein MvaT from Pseudomonas aeruginosa and demonstrate experimentally that its protomer exists in two different conformations, corresponding to two different functional states. In the half-opened state (dominant at low salt) the protein forms filaments along DNA, in the fully opened state (dominant at high salt) the protein bridges DNA. This switching is a direct effect of ionic strength on electrostatic interactions between the oppositely charged DNA binding and N-terminal domains of MvaT. The asymmetric charge distribution and intramolecular interactions are conserved among the H-NS family of proteins. Therefore, our study establishes a general paradigm for the molecular mechanistic basis of the osmosensitivity of H-NS proteins.
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Affiliation(s)
- Liang Qin
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Fredj Ben Bdira
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Yann G J Sterckx
- Laboratory of Medical Biochemistry, University of Antwerp, Campus Drie Eiken, University Square 1, 2610 Wilrijk, Belgium
| | - Alexander N Volkov
- VIB-VUB Structural Biology Research Center, Pleinlaan 2, 1050 Brussels, Belgium.,Jean Jeener NMR Centre, VUB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jocelyne Vreede
- Department of Computational Chemistry, Van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Gabriele Giachin
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - Peter van Schaik
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Remus T Dame
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
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25
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Tossounian MA, Khanh Truong AC, Buts L, Wahni K, Mourenza Á, Leermakers M, Vertommen D, Mateos LM, Volkov AN, Messens J. Methionine sulfoxide reductase B from Corynebacterium diphtheriae catalyzes sulfoxide reduction via an intramolecular disulfide cascade. J Biol Chem 2020; 295:3664-3677. [PMID: 31992594 DOI: 10.1074/jbc.ra119.012438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 12/27/2019] [Revised: 01/24/2020] [Indexed: 11/06/2022] Open
Abstract
Corynebacterium diphtheriae is a human pathogen that causes diphtheria. In response to immune system-induced oxidative stress, C. diphtheriae expresses antioxidant enzymes, among which are methionine sulfoxide reductase (Msr) enzymes, which are critical for bacterial survival in the face of oxidative stress. Although some aspects of the catalytic mechanism of the Msr enzymes have been reported, several details still await full elucidation. Here, we solved the solution structure of C. diphtheriae MsrB (Cd-MsrB) and unraveled its catalytic and oxidation-protection mechanisms. Cd-MsrB catalyzes methionine sulfoxide reduction involving three redox-active cysteines. Using NMR heteronuclear single-quantum coherence spectra, kinetics, biochemical assays, and MS analyses, we show that the conserved nucleophilic residue Cys-122 is S-sulfenylated after substrate reduction, which is then resolved by a conserved cysteine, Cys-66, or by the nonconserved residue Cys-127. We noted that the overall structural changes during the disulfide cascade expose the Cys-122-Cys-66 disulfide to recycling through thioredoxin. In the presence of hydrogen peroxide, Cd-MsrB formed reversible intra- and intermolecular disulfides without losing its Cys-coordinated Zn2+, and only the nonconserved Cys-127 reacted with the low-molecular-weight (LMW) thiol mycothiol, protecting it from overoxidation. In summary, our structure-function analyses reveal critical details of the Cd-MsrB catalytic mechanism, including a major structural rearrangement that primes the Cys-122-Cys-66 disulfide for thioredoxin reduction and a reversible protection against excessive oxidation of the catalytic cysteines in Cd-MsrB through intra- and intermolecular disulfide formation and S-mycothiolation.
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Affiliation(s)
- Maria-Armineh Tossounian
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussels, B-1050 Brussels, Belgium
| | - Anh-Co Khanh Truong
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussels, B-1050 Brussels, Belgium
| | - Lieven Buts
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussels, B-1050 Brussels, Belgium; Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussels, B-1050 Brussels, Belgium
| | - Khadija Wahni
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussels, B-1050 Brussels, Belgium
| | - Álvaro Mourenza
- Department of Molecular Biology, Area of Microbiology, University of León, 24071 León, Spain
| | - Martine Leermakers
- Analytical, Environmental and Geo-Chemistry (AMGC), Vrije Universiteit Brussels, Brussels, Belgium
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Luis Mariano Mateos
- Department of Molecular Biology, Area of Microbiology, University of León, 24071 León, Spain
| | - Alexander N Volkov
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussels, B-1050 Brussels, Belgium; Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussels, B-1050 Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussels, B-1050 Brussels, Belgium.
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26
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Shabaev AR, Kazantsev AN, Tarasov RS, Ruban EV, Lider RI, Iakhnis EI, Solobuev AI, Volkov AN, Mironov AV. [Surgical treatment of a patient with saccular arterial aneurysm of the cavernous-ophthalmic segment]. Angiol Sosud Khir 2020; 25:131-138. [PMID: 31855210 DOI: 10.33529/angio2019412] [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] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Presented in the article are the results of surgical management of a patient with an extremely rare pathology - a saccular arterial aneurysm of the cavernous-ophthalmic segment of the left internal carotid artery. We performed multistage open surgical intervention in the following scope: osteoplastic pterional craniotomy on the left, creation of a wide-lumen anastomosis between the left external carotid artery and M2 segment of the left middle cerebral artery with the use of the radial artery, ligation of the cervical portion of the left internal carotid artery and clipping of its supraclinoid portion. The chosen surgical policy made it possible to create sufficient volumetric blood flow through the shunt, comparable to the blood flow through the internal carotid artery, which helped avoid ischaemic stroke after exclusion of the aneurysm from circulation. A conclusion was drawn on efficacy of this method of treatment.
