1
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Zhang H, Lesnov GD, Subach OM, Zhang W, Kuzmicheva TP, Vlaskina AV, Samygina VR, Chen L, Ye X, Nikolaeva AY, Gabdulkhakov A, Papadaki S, Qin W, Borshchevskiy V, Perfilov MM, Gavrikov AS, Drobizhev M, Mishin AS, Piatkevich KD, Subach FV. Bright and stable monomeric green fluorescent protein derived from StayGold. Nat Methods 2024; 21:657-665. [PMID: 38409224 DOI: 10.1038/s41592-024-02203-y] [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: 07/20/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024]
Abstract
The high brightness and photostability of the green fluorescent protein StayGold make it a particularly attractive probe for long-term live-cell imaging; however, its dimeric nature precludes its application as a fluorescent tag for some proteins. Here, we report the development and crystal structures of a monomeric variant of StayGold, named mBaoJin, which preserves the beneficial properties of its precursor, while serving as a tag for structural proteins and membranes. Systematic benchmarking of mBaoJin against popular green fluorescent proteins and other recently introduced monomeric and pseudomonomeric derivatives of StayGold established mBaoJin as a bright and photostable fluorescent protein, exhibiting rapid maturation and high pH/chemical stability. mBaoJin was also demonstrated for super-resolution, long-term live-cell imaging and expansion microscopy. We further showed the applicability of mBaoJin for neuronal labeling in model organisms, including Caenorhabditis elegans and mice.
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Affiliation(s)
- Hanbin Zhang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Gleb D Lesnov
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Oksana M Subach
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Wenhao Zhang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Tatyana P Kuzmicheva
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Anna V Vlaskina
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Valeriya R Samygina
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
- Institute of Crystallography of Federal Research Scientific Center 'Crystallography and Photonics' of the Russian Academy of Sciences, Moscow, Russia
| | - Liangyi Chen
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Xianxin Ye
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Alena Yu Nikolaeva
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Stavrini Papadaki
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Wenming Qin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute CAS, Shanghai, China
| | | | - Maxim M Perfilov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Gavrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kiryl D Piatkevich
- School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China.
| | - Fedor V Subach
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia.
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2
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Subach OM, Vlaskina AV, Agapova YK, Nikolaeva AY, Varizhuk AM, Podgorny OV, Piatkevich KD, Patrushev MV, Boyko KM, Subach FV. YTnC2, an improved genetically encoded green calcium indicator based on toadfish troponin C. FEBS Open Bio 2023; 13:2047-2060. [PMID: 37650870 PMCID: PMC10626279 DOI: 10.1002/2211-5463.13702] [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: 06/01/2023] [Revised: 08/03/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023] Open
Abstract
Genetically encoded calcium indicators based on truncated troponin C are attractive probes for calcium imaging due to their relatively small molecular size and twofold reduced calcium ion buffering. However, the best-suited members of this family, YTnC and cNTnC, suffer from low molecular brightness, limited dynamic range, and/or poor sensitivity to calcium transients in neurons. To overcome these limitations, we developed an enhanced version of YTnC, named YTnC2. Compared with YTnC, YTnC2 had 5.7-fold higher molecular brightness and 6.4-fold increased dynamic range in vitro. YTnC2 was successfully used to reveal calcium transients in the cytosol and in the lumen of mitochondria of both mammalian cells and cultured neurons. Finally, we obtained and analyzed the crystal structure of the fluorescent domain of the YTnC2 mutant.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS TechnologiesNational Research Center “Kurchatov Institute”MoscowRussia
| | - Anna V. Vlaskina
- Complex of NBICS TechnologiesNational Research Center “Kurchatov Institute”MoscowRussia
| | - Yulia K. Agapova
- Complex of NBICS TechnologiesNational Research Center “Kurchatov Institute”MoscowRussia
| | - Alena Y. Nikolaeva
- Complex of NBICS TechnologiesNational Research Center “Kurchatov Institute”MoscowRussia
- Bach Institute of BiochemistryResearch Centre of Biotechnology of the Russian Academy of SciencesMoscowRussia
| | - Anna M. Varizhuk
- Federal Research and Clinical Center of Physical‐Chemical Medicine of Federal Medical Biological AgencyMoscowRussia
- Moscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Oleg V. Podgorny
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic ChemistryRASMoscowRussia
- Center for Precision Genome Editing and Genetic Technologies for BiomedicinePirogov Russian National Research Medical UniversityMoscowRussia
