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Prostova M, Kanevskaya A, Panteleev V, Lisitskaya L, Perfilova Tugaeva KV, Sluchanko NN, Esyunina D, Kulbachinskiy A. DNA-targeting short Argonautes complex with effector proteins for collateral nuclease activity and bacterial population immunity. Nat Microbiol 2024:10.1038/s41564-024-01654-5. [PMID: 38622379 DOI: 10.1038/s41564-024-01654-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/25/2023] [Accepted: 02/28/2024] [Indexed: 04/17/2024]
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 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.
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Affiliation(s)
- Maria Prostova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Anna Kanevskaya
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| | | | - Lidia Lisitskaya
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kristina V Perfilova Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Daria Esyunina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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2
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Egorkin NA, Dominnik EE, Maksimov EG, Sluchanko NN. Insights into the molecular mechanism of yellow cuticle coloration by a chitin-binding carotenoprotein in gregarious locusts. Commun Biol 2024; 7:448. [PMID: 38605243 PMCID: PMC11009388 DOI: 10.1038/s42003-024-06149-x] [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: 12/21/2023] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Carotenoids are hydrophobic pigments binding to diverse carotenoproteins, many of which remain unexplored. Focusing on yellow gregarious locusts accumulating cuticular carotenoids, here we use engineered Escherichia coli cells to reconstitute a functional water-soluble β-carotene-binding protein, BBP. HPLC and Raman spectroscopy confirmed that recombinant BBP avidly binds β-carotene, inducing the unusual vibronic structure of its absorbance spectrum, just like native BBP extracted from the locust cuticles. Bound to recombinant BBP, β-carotene exhibits pronounced circular dichroism and allows BBP to withstand heating (T0.5 = 68 °C), detergents and pH variations. Using bacteria producing distinct xanthophylls we demonstrate that, while β-carotene is the preferred carotenoid, BBP can also extract from membranes ketocarotenoids and, very poorly, hydroxycarotenoids. We show that BBP-carotenoid complex reversibly binds to chitin, but not to chitosan, implying the role for chitin acetyl groups in cuticular BBP deposition. Reconstructing such locust coloration mechanism in vitro paves the way for structural studies and BBP applications.
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Affiliation(s)
- Nikita A Egorkin
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- M.V. Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
| | - Eva E Dominnik
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- M.V. Lomonosov Moscow State University, Faculty of Chemistry, Moscow, Russia
| | - Eugene G Maksimov
- M.V. Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
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3
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Muranova LK, Vostrikova VM, Shatov VM, Sluchanko NN, Gusev NB. Interaction of the C-terminal immunoglobulin-like domains (Ig 22-24) of filamin C with human small heat shock proteins. Biochimie 2024; 219:146-154. [PMID: 38016530 DOI: 10.1016/j.biochi.2023.11.010] [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: 10/10/2023] [Revised: 11/18/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
Small heat shock proteins are the well-known regulators of the cytoskeleton integrity, yet their complexes with actin-binding proteins are underexplored. Filamin C, a dimeric 560 kDa protein, abundant in cardiac and skeletal muscles, crosslinks actin filaments and contributes to Z-disc formation and membrane-cytoskeleton attachment. Here, we analyzed the interaction of a human filamin C fragment containing immunoglobulin-like domains 22-24 (FLNC22-24) with five small heat shock proteins (HspB1, HspB5, HspB6, HspB7, HspB8) and their α-crystallin domains. On size-exclusion chromatography, only HspB7 or its α-crystallin domain formed complexes with FLNC22-24. Despite similar isoelectric points of the small heat shock proteins analyzed, only HspB7 and its α-crystallin domain interacted with FLNC22-24 on native gel electrophoresis. Crosslinking with glutaraldehyde confirmed the formation of complexes between HspB7 (or its α-crystallin domain) and the filamin С fragment, inhibiting intersubunit FLNC crosslinking. These data are consistent with the structure modeling using Alphafold. Thus, the C-terminal fragment (immunoglobulin-like domains 22-24) of filamin C contains the site for HspB7 (or its α-crystallin domain) interaction, which competes with FLNC22-24 dimerization and its probable interaction with different target proteins.
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Affiliation(s)
- Lydia K Muranova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russia
| | - Varvara M Vostrikova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russia
| | - Vladislav M Shatov
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia
| | - Nikolai B Gusev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russia.
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4
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Likkei K, Moldenhauer M, Tavraz NN, Egorkin NA, Slonimskiy YB, Maksimov EG, Sluchanko NN, Friedrich T. Elements of the C-terminal tail of a C-terminal domain homolog of the Orange Carotenoid Protein determining xanthophyll uptake from liposomes. Biochim Biophys Acta Bioenerg 2024:149043. [PMID: 38522658 DOI: 10.1016/j.bbabio.2024.149043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 03/26/2024]
Abstract
Carotenoids perform multifaceted roles in life ranging from coloration over light harvesting to photoprotection. The Orange Carotenoid Protein (OCP), a light-driven photoswitch involved in cyanobacterial photoprotection, accommodates a ketocarotenoid vital for its function. OCP extracts its ketocarotenoid directly from membranes, or accepts it from homologs of its C-terminal domain (CTDH). The CTDH from Anabaena (AnaCTDH) was shown to be important for carotenoid transfer and delivery from/to membranes. The C-terminal tail of AnaCTDH is a critical structural element likely serving as a gatekeeper and facilitator of carotenoid uptake from membranes. We investigated the impact of amino acid substitutions within the AnaCTDH-CTT on echinenone and canthaxanthin uptake from DOPC and DMPG liposomes. The transfer rate was uniformly reduced for substitutions of Arg-137 and Arg-138 to Gln or Ala, and depended on the lipid type, indicating a weaker interaction particularly with the lipid head group. Our results further suggest that Glu-132 has a membrane-anchoring effect on the PC lipids, specifically at the choline motif as inferred from the strongly different effects of the CTT variants on the extraction from the two liposome types. The substitution of Pro-130 by Gly suggests that the CTT is perpendicular to both the membrane and the main AnaCTDH protein during carotenoid extraction. Finally, the simultaneous mutation of Leu-133, Leu-134 and Leu-136 for alanines showed that the hydrophobicity of the CTT is crucial for carotenoid uptake. Since some substitutions accelerated carotenoid transfer into AnaCTDH while others slowed it down, carotenoprotein properties can be engineered toward the requirements of applications.
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Affiliation(s)
- Kristina Likkei
- Technische Universität Berlin, Institute of Chemistry, PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Marcus Moldenhauer
- Technische Universität Berlin, Institute of Chemistry, PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Neslihan N Tavraz
- Technische Universität Berlin, Institute of Chemistry, PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Nikita A Egorkin
- Federal Research Center of Biotechnology of the Russian Academy of Sciences, A.N. Bach Institute of Biochemistry, Leninsky Prospect 33-1, Moscow 119071, Russian Federation; Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1-12, Moscow 119991, Russian Federation
| | - Yury B Slonimskiy
- Federal Research Center of Biotechnology of the Russian Academy of Sciences, A.N. Bach Institute of Biochemistry, Leninsky Prospect 33-1, Moscow 119071, Russian Federation
| | - Eugene G Maksimov
- Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1-12, Moscow 119991, Russian Federation
| | - Nikolai N Sluchanko
- Federal Research Center of Biotechnology of the Russian Academy of Sciences, A.N. Bach Institute of Biochemistry, Leninsky Prospect 33-1, Moscow 119071, Russian Federation
| | - Thomas Friedrich
- Technische Universität Berlin, Institute of Chemistry, PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany.
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5
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Kapitonova AA, Perfilova KV, Cooley RB, Sluchanko NN. Phosphorylation code of human nucleophosmin includes four cryptic sites for hierarchical binding of 14-3-3 proteins. bioRxiv 2024:2024.02.13.580064. [PMID: 38405961 PMCID: PMC10888825 DOI: 10.1101/2024.02.13.580064] [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] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Nucleophosmin (NPM1) is the 46th most abundant human protein with many functions whose dysregulation leads to various cancers. Pentameric NPM1 resides in the nucleolus but can also shuttle to the cytosol. NPM1 is regulated by multisite phosphorylation, yet molecular consequences of site-specific NPM1 phosphorylation remain elusive. Here we identify four 14-3-3 protein binding sites in NPM1 concealed within its oligomerization and α-helical C-terminal domains that are found phosphorylated in vivo. By combining mutagenesis, in-cell phosphorylation and PermaPhos technology for site-directed incorporation of a non-hydrolyzable phosphoserine mimic, we show how phosphorylation promotes NPM1 monomerization and partial unfolding, to recruit 14-3-3 dimers with low-micromolar affinity. Using fluorescence anisotropy we quantified pairwise interactions of all seven human 14-3-3 isoforms with four recombinant NPM1 phosphopeptides and assessed their druggability by fusicoccin. This revealed a complex hierarchy of 14-3-3 affinities toward the primary (S48, S293) and secondary (S106, S260) sites, differentially modulated by the small molecule. As three of these 14-3-3 binding phospho-sites in NPM1 reside within signal sequences, this work highlights a key mechanism of NPM1 regulation by which NPM1 phosphorylation promotes 14-3-3 binding to control nucleocytoplasmic shuttling. It also provides further evidence that phosphorylation-induced structural rearrangements of globular proteins serve to expose otherwise cryptic 14-3-3-binding sites that are important for cellular function.
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Affiliation(s)
- Anna A. Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Kristina V. Perfilova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Richard B. Cooley
- GCE4All Center, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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6
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Sluchanko NN, Maksimov EG, Slonimskiy YB, Varfolomeeva LA, Bukhanko AY, Egorkin NA, Tsoraev GV, Khrenova MG, Ge B, Qin S, Boyko KM, Popov VO. Structural framework for the understanding spectroscopic and functional signatures of the cyanobacterial Orange Carotenoid Protein families. Int J Biol Macromol 2024; 254:127874. [PMID: 37939760 DOI: 10.1016/j.ijbiomac.2023.127874] [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: 09/14/2023] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
The Orange Carotenoid Protein (OCP) is a unique photoreceptor crucial for cyanobacterial photoprotection. Best studied Synechocystis sp. PCC 6803 OCP belongs to the large OCP1 family. Downregulated by the Fluorescence Recovery Protein (FRP) in low-light, high-light-activated OCP1 binds to the phycobilisomes and performs non-photochemical quenching. Recently discovered families OCP2 and OCP3 remain structurally and functionally underexplored, and no systematic comparative studies have ever been conducted. Here we present two first crystal structures of OCP2 from morphoecophysiologically different cyanobacteria and provide their comprehensive structural, spectroscopic and functional comparison with OCP1, the recently described OCP3 and all-OCP ancestor. Structures enable correlation of spectroscopic signatures with the effective number of hydrogen and discovered here chalcogen bonds anchoring the ketocarotenoid in OCP, as well as with the rotation of the echinenone's β-ionone ring in the CTD. Structural data also helped rationalize the observed differences in OCP/FRP and OCP/phycobilisome functional interactions. These data are expected to foster OCP research and applications in optogenetics, targeted carotenoid delivery and cyanobacterial biomass engineering.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Eugene G Maksimov
- M.V. Lomonosov Moscow State University, Faculty of Biology, Moscow 119991, Russia
| | - Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Larisa A Varfolomeeva
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Antonina Y Bukhanko
- M.V. Lomonosov Moscow State University, Faculty of Biology, Moscow 119991, Russia
| | - Nikita A Egorkin
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; M.V. Lomonosov Moscow State University, Faculty of Biology, Moscow 119991, Russia
| | - Georgy V Tsoraev
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Maria G Khrenova
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; Lomonosov Moscow State University, Chemistry Department, Moscow 119991, Russia
| | - Baosheng Ge
- China University of Petroleum (Huadong), College of Chemistry and Chemical Engineering, Qingdao 266580, People's Republic of China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, People's Republic of China.
| | - Konstantin M Boyko
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Vladimir O Popov
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; M.V. Lomonosov Moscow State University, Faculty of Biology, Moscow 119991, Russia
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7
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Likkei K, Moldenhauer M, Tavraz NN, Maksimov EG, Sluchanko NN, Friedrich T. Lipid composition and properties affect protein-mediated carotenoid uptake efficiency from membranes. Biochim Biophys Acta Biomembr 2024; 1866:184241. [PMID: 37866690 DOI: 10.1016/j.bbamem.2023.184241] [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] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/04/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
Carotenoids are pigments of diverse functions ranging from coloration over light-harvesting to photoprotection. Yet, the number of carotenoid-binding proteins, which mobilize these pigments in physiological media, is limited, and the mechanisms of carotenoid mobilization are still not well understood. The same applies for the determinants of carotenoid uptake from membranes into carotenoproteins, especially regarding the dependence on the chemical properties of membrane lipids. Here, we investigate xanthophyll uptake capacity and kinetics of a paradigmatic carotenoid-binding protein, the homolog of the Orange Carotenoid Protein's C-terminal domain from Anabaena sp. PCC 7120 (AnaCTDH), using liposomes formed from defined lipid species and loaded with canthaxanthin (CAN) and echinenone (ECN), respectively. Phospholipids with different chain length and degree of saturation were investigated. The composition of carotenoid-loaded liposomes directly affected the incorporation yield and storage ratio of CAN and ECN as well as the rate of carotenoid uptake by AnaCTDH. Generally, saturated PC lipids were identified as unsuitable, and a high phase transition temperature of the lipids negatively affected the carotenoid incorporation and storage yield. For efficient carotenoid transfer, the velocity increases with increasing chain length or membrane thickness. An average transfer yield of 93 % and 43 % were obtained for the formation of AnaCTDH(CAN) and AnaCTDH(ECN) holoproteins, respectively. In summary, the most suitable lipids for the formation of AnaCTDH(CAN/ECN) holoproteins by carotenoid transfer from artificial liposomes are phosphatidylcholine (18:1) and phosphatidylglycerol (14:0). Thus, these two lipids provide the best conditions for further investigation of lipid-protein interaction and the carotenoid uptake process.