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Affiliation(s)
- A R Shabaev
- Kemerovo Regional Clinical Cardiological Dispensary named after Academician L.S. Barbarash, Kemerovo, Russia; Research Institute for Complex Problems of Cardiovascular Diseases, Kemerovo, Russia
| | - A N Kazantsev
- Kemerovo Regional Clinical Cardiological Dispensary named after Academician L.S. Barbarash, Kemerovo, Russia; Research Institute for Complex Problems of Cardiovascular Diseases, Kemerovo, Russia
| | - R S Tarasov
- Research Institute for Complex Problems of Cardiovascular Diseases, Kemerovo, Russia
| | - E V Ruban
- Kemerovo Regional Clinical Cardiological Dispensary named after Academician L.S. Barbarash, Kemerovo, Russia
| | - R Iu Lider
- Kemerovo State Medical University of the RF Ministry of Public Health, Kemerovo, Russia
| | - E Ia Iakhnis
- Kemerovo State Medical University of the RF Ministry of Public Health, Kemerovo, Russia
| | - A I Solobuev
- Kemerovo State Medical University of the RF Ministry of Public Health, Kemerovo, Russia
| | - A N Volkov
- Kemerovo Regional Clinical Cardiological Dispensary named after Academician L.S. Barbarash, Kemerovo, Russia
| | - A V Mironov
- Kemerovo Regional Clinical Cardiological Dispensary named after Academician L.S. Barbarash, Kemerovo, Russia; Research Institute for Complex Problems of Cardiovascular Diseases, Kemerovo, Russia
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27
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Tarasov RS, Ivanov SV, Kazantsev AN, Volkov AN, Shabayev AR, Bakovskiy KV, Lider RY, Grachev KI. [Long-term outcomes of coronary artery bypass surgery in young patients]. Khirurgiia (Mosk) 2019:57-63. [PMID: 31714531 DOI: 10.17116/hirurgia201911157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To analyze long-term outcomes of CABG in young patients, incidence and structure of adverse cardiovascular events depending on patients' age. MATERIAL AND METHODS There were 175 young patients (up to 44 years old in accordance with WHO classification) who underwent CABG for the period from 2006 to 2016. The control group included 175 patients aged 45 years and older who were randomly selected among patients operated in the same period. Overall long-term follow-up period was 81.9±15.75 months (≈ 6.8 years). Data on long-term survival and adverse cardiovascular events were available in 86.3% of patients in general sample and 72.6% of young patients. RESULTS Young patients undergoing CABG were usually characterized by the absence of severe concomitant diseases, moderate coronary atherosclerosis by SYNTAX Score scale, high percentage of left ventricular aneurysm and previous PCI. Incidence and structure of in-hospital and long-term adverse cardiovascular events in young and older patients confirmed satisfactory results of CABG regardless age.
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Affiliation(s)
- R S Tarasov
- Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - S V Ivanov
- Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - A N Kazantsev
- Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - A N Volkov
- Kemerovo Regional Clinical Cardiology Dispensary, Kemerovo, Russia
| | - A R Shabayev
- Kemerovo Regional Clinical Cardiology Dispensary, Kemerovo, Russia
| | - K V Bakovskiy
- Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - R Yu Lider
- Kemerovo State Medical University of the Ministry of Health of the Russia, Kemerovo, Russia
| | - K I Grachev
- Kemerovo State Medical University of the Ministry of Health of the Russia, Kemerovo, Russia
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28
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Yoon JH, Kulesha AV, Lengyel-Zhand Z, Volkov AN, Rempillo JJ, D'Souza A, Costeas C, Chester C, Caselle ER, Makhlynets OV. Uno Ferro, a de novo Designed Protein, Binds Transition Metals with High Affinity and Stabilizes Semiquinone Radical Anion. Chemistry 2019; 25:15252-15256. [PMID: 31509280 DOI: 10.1002/chem.201904020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 09/02/2019] [Indexed: 11/07/2022]
Abstract
Metalloenzymes often utilize radicals in order to facilitate chemical reactions. Recently, DeGrado and co-workers have discovered that model proteins can efficiently stabilize semiquinone radical anion produced by oxidation of 3,5-di-tert-butylcatechol (DTBC) in the presence of two zinc ions. Here, we show that the number and the nature of metal ions have relatively minor effect on semiquinone stabilization in model proteins, with a single metal ion being sufficient for radical stabilization. The radical is stabilized by both metal ion, hydrophobic sequestration, and interactions with the hydrophilic residues in the protein interior resulting in a remarkable, nearly 500 mV change in the redox potential of the SQ. - /catechol couple compared to bulk aqueous solution. Moreover, we have created 4G-UFsc, a single metal ion-binding protein with pm affinity for zinc that is higher than any other reported model systems and is on par with many natural zinc-containing proteins. We expect that the robust and easy-to-modify DFsc/UFsc family of proteins will become a versatile tool for mechanistic model studies of metalloenzymes.
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Affiliation(s)
- Jennifer H Yoon
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Alona V Kulesha
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Zsofia Lengyel-Zhand
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Alexander N Volkov
- VIB Centre for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Pleinlaan 2, Brussels, 1050, Belgium.,Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium
| | - Joel J Rempillo
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Areetha D'Souza
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Christos Costeas
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Cara Chester
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Elizabeth R Caselle
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
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Rice HC, de Malmazet D, Schreurs A, Frere S, Van Molle I, Volkov AN, Creemers E, Vertkin I, Nys J, Ranaivoson FM, Comoletti D, Savas JN, Remaut H, Balschun D, Wierda KD, Slutsky I, Farrow K, De Strooper B, de Wit J. Secreted amyloid-β precursor protein functions as a GABA BR1a ligand to modulate synaptic transmission. Science 2019; 363:363/6423/eaao4827. [PMID: 30630900 DOI: 10.1126/science.aao4827] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/30/2018] [Accepted: 11/14/2018] [Indexed: 12/16/2022]
Abstract
Amyloid-β precursor protein (APP) is central to the pathogenesis of Alzheimer's disease, yet its physiological function remains unresolved. Accumulating evidence suggests that APP has a synaptic function mediated by an unidentified receptor for secreted APP (sAPP). Here we show that the sAPP extension domain directly bound the sushi 1 domain specific to the γ-aminobutyric acid type B receptor subunit 1a (GABABR1a). sAPP-GABABR1a binding suppressed synaptic transmission and enhanced short-term facilitation in mouse hippocampal synapses via inhibition of synaptic vesicle release. A 17-amino acid peptide corresponding to the GABABR1a binding region within APP suppressed in vivo spontaneous neuronal activity in the hippocampus of anesthetized Thy1-GCaMP6s mice. Our findings identify GABABR1a as a synaptic receptor for sAPP and reveal a physiological role for sAPP in regulating GABABR1a function to modulate synaptic transmission.