- Federal Center of Brain Research and Neurotechnologies of Federal Medical Biological AgencyMoscowRussia
| | - Kiryl D. Piatkevich
- School of Life SciencesWestlake UniversityHangzhouChina
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouChina
| | - Maxim V. Patrushev
- Complex of NBICS TechnologiesNational Research Center “Kurchatov Institute”MoscowRussia
| | - Konstantin M. Boyko
- Bach Institute of BiochemistryResearch Centre of Biotechnology of the Russian Academy of SciencesMoscowRussia
| | - Fedor V. Subach
- Complex of NBICS TechnologiesNational Research Center “Kurchatov Institute”MoscowRussia
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3
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Subach OM, Varfolomeeva L, Vlaskina AV, Agapova YK, Nikolaeva AY, Piatkevich KD, Patrushev MV, Boyko KM, Subach FV. FNCaMP, ratiometric green calcium indicator based on mNeonGreen protein. Biochem Biophys Res Commun 2023; 665:169-177. [PMID: 37163937 DOI: 10.1016/j.bbrc.2023.04.108] [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: 04/18/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/12/2023]
Abstract
Neurobiologists widely use green genetically encoded calcium indicators (GECIs) for visualization of neuronal activity. Among them, ratiometric GECIs allow imaging of both active and non-active neuronal populations. However, they are not popular, since their properties are inferior to intensiometric GCaMP series of GECIs. The most characterized and developed ratiometric green GECI is FGCaMP7. However, the dynamic range and sensitivity of its large Stock's shift green (LSS-Green) form is significantly lower than its Green form and its molecular design is not optimal. To address these drawbacks, we engineered a ratiometric green calcium indicator, called FNCaMP, which is based on bright mNeonGreen protein and calmodulin from A. niger and has optimal NTnC-like design. We compared the properties of the FNCaMP and FGCaMP7 indicators in vitro, in mammalian cells, and in neuronal cultures. Finally, we obtained and analyzed X-ray structure of the FNCaMP indicator.
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Affiliation(s)
- Oksana M Subach
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
| | - Larisa Varfolomeeva
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Anna V Vlaskina
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
| | - Yulia K Agapova
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
| | - Alena Y Nikolaeva
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia; Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Kiryl D Piatkevich
- School of Life Sciences, Westlake University, Hangzhou, 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China.
| | - Maxim V Patrushev
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Fedor V Subach
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
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4
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Boyko KM, Khrenova MG, Nikolaeva AY, Dorovatovskii PV, Vlaskina AV, Subach OM, Popov VO, Subach FV. Combined Structural and Computational Study of the mRubyFT Fluorescent Timer Locked in Its Blue Form. Int J Mol Sci 2023; 24:ijms24097906. [PMID: 37175610 PMCID: PMC10178504 DOI: 10.3390/ijms24097906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
The mRubyFT is a monomeric genetically encoded fluorescent timer based on the mRuby2 fluorescent protein, which is characterized by the complete maturation of the blue form with the subsequent conversion to the red one. It has higher brightness in mammalian cells and higher photostability compared with other fluorescent timers. A high-resolution structure is a known characteristic of the mRubyFT with the red form chromophore, but structural details of its blue form remain obscure. In order to obtain insight into this, we obtained an S148I variant of the mRubyFT (mRubyFTS148I) with the blocked over time blue form of the chromophore. X-ray data at a 1.8 Å resolution allowed us to propose a chromophore conformation and its interactions with the neighboring residues. The imidazolidinone moiety of the chromophore is completely matured, being a conjugated π-system. The methine bridge is not oxidized in the blue form bringing flexibility to the phenolic moiety that manifests itself in poor electron density. Integration of these data with the results of molecular dynamic simulation disclosed that the OH group of the phenolic moiety forms a hydrogen bond with the side chain of the T163 residue. A detailed comparison of mRubyFTS148I with other available structures of the blue form of fluorescent proteins, Blue102 and mTagBFP, revealed a number of characteristic differences. Molecular dynamic simulations with the combined quantum mechanic/molecular mechanic potentials demonstrated that the blue form exists in two protonation states, anion and zwitterion, both sharing enolate tautomeric forms of the C=C-O- fragment. These two forms have similar excitation energies, as evaluated by calculations. Finally, excited state molecular dynamic simulations showed that excitation of the chromophore in both protonation states leads to the same anionic fluorescent state. The data obtained shed light on the structural features and spectral properties of the blue form of the mRubyFT timer.