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Affiliation(s)
- Kristina Likkei
- Technische Universität Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Marcus Moldenhauer
- Technische Universität Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Neslihan N Tavraz
- Technische Universität Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Eugene G Maksimov
- Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1-12, Moscow 119991, Russia
| | - Nikolai N Sluchanko
- Federal Research Center of Biotechnology of the Russian Academy of Sciences, A.N. Bach Institute of Biochemistry, Leninsky Prospect 33-1, Moscow 119071, Russia
| | - Thomas Friedrich
- Technische Universität Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany.
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8
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Zlenko DV, Protasova EA, Tsoraev GV, Sluchanko NN, Cherepanov DA, Friedrich T, Ge B, Qin S, Maksimov EG, Rubin AB. Anti-stokes fluorescence of phycobilisome and its complex with the orange carotenoid protein. Biochim Biophys Acta Bioenerg 2024; 1865:149014. [PMID: 37739300 DOI: 10.1016/j.bbabio.2023.149014] [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] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/06/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Phycobilisomes (PBSs) are giant water-soluble light-harvesting complexes of cyanobacteria and red algae, consisting of hundreds of phycobiliproteins precisely organized to deliver the energy of absorbed light to chlorophyll chromophores of the photosynthetic electron-transport chain. Quenching the excess of excitation energy is necessary for the photoprotection of photosynthetic apparatus. In cyanobacteria, quenching of PBS excitation is provided by the Orange Carotenoid Protein (OCP), which is activated under high light conditions. In this work, we describe parameters of anti-Stokes fluorescence of cyanobacterial PBSs in quenched and unquenched states. We compare the fluorescence readout from entire phycobilisomes and their fragments. The obtained results revealed the heterogeneity of conformations of chromophores in isolated phycobiliproteins, while such heterogeneity was not observed in the entire PBS. Under excitation by low-energy quanta, we did not detect a significant uphill energy transfer from the core to the peripheral rods of PBS, while the one from the terminal emitters to the bulk allophycocyanin chromophores is highly probable. We show that this direction of energy migration does not eliminate fluorescence quenching in the complex with OCP. Thus, long-wave excitation provides new insights into the pathways of energy conversion in the phycobilisome.
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Affiliation(s)
- Dmitry V Zlenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Elena A Protasova
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Georgy V Tsoraev
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 142432 Moscow, Russia.; A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, 119991 Moscow, Russia
| | - Thomas Friedrich
- Technical University of Berlin, Institute of Chemistry PC 14, D-10623 Berlin, Germany
| | - Baosheng Ge
- China University of Petroleum (Huadong), College of Chemical Engineering, Qingdao 266580, PR China
| | - Song Qin
- China University of Petroleum (Huadong), College of Chemical Engineering, Qingdao 266580, PR China; Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China
| | - Eugene G Maksimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Andrew B Rubin
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
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9
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Tsoraev GV, Bukhanko AY, Mamchur AA, Yaroshevich IA, Sluchanko NN, Tseng HW, Moldenhauer M, Budisa N, Friedrich T, Maksimov EG. Intrinsic tryptophan fluorescence quenching by iodine in non-canonical amino acid reveals alteration of the hydrogen bond network in the photoactive orange carotenoid protein. Biochem Biophys Res Commun 2023; 683:149119. [PMID: 37862781 DOI: 10.1016/j.bbrc.2023.10.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
The Orange Carotenoid Protein (OCP) regulates cyanobacterial photosynthetic activity through photoactivation in intense light. A hydrogen bonding network involving the keto-carotenoid oxygen and Y201 and W288 residues prevents the spontaneous activation of dark-adapted OCP. To investigate the role of the hydrogen bonds in OCP photocycling, we introduced non-canonical amino acids near the keto-carotenoid, particularly iodine at the meta-position of Y201. This modification significantly increased the yield of red OCP photoproducts, albeit with a shorter lifetime. Changes in tryptophan fluorescence during photocycling influenced by the presence of iodine near W288 revealed interactions between Y201 and W288 in the absence of the carotenoid in the C-domain. We propose that upon the relaxation of red states, a ternary complex with the carotenoid is formed. Analysis of spectral signatures and interaction energies indicates that the specific iodo-tyrosine configuration enhances interactions between the carotenoid and W288.
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Affiliation(s)
- Georgy V Tsoraev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | | | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Hsueh-Wei Tseng
- Technical University of Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Marcus Moldenhauer
- Technical University of Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Thomas Friedrich
- Technical University of Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Eugene G Maksimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
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10
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Sluchanko NN, Kapitonova AA, Shulepko MA, Kukushkin ID, Kulbatskii DS, Tugaeva KV, Varfolomeeva LA, Minyaev ME, Boyko KM, Popov VO, Kirpichnikov MP, Lyukmanova EN. Crystal structure reveals canonical recognition of the phosphorylated cytoplasmic loop of human alpha7 nicotinic acetylcholine receptor by 14-3-3 protein. Biochem Biophys Res Commun 2023; 682:91-96. [PMID: 37804592 DOI: 10.1016/j.bbrc.2023.09.086] [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: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023]
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 (Q361RRCSLASVEMS372), known to be phosphorylated in vivo. We reconstructed the 14-3-3ζ/ICL peptide complex and determined its structure by X-ray crystallography, which confirmed the Ser365 phosphorylation-dependent canonical recognition of the ICL by 14-3-3. A common mechanism of nAChRs' regulation by ICL phosphorylation and 14-3-3 binding that potentially affects nAChR activity, stoichiometry, and surface expression is suggested.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Anna A Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Mikhail A Shulepko
- Faculty of Biology, MSU-BIT Shenzhen University, Shenzhen, 518172, China
| | - Ilya D Kukushkin
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow region, 141701, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Dmitrii S Kulbatskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Larisa A Varfolomeeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Mikhail E Minyaev
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin M Boyko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Vladimir O Popov
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia; Interdisciplinary Scientific and Educational School of Moscow University "Molecular Technologies of the Living Systems and Synthetic Biology", Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, Moscow, 119234, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia; Interdisciplinary Scientific and Educational School of Moscow University "Molecular Technologies of the Living Systems and Synthetic Biology", Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, Moscow, 119234, Russia
| | - Ekaterina N Lyukmanova
- Faculty of Biology, MSU-BIT Shenzhen University, Shenzhen, 518172, China; Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow region, 141701, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia; Interdisciplinary Scientific and Educational School of Moscow University "Molecular Technologies of the Living Systems and Synthetic Biology", Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, Moscow, 119234, Russia.
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11
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Jamgochian HH, Zamakhaev MV, Sluchanko NN, Goncharenko AV, Shumkov MS. Development of Heterologous Expression System and Optimization of the Method of Cholera Toxin β-Subunit Production in E. coli. Biochemistry (Mosc) 2023; 88:1304-1317. [PMID: 37770397 DOI: 10.1134/s0006297923090109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 09/30/2023]
Abstract
Cholera is a deadly infection disease, which is usually associated with low hygiene levels and limited access to high-quality drinking water. An effective way to prevent cholera is the use of vaccines. Among active vaccine components there is the CtxB protein (cholera toxin β-subunit). In the current work, we have developed a genetic system for production of the recombinant CtxB in E. coli cells and studied conditions for synthesis and purification of the target product at the laboratory scale. It has been found that the optimal algorithm for isolation of the recombinant protein is to grow E. coli culture in the synthetic M9 medium with glycerol, followed by CtxB purification out of the spent culture medium using Ni2+-chelate affinity chromatography techniques. Forty-eight hours after induction of CtxB expression, concentration of the target product could be up to 50 mg/liter in the culture medium. The CtxB protein retains its pentameric structure during expression and through purification. The latter makes it possible to consider the developed system as a promising tool for the industrial-level production of recombinant CtxB for medical and research purposes.
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Affiliation(s)
- Hamesd H Jamgochian
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Mikhail V Zamakhaev
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Nikolai N Sluchanko
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Anna V Goncharenko
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Mikhail S Shumkov
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
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12
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Kornilov FD, Slonimskiy YB, Lunegova DA, Egorkin NA, Savitskaya AG, Kleymenov SY, Maksimov EG, Goncharuk SA, Mineev KS, Sluchanko NN. Structural basis for the ligand promiscuity of the neofunctionalized, carotenoid-binding fasciclin domain protein AstaP. Commun Biol 2023; 6:471. [PMID: 37117801 PMCID: PMC10147662 DOI: 10.1038/s42003-023-04832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/10/2023] [Indexed: 04/30/2023] Open
Abstract
Fasciclins (FAS1) are ancient adhesion protein domains with no common small ligand binding reported. A unique microalgal FAS1-containing astaxanthin (AXT)-binding protein (AstaP) binds a broad repertoire of carotenoids by a largely unknown mechanism. Here, we explain the ligand promiscuity of AstaP-orange1 (AstaPo1) by determining its NMR structure in complex with AXT and validating this structure by SAXS, calorimetry, optical spectroscopy and mutagenesis. α1-α2 helices of the AstaPo1 FAS1 domain embrace the carotenoid polyene like a jaw, forming a hydrophobic tunnel, too short to cap the AXT β-ionone rings and dictate specificity. AXT-contacting AstaPo1 residues exhibit different conservation in AstaPs with the tentative carotenoid-binding function and in FAS1 proteins generally, which supports the idea of AstaP neofunctionalization within green algae. Intriguingly, a cyanobacterial homolog with a similar domain structure cannot bind carotenoids under identical conditions. These structure-activity relationships provide the first step towards the sequence-based prediction of the carotenoid-binding FAS1 members.
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Affiliation(s)
- Fedor D Kornilov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Daria A Lunegova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Nikita A Egorkin
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Anna G Savitskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia
| | - Sergey Yu Kleymenov
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 26 Vavilov Street, 119334, Moscow, Russia
| | - Eugene G Maksimov
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119991, Moscow, Russia
| | - Sergey A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia.
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.
