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Article ; Online: DNA-targeting short Argonautes complex with effector proteins for collateral nuclease activity and bacterial population immunity.

Prostova, Maria / Kanevskaya, Anna / Panteleev, Vladimir / Lisitskaya, Lidia / Perfilova Tugaeva, Kristina V / Sluchanko, Nikolai N / Esyunina, Daria / Kulbachinskiy, Andrey

Nature microbiology

2024

Abstract: Two prokaryotic defence systems, prokaryotic Argonautes (pAgos) and CRISPR-Cas, detect and cleave invader nucleic acids using complementary guides and the nuclease activities of pAgo or Cas proteins. However, not all pAgos are active nucleases. A large ... ...

Abstract	Two prokaryotic defence systems, prokaryotic Argonautes (pAgos) and CRISPR-Cas, detect and cleave invader nucleic acids using complementary guides and the nuclease activities of pAgo or Cas proteins. However, not all pAgos are active nucleases. A large clade of short pAgos bind nucleic acid guides but lack nuclease activity, suggesting a different mechanism of action. Here we investigate short pAgos associated with a putative effector nuclease, NbaAgo from Novosphingopyxis baekryungensis and CmeAgo from Cupriavidus metallidurans. We show that these pAgos form a heterodimeric complex with co-encoded effector nucleases (short prokaryotic Argonaute, DNase and RNase associated (SPARDA)). RNA-guided target DNA recognition unleashes the nuclease activity of SPARDA leading to indiscriminate collateral cleavage of DNA and RNA. Activation of SPARDA by plasmids or phages results in degradation of cellular DNA and cell death or dormancy, conferring target-specific population protection and expanding the range of known prokaryotic immune systems.
Language	English
Publishing date	2024-04-15
Publishing country	England
Document type	Journal Article
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-024-01654-5
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Article ; Online: Effect of Betaine and Arginine on Interaction of αB-Crystallin with Glycogen Phosphorylase

Eronina, Tatiana B / Mikhaylova, Valeriya V / Chebotareva, Natalia A / Tugaeva, Kristina V / Kurganov, Boris I

International journal of molecular sciences

2022 Volume 23, Issue 7

Abstract: Protein-protein interactions (PPIs) play an important role in many biological processes in a living cell. Among them chaperone-client interactions are the most important. In this work PPIs of αB-crystallin and glycogen ... ...

Abstract	Protein-protein interactions (PPIs) play an important role in many biological processes in a living cell. Among them chaperone-client interactions are the most important. In this work PPIs of αB-crystallin and glycogen phosphorylase
MeSH term(s)	Arginine ; Betaine/pharmacology ; Crystallins ; Glycogen Phosphorylase ; Humans ; Molecular Chaperones/metabolism
Chemical Substances	Crystallins ; Molecular Chaperones ; Betaine (3SCV180C9W) ; Arginine (94ZLA3W45F) ; Glycogen Phosphorylase (EC 2.4.1.-)
Language	English
Publishing date	2022-03-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23073816
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Article ; Online: Hierarchized phosphotarget binding by the seven human 14-3-3 isoforms.

Gogl, Gergo / Tugaeva, Kristina V / Eberling, Pascal / Kostmann, Camille / Trave, Gilles / Sluchanko, Nikolai N

Nature communications

2021 Volume 12, Issue 1, Page(s) 1677

Abstract: The seven 14-3-3 isoforms are highly abundant human proteins encoded by similar yet distinct genes. 14-3-3 proteins recognize phosphorylated motifs within numerous human and viral proteins. Here, we analyze by X-ray crystallography, fluorescence ... ...