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Affiliation(s)
- Heather C Rice
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Daniel de Malmazet
- Neuro-Electronics Research Flanders, Leuven, Belgium.,Department of Biology, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - An Schreurs
- Brain & Cognition, KU Leuven, Leuven, Belgium
| | - Samuel Frere
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Inge Van Molle
- VIB-VUB Structural Biology Research Center, Brussels, Belgium
| | - Alexander N Volkov
- VIB-VUB Structural Biology Research Center, Brussels, Belgium.,Jean Jeener NMR Centre, VUB, Brussels, Belgium
| | - Eline Creemers
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Irena Vertkin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Julie Nys
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Fanomezana M Ranaivoson
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers University, NJ, USA
| | - Davide Comoletti
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers University, NJ, USA.,Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, NJ, USA
| | - Jeffrey N Savas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Han Remaut
- VIB-VUB Structural Biology Research Center, Brussels, Belgium
| | | | - Keimpe D Wierda
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Inna Slutsky
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Karl Farrow
- Neuro-Electronics Research Flanders, Leuven, Belgium.,Department of Biology, Leuven Brain Institute, KU Leuven, Leuven, Belgium.,VIB, Leuven, Belgium.,imec, Leuven, Belgium
| | - Bart De Strooper
- VIB Center for Brain & Disease Research, Leuven, Belgium. .,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium.,UK-Dementia Research Institute at University College London, UK
| | - Joris de Wit
- VIB Center for Brain & Disease Research, Leuven, Belgium. .,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
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Volkov AN, Khabieva SM, Smirnova EY, Larionov AV. [The genetic diagnostics of mutations UGT1A1 in practice of modern medicine.]. Klin Lab Diagn 2019; 63:186-192. [PMID: 30673201 DOI: 10.18821/0869-2084-2018-63-3-186-192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 11/22/2017] [Indexed: 11/17/2022]
Abstract
The detection of mutations of the gene of UDF-glucuronyltransferase A1 (UGT1A1) has an important practical value. The carriers of mutant genotypes, mainly *28/*28, are characterized by a reduced function of glucuronidation and excretion of a number of endogenous and exogenous toxins. A precise association of particular forms of benign hyperbilirubinemia (especially Gilbert's syndrome) with mutations in promoter and exonic areas of UGT1A1 is established. On the other hand, carriers of various genotypes of UGT1A1 differ significantly in metabolism characteristics of a number of common medications (irinotecan, belinostat, etc.), that requires a dosage of these medications considering individual genetic status of patient. The analysis of modern technical solutions for genetic diagnostics of UGT1A1 mutations is carried out. The particular attention is paid to discussion of national developments for genetic typing of UGT1A1. The conclusion is made concerning small assortment of corresponding test-systems of Russian production. In some cases, there is no data about their main analytical and diagnostic characteristics. When developing design of diagnosticums, various methodological approaches are applied that allow to potential consumers to choose depending on financial technical capabilities of laboratory, amount of implemented analyses, qualification of personnel. To support UGT1A1 research instrumentally, laboratory equipment of national manufacturers can be sufficient that would permit to organize entire analytical cycle on the basis of import substitution principle.
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Affiliation(s)
- A N Volkov
- The Federal State Budget Educational Institution of Higher Education "The Kemerovo State Medical University" of Minzdrav of Russia, 650029, Kemerovo, Russia.,The Federal State Budget Educational Institution of Higher Education "The Kemerovo State University", 650043, Kemerovo, Russia
| | - S M Khabieva
- The Federal State Budget Educational Institution of Higher Education "The Kemerovo State University", 650043, Kemerovo, Russia
| | - E Yu Smirnova
- The Federal State Budget Educational Institution of Higher Education "The Kemerovo State University", 650043, Kemerovo, Russia
| | - A V Larionov
- The Federal State Budget Educational Institution of Higher Education "The Kemerovo State University", 650043, Kemerovo, Russia
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31
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Kalyakin AS, Lyagaeva JY, Volkov AN, Medvedev DA. Unusual oxygen detection by means of a solid state sensor based on a CaZr0.9In0.1O3–δ proton-conducting electrolyte. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Sedykh DY, Kazantsev AN, Tarasov RS, Kashtalap VV, Volkov AN, Grachev KI, Shabayev AR, Barbarash OL. [Predictors of Progressive Course of Multifocal Atherosclerosis in Patients With Myocardial Infarction]. ACTA ACUST UNITED AC 2019; 59:36-44. [PMID: 31131766 DOI: 10.18087/cardio.2019.5.10257] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 05/25/2019] [Indexed: 11/18/2022]
Abstract
PURPOSE Determination of clinical and instrumental predictors of progressive course of multifocal atherosclerosis (MFA) in patients one year after myocardial infarction (MI), initially having hemodynamically insignificant stenoses of carotid arteries. MATERIALS AND METHODS From database of patients with acute coronary syndrome treated in the Kemerovo Regional Clinical Cardiac Dispensary in 2009-2010 we selected for this study 141 patients with verified diagnosis of MI and hemodynamically insignificant lesions in the internal carotid artery (ICA) (stenosis up ≤ 55 %). All patients had coronary atherosclerosis verified on coronary angiography at admission because of MI. A multivariate analysis of possible predictors of the progressive course of multifocal atherosclerosis was made based on assessment of the development of cardiovascular complications (CVC) (death, MI, stroke and transient cerebral circulatory attacks [TIA]), as well as revascularizations and negative dynamics of parameters of color duplex scanning (CDS) of ICA during one year after MI. RESULTS One year after MI the overall incidence of CVC was 16.3 % (n=23). Structure of registered events was as follows: death from MI 7.1 % (n=10), deaths from stroke 2.1 % (n=3) and other causes 2.1 % (n=3), non-fatal MI 5.0 % (n=7), non-fatal stroke / TIA 2.1 % (n=3), carotid revascularization 2.8 % (n=4), coronary revascularization 14.9 % (n=21). CDC of ICAs was repeated in 125 patients. There were 17 (13.6 %) cases of progression of carotid atherosclerosis in the form of de novo bilateral stenoses in 14 (11.2 %) patients, stenoses in the left and right ICA 1 patient and 2 patients, respectively. The following predictors of progression of atherosclerosis of cerebral arteries were identified: family history of cardiovascular diseases (CVD),ICA stenosis ≥45 %, baseline circular atherosclerotic plaque (ASP). Predictors of high risk of stroke were family history of CVD, history of stroke,ICA stenosis ≥45 %, heterogeneous hypoechoic ASP. As predictors of lethal outcome, we identified history of MI, high functional class of angina preceding the index MI, severe coronary vascular bed involvement (SYNTAX score >23), presence of any bilateral atherosclerotic lesion in ICAs, and heterogeneous hypoechoic ASP. Assessment of the contribution of adherence to therapy in the prognosis 1 year after hospital discharge was fulfilled in 125 alive patients. It allowed to conclude that patients with progression of atherosclerosis and nonfatal CVC were characterized by insufficient adherence to standard therapy. CONCLUSION Predictors of the progressive course of multifocal atherosclerosis during one year after MI were identified in this study. It is necessary to strengthen therapeutic and preventive measures aimed at minimization of the impact of these factors in this category of patients.