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13
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Zhu P, Stanisheuski S, Franklin R, Vogel A, Vesely CH, Reardon P, Sluchanko NN, Beckman JS, Karplus PA, Mehl RA, Cooley RB. Autonomous Synthesis of Functional, Permanently Phosphorylated Proteins for Defining the Interactome of Monomeric 14-3-3ζ. ACS Cent Sci 2023; 9:816-835. [PMID: 37122473 PMCID: PMC10141581 DOI: 10.1021/acscentsci.3c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Indexed: 05/03/2023]
Abstract
14-3-3 proteins are dimeric hubs that bind hundreds of phosphorylated "clients" to regulate their function. Installing stable, functional mimics of phosphorylated amino acids into proteins offers a powerful strategy to study 14-3-3 function in cellular-like environments, but a previous genetic code expansion (GCE) system to translationally install nonhydrolyzable phosphoserine (nhpSer), with the γ-oxygen replaced with CH2, site-specifically into proteins has seen limited usage. Here, we achieve a 40-fold improvement in this system by engineering into Escherichia coli a six-step biosynthetic pathway that produces nhpSer from phosphoenolpyruvate. Using this autonomous "PermaPhos" expression system, we produce three biologically relevant proteins with nhpSer and confirm that nhpSer mimics the effects of phosphoserine for activating GSK3β phosphorylation of the SARS-CoV-2 nucleocapsid protein, promoting 14-3-3/client complexation, and monomerizing 14-3-3 dimers. Then, to understand the biological function of these phosphorylated 14-3-3ζ monomers (containing nhpSer at Ser58), we isolate its interactome from HEK293T lysates and compare it with that of wild-type 14-3-3ζ. These data identify two new subsets of 14-3-3 client proteins: (i) those that selectively bind dimeric 14-3-3ζ and (ii) those that selectively bind monomeric 14-3-3ζ. We discover that monomeric-but not dimeric-14-3-3ζ interacts with cereblon, an E3 ubiquitin-ligase adaptor protein of pharmacological interest.
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Affiliation(s)
- Phillip Zhu
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Stanislau Stanisheuski
- Department
of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Rachel Franklin
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Amber Vogel
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Cat Hoang Vesely
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Patrick Reardon
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Nikolai N. Sluchanko
- A.N.
Bach Institute of Biochemistry, Federal Research Center of Biotechnology
of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Joseph S. Beckman
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- e-MSion
Inc., 2121 NE Jack London
St., Corvallis, Oregon 97330, United States
| | - P. Andrew Karplus
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Ryan A. Mehl
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Richard B. Cooley
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
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14
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Lee E, Redzic JS, Saviola AJ, Li X, Ebmeier CC, Kutateladze T, Hansen KC, Zhao R, Ahn N, Sluchanko NN, Eisenmesser E. Molecular insight into the specific interactions of the SARS-Coronavirus-2 nucleocapsid with RNA and host protein. Protein Sci 2023; 32:e4603. [PMID: 36807437 PMCID: PMC10019451 DOI: 10.1002/pro.4603] [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: 12/20/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid protein is the most abundantly expressed viral protein during infection where it targets both RNA and host proteins. However, identifying how a single viral protein interacts with so many different targets remains a challenge, providing the impetus here for identifying the interaction sites through multiple methods. Through a combination of nuclear magnetic resonance (NMR), electron microscopy, and biochemical methods, we have characterized nucleocapsid interactions with RNA and with three host proteins, which include human cyclophilin-A, Pin1, and 14-3-3τ. Regarding RNA interactions, the nucleocapsid protein N-terminal folded domain preferentially interacts with smaller RNA fragments relative to the C-terminal region, suggesting an initial RNA engagement is largely dictated by this N-terminal region followed by weaker interactions to the C-terminal region. The nucleocapsid protein forms 10 nm ribonuclear complexes with larger RNA fragments that include 200 and 354 nucleic acids, revealing its potential diversity in sequestering different viral genomic regions during viral packaging. Regarding host protein interactions, while the nucleocapsid targets all three host proteins through its serine-arginine-rich region, unstructured termini of the nucleocapsid protein also engage host cyclophilin-A and host 14-3-3τ. Considering these host proteins play roles in innate immunity, the SARS-CoV-2 nucleocapsid protein may block the host response by competing interactions. Finally, phosphorylation of the nucleocapsid protein quenches an inherent dynamic exchange process within its serine-arginine-rich region. Our studies identify many of the diverse interactions that may be important for SARS-CoV-2 pathology during infection.
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Affiliation(s)
- Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | | | - Tatiana Kutateladze
- Department of PharmacologySchool of Medicine, University of Colorado DenverAuroraColoradoUSA
| | - Kirk Charles Hansen
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Natalie Ahn
- Department of BiochemistryUniversity of Colorado BoulderBoulderColoradoUSA
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of SciencesMoscowRussia
| | - Elan Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
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15
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Pishchalnikov RY, Yaroshevich IA, Zlenko DV, Tsoraev GV, Osipov EM, Lazarenko VA, Parshina EY, Chesalin DD, Sluchanko NN, Maksimov EG. The role of the local environment on the structural heterogeneity of carotenoid β-ionone rings. Photosynth Res 2023; 156:3-17. [PMID: 36063303 DOI: 10.1007/s11120-022-00955-2] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Our analysis of the X-ray crystal structure of canthaxanthin (CAN) showed that its ketolated β-ionone rings can adopt two energetically equal, but structurally distinct puckers. Quantum chemistry calculations revealed that the potential energy surface of the β-ionone ring rotation over the plane of the conjugated π-system in carotenoids depends on the pucker state of the β-ring. Considering different pucker states and β-ionone ring rotation, we found six separate local minima on the potential energy surface defining the geometry of the keto-β-ionone ring-two cis and one trans orientation for each of two pucker states. We observed a small difference in energy and no difference in relative orientation for the cis-minima, but a pronounced difference for the position of trans-minimum in alternative pucker configurations. An energetic advantage of β-ionone ring rotation from a specific pucker type can reach up to 8 kJ/mol ([Formula: see text]). In addition, we performed the simulation of linear absorption of CAN in hexane and in a unit cell of the CAN crystal. The electronic energies of [Formula: see text] transition were estimated both for the CAN monomer and in the CAN crystal. The difference between them reached [Formula: see text], which roughly corresponds to the energy gap between A and B pucker states predicted by theoretical estimations. Finally, we have discussed the importance of such effects for biological systems whose local environment determines conformational mobility, and optical/functional characteristics of carotenoid.
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Affiliation(s)
- Roman Y Pishchalnikov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str., 38, Moscow, Russia, 119991.
| | - Igor A Yaroshevich
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Dmitry V Zlenko
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
- A.N. Severtsov Institute of Ecology and Evolution (IEE), RAS, Moscow, Russia, 117071
| | - Georgy V Tsoraev
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Evgenii M Osipov
- Laboratory for Biocrystallography, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Vladimir A Lazarenko
- National Research Center "Kurchatov Institute", 1 Akademika Kurchatova Pl., Moscow, Russia, 123182
| | - Evgenia Yu Parshina
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Denis D Chesalin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str., 38, Moscow, Russia, 119991
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia, 119071
| | - Eugene G Maksimov
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
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16
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Tsoraev GV, Bukhanko A, Budylin GS, Shirshin EA, Slonimskiy YB, Sluchanko NN, Kloz M, Cherepanov DA, Shakina YV, Ge B, Moldenhauer M, Friedrich T, Golub M, Pieper J, Maksimov EG, Rubin AB. Stages of OCP-FRP Interactions in the Regulation of Photoprotection in Cyanobacteria, Part 1: Time-Resolved Spectroscopy. J Phys Chem B 2023; 127:1890-1900. [PMID: 36799909 DOI: 10.1021/acs.jpcb.2c07189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Most cyanobacteria utilize a water-soluble Orange Carotenoid Protein (OCP) to protect their light-harvesting complexes from photodamage. The Fluorescence Recovery Protein (FRP) is used to restore photosynthetic activity by inactivating OCP via dynamic OCP-FRP interactions, a multistage process that remains underexplored. In this work, applying time-resolved spectroscopy, we demonstrate that the interaction of FRP with the photoactivated OCP begins early in the photocycle. Interacting with the compact OCP state, FRP completely prevents the possibility of OCP domain separation and formation of the signaling state capable of interacting with the antenna. The structural element that prevents FRP binding and formation of the complex is the short α-helix at the beginning of the N-terminal domain of OCP, which masks the primary site in the C-terminal domain of OCP. We determined the rate of opening of this site and show that it remains exposed long after the relaxation of the red OCP states. Observations of the OCP transitions on the ms time scale revealed that the relaxation of the orange photocycle intermediates is accompanied by an increase in the interaction of the carotenoid keto group with the hydrogen bond donor tyrosine-201. Our data refine the current model of photoinduced OCP transitions and the interaction of its intermediates with FRP.
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Affiliation(s)
- Georgy V Tsoraev
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Antonina Bukhanko
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Gleb S Budylin
- Faculty of Physics, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia.,Laboratory of Clinical Biophotonics, Scientific and Technological Biomedical Park, Sechenov University, 119435 Moscow, Russia
| | - Evgeny A Shirshin
- Faculty of Physics, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Miroslav Kloz
- ELI-Beamlines, Institute of Physics, Dolní Břežany, 252 41 Czech Republic
| | - Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 142432 Moscow, Russia.,A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, 119991 Moscow, Russia
| | | | - Baosheng Ge
- China University of Petroleum (Huadong), College of Chemical Engineering, Qingdao 266580, PR China
| | - Marcus Moldenhauer
- Technische Universität Berlin, Institute of Chemistry PC14, 10623 Berlin, Germany
| | - Thomas Friedrich
- Technische Universität Berlin, Institute of Chemistry PC14, 10623 Berlin, Germany
| | - Maksym Golub
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
| | - Jörg Pieper
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
| | - Eugene G Maksimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Andrew B Rubin
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
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17
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Zhu P, Nguyen KT, Estelle AB, Sluchanko NN, Mehl RA, Cooley RB. Genetic encoding of 3-nitro-tyrosine reveals the impacts of 14-3-3 nitration on client binding and dephosphorylation. Protein Sci 2023; 32:e4574. [PMID: 36691781 PMCID: PMC9926477 DOI: 10.1002/pro.4574] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023]
Abstract
14-3-3 proteins are central hub regulators of hundreds of phosphorylated "client" proteins. They are subject to over 60 post-translational modifications (PTMs), yet little is known how these PTMs alter 14-3-3 function and its ability to regulate downstream signaling pathways. An often neglected, but well-documented 14-3-3 PTM found under physiological and immune-stimulatory conditions is the conversion of tyrosine to 3-nitro-tyrosine at several Tyr sites, two of which are located at sites considered important for 14-3-3 function: Y130 (β-isoform numbering) is located in the primary phospho-client peptide-binding groove, while Y213 is found on a secondary binding site that engages with clients for full 14-3-3/client complex formation and client regulation. By genetically encoding 3-nitro-tyrosine, we sought to understand if nitration at Y130 and Y213 effectively modulated 14-3-3 structure, function, and client complexation. The 1.5 Å resolution crystal structure of 14-3-3 nitrated at Y130 showed the nitro group altered the conformation of key residues in the primary binding site, while functional studies confirmed client proteins failed to bind this variant of 14-3-3. But, in contrast to other client-binding deficient variants, it did not localize to the nucleus. The 1.9 Å resolution structure of 14-3-3 nitrated at Y213 revealed unusual flexibility of its C-terminal α-helix resulting in domain swapping, suggesting additional structural plasticity though its relevance is not clear as this nitrated form retained its ability to bind clients. Collectively, our data suggest that nitration of 14-3-3 will alter downstream signaling systems, and if uncontrolled could result in global dysregulation of the 14-3-3 interactome.
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Affiliation(s)
- Phillip Zhu
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Kyle T. Nguyen
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Aidan B. Estelle
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology of the Russian Academy of SciencesA.N. Bach Institute of BiochemistryMoscowRussia
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Richard B. Cooley
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
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18
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Gayer AV, Yakimov BP, Sluchanko NN, Shirshin EA. Multifarious analytical capabilities of the UV/Vis protein fluorescence in blood plasma. Spectrochim Acta A Mol Biomol Spectrosc 2023; 286:122028. [PMID: 36327910 DOI: 10.1016/j.saa.2022.122028] [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] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/09/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Autofluorescence of blood plasma has been broadly considered as a prospective disease screening method. However, the assessment of such intrinsic fluorescence is mostly phenomenological, and its origin is still not fully understood, complicating its use in the clinical practice. Here we present the detailed evaluation of analytical capabilities, variability, and formation of blood plasma protein fluorescence based on the open dataset of excitation-emission matrices measured for ∼300 patients with suspected colorectal cancer, and our supporting model experiments. Using high-resolution size-exclusion chromatography coupled with comprehensive spectral analysis, we demonstrate, for the first time, the dominant role of HSA in the formation of blood plasma fluorescence in the visible spectral range (excitation wavelength >350 nm), presumably caused by its oxidative modifications. Furthermore, the diagnostic value of the tryptophan emission, as well as of the tyrosine fluorescence and visible fluorescence of proteins is shown by building a tree-based classification model that uses a small subset of physically interpretable fluorescence features for distinguishing between the control group and cancer patients with >80% accuracy. The obtained results extend current understanding and approaches used for the analysis of blood plasma fluorescence and pave the way for novel autofluorescence-based disease screening methods.