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Affiliation(s)
- Konstantin M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt. 33, bld. 2, 119071 Moscow, Russia
| | - Maria G Khrenova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt. 33, bld. 2, 119071 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119992 Moscow, Russia
| | - Alena Y Nikolaeva
- National Research Centre "Kurchatov Institute", Kurchatov Complex NBICS-Technologies, Akad. Kurchatova sqr., 1, 123182 Moscow, Russia
| | - Pavel V Dorovatovskii
- National Research Centre "Kurchatov Institute", Kurchatov Complex NBICS-Technologies, Akad. Kurchatova sqr., 1, 123182 Moscow, Russia
| | - Anna V Vlaskina
- National Research Centre "Kurchatov Institute", Kurchatov Complex NBICS-Technologies, Akad. Kurchatova sqr., 1, 123182 Moscow, Russia
| | - Oksana M Subach
- National Research Centre "Kurchatov Institute", Kurchatov Complex NBICS-Technologies, Akad. Kurchatova sqr., 1, 123182 Moscow, Russia
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt. 33, bld. 2, 119071 Moscow, Russia
- National Research Centre "Kurchatov Institute", Kurchatov Complex NBICS-Technologies, Akad. Kurchatova sqr., 1, 123182 Moscow, Russia
| | - Fedor V Subach
- National Research Centre "Kurchatov Institute", Kurchatov Complex NBICS-Technologies, Akad. Kurchatova sqr., 1, 123182 Moscow, Russia
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5
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Subach OM, Vlaskina AV, Agapova YK, Nikolaeva AY, Anokhin KV, Piatkevich KD, Patrushev MV, Boyko KM, Subach FV. Blue-to-Red TagFT, mTagFT, mTsFT, and Green-to-FarRed mNeptusFT2 Proteins, Genetically Encoded True and Tandem Fluorescent Timers. Int J Mol Sci 2023; 24:ijms24043279. [PMID: 36834686 PMCID: PMC9963904 DOI: 10.3390/ijms24043279] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
True genetically encoded monomeric fluorescent timers (tFTs) change their fluorescent color as a result of the complete transition of the blue form into the red form over time. Tandem FTs (tdFTs) change their color as a consequence of the fast and slow independent maturation of two forms with different colors. However, tFTs are limited to derivatives of the mCherry and mRuby red fluorescent proteins and have low brightness and photostability. The number of tdFTs is also limited, and there are no blue-to-red or green-to-far-red tdFTs. tFTs and tdFTs have not previously been directly compared. Here, we engineered novel blue-to-red tFTs, called TagFT and mTagFT, which were derived from the TagRFP protein. The main spectral and timing characteristics of the TagFT and mTagFT timers were determined in vitro. The brightnesses and photoconversions of the TagFT and mTagFT tFTs were characterized in live mammalian cells. The engineered split version of the TagFT timer matured in mammalian cells at 37 °C and allowed the detection of interactions between two proteins. The TagFT timer under the control of the minimal arc promoter, successfully visualized immediate-early gene induction in neuronal cultures. We also developed and optimized green-to-far-red and blue-to-red tdFTs, named mNeptusFT and mTsFT, which were based on mNeptune-sfGFP and mTagBFP2-mScarlet fusion proteins, respectively. We developed the FucciFT2 system based on the TagFT-hCdt1-100/mNeptusFT2-hGeminin combination, which could visualize the transitions between the G1 and S/G2/M phases of the cell cycle with better resolution than the conventional Fucci system because of the fluorescent color changes of the timers over time in different phases of the cell cycle. Finally, we determined the X-ray crystal structure of the mTagFT timer and analyzed it using directed mutagenesis.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Yulia K. Agapova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Konstantin V. Anokhin
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Kiryl D. Piatkevich
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Maxim V. Patrushev
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
- Correspondence: ; Tel.: +7-499-196-7100-3389
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6
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Subach OM, Vlaskina AV, Agapova YK, Korzhenevskiy DA, Nikolaeva AY, Varizhuk AM, Subach MF, Patrushev MV, Piatkevich KD, Boyko KM, Subach FV. cNTnC and fYTnC2, Genetically Encoded Green Calcium Indicators Based on Troponin C from Fast Animals. Int J Mol Sci 2022; 23:ijms232314614. [PMID: 36498942 PMCID: PMC9741049 DOI: 10.3390/ijms232314614] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