Abstract	The seven 14-3-3 isoforms are highly abundant human proteins encoded by similar yet distinct genes. 14-3-3 proteins recognize phosphorylated motifs within numerous human and viral proteins. Here, we analyze by X-ray crystallography, fluorescence polarization, mutagenesis and fusicoccin-mediated modulation the structural basis and druggability of 14-3-3 binding to four E6 oncoproteins of tumorigenic human papillomaviruses. 14-3-3 isoforms bind variant and mutated phospho-motifs of E6 and unrelated protein RSK1 with different affinities, albeit following an ordered affinity ranking with conserved relative K
MeSH term(s)	14-3-3 Proteins/chemistry ; 14-3-3 Proteins/metabolism ; Amino Acid Sequence ; Crystallography, X-Ray ; Humans ; Papillomaviridae ; Phosphoproteins ; Phosphorylation ; Protein Binding ; Protein Isoforms/metabolism
Chemical Substances	14-3-3 Proteins ; Phosphoproteins ; Protein Isoforms
Language	English
Publishing date	2021-03-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-21908-8
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Article ; Online: Crystal structure of human 14-3-3ζ complexed with the noncanonical phosphopeptide from proapoptotic BAD.

Sluchanko, Nikolai N / Tugaeva, Kristina V / Gushchin, Ivan / Remeeva, Alina / Kovalev, Kirill / Cooley, Richard B

Biochemical and biophysical research communications

2021 Volume 583, Page(s) 100–105

Abstract: Several signaling pathways control phosphorylation of the proapoptotic protein BAD and its phosphorylation-dependent association with 14-3-3 proteins in the cytoplasm. The stability of the 14-3-3/BAD complex determines the cell fate: unphosphorylated BAD ...

Abstract	Several signaling pathways control phosphorylation of the proapoptotic protein BAD and its phosphorylation-dependent association with 14-3-3 proteins in the cytoplasm. The stability of the 14-3-3/BAD complex determines the cell fate: unphosphorylated BAD escapes from 14-3-3, migrates to the mitochondria and initiates apoptosis. While the 14-3-3/BAD interaction represents a promising drug target, it lacks structural characterization. Among several phosphosites identified in vivo, Ser75 and Ser99 of human BAD match the consensus sequence RXXpSXP recognized by 14-3-3 and, therefore, represent canonical 14-3-3-binding sites. Yet, BAD contains other serines phosphorylatable in vivo, whose role is less understood. Here, we report a 2.36 Å crystal structure of 14-3-3ζ complexed with a BAD fragment which includes residues Ser74 and Ser75, both being substrates for protein kinases. While the BAD peptide is anchored to 14-3-3 by phosphoserine as expected, the BAD peptide was unexpectedly phosphorylated at Ser74 instead of Ser75, revealing noncanonical binding within the amphipathic groove and leading to a one-step positional shift and reorganization of the interface. This observation exemplifies plasticity of the amphipathic 14-3-3 groove in accommodating various peptides and suggests the redundancy of Ser74 and Ser75 phosphosites with respect to binding of BAD to 14-3-3.
Language	English
Publishing date	2021-10-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2021.10.053
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Article ; Online: Effect of Trehalose on Oligomeric State and Anti-Aggregation Activity of αB-Crystallin.

Chebotareva, Natalia A / Eronina, Tatiana B / Mikhaylova, Valeriya V / Roman, Svetlana G / Tugaeva, Kristina V / Kurganov, Boris I

Biochemistry. Biokhimiia

2022 Volume 87, Issue 2, Page(s) 121–130

Abstract: αB-Crystallin (αB-Cr), one of the main crystalline lens proteins, along with other crystallins maintains lens transparency suppressing protein aggregation and thus preventing cataractogenesis. αB-Cr belongs to the class of molecular chaperones; being ... ...