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Affiliation(s)
- Alexey V Gayer
- Faculty of Physics, M.V. Lomonosov Moscow State University, 1-2 Leninskie Gory, Moscow 119991, Russia; Laboratory of Clinical Biophotonics, Biomedical Science and Technology Park, Sechenov First Moscow State Medical University, Trubetskaya 8, Moscow 119048, Russia
| | - Boris P Yakimov
- Faculty of Physics, M.V. Lomonosov Moscow State University, 1-2 Leninskie Gory, Moscow 119991, Russia; Laboratory of Clinical Biophotonics, Biomedical Science and Technology Park, Sechenov First Moscow State Medical University, Trubetskaya 8, Moscow 119048, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Evgeny A Shirshin
- Faculty of Physics, M.V. Lomonosov Moscow State University, 1-2 Leninskie Gory, Moscow 119991, Russia; Laboratory of Clinical Biophotonics, Biomedical Science and Technology Park, Sechenov First Moscow State Medical University, Trubetskaya 8, Moscow 119048, Russia.
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19
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Tugaeva KV, Sysoev AA, Kapitonova AA, Smith JLR, Zhu P, Cooley RB, Antson AA, Sluchanko NN. Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation. J Mol Biol 2023; 435:167891. [PMID: 36427566 PMCID: PMC9683861 DOI: 10.1016/j.jmb.2022.167891] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/06/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022]
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.
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Affiliation(s)
- Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Andrey A Sysoev
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anna A Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Phillip Zhu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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20
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Moldenhauer M, Tseng HW, Kraskov A, Tavraz NN, Yaroshevich IA, Hildebrandt P, Sluchanko NN, Hochberg GA, Essen LO, Budisa N, Korf L, Maksimov EG, Friedrich T. Parameterization of a single H-bond in Orange Carotenoid Protein by atomic mutation reveals principles of evolutionary design of complex chemical photosystems. Front Mol Biosci 2023; 10:1072606. [PMID: 36776742 PMCID: PMC9909426 DOI: 10.3389/fmolb.2023.1072606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction: Dissecting the intricate networks of covalent and non-covalent interactions that stabilize complex protein structures is notoriously difficult and requires subtle atomic-level exchanges to precisely affect local chemical functionality. The function of the Orange Carotenoid Protein (OCP), a light-driven photoswitch involved in cyanobacterial photoprotection, depends strongly on two H-bonds between the 4-ketolated xanthophyll cofactor and two highly conserved residues in the C-terminal domain (Trp288 and Tyr201). Method: By orthogonal translation, we replaced Trp288 in Synechocystis OCP with 3-benzothienyl-L-alanine (BTA), thereby exchanging the imino nitrogen for a sulphur atom. Results: Although the high-resolution (1.8 Å) crystal structure of the fully photoactive OCP-W288_BTA protein showed perfect isomorphism to the native structure, the spectroscopic and kinetic properties changed distinctly. We accurately parameterized the effects of the absence of a single H-bond on the spectroscopic and thermodynamic properties of OCP photoconversion and reveal general principles underlying the design of photoreceptors by natural evolution. Discussion: Such "molecular surgery" is superior over trial-and-error methods in hypothesis-driven research of complex chemical systems.
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Affiliation(s)
- Marcus Moldenhauer
- Department of Bioenergetics, Institute of Chemistry PC 14, Technische Universität Berlin, Berlin, Germany
| | - Hsueh-Wei Tseng
- Department of Biocatalysis, Institute of Chemistry L1, Technische Universität Berlin, Berlin, Germany
| | - Anastasia Kraskov
- Department of Bioenergetics, Institute of Chemistry PC 14, Technische Universität Berlin, Berlin, Germany
| | - Neslihan N. Tavraz
- Department of Bioenergetics, Institute of Chemistry PC 14, Technische Universität Berlin, Berlin, Germany
| | - Igor A. Yaroshevich
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Peter Hildebrandt
- Department of Bioenergetics, Institute of Chemistry PC 14, Technische Universität Berlin, Berlin, Germany
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center Fundamentals of Biotechnology of Russian Academy of Sciences, Moscow, Russia
| | - Georg A. Hochberg
- Max-Planck-Institute of Terrestrial Microbiology, Evolutionary Biochemistry Group, Marburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry and Unit for Structural Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Nediljko Budisa
- Department of Biocatalysis, Institute of Chemistry L1, Technische Universität Berlin, Berlin, Germany,Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Lukas Korf
- Department of Chemistry and Unit for Structural Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Eugene G. Maksimov
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Thomas Friedrich
- Department of Bioenergetics, Institute of Chemistry PC 14, Technische Universität Berlin, Berlin, Germany,*Correspondence: Thomas Friedrich,
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21
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Shatov VM, Muranova LK, Zamotina MA, Sluchanko NN, Gusev NB. α-Crystallin Domains of Five Human Small Heat Shock Proteins (sHsps) Differ in Dimer Stabilities and Ability to Incorporate Themselves into Oligomers of Full-Length sHsps. Int J Mol Sci 2023; 24:ijms24021085. [PMID: 36674601 PMCID: PMC9860685 DOI: 10.3390/ijms24021085] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 01/08/2023] Open
Abstract
The α-crystallin domain (ACD) is the hallmark of a diverse family of small heat shock proteins (sHsps). We investigated some of the ACD properties of five human sHsps as well as their interactions with different full-length sHsps. According to size-exclusion chromatography, at high concentrations, the ACDs of HspB1 (B1ACD), HspB5 (B5ACD) and HspB6 (B6ACD) formed dimers of different stabilities, which, upon dilution, dissociated to monomers to different degrees. Upon dilution, the B1ACD dimers possessed the highest stabilities, and those of B6ACD had the lowest. In striking contrast, the ACDs of HspB7 (B7ACD) and HspB8 (B8ACD) formed monomers in the same concentration range, which indicated the compromised stabilities of their dimer interfaces. B1ACD, B5ACD and B6ACD transiently interacted with full-length HspB1 and HspB5, which are known to form large oligomers, and modulated their oligomerization behavior. The small oligomers formed by the 3D mutant of HspB1 (mimicking phosphorylation at Ser15, Ser78 and Ser82) effectively interacted with B1ACD, B5ACD and B6ACD, incorporating these α-crystallin domains into their structures. The inherently dimeric full-length HspB6 readily formed heterooligomeric complexes with B1ACD and B5ACD. In sharp contrast to the abovementioned ACDs, B7ACD and B8ACD were unable to interact with full-length HspB1, the 3D mutant of HspB1, HspB5 or HspB6. Thus, their high sequence homology notwithstanding, B7ACD and B8ACD differ from the other three ACDs in their inability to form dimers and interact with the full-length small heat shock proteins. Having conservative primary structures and being apparently similar, the ACDs of the different sHsps differ in terms of their dimer stabilities, which can influence the heterooligomerization preferences of sHsps.
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Affiliation(s)
- Vladislav M. Shatov
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russia
| | - Lydia K. Muranova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russia
| | - Maria A. Zamotina
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russia
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, Moscow 119071, Russia
| | - Nikolai B. Gusev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russia
- Correspondence: ; Tel.: +7-495-939-2747
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22
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Sluchanko NN, Slonimskiy YB, Egorkin NA, Varfolomeeva LA, Faletrov YV, Moysenovich AM, Parshina EY, Friedrich T, Maksimov EG, Boyko KM, Popov VO. Silkworm carotenoprotein as an efficient carotenoid extractor, solubilizer and transporter. Int J Biol Macromol 2022; 223:1381-1393. [PMID: 36395947 DOI: 10.1016/j.ijbiomac.2022.11.093] [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: 08/18/2022] [Revised: 10/31/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
Found in many organisms, water-soluble carotenoproteins are prospective antioxidant nanocarriers for biomedical applications. Yet, the toolkit of characterized carotenoproteins is rather limited: such proteins are either too specific binders of only few different carotenoids, or their ability to transfer carotenoids to various acceptor systems is unknown. Here, by focusing on a recently characterized recombinant ~27-kDa Carotenoid-Binding Protein from Bombyx mori (BmCBP) [Slonimskiy et al., International Journal of Biological Macromolecules 214 (2022): 664-671], we analyze its carotenoid-binding repertoire and potential as a carotenoid delivery module. We show that BmCBP forms productive complexes with both hydroxyl- and ketocarotenoids - lutein, zeaxanthin, astaxanthin, canthaxanthin and a smaller antioxidant, aporhodoxanthinone, but not with β-carotene or retinal, which defines its broad ligand specificity toward xanthophylls valuable to human health. Moreover, the His-tagged BmCBP apoform is capable of cost-efficient and scalable enrichment of xanthophylls from various crude methanolic herbal extracts. Upon carotenoid binding, BmCBP remains monomeric and shows a remarkable ability to dynamically shuttle carotenoids to biological membrane models and to unrelated carotenoproteins, which in particular makes from the cyanobacterial Orange Carotenoid Protein a blue-light controlled photoswitch. Furthermore, administration of BmCBP loaded by zeaxanthin stimulates fibroblast growth, which is attractive for cell- and tissue-based assays.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation.
| | - Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Nikita A Egorkin
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Larisa A Varfolomeeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Yaroslav V Faletrov
- Research Institute for Physical Chemical Problems, Belarusian State University, Minsk, Belarus
| | - Anastasia M Moysenovich
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119991 Moscow, Russian Federation
| | - Evgenia Yu Parshina
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119991 Moscow, Russian Federation
| | - Thomas Friedrich
- Technical University of Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Eugene G Maksimov
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119991 Moscow, Russian Federation
| | - Konstantin M Boyko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Vladimir O Popov
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation; M.V. Lomonosov Moscow State University, Faculty of Biology, 119991 Moscow, Russian Federation
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23
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Slonimskiy YB, Zupnik AO, Varfolomeeva LA, Boyko KM, Maksimov EG, Sluchanko NN. A primordial Orange Carotenoid Protein: Structure, photoswitching activity and evolutionary aspects. Int J Biol Macromol 2022; 222:167-180. [PMID: 36165868 DOI: 10.1016/j.ijbiomac.2022.09.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/28/2022]
Abstract
Cyanobacteria are photosynthesizing prokaryotes responsible for the Great Oxygenation Event on Earth ~2.5 Ga years ago. They use a specific photoprotective mechanism based on the 35-kDa photoactive Orange Carotenoid Protein (OCP), a promising target for developing novel optogenetic tools and for biomass engineering. The two-domain OCP presumably stems from domain fusion, yet the primitive thylakoid-less cyanobacteria Gloeobacter encodes a complete OCP. Its photosynthesis regulation lacks the so-called Fluorescence Recovery Protein (FRP), which in Synechocystis inhibits OCP-mediated phycobilisome fluorescence quenching, and Gloeobacter OCP belongs to the recently defined, heterogeneous clade OCPX (GlOCPX), the least characterized compared to OCP2 and especially OCP1 clades. Here, we describe the first crystal structure of OCPX, which explains unique functional adaptations of Gloeobacter OCPX compared to OCP1 from Synechocystis. We show that monomeric GlOCPX exploits a remarkable intramolecular locking mechanism stabilizing its dark-adapted state and exhibits drastically accelerated, less temperature-dependent recovery after photoactivation. While GlOCPX quenches Synechocystis phycobilisomes similar to Synechocystis OCP1, it evades interaction with and regulation by FRP from other species and likely uses alternative mechanisms for fluorescence recovery. This analysis of a primordial OCPX sheds light on its evolution, rationalizing renaming and subdivision of the OCPX clade into subclades - OCP3a, OCP3b, OCP3c.
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Affiliation(s)
- Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Andrei O Zupnik
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Larisa A Varfolomeeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Konstantin M Boyko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Eugene G Maksimov
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119991 Moscow, Russian Federation
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation.