NTnC-like green fluorescent genetically encoded calcium indicators (GECIs) with two calcium ion binding sites were constructed using the insertion of truncated troponin C (TnC) from Opsanus tau into green fluorescent proteins (GFPs). These GECIs are small proteins containing the N- and C-termini of GFP; they exert a limited effect on the cellular free calcium ion concentration; and in contrast to calmodulin-based calcium indicators they lack undesired interactions with intracellular proteins in neurons. The available TnC-based NTnC or YTnC GECIs had either an inverted response and high brightness but a limited dynamic range or a positive response and fast kinetics in neurons but lower brightness and an enhanced but still limited dF/F dynamic range. Here, we solved the crystal structure of NTnC at 2.5 Å resolution. Based on this structure, we developed positive NTnC2 and inverted iNTnC2 GECIs with a large dF/F dynamic range in vitro but very slow rise and decay kinetics in neurons. To overcome their slow responsiveness, we swapped TnC from O. tau in NTnC2 with truncated troponin C proteins from the muscles of fast animals, namely, the falcon, hummingbird, cheetah, bat, rattlesnake, and ant, and then optimized the resulting constructs using directed molecular evolution. Characterization of the engineered variants using purified proteins, mammalian cells, and neuronal cultures revealed cNTnC GECI with truncated TnC from Calypte anna (hummingbird) to have the largest dF/F fluorescence response and fast dissociation kinetics in neuronal cultures. In addition, based on the insertion of truncated TnCs from fast animals into YTnC2, we developed fYTnC2 GECI with TnC from Falco peregrinus (falcon). The purified proteins cNTnC and fYTnC2 had 8- and 6-fold higher molecular brightness and 7- and 6-fold larger dF/F responses to the increase in Ca2+ ion concentration than YTnC, respectively. cNTnC GECI was also 4-fold more photostable than YTnC and fYTnC2 GECIs. Finally, we assessed the developed GECIs in primary mouse neuronal cultures stimulated with an external electric field; in these conditions, cNTnC had a 2.4-fold higher dF/F fluorescence response than YTnC and fYTnC2 and was the same or slightly slower (1.4-fold) than fYTnC2 and YTnC in the rise and decay half-times, respectively.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Yuliya K. Agapova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Dmitriy A. Korzhenevskiy
- Laboratory of Electrophysiology, Federal Center of Brain Research and Neurotechnologies, Ostrovityanova Str. 1, Bld. 10, Moscow 125367, Russia
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Anna M. Varizhuk
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Str. 1a, Moscow 119435, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Maksim F. Subach
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Maxim V. Patrushev
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Kiryl D. Piatkevich
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow 119071, Russia
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
- Correspondence: ; Tel.: +7-499-196-7100-3389
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7
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Subach OM, Tashkeev A, Vlaskina AV, Petrenko DE, Gaivoronskii FA, Nikolaeva AY, Ivashkina OI, Anokhin KV, Popov VO, Boyko KM, Subach FV. The mRubyFT Protein, Genetically Encoded Blue-to-Red Fluorescent Timer. Int J Mol Sci 2022; 23:ijms23063208. [PMID: 35328628 PMCID: PMC8952768 DOI: 10.3390/ijms23063208] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 11/26/2022] Open
Abstract
Genetically encoded monomeric blue-to-red fluorescent timers (mFTs) change their fluorescent color over time. mCherry-derived mFTs were used for the tracking of the protein age, visualization of the protein trafficking, and labeling of engram cells. However, the brightness of the blue and red forms of mFTs are 2–3- and 5–7-fold dimmer compared to the brightness of the enhanced green fluorescent protein (EGFP). To address this limitation, we developed a blue-to-red fluorescent timer, named mRubyFT, derived from the bright mRuby2 red fluorescent protein. The blue form of mRubyFT reached its maximum at 5.7 h and completely transformed into the red form that had a maturation half-time of 15 h. Blue and red forms of purified mRubyFT were 4.1-fold brighter and 1.3-fold dimmer than the respective forms of the mCherry-derived Fast-FT timer in vitro. When expressed in mammalian cells, both forms of mRubyFT were 1.3-fold brighter than the respective forms of Fast-FT. The violet light-induced blue-to-red photoconversion was 4.2-fold less efficient in the case of mRubyFT timer compared to the same photoconversion of the Fast-FT timer. The timer behavior of mRubyFT was confirmed in mammalian cells. The monomeric properties of mRubyFT allowed the labeling and confocal imaging of cytoskeleton proteins in live mammalian cells. The X-ray structure of the red form of mRubyFT at 1.5 Å resolution was obtained and analyzed. The role of the residues from the chromophore surrounding was studied using site-directed mutagenesis.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (D.E.P.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Aleksandr Tashkeev
- Unit of Animal Genomics, GIGA Research Center, University of Liège, 4000 Liege, Belgium;
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (D.E.P.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Dmitry E. Petrenko
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (D.E.P.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Filipp A. Gaivoronskii
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (F.A.G.); (K.M.B.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (D.E.P.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (F.A.G.); (K.M.B.)