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Affiliation(s)
- D Yu Sedykh
- Research Institute for Complex Issues of Cardiovascular Diseases; Kemerovo Regional Clinical Cardiology Dispensary
| | - A N Kazantsev
- Research Institute for Complex Issues of Cardiovascular Diseases; Kemerovo Regional Clinical Cardiology Dispensary
| | - R S Tarasov
- Research Institute for Complex Issues of Cardiovascular Diseases
| | - V V Kashtalap
- Research Institute for Complex Issues of Cardiovascular Diseases; Kemerovo State Medical University
| | - A N Volkov
- Kemerovo Regional Clinical Cardiology Dispensary
| | | | - A R Shabayev
- Research Institute for Complex Issues of Cardiovascular Diseases; Kemerovo Regional Clinical Cardiology Dispensary
| | - O L Barbarash
- Research Institute for Complex Issues of Cardiovascular Diseases; Kemerovo State Medical University
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Caselle EA, Yoon JH, Bhattacharya S, Rempillo JJL, Lengyel Z, D'Souza A, Moroz YS, Tolbert PL, Volkov AN, Forconi M, Castañeda CA, Makhlynets OV, Korendovych IV. Front Cover: Kemp Eliminases of the AlleyCat Family Possess High Substrate Promiscuity (ChemCatChem 5/2019). ChemCatChem 2019. [DOI: 10.1002/cctc.201900266] [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: 11/06/2022]
Affiliation(s)
- Elizabeth A. Caselle
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Jennifer H. Yoon
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Sagar Bhattacharya
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Joel J. L. Rempillo
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Zsófia Lengyel
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Areetha D'Souza
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Yurii S. Moroz
- Department of ChemistryTaras Shevchenko National University of Kyiv 64 Volodymyrska St. Kyiv 01601 Ukraine
| | - Patricia L. Tolbert
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Alexander N. Volkov
- VIB Centre for Structural BiologyVlaams Instituut voor Biotechnologie (VIB) Pleinlaan 2 Brussels 1050 Belgium
- Jean Jeener NMR CetreVrije Universiteit Brussel (VUB) Pleinlaan 2 Brussels 1050 Belgium
| | - Marcello Forconi
- Department of Chemistry and BiochemistryCollege of Charleston 66 George St. Charleston SC 29424 USA
| | - Carlos A. Castañeda
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Olga V. Makhlynets
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Ivan V. Korendovych
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
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34
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Caselle EA, Yoon JH, Bhattacharya S, Rempillo JJL, Lengyel Z, D'Souza A, Moroz YS, Tolbert PL, Volkov AN, Forconi M, Castañeda CA, Makhlynets OV, Korendovych IV. Kemp Eliminases of the AlleyCat Family Possess High Substrate Promiscuity. ChemCatChem 2019. [DOI: 10.1002/cctc.201900269] [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: 11/06/2022]
Affiliation(s)
- Elizabeth A. Caselle
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Jennifer H. Yoon
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Sagar Bhattacharya
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Joel J. L. Rempillo
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Zsófia Lengyel
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Areetha D'Souza
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Yurii S. Moroz
- Department of ChemistryTaras Shevchenko National University of Kyiv 64 Volodymyrska St. Kyiv 01601 Ukraine
| | - Patricia L. Tolbert
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Alexander N. Volkov
- VIB Centre for Structural BiologyVlaams Instituut voor Biotechnologie (VIB) Pleinlaan 2 Brussels 1050 Belgium
- Jean Jeener NMR CetreVrije Universiteit Brussel (VUB) Pleinlaan 2 Brussels 1050 Belgium
| | - Marcello Forconi
- Department of Chemistry and BiochemistryCollege of Charleston 66 George St. Charleston SC 29424 USA
| | - Carlos A. Castañeda
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Olga V. Makhlynets
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
| | - Ivan V. Korendovych
- Department of ChemistrySyracuse University 111 College Place, Syracuse NY 13244 USA
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35
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Caselle EA, Yoon JH, Bhattacharya S, Rempillo JJ, Lengyel Z, D’Souza A, Moroz YS, Tolbert PL, Volkov AN, Forconi M, Castañeda CA, Makhlynets OV, Korendovych IV. Kemp Eliminases of the AlleyCat Family Possess High Substrate Promiscuity. ChemCatChem 2019; 11:1425-1430. [PMID: 31788134 PMCID: PMC6884320 DOI: 10.1002/cctc.201801994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Indexed: 10/21/2023]
Abstract
Minimalist enzymes designed to catalyze model reactions provide useful starting points for creating catalysts for practically important chemical transformations. We have shown that Kemp eliminases of the AlleyCat family facilitate conversion of leflunomide (an immunosupressor pro-drug) to its active form teriflunomide with outstanding rate enhancement (nearly four orders of magnitude) and catalytic proficiency (more than seven orders of magnitude) without any additional optimization. This remarkable activity is achieved by properly positioning the substrate in close proximity to the catalytic glutamate with very high pKa.