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24
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Semenov AN, Gvozdev DA, Zlenko DV, Protasova EA, Khashimova AR, Parshina EY, Baizhumanov AA, Lotosh NY, Kim EE, Kononevich YN, Pakhomov AA, Selishcheva AA, Sluchanko NN, Shirshin EA, Maksimov EG. Modulation of Membrane Microviscosity by Protein-Mediated Carotenoid Delivery as Revealed by Time-Resolved Fluorescence Anisotropy. Membranes (Basel) 2022; 12:905. [PMID: 36295665 PMCID: PMC9609150 DOI: 10.3390/membranes12100905] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Carotenoids are potent antioxidants with a wide range of biomedical applications. However, their delivery into human cells is challenging and relatively inefficient. While the use of natural water-soluble carotenoproteins capable to reversibly bind carotenoids and transfer them into membranes is promising, the quantitative estimation of the delivery remains unclear. In the present work, we studied echinenone (ECN) delivery by cyanobacterial carotenoprotein AnaCTDH (C-terminal domain homolog of the Orange Carotenoid Protein from Anabaena), into liposome membranes labelled with BODIPY fluorescent probe. We observed that addition of AnaCTDH-ECN to liposomes led to the significant changes in the fast-kinetic component of the fluorescence decay curve, pointing on the dipole-dipole interactions between the probe and ECN within the membrane. It may serve as an indirect evidence of ECN delivery into membrane. To study the delivery in detail, we carried out molecular dynamics modeling of the localization of ECN within the lipid bilayer and calculate its orientation factor. Next, we exploited FRET to assess concentration of ECN delivered by AnaCTDH. Finally, we used time-resolved fluorescence anisotropy to assess changes in microviscosity of liposomal membranes. Incorporation of liposomes with β-carotene increased membrane microviscosity while the effect of astaxanthin and its mono- and diester forms was less pronounced. At temperatures below 30 °C addition of AnaCTDH-ECN increased membrane microviscosity in a concentration-dependent manner, supporting the protein-mediated carotenoid delivery mechanism. Combining all data, we propose FRET-based analysis and assessment of membrane microviscosity as potent approaches to characterize the efficiency of carotenoids delivery into membranes.
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Affiliation(s)
- Alexey N. Semenov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Danil A. Gvozdev
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Dmitry V. Zlenko
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Elena A. Protasova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Anastasia R. Khashimova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Evgenia Yu. Parshina
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Adil A. Baizhumanov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Natalia Yu. Lotosh
- National Research Center “Kurchatov Institute”, 1 Acad. Kurchatov Sq., Moscow 123182, Russia
| | - Eleonora E. Kim
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
| | - Yuriy N. Kononevich
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey A. Pakhomov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
- M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alla A. Selishcheva
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
- National Research Center “Kurchatov Institute”, 1 Acad. Kurchatov Sq., Moscow 123182, Russia
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology, Russian Academy of Sciences, 33 Leninsky Prospect, Moscow 119071, Russia
| | - Evgeny A. Shirshin
- Faculty of Physics, M.V. Lomonosov Moscow State University, 1-2 Leninskie Gory St., Moscow 119991, Russia
- Laboratory of Clinical Biophotonics, Biomedical Science and Technology Park, I.M. Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, Moscow 119991, Russia
- Institute of Spectroscopy, Russian Academy of Sciences, 5 Fizicheskaya Str., Troitsk, Moscow 108840, Russia
| | - Eugene G. Maksimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
- Faculty of Physics, M.V. Lomonosov Moscow State University, 1-2 Leninskie Gory St., Moscow 119991, Russia
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25
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Tsoraev GV, Protasova EA, Klimanova EA, Ryzhykau YL, Kuklin AI, Semenov YS, Ge B, Li W, Qin S, Friedrich T, Sluchanko NN, Maksimov EG. Anti-Stokes fluorescence excitation reveals conformational mobility of the C-phycocyanin chromophores. Struct Dyn 2022; 9:054701. [PMID: 36065339 PMCID: PMC9440762 DOI: 10.1063/4.0000164] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/08/2022] [Indexed: 05/15/2023]
Abstract
The structural organization of natural pigment-protein complexes provides a specific environment for the chromophore groups. Yet, proteins are inherently dynamic and conformationally mobile. In this work, we demonstrate the heterogeneity of chromophores of C-phycocyanin (C-PC) from Arthrospira platensis. Part of the population of trimeric C-PC is subject to spontaneous disturbances of protein-protein interactions resulting in increased conformational mobility of the chromophores. Upon fluorescence excitation in the visible range, the spectral signatures of these poorly populated states are masked by bulk chromophore states, but the former could be clearly discriminated when the fluorescence is excited by near-infrared quanta. Such selective excitation of conformationally mobile C-PC chromophores is due to the structure of their S1 level, which is characterized by a significantly broadened spectral line. We demonstrate that the anti-Stokes C-PC fluorescence is the result of single-photon absorption. By combining spectral and structural methods, we characterize four distinct states of C-PC chromophores emitting at 620, 650, 665, and 720 nm and assigned the fast component in the anti-Stokes fluorescence decay kinetics in the range of 690-750 nm to the chromophores with increased conformational mobility. Our data suggest that the spectral and temporal characteristics of the anti-Stokes fluorescence can be used to study protein dynamics and develop methods to visualize local environment parameters such as temperature.
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Affiliation(s)
- Georgy V. Tsoraev
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Elena A. Protasova
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | | | | | | | - Yury S. Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Baosheng Ge
- China University of Petroleum (Huadong), College of Chemical Engineering, Qingdao 266580, People's Republic of China
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, People's Republic of China
| | | | - Thomas Friedrich
- Technical University of Berlin, Institute of Chemistry PC 14, D-10623 Berlin, Germany
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Eugene G. Maksimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Author to whom correspondence should be addressed:. Tel.: +7 (926) 735–04-37
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26
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Kapitonova AA, Tugaeva KV, Varfolomeeva LA, Boyko KM, Cooley RB, Sluchanko NN. Structural basis for the recognition by 14-3-3 proteins of a conditional binding site within the oligomerization domain of human nucleophosmin. Biochem Biophys Res Commun 2022; 627:176-183. [PMID: 36041327 DOI: 10.1016/j.bbrc.2022.08.047] [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: 08/10/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022]
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.
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Affiliation(s)
- Anna A Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Larisa A Varfolomeeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Konstantin M Boyko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.
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27
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Slonimskiy YB, Egorkin NA, Ashikhmin AA, Friedrich T, Maksimov EG, Sluchanko NN. Reconstitution of the functional carotenoid-binding protein from silkworm in E. coli. Int J Biol Macromol 2022; 214:664-671. [PMID: 35753519 DOI: 10.1016/j.ijbiomac.2022.06.135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 04/14/2022] [Revised: 06/02/2022] [Accepted: 06/20/2022] [Indexed: 12/16/2022]
Abstract
Natural water-soluble carotenoproteins are promising antioxidant nanocarriers for biomedical applications. The Carotenoid-Binding Protein from silkworm Bombyx mori (BmCBP) is responsible for depositing carotenoids in cocoons. This determines the silk coloration, which is relevant for sericulture for four thousand years. While BmCBP function is well-characterized by molecular genetics, its structure and carotenoid-binding mechanism remain to be studied. To facilitate this, here we report on successful production of soluble BmCBP in Escherichia coli, its purification and characterization. According to CD spectroscopy and SEC-MALS, this protein folds into a ~ 27-kDa monomer capable of dose-dependent binding of lutein, a natural BmCBP ligand, in vitro. Binding leads to a >10 nm red-shift of the carotenoid absorbance and quenches tryptophan fluorescence of BmCBP. Using zeaxanthin, a close lutein isomer that can be stably produced in engineered E.coli strains, we successfully reconstitute the BmCBP holoform and characterize its properties. While BmCBP successfully matures into the holoform, BmCBP-zeaxanthin complexes are contaminated by the apoform. We demonstrate that the yield of the holoform can be increased by adding bovine serum albumin during cell lysis and that the remaining BmCBP apoform is efficiently removed using hydroxyapatite chromatography. Bacterial production of BmCBP paves the way for its structural studies and applications.
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Affiliation(s)
- Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Nikita A Egorkin
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Aleksandr A Ashikhmin
- Federal Research Center Pushchino Scientific Center Russian Academy of Sciences, Institute of Basic Biological Problems of Russian Academy of Sciences, Institutskaya, 2, Pushchino, Moscow 142290, Russia
| | - Thomas Friedrich
- Technical University of Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Eugene G Maksimov
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119991 Moscow, Russian Federation
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation.
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Abstract
Being phosphopeptide-binding hubs, 14-3-3 proteins coordinate multiple cellular processes in eukaryotes, including the regulation of apoptosis, cell cycle, ion channels trafficking, transcription, signal transduction, and hormone biosynthesis. Forming constitutive α-helical dimers, 14-3-3 proteins predominantly recognize specifically phosphorylated Ser/Thr sites within their partners; this generally stabilizes phosphotarget conformation and affects its activity, intracellular distribution, dephosphorylation, degradation and interactions with other proteins. Not surprisingly, 14-3-3 complexes are involved in the development of a range of diseases and are considered promising drug targets. The wide interactome of 14-3-3 proteins encompasses hundreds of different phosphoproteins, for many of which the interaction is well-documented in vitro and in vivo but lack the structural data that would help better understand underlying regulatory mechanisms and develop new drugs. Despite obtaining structural information on 14-3-3 complexes is still lagging behind the research of 14-3-3 interactions on a proteome-wide scale, recent works provided some advances, including methodological improvements and accumulation of new interesting structural data, that are discussed in this review.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russian Federation.
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Zhu P, Franklin R, Vogel A, Stanisheuski S, Reardon P, Sluchanko NN, Beckman JS, Karplus PA, Mehl RA, Cooley RB. PermaPhos Ser : autonomous synthesis of functional, permanently phosphorylated proteins. bioRxiv 2021:2021.10.22.465468. [PMID: 34931187 PMCID: PMC8687462 DOI: 10.1101/2021.10.22.465468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Installing stable, functional mimics of phosphorylated amino acids into proteins offers a powerful strategy to study protein regulation. Previously, a genetic code expansion (GCE) system was developed to translationally install non-hydrolyzable phosphoserine (nhpSer), with the γ-oxygen replaced with carbon, but it has seen limited usage. Here, we achieve a 40-fold improvement in this system by engineering into Escherichia coli a biosynthetic pathway that produces nhpSer from the central metabolite phosphoenolpyruvate. Using this "PermaPhos Ser " system - an autonomous 21-amino acid E. coli expression system for incorporating nhpSer into target proteins - we show that nhpSer faithfully mimics the effects of phosphoserine in three stringent test cases: promoting 14-3-3/client complexation, disrupting 14-3-3 dimers, and activating GSK3β phosphorylation of the SARS-CoV-2 nucleocapsid protein. This facile access to nhpSer containing proteins should allow nhpSer to replace Asp and Glu as the go-to pSer phosphomimetic for proteins produced in E. coli .