Abstract	αB-Crystallin (αB-Cr), one of the main crystalline lens proteins, along with other crystallins maintains lens transparency suppressing protein aggregation and thus preventing cataractogenesis. αB-Cr belongs to the class of molecular chaperones; being expressed in many tissues it has a dynamic quaternary structure, which is essential for its chaperone-like activity. Shift in the equilibrium between ensembles of oligomers of different size allows regulating the chaperone activity. Trehalose is known to inhibit protein aggregation in vivo and in vitro, and it is widely used in biotechnology. The results of studying the effect of trehalose on the chaperone-like activity of crystallins can serve as a basis for the design of drugs delaying cataractogenesis. We have studied the trehalose effect on the quaternary structure and anti-aggregation activity of αB-Cr using muscle glycogen phosphorylase b (Phb) as a target protein. According to the dynamic light scattering data, trehalose affects the nucleation stage of Phb thermal aggregation at 48°C, and an increase in the αB-Cr adsorption capacity (AC
MeSH term(s)	Crystallins/metabolism ; Molecular Chaperones/metabolism ; Protein Aggregates ; Protein Folding ; Trehalose/pharmacology ; alpha-Crystallin B Chain/metabolism
Chemical Substances	Crystallins ; Molecular Chaperones ; Protein Aggregates ; alpha-Crystallin B Chain ; Trehalose (B8WCK70T7I)
Language	English
Publishing date	2022-05-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	1109-5
ISSN	1608-3040 ; 0006-2979 ; 0320-9717
ISSN (online)	1608-3040
ISSN	0006-2979 ; 0320-9717
DOI	10.1134/S0006297922020043
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Article ; Online: Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation.

Tugaeva, Kristina V / Sysoev, Andrey A / Kapitonova, Anna A / Smith, Jake L R / Zhu, Phillip / Cooley, Richard B / Antson, Alfred A / Sluchanko, Nikolai N

Journal of molecular biology

2022 Volume 435, Issue 2, Page(s) 167891

Abstract: Phosphorylation of SARS-CoV-2 nucleoprotein recruits human cytosolic 14-3-3 proteins playing a well-recognized role in replication of many viruses. Here we use genetic code expansion to demonstrate that 14-3-3 binding is triggered by phosphorylation of ... ...

Abstract	Phosphorylation of SARS-CoV-2 nucleoprotein recruits human cytosolic 14-3-3 proteins playing a well-recognized role in replication of many viruses. Here we use genetic code expansion to demonstrate that 14-3-3 binding is triggered by phosphorylation of SARS-CoV-2 nucleoprotein at either of two pseudo-repeats centered at Ser197 and Thr205. According to fluorescence anisotropy measurements, the pT205-motif,presentin SARS-CoV-2 but not in SARS-CoV, is preferred over the pS197-motif by all seven human 14-3-3 isoforms, which collectively display an unforeseen pT205/pS197 peptide binding selectivity hierarchy. Crystal structures demonstrate that pS197 and pT205 are mutually exclusive 14-3-3-binding sites, whereas SAXS and biochemical data obtained on the full protein-protein complex indicate that 14-3-3 binding occludes the Ser/Arg-rich region of the nucleoprotein, inhibiting its dephosphorylation. This Ser/Arg-rich region is highly prone to mutations, as exemplified by the Omicron and Delta variants, with our data suggesting that the strength of 14-3-3/nucleoprotein interaction can be linked with the replicative fitness of the virus.
MeSH term(s)	Humans ; 14-3-3 Proteins/metabolism ; COVID-19/virology ; Mutation ; Nucleoproteins/genetics ; Nucleoproteins/metabolism ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Scattering, Small Angle ; X-Ray Diffraction ; Coronavirus Nucleocapsid Proteins/genetics ; Coronavirus Nucleocapsid Proteins/metabolism
Chemical Substances	14-3-3 Proteins ; Nucleoproteins ; nucleocapsid phosphoprotein, SARS-CoV-2 ; Coronavirus Nucleocapsid Proteins
Language	English
Publishing date	2022-11-24
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167891
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Article ; Online: Structural basis for the recognition by 14-3-3 proteins of a conditional binding site within the oligomerization domain of human nucleophosmin.