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Affiliation(s)
- Elizabeth A. Caselle
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Jennifer H. Yoon
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Sagar Bhattacharya
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Joel J.L. Rempillo
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Zsófia Lengyel
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Areetha D’Souza
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Yurii S. Moroz
- Department of Chemistry, Taras Shevchenko National University of Kyiv, 64 Volodymyrska St., Kyiv 01601, Ukraine
| | - Patricia L. Tolbert
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Alexander N. Volkov
- VIB Centre for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Pleinlaan 2, Brussels 1050, Belgium
- Jean Jeener NMR Cetre, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels 1050, Belgium
| | - Marcello Forconi
- Department of Chemistry and Biochemistry, College of Charleston, 66 George St. Charleston, SC 29424, USA
| | - Carlos A. Castañeda
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Olga V. Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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Kazantsev AN, Tarasov RS, Burkov NN, Volkov AN, Grachev KI, Iakhnis EI, Lider RI, Shabaev AR, Barbarash LS. [In-hospital outcomes of transcutaneous coronary intervention and carotid endarterectomy in hybrid and staged regimens]. Angiol Sosud Khir 2019; 25:101-107. [PMID: 30994615 DOI: 10.33529/angio2019114] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The aim of this study was comparative assessment of in-hospital outcomes after hybrid and staged surgical management of patients presenting with haemodynamically significant lesions of the coronary (CA) and brachiocephalic arteries (BCA) treated by means of either endovascular or surgical techniques. Over the period from 2010 to 2017, we operated on a total of 197 patients with stenotic lesions of the carotid and coronary arteries. The strategy of revascularization included transcutaneous coronary intervention (TCI) and carotid endarterectomy (CEA). Of these, 73 (37%) patients underwent staged revascularization of the brain and myocardium in various sequence (TCI-CEA or CEA-TCI), with a mean interval between the operations amounting to 9.89±7.36 months. Unfavourable outcomes were regarded as the development of such significant cardiovascular events as myocardial infarction (MI), acute impairment of cerebral circulation, death, repeat unplanned revascularization. For hybrid strategy (TCI+CEA) the index period of assessing the outcomes was the single in-hospital period, whereas for the staged strategy it was the time period beginning from the in-hospital period of the primary operation and ending by the in-hospital period of the second stage. The groups were comparable by the absolute majority of the parameters. More than half of the patients were elderly males. One third had a history of MI. The findings of coronary angiography most often revealed lesions of 1-2 CAs. The average parameters of carotid artery stenosis, according to the BCA angiography varied from 74.9 to 82.6%, with bilateral occlusive stenotic lesions being revealed in every third patient. In connection with more frequent involvement of 1-2 CAs the patients underwent implantation of 1-2 stents. In our sample we used a total of 247 stents. Of these, 119 were uncoated and 128 were drug-eluting stents. No between-group significant differences in the development of unfavourable cardiovascular events during the in-hospital postoperative period were revealed. However, despite this, a pronounced negative tendency of the complication rate was noted in the group of staged revascularization. Non-optimal time intervals between the stages of the operations in a third of cases exceeded one year on the patient's own initiative. Nearly a quarter of patients did not come for the second stage of revascularization. An important finding of our study was no increase in the risk of stent thrombosis in hybrid operations compared with the staged approach, despite administration of a loading dose of clopidogrel after CEA, but not before TCI. Another significant result was the fact of greater availability of revascularization of the myocardium and the brain within the framework of the hybrid strategy as compared with the staged one, which may play an important role in prevention of ischaemic unfavourable events in the remote period of follow up.
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Affiliation(s)
- A N Kazantsev
- Research Institute for Complex Problems of Cardiovascular Diseases, Kemerovo, Russia
| | - R S Tarasov
- Research Institute for Complex Problems of Cardiovascular Diseases, Kemerovo, Russia
| | - N N Burkov
- Research Institute for Complex Problems of Cardiovascular Diseases, Kemerovo, Russia
| | - A N Volkov
- Kemerovo Regional Clinical Cardiological Dispensary named after Academician L.S. Barbarash, Kemerovo, Russia
| | - K I Grachev
- Kemerovo State Medical University of the RF Ministry of Public Health, Kemerovo, Russia
| | - E Ia Iakhnis
- Kemerovo State Medical University of the RF Ministry of Public Health, Kemerovo, Russia
| | - R Iu Lider
- Kemerovo State Medical University of the RF Ministry of Public Health, Kemerovo, Russia
| | - A R Shabaev
- Kemerovo Regional Clinical Cardiological Dispensary named after Academician L.S. Barbarash, Kemerovo, Russia
| | - L S Barbarash
- Research Institute for Complex Problems of Cardiovascular Diseases, Kemerovo, Russia
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Nguyen HH, Volkov AN, Vandenbussche G, Tompa P, Pauwels K. In vivo biotinylated calpastatin improves the affinity purification of human m-calpain. Protein Expr Purif 2018; 145:77-84. [PMID: 29339216 DOI: 10.1016/j.pep.2018.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 11/15/2017] [Revised: 12/14/2017] [Accepted: 01/05/2018] [Indexed: 12/31/2022]
Abstract
Recently we established a novel affinity purification method for calpain by exploiting the specific and reversible binding properties of its intrinsically disordered protein inhibitor, calpastatin. The immobilization strategy relied on the strength and specificity of the biotin - streptavidin interaction. Here, we report an improved and optimized method that even enables the general applicability of in vivo biotinylated (intrinsically disordered) proteins in any affinity capture strategy. Since in vitro chemical biotinylation is only accomplished with reagents that lack exact site specificity, it can not only cause sample heterogeneity but it can also hamper the functionality of the biotinylated molecules. Therefore, we have developed a recombinant expression protocol to produce in vivo biotinylated human calpastatin domain 1 (hCSD1) in Escherichia coli. We have experimentally verified that the biotinylated polypeptide tag is compatible with the intrinsically disordered state of hCSD1 and that it does not influence the functional properties of this intrinsically disordered protein (IDP). The in vivo biotinylated hCSD1 was then used without the need of any prepurification step prior to the affinity capturing of its substrate, human m-calpain. This leads to a simplified purification strategy that allows capturing the calpain efficiently from a complex biological mixture with only a single chromatogaphic step and in a considerably reduced timeframe. Our approach is generally applicable through the in vivo biotinylation of any IDP of interest, and its practical implementation will showcase the power to exploit the properties of IDPs in affinity capture strategies.
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Affiliation(s)
- Hung Huy Nguyen
- VIB - VUB Centre for Structural Biology (VIB CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium; Structural Biology Brussels (SBB), Department of Biotechnology (DBIT), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Alexander N Volkov
- VIB - VUB Centre for Structural Biology (VIB CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium; Structural Biology Brussels (SBB), Department of Biotechnology (DBIT), Vrije Universiteit Brussel (VUB), Brussels, Belgium; Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Guy Vandenbussche
- Laboratory for the Structure and Function of Biological Membranes, Centre for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Peter Tompa
- VIB - VUB Centre for Structural Biology (VIB CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium; Structural Biology Brussels (SBB), Department of Biotechnology (DBIT), Vrije Universiteit Brussel (VUB), Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Kris Pauwels
- VIB - VUB Centre for Structural Biology (VIB CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium; Structural Biology Brussels (SBB), Department of Biotechnology (DBIT), Vrije Universiteit Brussel (VUB), Brussels, Belgium.