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Affiliation(s)
- Phillip Zhu
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Rachel Franklin
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Amber Vogel
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Stanislau Stanisheuski
- Oregon State University, Department of Chemistry, 153 Gilbert Hall, Oregon State University, Corvallis, Oregon 97331
| | - Patrick Reardon
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Joseph S. Beckman
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
- e-MSion Inc., 2121 NE Jack London St, Corvallis, Oregon 97330
| | - P. Andrew Karplus
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Ryan A. Mehl
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Richard B. Cooley
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
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30
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Sluchanko NN, Tugaeva KV, Gushchin I, Remeeva A, Kovalev K, Cooley RB. Crystal structure of human 14-3-3ζ complexed with the noncanonical phosphopeptide from proapoptotic BAD. Biochem Biophys Res Commun 2021; 583:100-105. [PMID: 34735870 DOI: 10.1016/j.bbrc.2021.10.053] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 10/20/2022]
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.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Kirill Kovalev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia; European Molecular Biology Laboratory, 22607, Hamburg, Germany
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
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Slonimskiy YB, Egorkin NA, Friedrich T, Maksimov EG, Sluchanko NN. Microalgal protein AstaP is a potent carotenoid solubilizer and delivery module with a broad carotenoid binding repertoire. FEBS J 2021; 289:999-1022. [PMID: 34582628 DOI: 10.1111/febs.16215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/09/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022]
Abstract
Carotenoids are lipophilic substances with many biological functions, from coloration to photoprotection. Being potent antioxidants, carotenoids have multiple biomedical applications, including the treatment of neurodegenerative disorders and retina degeneration. Nevertheless, the delivery of carotenoids is substantially limited by their poor solubility in the aqueous phase. Natural water-soluble carotenoproteins can facilitate this task, necessitating studies on their ability to uptake and deliver carotenoids. One such promising carotenoprotein, AstaP (astaxanthin-binding protein), was recently identified in eukaryotic microalgae, but its structure and functional properties remained largely uncharacterized. By using a correctly folded recombinant protein, here we show that AstaP is an efficient carotenoid solubilizer that can stably bind not only astaxanthin but also zeaxanthin, canthaxanthin, and, to a lesser extent, β-carotene, that is, carotenoids especially valuable to human health. AstaP accepts carotenoids provided as acetone solutions or embedded in membranes, forming carotenoid-protein complexes with an apparent stoichiometry of 1:1. We successfully produced AstaP holoproteins in specific carotenoid-producing strains of Escherichia coli, proving it is amenable to cost-efficient biotechnology processes. Regardless of the carotenoid type, AstaP remains monomeric in both apo- and holoform, while its rather minimalistic mass (~ 20 kDa) makes it an especially attractive antioxidant delivery module. In vitro, AstaP transfers different carotenoids to liposomes and to unrelated proteins from cyanobacteria, which can modulate their photoactivity and/or oligomerization. These findings expand the toolkit of the characterized carotenoid binding proteins and outline the perspective of the use of AstaP as a unique monomeric antioxidant nanocarrier with an extensive carotenoid binding repertoire.
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Affiliation(s)
- Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Nikita A Egorkin
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Thomas Friedrich
- Institute of Chemistry PC 14, Technical University of Berlin, Berlin, Germany
| | - Eugene G Maksimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russian Federation
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
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32
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Shatov VM, Sluchanko NN, Gusev NB. Replacement of Arg in the conserved N-terminal RLFDQxFG motif affects physico-chemical properties and chaperone-like activity of human small heat shock protein HspB8 (Hsp22). PLoS One 2021; 16:e0253432. [PMID: 34143841 PMCID: PMC8213154 DOI: 10.1371/journal.pone.0253432] [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: 03/28/2021] [Accepted: 06/04/2021] [Indexed: 01/06/2023] Open
Abstract
The small heat shock protein (sHsp) called HspB8 (formerly, Hsp22) is one of the least typical sHsp members, whose oligomerization status remains debatable. Here we analyze the effect of mutations in a highly conservative sequence located in the N-terminal domain of human HspB8 on its physico-chemical properties and chaperone-like activity. According to size-exclusion chromatography coupled to multi-angle light scattering, the wild type (WT) HspB8 is present as dominating monomeric species (~24 kDa) and a small fraction of oligomers (~60 kDa). The R29A amino acid substitution leads to the predominant formation of 60-kDa oligomers, leaving only a small fraction of monomers. Deletion of the 28–32 pentapeptide (Δ mutant) results in the formation of minor quantities of dimers (~49 kDa) and large quantities of the 24-kDa monomers. Both the WT protein and its Δ mutant efficiently bind a hydrophobic probe bis-ANS and are relatively rapidly hydrolyzed by chymotrypsin, whereas the R29A mutant weakly binds bis-ANS and resists chymotrypsinolysis. In contrast to HspB8 WT and its Δ mutant, which are well phosphorylated by cAMP-dependent and ERK1 protein kinases, the R29A mutant is poorly phosphorylated. R29A mutation affects the chaperone-like activity of HspB8 measured in vitro. It is concluded that the irreplaceable Arg residue located in the only highly conservative motif in the N-terminal domain of all sHsp proteins affects the oligomeric structure and key properties of HspB8.
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Affiliation(s)
- Vladislav M. Shatov
- Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russian Federation
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Nikolai B. Gusev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russian Federation
- * E-mail:
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33
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Yaroshevich IA, Maksimov EG, Sluchanko NN, Zlenko DV, Stepanov AV, Slutskaya EA, Slonimskiy YB, Botnarevskii VS, Remeeva A, Gushchin I, Kovalev K, Gordeliy VI, Shelaev IV, Gostev FE, Khakhulin D, Poddubnyy VV, Gostev TS, Cherepanov DA, Polívka T, Kloz M, Friedrich T, Paschenko VZ, Nadtochenko VA, Rubin AB, Kirpichnikov MP. Role of hydrogen bond alternation and charge transfer states in photoactivation of the Orange Carotenoid Protein. Commun Biol 2021; 4:539. [PMID: 33972665 PMCID: PMC8110590 DOI: 10.1038/s42003-021-02022-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 09/03/2020] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
Here, we propose a possible photoactivation mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP), suggesting that the reaction involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. Taking advantage of engineering an OCP variant carrying the Y201W mutation, which shows superior spectroscopic and structural properties, it is shown that the presence of Trp201 augments the impact of one critical H-bond between the ketocarotenoid and the protein. This confers an unprecedented homogeneity of the dark-adapted OCP state and substantially increases the yield of the excited photoproduct S*, which is important for the productive photocycle to proceed. A 1.37 Å crystal structure of OCP Y201W combined with femtosecond time-resolved absorption spectroscopy, kinetic analysis, and deconvolution of the spectral intermediates, as well as extensive quantum chemical calculations incorporating the effect of the local electric field, highlighted the role of charge-transfer states during OCP photoconversion. Yaroshevich et al. present a chemical reaction mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP). They find that photoactivation critically involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. This study suggests the role of charge-transfer states during OCP photoconversion.
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Affiliation(s)
- Igor A Yaroshevich
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Eugene G Maksimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia. .,A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V Zlenko
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey V Stepanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A Slutskaya
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yury B Slonimskiy
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Viacheslav S Botnarevskii
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany.,Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ivan V Shelaev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Fedor E Gostev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Timofey S Gostev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Moscow, Russia
| | - Tomáš Polívka
- Institute of Physics, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Miroslav Kloz
- ELI-Beamlines, Institute of Physics, Praha, Czech Republic
| | - Thomas Friedrich
- Technische Universität Berlin, Institute of Chemistry PC14, Berlin, Germany
| | | | - Victor A Nadtochenko
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Andrew B Rubin
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail P Kirpichnikov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Tugaeva KV, Hawkins DEDP, Smith JLR, Bayfield OW, Ker DS, Sysoev AA, Klychnikov OI, Antson AA, Sluchanko NN. The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins. J Mol Biol 2021; 433:166875. [PMID: 33556408 PMCID: PMC7863765 DOI: 10.1016/j.jmb.2021.166875] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [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: 01/14/2021] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/24/2022]
Abstract
The coronavirus nucleocapsid protein (N) controls viral genome packaging and contains numerous phosphorylation sites located within unstructured regions. Binding of phosphorylated SARS-CoV N to the host 14-3-3 protein in the cytoplasm was reported to regulate nucleocytoplasmic N shuttling. All seven isoforms of the human 14-3-3 are abundantly present in tissues vulnerable to SARS-CoV-2, where N can constitute up to ~1% of expressed proteins during infection. Although the association between 14-3-3 and SARS-CoV-2 N proteins can represent one of the key host-pathogen interactions, its molecular mechanism and the specific critical phosphosites are unknown. Here, we show that phosphorylated SARS-CoV-2 N protein (pN) dimers, reconstituted via bacterial co-expression with protein kinase A, directly associate, in a phosphorylation-dependent manner, with the dimeric 14-3-3 protein, but not with its monomeric mutant. We demonstrate that pN is recognized by all seven human 14-3-3 isoforms with various efficiencies and deduce the apparent KD to selected isoforms, showing that these are in a low micromolar range. Serial truncations pinpointed a critical phosphorylation site to Ser197, which is conserved among related zoonotic coronaviruses and located within the functionally important, SR-rich region of N. The relatively tight 14-3-3/pN association could regulate nucleocytoplasmic shuttling and other functions of N via occlusion of the SR-rich region, and could also hijack cellular pathways by 14-3-3 sequestration. As such, the assembly may represent a valuable target for therapeutic intervention.
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Affiliation(s)
- Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - De-Sheng Ker
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Andrey A Sysoev
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Oleg I Klychnikov
- Department of Biochemistry, School of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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Maksimov EG, Laptev GY, Blokhin DS, Klochkov VV, Slonimskiy YB, Sluchanko NN, Friedrich T, Chang CF, Polshakov VI. NMR resonance assignment and backbone dynamics of a C-terminal domain homolog of orange carotenoid protein. Biomol NMR Assign 2021; 15:17-23. [PMID: 32939684 DOI: 10.1007/s12104-020-09976-1] [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: 08/01/2020] [Accepted: 09/11/2020] [Indexed: 05/15/2023]
Abstract
Photoprotection in cyanobacteria is mediated by the Orange Carotenoid Protein (OCP), a two-domain photoswitch which has multiple natural homologs of its N- and C-terminal domains. Recently, it was demonstrated that C-terminal domain homologs (CTDHs) of OCP are standalone carotenoproteins participating in multidirectional carotenoid transfer between membranes and proteins. Non-covalent embedment of a ketocarotenoid causes dimerization of the small 16-kDa water-soluble CTDH protein; however, dynamic interactions of CTDH with membranes and other proteins apparently require the monomeric state. Although crystallography recently provided static snapshots of the Anabaena CTDH (AnaCTDH) spatial structure in the apo-form, which predicted mobility of some putative functional segments, no crystallographic information on the holo-form of CTDH is presently available. In order to use NMR techniques to cope with the dynamics of the AnaCTDH protein, it was necessary to obtain 1H, 13C and 15N resonance assignments. AnaCTDH samples enriched with 13C and 15N isotopes were prepared using recombinant protein expression, and NMR resonance assignment was achieved for more than 90% of the residues. The obtained results revealed that the structure of AnaCTDH in solution and in the crystal are largely equivalent. Together with 15N NMR relaxation experiments, our data shed light on the AnaCTDH dynamics and provide the platform for the subsequent analysis of the holo-CTDH structure in solution, for the better understanding of light-triggered protein-protein interactions and the development of antioxidant nanocarriers for biomedical applications in the future.
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Affiliation(s)
- Eugene G Maksimov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991.
- A.N. Bach Institute of Biochemistry, Federal Research Center, "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia, 119071.
- Laboratory of Physical Chemistry of Biomembranes, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991.
| | - Gennady Yu Laptev
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Dmitriy S Blokhin
- NMR Laboratory, Institute of Physics, Kazan Federal University, 18 Kremlevskaya st., Kazan, Russia, 420008
| | - Vladimir V Klochkov
- NMR Laboratory, Institute of Physics, Kazan Federal University, 18 Kremlevskaya st., Kazan, Russia, 420008
| | - Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center, "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia, 119071
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center, "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia, 119071
| | - Thomas Friedrich
- Institute of Chemistry PC 14, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Vladimir I Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991.
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Gogl G, Tugaeva KV, Eberling P, Kostmann C, Trave G, Sluchanko NN. Hierarchized phosphotarget binding by the seven human 14-3-3 isoforms. Nat Commun 2021; 12:1677. [PMID: 33723253 PMCID: PMC7961048 DOI: 10.1038/s41467-021-21908-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
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 KD ratios. Remarkably, 14-3-3 isoforms obey the same hierarchy when binding to most of their established targets, as supported by literature and a recent human complexome map. This knowledge allows predicting proportions of 14-3-3 isoforms engaged with phosphoproteins in various tissues. Notwithstanding their individual functions, cellular concentrations of 14-3-3 may be collectively adjusted to buffer the strongest phosphorylation outbursts, explaining their expression variations in different tissues and tumors.
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Affiliation(s)
- Gergo Gogl
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France.
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Pascal Eberling
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| | - Camille Kostmann
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| | - Gilles Trave
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
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Kulbatskii DS, Shulepko MA, Sluchanko NN, Yablokov EO, Kamyshinsky RA, Chesnokov YM, Kirpichnikov MP, Lyukmanova EN. Efficient screening of ligand-receptor complex formation using fluorescence labeling and size-exclusion chromatography. Biochem Biophys Res Commun 2020; 532:127-133. [PMID: 32828540 DOI: 10.1016/j.bbrc.2020.08.021] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 11/19/2022]
Abstract
Evidence of a complex formation is a crucial step in the structural studies of ligand-receptor interactions. Here we presented a simple and fast approach for qualitative screening of the complex formation between the chimeric extracellular domain of the nicotinic acetylcholine receptor (α7-ECD) and three-finger proteins. Complex formation of snake toxins α-Bgtx and WTX, as well as of recombinant analogs of human proteins Lynx1 and SLURP-1, with α7-ECD was confirmed using fluorescently labeled ligands and size-exclusion chromatography with simultaneous absorbance and fluorescence detection. WTX/α7-ECD complex formation also was confirmed by cryo-EM. The proposed approach could easily be adopted to study the interaction of other receptors with their ligands.