Kapitonova, Anna A / Tugaeva, Kristina V / Varfolomeeva, Larisa A / Boyko, Konstantin M / Cooley, Richard B / Sluchanko, Nikolai N

Biochemical and biophysical research communications

2022 Volume 627, Page(s) 176–183

Abstract: Nucleophosmin 1 (NPM1) is a multifunctional protein regulating ribosome biogenesis, centrosome duplication and chromatin remodeling. Being a major nucleolar protein, NPM1 can migrate to the nucleus and the cytoplasm, which is controlled by changes of ... ...

Abstract	Nucleophosmin 1 (NPM1) is a multifunctional protein regulating ribosome biogenesis, centrosome duplication and chromatin remodeling. Being a major nucleolar protein, NPM1 can migrate to the nucleus and the cytoplasm, which is controlled by changes of NPM1 oligomerization and interaction with other cell factors. NPM1 forms a stable pentamer with its N-terminal structured domain, where two nuclear export signals and several phosphorylation sites reside. This domain undergoes dissociation and disordering upon Ser48 phosphorylation in the subunit interface. Recent studies indicated that Ser48 is important for NPM1 interaction with other proteins including 14-3-3, the well-known phosphoserine/phosphothreonine binders, but the structural basis for 14-3-3/NPM1 interaction remained unaddressed. By fusing human 14-3-3ζ with an NPM1 segment surrounding Ser48, which was phosphorylated inside Escherichia coli cells by co-expressed protein kinase A, here we obtained the desired protein/phosphopeptide complex and determined its crystal structure. While biochemical data indicated that the interaction is driven by Ser48 phosphorylation, the crystallographic 14-3-3/phosphopeptide interface reveals an NPM1 conformation distinctly different from that in the NPM1 pentamer. Given the canonical phosphopeptide-binding mode observed in our crystal structure, Ser48 emerges as a conditional binding site whose recognition by 14-3-3 proteins is enabled by NPM1 phosphorylation, disassembly and disordering under physiological circumstances.
MeSH term(s)	14-3-3 Proteins/metabolism ; Binding Sites ; Humans ; Nuclear Proteins/metabolism ; Nucleophosmin ; Phosphopeptides
Chemical Substances	14-3-3 Proteins ; Nuclear Proteins ; Phosphopeptides ; Nucleophosmin (117896-08-9)
Language	English
Publishing date	2022-08-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2022.08.047
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Article ; Online: Hierarchized phosphotarget binding by the seven human 14-3-3 isoforms

Gergo Gogl / Kristina V. Tugaeva / Pascal Eberling / Camille Kostmann / Gilles Trave / Nikolai N. Sluchanko

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 12

Abstract: 14-3-3 proteins recognize phosphorylated motifs within numerous protein partners. Here, the authors characterize the binding of all human 14-3-3 isoforms to four E6 oncoproteins, and identify a fixed order of 14-3-3 binding affinities that is conserved ... ...

Abstract	14-3-3 proteins recognize phosphorylated motifs within numerous protein partners. Here, the authors characterize the binding of all human 14-3-3 isoforms to four E6 oncoproteins, and identify a fixed order of 14-3-3 binding affinities that is conserved in 14-3-3:phosphoprotein interactions across the proteome.
Keywords	Science ; Q
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Crystal structure reveals canonical recognition of the phosphorylated cytoplasmic loop of human alpha7 nicotinic acetylcholine receptor by 14-3-3 protein.

Sluchanko, Nikolai N / Kapitonova, Anna A / Shulepko, Mikhail A / Kukushkin, Ilya D / Kulbatskii, Dmitrii S / Tugaeva, Kristina V / Varfolomeeva, Larisa A / Minyaev, Mikhail E / Boyko, Konstantin M / Popov, Vladimir O / Kirpichnikov, Mikhail P / Lyukmanova, Ekaterina N

Biochemical and biophysical research communications

2023 Volume 682, Page(s) 91–96

Abstract: Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels composed of five homologous subunits. The homopentameric α7-nAChR, abundantly expressed in the brain, is involved in the regulation of the neuronal plasticity and memory and ... ...