| | - Olga I. Ivashkina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (D.E.P.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia;
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Konstantin V. Anokhin
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia;
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir O. Popov
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (D.E.P.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (F.A.G.); (K.M.B.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (F.A.G.); (K.M.B.)
- Moscow Institute of Physics and Technology, Institutsky Lane 9, Dolgoprudny, 141700 Moscow, Russia
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (D.E.P.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Correspondence: ; Tel.: +7-499-196-7100-3389
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Subach OM, Vlaskina AV, Agapova YK, Dorovatovskii PV, Nikolaeva AY, Ivashkina OI, Popov VO, Piatkevich KD, Khrenova MG, Smirnova TA, Boyko KM, Subach FV. LSSmScarlet, dCyRFP2s, dCyOFP2s and CRISPRed2s, Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift. Int J Mol Sci 2021; 22:12887. [PMID: 34884694 PMCID: PMC8657457 DOI: 10.3390/ijms222312887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/20/2021] [Accepted: 11/24/2021] [Indexed: 11/24/2022] Open
Abstract
Genetically encoded red fluorescent proteins with a large Stokes shift (LSSRFPs) can be efficiently co-excited with common green FPs both under single- and two-photon microscopy, thus enabling dual-color imaging using a single laser. Recent progress in protein development resulted in a great variety of novel LSSRFPs; however, the selection of the right LSSRFP for a given application is hampered by the lack of a side-by-side comparison of the LSSRFPs' performance. In this study, we employed rational design and random mutagenesis to convert conventional bright RFP mScarlet into LSSRFP, called LSSmScarlet, characterized by excitation/emission maxima at 470/598 nm. In addition, we utilized the previously reported LSSRFPs mCyRFP1, CyOFP1, and mCRISPRed as templates for directed molecular evolution to develop their optimized versions, called dCyRFP2s, dCyOFP2s and CRISPRed2s. We performed a quantitative assessment of the developed LSSRFPs and their precursors in vitro on purified proteins and compared their brightness at 488 nm excitation in the mammalian cells. The monomeric LSSmScarlet protein was successfully utilized for the confocal imaging of the structural proteins in live mammalian cells and multicolor confocal imaging in conjugation with other FPs. LSSmScarlet was successfully applied for dual-color two-photon imaging in live mammalian cells. We also solved the X-ray structure of the LSSmScarlet protein at the resolution of 1.4 Å that revealed a hydrogen bond network supporting excited-state proton transfer (ESPT). Quantum mechanics/molecular mechanics molecular dynamic simulations confirmed the ESPT mechanism of a large Stokes shift. Structure-guided mutagenesis revealed the role of R198 residue in ESPT that allowed us to generate a variant with improved pH stability. Finally, we showed that LSSmScarlet protein is not appropriate for STED microscopy as a consequence of LSSRed-to-Red photoconversion with high-power 775 nm depletion light.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Yuliya K. Agapova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Pavel V. Dorovatovskii
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
| | - Olga I. Ivashkina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir O. Popov
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kiryl D. Piatkevich
- School of Life Sciences, Westlake University, Hangzhou 310024, China;
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Tatiana A. Smirnova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