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38
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Volkov AN, Rytenkova OI, Babarykina TA, Lysenko DI. [The cytogenetic diagnostic of chromosome anomalies under non-developing pregnancy.]. Klin Lab Diagn 2017; 62:553-556. [PMID: 30807055 DOI: 10.18821/0869-2084-2017-62-9-553-556] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 04/15/2017] [Indexed: 06/09/2023]
Abstract
The purpose of the study is to analyze qualitative and quantitative characteristics of chromosome anomalies in abortus under undeveloped pregnancy. The cytogenetic analysis was implemented concerning embryonic material obtained after artificial abortion of undeveloped pregnancy in 57 women. The percentage of abnormal karyotypes made up to 67.3%. The number abnormalities prevailed among chromosome disorders. The structural alterations of chromosomes occurred significantly rarely. The cytogenetic analysis of abortion material can become a valuable diagnostic tool permitting to establish the role of genetic factors in termination of pregnancy both in cases of natural conception and application of ART.
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Affiliation(s)
- A N Volkov
- The Kemerovskii state medical university of Minzdrav of Russia, 650029, Kemerovo, Russia
- The Kemerovskii state university, 650043, Kemerovo, Russia
| | - O I Rytenkova
- The Kemerovskaia oblast clinical hospital, 650000, Kemerovo, Russia
| | - T A Babarykina
- The Kemerovskaia oblast clinical hospital, 650000, Kemerovo, Russia
| | - D I Lysenko
- The Kemerovskaia oblast clinical hospital, 650000, Kemerovo, Russia
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Abstract
Sugar binding by a cell surface ∼29 kDa lectin (RSL) from the bacterium Ralstonia solanacearum was characterized by NMR spectroscopy. The complexes formed with four monosaccharides and four fucosides were studied. Complete resonance assignments and backbone dynamics were determined for RSL in the sugar-free form and when bound to l-fucose or d-mannose. RSL was found to interact with both the α- and the β-anomer of l-fucose and the "fucose like" sugars d-arabinose and l-galactose. Peak splitting was observed for some resonances of the binding site residues. The assignment of the split signals to the α- or β-anomer was confirmed by comparison with the spectra of RSL bound to methyl-α-l-fucoside or methyl-β-l-fucoside. The backbone dynamics of RSL were sensitive to the presence of ligand, with the protein adopting a more compact structure upon binding to l-fucose. Taking advantage of tryptophan residues in the binding sites, we show that the indole resonance is an excellent reporter on ligand binding. Each sugar resulted in a distinct signature of chemical shift perturbations, suggesting that tryptophan signals are a sufficient probe of sugar binding.
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Affiliation(s)
- Paweł M Antonik
- School of Chemistry, National University of Ireland Galway , University Road, Galway, Ireland.,Department of Food BioSciences, Teagasc Food Research Centre , Ashtown, Dublin 15, Ireland
| | - Alexander N Volkov
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussels, Belgium.,Structural Biology Research Centre, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Ursula N Broder
- School of Chemistry, National University of Ireland Galway , University Road, Galway, Ireland
| | - Daniele Lo Re
- School of Chemistry, National University of Ireland Galway , University Road, Galway, Ireland
| | - Nico A J van Nuland
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussels, Belgium.,Structural Biology Research Centre, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway , University Road, Galway, Ireland
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40
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Volkov AN. [The fixed human lymphocytes as a source of DNA for polymerase chain reaction diagnostic.]. Klin Lab Diagn 2016; 61:819-821. [PMID: 31536692 DOI: 10.18821/0869-2084-2016-61-12-819-821] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 05/15/2016] [Indexed: 06/10/2023]
Abstract
The article presents the results of studying of quantitative and qualitative characteristics of DNA samples separated by sorbate technique from human lymphocytes went through ethanol acetic fixation for preparation of cytogenetic specimen. The concentration of DNA varied within range 18.9-213.2 ng per mkl. The rate A260/A280 amounted to 1.47-2.53. All samples were found suitable for application of polymerase chain reaction during detection of AZF-deletions of Y-chromosome. The considered mode of separation of DNA is highly efficient in respect of fixed lymphocytes and it can be applied in medical biologic studies.
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Affiliation(s)
- A N Volkov
- The Kemerovskii state medical university of Minzdrav of Russia, 650066, Kemerovo, Russia
- The Kemerovskii state university, 650043, Kemerovo, Russia
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41
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Abstract
Many biomolecular interactions proceed via lowly populated, transient intermediates. Believed to facilitate formation of a productive complex, these short-lived species are inaccessible to conventional biophysical and structural techniques and, until recently, could only be studied by theoretical simulations. Recent development of experimental approaches sensitive to the presence of minor species--in particular paramagnetic relaxation enhancement (PRE) NMR spectroscopy--has enabled direct visualization and detailed characterization of such lowly populated states. Collectively referred to as an encounter complex, the binding intermediates are particularly important in transient protein interactions, such as those orchestrating signaling cascades or energy-generating electron transfer (ET) chains. Here I discuss encounter complexes of redox proteins mediating biological ET reactions, which are essential for many vital cellular activities including oxidative phosphorylation and photosynthesis. In particular, this Account focuses on the complex of cytochrome c (Cc) and cytochrome c peroxidase (CcP), which is a paradigm of biomolecular ET and an attractive system for studying protein binding and enzymatic catalysis. The Cc-CcP complex formation proceeds via an encounter state, consisting of multiple protein-protein orientations sampled in the search of the dominant, functionally active bound form and exhibiting a broad spatial distribution, in striking agreement with earlier theoretical simulations. At low ionic strength, CcP binds another Cc molecule to form a weak ternary complex, initially inferred from kinetics experiments and postulated to account for the measured ET activity. Despite strenuous efforts, the ternary complex could not be observed directly and remained eagerly sought for the past two decades. Very recently, we have solved its structure in solution and shown that it consists of two binding forms: the dominant, ET-inactive geometry and an ensemble of lowly populated species with short separations between Cc and CcP cofactors, which summarily account for the measured ET rate. Unlike most protein complexes, which require accurate alignment of the binding surfaces in a single, well-defined orientation to carry out their function, redox proteins can form multiple productive complexes. As fast ET will occur any time the redox centers of the binding partners are close enough to ensure efficient electron tunneling across the interface, many protein-protein orientations are expected to be ET active. The present analysis confirms that the low-occupancy states can support the functional ET activity and contribute to the stability of redox protein complexes. As illustrated here, boundaries between the dominant and the encounter forms become blurred for many dynamic ET systems, which are more aptly described by ensembles of functionally and structurally heterogeneous bound forms.