Abstract	Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels composed of five homologous subunits. The homopentameric α7-nAChR, abundantly expressed in the brain, is involved in the regulation of the neuronal plasticity and memory and undergoes phosphorylation by protein kinase A (PKA). Here, we extracted native α7-nAChR from murine brain, validated its assembly by cryo-EM and showed that phosphorylation by PKA in vitro enables its interaction with the abundant human brain protein 14-3-3ζ. Bioinformatic analysis narrowed the putative 14-3-3-binding site down to the fragment of the intracellular loop (ICL) containing Ser365 (Q
MeSH term(s)	Animals ; Humans ; Mice ; 14-3-3 Proteins/metabolism ; alpha7 Nicotinic Acetylcholine Receptor/metabolism ; Binding Sites ; Cytoplasm/metabolism ; Receptors, Nicotinic/metabolism
Chemical Substances	14-3-3 Proteins ; alpha7 Nicotinic Acetylcholine Receptor ; Receptors, Nicotinic ; Chrna7 protein, human
Language	English
Publishing date	2023-09-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2023.09.086
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Article ; Online: Design, expression, purification and crystallization of human 14-3-3ζ protein chimera with phosphopeptide from proapoptotic protein BAD.

Tugaeva, Kristina V / Remeeva, Alina / Gushchin, Ivan / Cooley, Richard B / Sluchanko, Nikolai N

Protein expression and purification

2020 Volume 175, Page(s) 105707

Abstract: 14-3-3 protein isoforms regulate multiple processes in eukaryotes, including apoptosis and cell division. 14-3-3 proteins preferentially recognize phosphorylated unstructured motifs, justifying the protein-peptide binding approach to study 14-3-3/ ... ...

Abstract	14-3-3 protein isoforms regulate multiple processes in eukaryotes, including apoptosis and cell division. 14-3-3 proteins preferentially recognize phosphorylated unstructured motifs, justifying the protein-peptide binding approach to study 14-3-3/phosphotarget complexes. Tethering of human 14-3-3σ with partner phosphopeptides via a short linker has provided structural information equivalent to the use of synthetic phosphopeptides, simultaneously facilitating purification and crystallization. Nevertheless, the broader applicability to other 14-3-3 isoforms and phosphopeptides was unclear. Here, we designed a novel 14-3-3ζ chimera with a conserved phosphopeptide from BAD, whose complex with 14-3-3 is a gatekeeper of apoptosis regulation. The chimera could be bacterially expressed and purified without affinity tags. Co-expressed PKA efficiently phosphorylates BAD within the chimera and blocks its interaction with a known 14-3-3 phosphotarget, suggesting occupation of the 14-3-3 grooves by the tethered BAD phosphopeptide. Efficient crystallization of the engineered protein suggests suitability of the "chimeric" approach for studies of other relevant 14-3-3 complexes.
MeSH term(s)	14-3-3 Proteins/biosynthesis ; 14-3-3 Proteins/chemistry ; 14-3-3 Proteins/genetics ; 14-3-3 Proteins/isolation & purification ; Crystallography, X-Ray ; Humans ; Protein Engineering ; Recombinant Fusion Proteins/biosynthesis ; Recombinant Fusion Proteins/chemistry ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/isolation & purification ; bcl-Associated Death Protein/biosynthesis ; bcl-Associated Death Protein/chemistry ; bcl-Associated Death Protein/genetics ; bcl-Associated Death Protein/isolation & purification
Chemical Substances	14-3-3 Proteins ; BAD protein, human ; Recombinant Fusion Proteins ; YWHAZ protein, human ; bcl-Associated Death Protein
Language	English
Publishing date	2020-07-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1055455-5
ISSN	1096-0279 ; 1046-5928
ISSN (online)	1096-0279
ISSN	1046-5928
DOI	10.1016/j.pep.2020.105707
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