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Affiliation(s)
- D S Kulbatskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - M A Shulepko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - N N Sluchanko
- A. N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect 33, Building 1, Moscow, 119071, Russia
| | - E O Yablokov
- Federal State Budgetary Institution "V.N. Orekhovich Research Institute of Biomedical Chemistry", Pogodinskaya 10k8, Moscow, 119121, Russia
| | - R A Kamyshinsky
- National Research Center "Kurchatov Institute", Academic Kurchatov Sq. 1, Moscow, 123182, Russia; Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Leninskiy Prospect 59, Moscow, 119333, Russia
| | - Y M Chesnokov
- National Research Center "Kurchatov Institute", Academic Kurchatov Sq. 1, Moscow, 123182, Russia; Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Leninskiy Prospect 59, Moscow, 119333, Russia
| | - M P Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia; Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1k12, Moscow, 119192, Russia
| | - E N Lyukmanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia; Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1k12, Moscow, 119192, Russia.
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Slonimskiy YB, Maksimov EG, Sluchanko NN. Fluorescence recovery protein: a powerful yet underexplored regulator of photoprotection in cyanobacteria†. Photochem Photobiol Sci 2020; 19:763-775. [PMID: 33856677 DOI: 10.1039/d0pp00015a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/03/2020] [Indexed: 01/17/2023]
Abstract
Cyanobacteria utilize an elegant photoprotection mechanism mediated by the photoactive Orange Carotenoid Protein (OCP), which upon binding dissipates excess energy from light-harvesting complexes, phycobilisomes. The OCP activity is efficiently regulated by its partner, the Fluorescence Recovery Protein (FRP). FRP accelerates OCP conversion to the resting state, thus counteracting the OCP-mediated photoprotection. Behind the deceptive simplicity of such regulation is hidden a multistep process involving dramatic conformational rearrangements in OCP and FRP, the details of which became clearer only a decade after the FRP discovery. Yet many questions regarding the functioning of FRP have remained controversial. In this review, we summarize the current knowledge and understanding of the FRP role in cyanobacterial photoprotection as well as its evolutionary history that presumably lies far beyond cyanobacteria.
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Affiliation(s)
- Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russian Federation.,M. V. Lomonosov Moscow State University, Department of Biochemistry, Faculty of Biology, 119991, Moscow, Russian Federation
| | - Eugene G Maksimov
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russian Federation.,M. V. Lomonosov Moscow State University, Department of Biophysics, Faculty of Biology, 119991, Moscow, Russian Federation
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russian Federation. .,M. V. Lomonosov Moscow State University, Department of Biophysics, Faculty of Biology, 119991, Moscow, Russian Federation.
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Maksimov EG, Zamaraev AV, Parshina EY, Slonimskiy YB, Slastnikova TA, Abdrakhmanov AA, Babaev PA, Efimova SS, Ostroumova OS, Stepanov AV, Slutskaya EA, Ryabova AV, Friedrich T, Sluchanko NN. Soluble Cyanobacterial Carotenoprotein as a Robust Antioxidant Nanocarrier and Delivery Module. Antioxidants (Basel) 2020; 9:antiox9090869. [PMID: 32942578 PMCID: PMC7555398 DOI: 10.3390/antiox9090869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 08/18/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 01/04/2023] Open
Abstract
To counteract oxidative stress, antioxidants including carotenoids are highly promising, yet their exploitation is drastically limited by the poor bioavailability and fast photodestruction, whereas current delivery systems are far from being efficient. Here we demonstrate that the recently discovered nanometer-sized water-soluble carotenoprotein from Anabaena sp. PCC 7120 (termed AnaCTDH) transiently interacts with liposomes to efficiently extract carotenoids via carotenoid-mediated homodimerization, yielding violet–purple protein samples. We characterize the spectroscopic properties of the obtained pigment–protein complexes and the thermodynamics of liposome–protein carotenoid transfer and demonstrate the delivery of carotenoid echinenone from AnaCTDH into liposomes with an efficiency of up to 70 ± 3%. Most importantly, we show efficient carotenoid delivery to membranes of mammalian cells, which provides protection from reactive oxygen species (ROS). Incubation of neuroblastoma cell line Tet21N in the presence of 1 μM AnaCTDH binding echinenone decreased antimycin A ROS production by 25% (p < 0.05). The described carotenoprotein may be considered as part of modular systems for the targeted antioxidant delivery.
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Affiliation(s)
- Eugene G. Maksimov
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (E.Y.P.); (P.A.B.); (N.N.S.)
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
- Correspondence: ; Tel.: +7-926-735-04-37
| | - Alexey V. Zamaraev
- Faculty of Basic Medicine, MV Lomonosov Moscow State University, 117192 Moscow, Russia; (A.V.Z.); (A.A.A.)
- Center for Strategic Planning and Management of Medical and Biological Health Risks, 119121 Moscow, Russia
| | - Evgenia Yu. Parshina
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (E.Y.P.); (P.A.B.); (N.N.S.)
| | - Yury B. Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | | | - Alibek A. Abdrakhmanov
- Faculty of Basic Medicine, MV Lomonosov Moscow State University, 117192 Moscow, Russia; (A.V.Z.); (A.A.A.)
| | - Pavel A. Babaev
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (E.Y.P.); (P.A.B.); (N.N.S.)
| | - Svetlana S. Efimova
- Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia; (S.S.E.); (O.S.O.)
| | - Olga S. Ostroumova
- Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia; (S.S.E.); (O.S.O.)
| | - Alexey V. Stepanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.V.S.); (E.A.S.)
| | - Ekaterina A. Slutskaya
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.V.S.); (E.A.S.)
| | - Anastasia V. Ryabova
- A.M. Prokhorov General Physics Institute, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Thomas Friedrich
- Institute of Chemistry PC 14, Department of Bioenergetics, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nikolai N. Sluchanko
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (E.Y.P.); (P.A.B.); (N.N.S.)
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
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Tugaeva KV, Titterington J, Sotnikov DV, Maksimov EG, Antson AA, Sluchanko NN. Molecular basis for the recognition of steroidogenic acute regulatory protein by the 14‐3‐3 protein family. FEBS J 2020; 287:3944-3966. [DOI: 10.1111/febs.15474] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 07/01/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Kristina V. Tugaeva
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
- Department of Biochemistry School of Biology M.V. Lomonosov Moscow State University Russia
| | - James Titterington
- York Structural Biology Laboratory Department of Chemistry University of York UK
| | - Dmitriy V. Sotnikov
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
| | - Eugene G. Maksimov
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
- Department of Biophysics School of Biology M.V. Lomonosov Moscow State University Russia
| | - Alfred A. Antson
- York Structural Biology Laboratory Department of Chemistry University of York UK
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
- Department of Biophysics School of Biology M.V. Lomonosov Moscow State University Russia
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Maksimov EG, Protasova EA, Tsoraev GV, Yaroshevich IA, Maydykovskiy AI, Shirshin EA, Gostev TS, Jelzow A, Moldenhauer M, Slonimskiy YB, Sluchanko NN, Friedrich T. Probing of carotenoid-tryptophan hydrogen bonding dynamics in the single-tryptophan photoactive Orange Carotenoid Protein. Sci Rep 2020; 10:11729. [PMID: 32678150 PMCID: PMC7366913 DOI: 10.1038/s41598-020-68463-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 03/10/2020] [Accepted: 06/25/2020] [Indexed: 01/07/2023] Open
Abstract
The photoactive Orange Carotenoid Protein (OCP) plays a key role in cyanobacterial photoprotection. In OCP, a single non-covalently bound keto-carotenoid molecule acts as a light intensity sensor, while the protein is responsible for forming molecular contacts with the light-harvesting antenna, the fluorescence of which is quenched by OCP. Activation of this physiological interaction requires signal transduction from the photoexcited carotenoid to the protein matrix. Recent works revealed an asynchrony between conformational transitions of the carotenoid and the protein. Intrinsic tryptophan (Trp) fluorescence has provided valuable information about the protein part of OCP during its photocycle. However, wild-type OCP contains five Trp residues, which makes extraction of site-specific information impossible. In this work, we overcame this problem by characterizing the photocycle of a fully photoactive OCP variant (OCP-3FH) with only the most critical tryptophan residue (Trp-288) in place. Trp-288 is of special interest because it forms a hydrogen bond to the carotenoid's keto-oxygen to keep OCP in its dark-adapted state. Using femtosecond pump-probe fluorescence spectroscopy we analyzed the photocycle of OCP-3FH and determined the formation rate of the very first intermediate suggesting that generation of the recently discovered S* state of the carotenoid in OCP precedes the breakage of the hydrogen bonds. Therefore, following Trp fluorescence of the unique photoactive OCP-3FH variant, we identified the rate of the H-bond breakage and provided novel insights into early events accompanying photoactivation of wild-type OCP.
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Affiliation(s)
- Eugene G. Maksimov
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia ,0000 0004 0468 2555grid.425156.1A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Elena A. Protasova
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Georgy V. Tsoraev
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Igor A. Yaroshevich
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anton I. Maydykovskiy
- 0000 0001 2342 9668grid.14476.30Department of Quantum Electronics, Faculty of Physics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Evgeny A. Shirshin
- 0000 0001 2342 9668grid.14476.30Department of Quantum Electronics, Faculty of Physics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Timofey S. Gostev
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | | | - Marcus Moldenhauer
- 0000 0001 2292 8254grid.6734.6Technical University of Berlin, Institute of Chemistry PC 14, Straße des des 17. Juni 135, 10623 Berlin, Germany
| | - Yury B. Slonimskiy
- 0000 0004 0468 2555grid.425156.1A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Nikolai N. Sluchanko
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia ,0000 0004 0468 2555grid.425156.1A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Thomas Friedrich
- 0000 0001 2292 8254grid.6734.6Technical University of Berlin, Institute of Chemistry PC 14, Straße des des 17. Juni 135, 10623 Berlin, Germany
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Slonimskiy YB, Maksimov EG, Lukashev EP, Moldenhauer M, Friedrich T, Sluchanko NN. Engineering the photoactive orange carotenoid protein with redox-controllable structural dynamics and photoprotective function. Biochim Biophys Acta Bioenerg 2020; 1861:148174. [PMID: 32059843 DOI: 10.1016/j.bbabio.2020.148174] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 02/02/2020] [Accepted: 02/10/2020] [Indexed: 01/01/2023]
Abstract
Photosynthesis requires various photoprotective mechanisms for survival of organisms in high light. In cyanobacteria exposed to high light, the Orange Carotenoid Protein (OCP) is reversibly photoswitched from the orange (OCPO) to the red (OCPR) form, the latter binds to the antenna (phycobilisomes, PBs) and quenches its overexcitation. OCPR accumulation implicates restructuring of a compact dark-adapted OCPO state including detachment of the N-terminal extension (NTE) and separation of protein domains, which is reversed by interaction with the Fluorescence Recovery Protein (FRP). OCP phototransformation supposedly occurs via an intermediate characterized by an OCPR-like absorption spectrum and an OCPO-like protein structure, but the hierarchy of steps remains debatable. Here, we devise and analyze an OCP variant with the NTE trapped on the C-terminal domain (CTD) via an engineered disulfide bridge (OCPCC). NTE trapping preserves OCP photocycling within the compact protein structure but precludes functional interaction with PBs and especially FRP, which is completely restored upon reduction of the disulfide bridge. Non-interacting with the dark-adapted oxidized OCPCC, FRP binds reduced OCPCC nearly as efficiently as OCPO devoid of the NTE, suggesting that the low-affinity FRP binding to OCPO is realized via NTE displacement. The low efficiency of excitation energy transfer in complexes between PBs and oxidized OCPCC indicates that OCPCC binds to PBs in an orientation suboptimal for quenching PBs fluorescence. Our approach supports the presence of the OCPR-like intermediate in the OCP photocycle and shows effective uncoupling of spectral changes from functional OCP photoactivation, enabling redox control of its structural dynamics and function.