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Affiliation(s)
- Alexander N. Volkov
- Jean Jeener NMR Centre, Structural
Biology Brussels, Vrije Universiteit Brussel, and Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
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42
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Affiliation(s)
- Yann G. J. Sterckx
- Research
Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural
Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Alexander N. Volkov
- Structural
Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Jean
Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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43
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Sterckx YGJ, Volkov AN, Vranken WF, Kragelj J, Jensen MR, Buts L, Garcia-Pino A, Jové T, Van Melderen L, Blackledge M, van Nuland NAJ, Loris R. Small-angle X-ray scattering- and nuclear magnetic resonance-derived conformational ensemble of the highly flexible antitoxin PaaA2. Structure 2014; 22:854-65. [PMID: 24768114 DOI: 10.1016/j.str.2014.03.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 03/14/2014] [Accepted: 03/15/2014] [Indexed: 11/26/2022]
Abstract
Antitoxins from prokaryotic type II toxin-antitoxin modules are characterized by a high degree of intrinsic disorder. The description of such highly flexible proteins is challenging because they cannot be represented by a single structure. Here, we present a combination of SAXS and NMR data to describe the conformational ensemble of the PaaA2 antitoxin from the human pathogen E. coli O157. The method encompasses the use of SAXS data to filter ensembles out of a pool of conformers generated by a custom NMR structure calculation protocol and the subsequent refinement by a block jackknife procedure. The final ensemble obtained through the method is validated by an established residual dipolar coupling analysis. We show that the conformational ensemble of PaaA2 is highly compact and that the protein exists in solution as two preformed helices, connected by a flexible linker, that probably act as molecular recognition elements for toxin inhibition.
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Affiliation(s)
- Yann G J Sterckx
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Wim F Vranken
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Jaka Kragelj
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel CNRS-CEA-UJF UMR 5075, 41 Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Malene Ringkjøbing Jensen
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel CNRS-CEA-UJF UMR 5075, 41 Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Lieven Buts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Abel Garcia-Pino
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Thomas Jové
- Laboratoire de Génétique et Physiologie Bactérienne, Institut de Biologie et de Médecine Moléculaires Faculté des Sciences, Université Libre de Bruxelles, 12 Rue des Professeurs Jeener et Brachet, B-6041 Gosselies, Belgium
| | - Laurence Van Melderen
- Laboratoire de Génétique et Physiologie Bactérienne, Institut de Biologie et de Médecine Moléculaires Faculté des Sciences, Université Libre de Bruxelles, 12 Rue des Professeurs Jeener et Brachet, B-6041 Gosselies, Belgium
| | - Martin Blackledge
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel CNRS-CEA-UJF UMR 5075, 41 Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Nico A J van Nuland
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium.
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44
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Vanwetswinkel S, Volkov AN, Sterckx YGJ, Garcia-Pino A, Buts L, Vranken WF, Bouckaert J, Roy R, Wyns L, van Nuland NAJ. Study of the structural and dynamic effects in the FimH adhesin upon α-d-heptyl mannose binding. J Med Chem 2014; 57:1416-27. [PMID: 24476493 DOI: 10.1021/jm401666c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Uropathogenic Escherichia coli cause urinary tract infections by adhering to mannosylated receptors on the human urothelium via the carbohydrate-binding domain of the FimH adhesin (FimHL). Numerous α-d-mannopyranosides, including α-d-heptyl mannose (HM), inhibit this process by interacting with FimHL. To establish the molecular basis of the high-affinity HM binding, we solved the solution structure of the apo form and the crystal structure of the FimHL-HM complex. NMR relaxation analysis revealed that protein dynamics were not affected by the sugar binding, yet HM addition promoted protein dimerization, which was further confirmed by small-angle X-ray scattering. Finally, to address the role of Y48, part of the "tyrosine gate" believed to govern the affinity and specificity of mannoside binding, we characterized the FimHL Y48A mutant, whose conformational, dynamical, and HM binding properties were found to be very similar to those of the wild-type protein.
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Affiliation(s)
- Sophie Vanwetswinkel
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussels, Belgium
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45
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Vanwetswinkel S, van Nuland NAJ, Volkov AN. Paramagnetic properties of the low- and high-spin states of yeast cytochrome c peroxidase. J Biomol NMR 2013; 57:21-26. [PMID: 23832496 DOI: 10.1007/s10858-013-9760-8] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 06/26/2013] [Indexed: 06/02/2023]
Abstract
Here we describe paramagnetic NMR analysis of the low- and high-spin forms of yeast cytochrome c peroxidase (CcP), a 34 kDa heme enzyme involved in hydroperoxide reduction in mitochondria. Starting from the assigned NMR spectra of a low-spin CN-bound CcP and using a strategy based on paramagnetic pseudocontact shifts, we have obtained backbone resonance assignments for the diamagnetic, iron-free protein and the high-spin, resting-state enzyme. The derived chemical shifts were further used to determine low- and high-spin magnetic susceptibility tensors and the zero-field splitting constant (D) for the high-spin CcP. The D value indicates that the latter contains a hexacoordinate heme species with a weak field ligand, such as water, in the axial position. Being one of the very few high-spin heme proteins analyzed in this fashion, the resting state CcP expands our knowledge of the heme coordination chemistry in biological systems.