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Petrenko DE, Timofeev VI, Britikov VV, Britikova EV, Kleymenov SY, Vlaskina AV, Kuranova IP, Mikhailova AG, Rakitina TV. First Crystal Structure of Bacterial Oligopeptidase B in an Intermediate State: The Roles of the Hinge Region Modification and Spermine. Biology (Basel) 2021; 10:biology10101021. [PMID: 34681120 PMCID: PMC8533160 DOI: 10.3390/biology10101021] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Oligopeptidase B is a two-domain, trypsin-like peptidase from parasitic protozoa and bacteria which belongs to the least studied group of prolyloligopeptidases. In this study, we describe for the first time a crystal structure of bacterial oligopeptidase B and compare it with those of protozoan oligopeptidases B and related prolyloligopeptidases. The enzyme was crystallized in the presence of spermine and contained a modified sequence of the interdomain linker. Both factors were key for crystallization. The structure showed an uncommon intermediate conformation with a domain arrangement intermediate between open and closed conformations found in the crystals of ligand-free and inhibitor-bound prolyloligopeptidases, respectively. To evaluate the impact of the modification and spermine in the obtained conformation, small-angle X-ray scattering was applied, which showed that in solution wild-type enzymes adopt the open conformation and spermine causes a transition to the intermediate state, while the modification is associated with a partial transition. We suggest that spermine-dependent conformational transition replicates the behavior of the enzyme in bacterial cells and the intermediate state, which is rarely detected in vitro, and might be widely distributed in vivo, and so should be considered during computational studies, including those aimed wanting to develop the small molecule inhibitors targeting prolyloligopeptidases. Abstract Oligopeptidase B (OpB) is a two-domain, trypsin-like serine peptidase belonging to the S9 prolyloligopeptidase (POP) family. Two domains are linked by a hinge region that participates in the transition of the enzyme between two major states—closed and open—in which domains and residues of the catalytic triad are located close to each other and separated, respectively. In this study, we described, for the first time, a structure of OpB from bacteria obtained for an enzyme from Serratia proteomaculans with a modified hinge region (PSPmod). PSPmod was crystallized in a conformation characterized by a disruption of the catalytic triad together with a domain arrangement intermediate between open and closed states found in crystals of ligand-free and inhibitor-bound POP, respectively. Two additional derivatives of PSPmod were crystallized in the same conformation. Neither wild-type PSP nor its corresponding mutated variants were susceptible to crystallization, indicating that the hinge region modification was key in the crystallization process. The second key factor was suggested to be polyamine spermine since all crystals were grown in its presence. The influences of the hinge region modification and spermine on the conformational state of PSP in solution were evaluated by small-angle X-ray scattering. SAXS showed that, in solution, wild-type PSP adopted the open state, spermine caused the conformational transition to the intermediate state, and spermine-free PSPmod contained molecules in the open and intermediate conformations in dynamic equilibrium.
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Affiliation(s)
- Dmitry E. Petrenko
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (D.E.P.); (A.V.V.)
| | - Vladimir I. Timofeev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, 117997 Moscow, Russia;
- Federal Scientific Research Center “Crystallography and Photonics”, RAS, 119333 Moscow, Russia;
- Correspondence: (V.I.T.); (T.V.R.)
| | - Vladimir V. Britikov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (V.V.B.); (E.V.B.)
| | - Elena V. Britikova
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (V.V.B.); (E.V.B.)
| | - Sergey Y. Kleymenov
- Bach Institute of Biochemistry, Federal Research Center “Fundamentals of Biotechnology”, RAS, 119071 Moscow, Russia;
- Koltzov Institute of Developmental Biology, RAS, 119334 Moscow, Russia
| | - Anna V. Vlaskina
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (D.E.P.); (A.V.V.)
| | - Inna P. Kuranova
- Federal Scientific Research Center “Crystallography and Photonics”, RAS, 119333 Moscow, Russia;
| | - Anna G. Mikhailova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, 117997 Moscow, Russia;
| | - Tatiana V. Rakitina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, 117997 Moscow, Russia;
- Correspondence: (V.I.T.); (T.V.R.)