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Affiliation(s)
- Yury B Slonimskiy
- Protein-Protein Interactions Unit, A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation; Department of Biochemistry, Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russian Federation
| | - Eugene G Maksimov
- Protein-Protein Interactions Unit, A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation; Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russian Federation
| | - Evgeny P Lukashev
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russian Federation
| | - Marcus Moldenhauer
- Technische Universität Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Thomas Friedrich
- Technische Universität Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Nikolai N Sluchanko
- Protein-Protein Interactions Unit, A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation; Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russian Federation.
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Faletrov YV, Efimova VS, Horetski MS, Tugaeva KV, Frolova NS, Lin Q, Isaeva LV, Rubtsov MA, Sluchanko NN, Novikova LA, Shkumatov VM. New 20-hydroxycholesterol-like compounds with fluorescent NBD or alkyne labels: Synthesis, in silico interactions with proteins and uptake by yeast cells. Chem Phys Lipids 2019; 227:104850. [PMID: 31836520 DOI: 10.1016/j.chemphyslip.2019.104850] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/07/2023]
Abstract
20-hydroxycholesterol is a signaling oxysterol with immunomodulating functions and, thus, structural analogues with reporter capabilities could be useful for studying and modulating the cellular processes concerned. We have synthesized three new 20-hydroxycholesterol-like pregn-5-en-3β-ol derivatives with fluorescent 7-nitrobenzofurazan (NBD) or Raman-sensitive alkyne labels in their side-chains. In silico computations demonstrated the compounds possess good membrane permeability and can bind within active sites of known 20-hydroxycholesterol targets (e.g. Smoothened and yeast Osh4) and some other sterol-binding proteins (human LXRβ and STARD1; yeast START-kins Lam4S2 and Lam2S2). Having found good predicted membrane permeability and binding to some yeast proteins, we tested the compounds on microorganisms. Fluorescent microscopy indicated the uptake of the steroids by both Saccharomyces cerevisiae and Yarrowia lipolytica, whereas only S. cerevisiae demonstrated conversion of the compounds into 3-O-acetates, likely because 3-O-acetyltransferase Atf2p is present only in its genome. The new compounds provide new options to study the uptake, intracellular distribution and metabolism of sterols in yeast cells as well as might be used as ligands for sterol-binding proteins.
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Affiliation(s)
- Yaroslav V Faletrov
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus; Faculty of Chemistry, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus
| | - Vera S Efimova
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia
| | - Matvey S Horetski
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus; Faculty of Chemistry, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Pr. 33, Moscow, 119071, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia
| | - Nina S Frolova
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus
| | - Quingquing Lin
- Faculty of Chemistry, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus
| | - Ludmila V Isaeva
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia
| | - Mikhail A Rubtsov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia; Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia; Lomonosov Moscow State University, Laboratoire Franco-Russe de Recherches en Oncologie, Moscow, 119234, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Pr. 33, Moscow, 119071, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia
| | - Ludmila A Novikova
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia
| | - Vladimir M Shkumatov
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus; Faculty of Chemistry, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus.
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Pishchalnikov RY, Yaroshevich IA, Slastnikova TA, Ashikhmin AA, Stepanov AV, Slutskaya EA, Friedrich T, Sluchanko NN, Maksimov EG. Structural peculiarities of keto-carotenoids in water-soluble proteins revealed by simulation of linear absorption. Phys Chem Chem Phys 2019; 21:25707-25719. [PMID: 31720635 DOI: 10.1039/c9cp04508b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To prevent irreversible damage caused by an excess of incident light, the photosynthetic machinery of many cyanobacteria uniquely utilizes the water-soluble orange carotenoid protein (OCP) containing a single keto-carotenoid molecule. This molecule is non-covalently embedded into the two OCP domains which are interconnected by a flexible linker. The phenomenon of OCP photoactivation, causing significant changes in carotenoid absorption in the orange and red form of OCP, is currently being thoroughly studied. Numerous additional spectral forms of natural and synthetic OCP-like proteins have been unearthed. The optical properties of carotenoids are strongly determined by the interaction of their electronic states with vibrational modes, the surrounding protein matrix, and the solvent. In this work, the effects of the pigment-protein interaction and vibrational relaxation in OCP were studied by computational simulation of linear absorption. Taking into account Raman spectroscopy data and applying the multimode Brownian oscillator model as well as the cumulant expansion technique, we have calculated a set of characteristic microparameters sufficient to demarcate different carotenoid states in OCP forms, using the model carotenoids spheroidene and spheroidenone in methanol/acetone solution as benchmarks. The most crucial microparameters, which determine the effect of solvent and protein environment, are the Huang-Rhys factors and the frequencies of C[double bond, length as m-dash]C and C-C stretching modes, the low-frequency mode and the FWHM due to inhomogeneous line broadening. Considering the difference of linear absorption between spheroidene and spheroidenone, which remarkably resembles the photoinduced changes of OCP absorption, and applying quantum chemical calculations, we discuss structural and functional determinants of carotenoid binding proteins.
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Affiliation(s)
- Roman Y Pishchalnikov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str., 38, 119991, Moscow, Russia.
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Tugaeva KV, Kalacheva DI, Cooley RB, Strelkov SV, Sluchanko NN. Concatenation of 14-3-3 with partner phosphoproteins as a tool to study their interaction. Sci Rep 2019; 9:15007. [PMID: 31628352 PMCID: PMC6802120 DOI: 10.1038/s41598-019-50941-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 08/28/2019] [Accepted: 09/20/2019] [Indexed: 01/08/2023] Open
Abstract
Regulatory 14-3-3 proteins interact with a plethora of phosphorylated partner proteins, however 14-3-3 complexes feature intrinsically disordered regions and often a transient type of interactions making structural studies difficult. Here we engineer and examine a chimera of human 14-3-3 tethered to a nearly complete partner HSPB6 which is phosphorylated by protein kinase A (PKA). HSPB6 includes a long disordered N-terminal domain (NTD), a phosphorylation motif around Ser16, and a core α-crystallin domain (ACD) responsible for dimerisation. The chosen design enables an unstrained binding of pSer16 in each 1433 subunit and secures the correct 2:2 stoichiometry. Differential scanning calorimetry, limited proteolysis and small-angle X-ray scattering (SAXS) support the proper folding of both the 14-3-3 and ACD dimers within the chimera, and indicate that the chimera retains the overall architecture of the native complex of 14-3-3 and phosphorylated HSPB6 that has recently been resolved using crystallography. At the same time, the SAXS data highlight the weakness of the secondary interface between the ACD dimer and the C-terminal lobe of 14-3-3 observed in the crystal structure. Applied to other 14-3-3 complexes, the chimeric approach may help probe the stability and specificity of secondary interfaces for targeting them with small molecules in the future.
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Affiliation(s)
- Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.,Department of Biochemistry, School of Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Daria I Kalacheva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.,Department of Biochemistry, School of Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Sergei V Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000, Leuven, Belgium
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia. .,Department of Biophysics, School of Biology, M.V. Lomonosov Moscow State University, 119992, Moscow, Russia.
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Eronina TB, Mikhaylova VV, Chebotareva NA, Shubin VV, Sluchanko NN, Kurganov BI. Comparative effects of trehalose and 2-hydroxypropyl-β-cyclodextrin on aggregation of UV-irradiated muscle glycogen phosphorylase b. Biochimie 2019; 165:196-205. [DOI: 10.1016/j.biochi.2019.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/06/2019] [Indexed: 01/14/2023]
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Maksimov EG, Li WJ, Protasova EA, Friedrich T, Ge B, Qin S, Sluchanko NN. Hybrid coupling of R-phycoerythrin and the orange carotenoid protein supports the FRET-based mechanism of cyanobacterial photoprotection. Biochem Biophys Res Commun 2019; 516:699-704. [DOI: 10.1016/j.bbrc.2019.06.098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 06/18/2019] [Indexed: 12/31/2022]
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Abstract
Steroidogenesis takes place mainly in adrenal and gonadal cells that produce a variety of structurally similar hormones regulating numerous body functions. The rate-limiting stage of steroidogenesis is cholesterol delivery to the inner mitochondrial membrane, where it is converted by cytochrome P450scc into pregnenolone, a common precursor of all steroid hormones. The major role of supplying mitochondria with cholesterol belongs to steroidogenic acute regulatory protein (STARD1). STARD1, which is synthesized de novo as a precursor containing mitochondrial localization sequence and sterol-binding domain, significantly accelerates cholesterol transport and production of pregnenolone. Despite a tremendous interest in STARD1 fueled by its involvement in hereditary diseases and extensive efforts of numerous laboratories worldwide, many aspects of STARD1 structure, functioning, and regulation remain obscure and debatable. This review presents current concepts on the structure of STARD1 and other lipid transfer proteins, the role of STARD1 in steroidogenesis, and the mechanism of its functioning, as well as identifies the most controversial and least studied questions related to the activity of this protein.
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Affiliation(s)
- K V Tugaeva
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia. .,Lomonosov Moscow State University, Biological Faculty, Department of Biochemistry, Moscow, 119234, Russia
| | - N N Sluchanko
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia. .,Lomonosov Moscow State University, Biological Faculty, Department of Biophysics, Moscow, 119991, Russia
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Abstract
Protein-protein interactions (PPIs) mediate a variety of cellular processes and form complex networks, where connectivity is achieved owing to the "hub" proteins whose interaction with multiple protein partners is facilitated by the intrinsically disordered protein regions (IDPRs) and posttranslational modifications (PTMs). Universal regulatory proteins of the eukaryotic 14-3-3 family nicely exemplify these concepts and are the focus of this chapter. The extremely wide interactome of 14-3-3 proteins is characterized by high levels of intrinsic disorder (ID) enabling protein phosphorylation and consequent specific binding to the well-structured 14-3-3 dimers, one of the first phosphoserine/phosphothreonine binding modules discovered. However, high ID enrichment also challenges structural studies, thereby limiting the progress in the development of small molecule modulators of the key 14-3-3 PPIs of increased medical importance. Besides the well-known structural flexibility of their variable C-terminal tails, recent studies revealed the strong and conserved ID propensity hidden in the N-terminal segment of 14-3-3 proteins (~40 residues), normally forming the α-helical dimerization region, that may have a potential role for the dimer/monomer dynamics and recently reported moonlighting chaperone-like activity of these proteins. We review the role of ID in the 14-3-3 structure, their interactome, and also in selected 14-3-3 complexes. In addition, we discuss approaches that, in the future, may help minimize the disproportion between the large amount of known 14-3-3 partners and the small number of 14-3-3 complexes characterized with atomic precision, to unleash the whole potential of 14-3-3 PPIs as drug targets.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation; Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russian Federation.
| | - Diego M Bustos
- Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
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Slonimskiy YB, Muzzopappa F, Maksimov EG, Wilson A, Friedrich T, Kirilovsky D, Sluchanko NN. Light‐controlled carotenoid transfer between water‐soluble proteins related to cyanobacterial photoprotection. FEBS J 2019; 286:1908-1924. [DOI: 10.1111/febs.14803] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/07/2019] [Accepted: 03/05/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Yury B. Slonimskiy
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
- Department of Biochemistry Faculty of Biology M.V. Lomonosov Moscow State University Russia
| | - Fernando Muzzopappa
- Institute for Integrative Biology of the Cell (I2BC) CEA CNRS Université Paris‐Sud Université Paris‐Saclay Gif sur Yvette France
| | - Eugene G. Maksimov
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
- Department of Biophysics Faculty of Biology M.V. Lomonosov Moscow State University Russia
| | - Adjélé Wilson
- Institute for Integrative Biology of the Cell (I2BC) CEA CNRS Université Paris‐Sud Université Paris‐Saclay Gif sur Yvette France
| | - Thomas Friedrich
- Institute of Chemistry PC 14 Technical University of Berlin Germany
| | - Diana Kirilovsky
- Institute for Integrative Biology of the Cell (I2BC) CEA CNRS Université Paris‐Sud Université Paris‐Saclay Gif sur Yvette France
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
- Department of Biophysics Faculty of Biology M.V. Lomonosov Moscow State University Russia
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