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Affiliation(s)
- Sophie Vanwetswinkel
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
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46
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Volkov AN, van Nuland NAJ. Solution NMR study of the yeast cytochrome c peroxidase: cytochrome c interaction. J Biomol NMR 2013; 56:255-263. [PMID: 23708935 DOI: 10.1007/s10858-013-9744-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/13/2013] [Indexed: 06/02/2023]
Abstract
Here we present a solution NMR study of the complex between yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP), a paradigm for understanding the biological electron transfer. Performed for the first time, the CcP-observed heteronuclear NMR experiments were used to probe the Cc binding in solution. Combining the Cc- and CcP-detected experiments, the binding interface on both proteins was mapped out, confirming that the X-ray structure of the complex is maintained in solution. Using NMR titrations and chemical shift perturbation analysis, we show that the interaction is independent of the CcP spin-state and is only weakly affected by the Cc redox state. Based on these findings, we argue that the complex of the ferrous Cc and the cyanide-bound CcP is a good mimic of the catalytically-active Cc-CcP compound I species. Finally, no chemical shift perturbations due to the Cc binding at the low-affinity CcP site were observed at low ionic strength. We discuss possible reasons for the absence of the effects and outline future research directions.
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Affiliation(s)
- Alexander N Volkov
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
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47
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Volkov AN, Wohlkonig A, Soror SH, van Nuland NAJ. Expression, Purification, Characterization, and Solution Nuclear Magnetic Resonance Study of Highly Deuterated Yeast Cytochrome c Peroxidase with Enhanced Solubility. Biochemistry 2013; 52:2165-75. [DOI: 10.1021/bi400220w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander N. Volkov
- Jean Jeener NMR Centre, Structural
Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Molecular Recognition Unit,
Department of Structural Biology, VIB,
Pleinlaan 2, 1050 Brussels, Belgium
| | - Alexandre Wohlkonig
- JAST lab, Department of Structural
Biology, VIB, Pleinlaan 2, 1050 Brussels,
Belgium
| | - Sameh H. Soror
- JAST lab, Department of Structural
Biology, VIB, Pleinlaan 2, 1050 Brussels,
Belgium
- Department of Biochemistry
and
Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Nico A. J. van Nuland
- Jean Jeener NMR Centre, Structural
Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Molecular Recognition Unit,
Department of Structural Biology, VIB,
Pleinlaan 2, 1050 Brussels, Belgium
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48
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Abstract
Lying at the heart of many vital cellular processes such as photosynthesis and respiration, biological electron transfer (ET) is mediated by transient interactions among proteins that recognize multiple binding partners. Accurate description of the ET complexes – necessary for a comprehensive understanding of the cellular signaling and metabolism – is compounded by their short lifetimes and pronounced binding promiscuity. Here, we used a computational approach relying solely on the steric properties of the individual proteins to predict the ET properties of protein complexes constituting the functional interactome of the eukaryotic cytochrome c (Cc). Cc is a small, soluble, highly-conserved electron carrier protein that coordinates the electron flow among different redox partners. In eukaryotes, Cc is a key component of the mitochondrial respiratory chain, where it shuttles electrons between its reductase and oxidase, and an essential electron donor or acceptor in a number of other redox systems. Starting from the structures of individual proteins, we performed extensive conformational sampling of the ET-competent binding geometries, which allowed mapping out functional epitopes in the Cc complexes, estimating the upper limit of the ET rate in a given system, assessing ET properties of different binding stoichiometries, and gauging the effect of domain mobility on the intermolecular ET. The resulting picture of the Cc interactome 1) reveals that most ET-competent binding geometries are located in electrostatically favorable regions, 2) indicates that the ET can take place from more than one protein-protein orientation, and 3) suggests that protein dynamics within redox complexes, and not the electron tunneling event itself, is the rate-limiting step in the intermolecular ET. Further, we show that the functional epitope size correlates with the extent of dynamics in the Cc complexes and thus can be used as a diagnostic tool for protein mobility. A number of vital cellular processes such as respiration, photosynthesis, and multifarious metabolic conversions rely on a long-range electron transfer (ET) among protein molecules. Full understanding of the biological ET requires accurate description of the redox protein complexes, which is hampered by their pronounced mobility and short lifetimes. Here we used a simple computational approach to predict the ET properties of the physiological protein complexes of cytochrome c (Cc) – a small electron carrier that coordinates the electron flow among different redox partners. By performing extensive conformational sampling of the possible binding geometries, we mapped out functional epitopes in the Cc complexes and assessed their ET properties. Our study suggests that protein dynamics within redox complexes is the rate-limiting step in the intermolecular ET and indicates that the functional epitope size correlates with the extent of dynamics in the Cc complexes. We believe that the latter finding can be used as a diagnostic tool for protein mobility and expect that this work will engender future studies of the intermolecular ET in biological networks.
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Affiliation(s)
- Alexander N Volkov
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Belgium.
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49
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Volkov AN, Vanwetswinkel S, Van de Water K, van Nuland NAJ. Redox-dependent conformational changes in eukaryotic cytochromes revealed by paramagnetic NMR spectroscopy. J Biomol NMR 2012; 52:245-256. [PMID: 22318343 DOI: 10.1007/s10858-012-9607-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 01/15/2012] [Indexed: 05/31/2023]
Abstract
Cytochrome c (Cc) is a soluble electron carrier protein, transferring reducing equivalents between Cc reductase and Cc oxidase in eukaryotes. In this work, we assessed the structural differences between reduced and oxidized Cc in solution by paramagnetic NMR spectroscopy. First, we have obtained nearly-complete backbone NMR resonance assignments for iso-1-yeast Cc and horse Cc in both oxidation states. These were further used to derive pseudocontact shifts (PCSs) arising from the paramagnetic haem group. Then, an extensive dataset comprising over 450 measured PCSs and high-resolution X-ray and solution NMR structures of both proteins were used to define the anisotropic magnetic susceptibility tensor, Δχ. For most nuclei, the PCSs back-calculated from the Δχ tensor are in excellent agreement with the experimental PCS values. However, several contiguous stretches-clustered around G41, N52, and A81-exhibit large deviations both in yeast and horse Cc. This behaviour is indicative of redox-dependent structural changes, the extent of which is likely conserved in the protein family. We propose that the observed discrepancies arise from the changes in protein dynamics and discuss possible functional implications.
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Affiliation(s)
- Alexander N Volkov
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Belgium
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50
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Volkov AN, Nicholls P, Worrall JA. The complex of cytochrome c and cytochrome c peroxidase: The end of the road? Biochimica et Biophysica Acta (BBA) - Bioenergetics 2011; 1807:1482-503. [DOI: 10.1016/j.bbabio.2011.07.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 11/25/2022]
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