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Barykina NV, Sotskov VP, Gruzdeva AM, Wu YK, Portugues R, Subach OM, Chefanova ES, Plusnin VV, Ivashkina OI, Anokhin KV, Vlaskina AV, Korzhenevskiy DA, Nikolaeva AY, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Subach FV. FGCaMP7, an Improved Version of Fungi-Based Ratiometric Calcium Indicator for In Vivo Visualization of Neuronal Activity. Int J Mol Sci 2020; 21:ijms21083012. [PMID: 32344594 PMCID: PMC7215472 DOI: 10.3390/ijms21083012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 01/06/2023] Open
Abstract
Genetically encoded calcium indicators (GECIs) have become a widespread tool for the visualization of neuronal activity. As compared to popular GCaMP GECIs, the FGCaMP indicator benefits from calmodulin and M13-peptide from the fungi Aspergillus niger and Aspergillus fumigatus, which prevent its interaction with the intracellular environment. However, FGCaMP exhibits a two-phase fluorescence behavior with the variation of calcium ion concentration, has moderate sensitivity in neurons (as compared to the GCaMP6s indicator), and has not been fully characterized in vitro and in vivo. To address these limitations, we developed an enhanced version of FGCaMP, called FGCaMP7. FGCaMP7 preserves the ratiometric phenotype of FGCaMP, with a 3.1-fold larger ratiometric dynamic range in vitro. FGCaMP7 demonstrates 2.7- and 8.7-fold greater photostability compared to mEGFP and mTagBFP2 fluorescent proteins in vitro, respectively. The ratiometric response of FGCaMP7 is 1.6- and 1.4-fold higher, compared to the intensiometric response of GCaMP6s, in non-stimulated and stimulated neuronal cultures, respectively. We reveal the inertness of FGCaMP7 to the intracellular environment of HeLa cells using its truncated version with a deleted M13-like peptide; in contrast to the similarly truncated variant of GCaMP6s. We characterize the crystal structure of the parental FGCaMP indicator. Finally, we test the in vivo performance of FGCaMP7 in mouse brain using a two-photon microscope and an NVista miniscope; and in zebrafish using two-color ratiometric confocal imaging.
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Affiliation(s)
- Natalia V. Barykina
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia; (N.V.B.); (O.I.I.); (K.V.A.)
| | - Vladimir P. Sotskov
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
| | - Anna M. Gruzdeva
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; (Y.K.W.); (R.P.)
| | - You Kure Wu
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; (Y.K.W.); (R.P.)
| | - Ruben Portugues
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; (Y.K.W.); (R.P.)
- Institute of Neuroscience, Technical University of Munich, 80802 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Elizaveta S. Chefanova
- Department of NBIC-technologies, Moscow Institute of Physics and Technology, 123182 Moscow, Russia;
| | - Viktor V. Plusnin
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Department of NBIC-technologies, Moscow Institute of Physics and Technology, 123182 Moscow, Russia;
| | - Olga I. Ivashkina
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia; (N.V.B.); (O.I.I.); (K.V.A.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Konstantin V. Anokhin
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia; (N.V.B.); (O.I.I.); (K.V.A.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Dmitry A. Korzhenevskiy
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Tatiana V. Rakitina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Laboratory of Hormonal Regulation Proteins, M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Anna M. Varizhuk
- Department of Biophysics, Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.M.V.); (G.E.P.)
- Department of Biophysics, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119435 Moscow, Russia
| | - Galina E. Pozmogova
- Department of Biophysics, Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.M.V.); (G.E.P.)
- Department of Biophysics, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119435 Moscow, Russia
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Correspondence: ; Tel.: +07-499-196-7100-3389
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11
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Subach OM, Sotskov VP, Plusnin VV, Gruzdeva AM, Barykina NV, Ivashkina OI, Anokhin KV, Nikolaeva AY, Korzhenevskiy DA, Vlaskina AV, Lazarenko VA, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Podgorny OV, Piatkevich KD, Boyden ES, Subach FV. Novel Genetically Encoded Bright Positive Calcium Indicator NCaMP7 Based on the mNeonGreen Fluorescent Protein. Int J Mol Sci 2020; 21:ijms21051644. [PMID: 32121243 PMCID: PMC7084697 DOI: 10.3390/ijms21051644] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 02/08/2020] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 12/21/2022] Open
Abstract
Green fluorescent genetically encoded calcium indicators (GECIs) are the most popular tool for visualization of calcium dynamics in vivo. However, most of them are based on the EGFP protein and have similar molecular brightnesses. The NTnC indicator, which is composed of the mNeonGreen fluorescent protein with the insertion of troponin C, has higher brightness as compared to EGFP-based GECIs, but shows a limited inverted response with an ΔF/F of 1. By insertion of a calmodulin/M13-peptide pair into the mNeonGreen protein, we developed a green GECI called NCaMP7. In vitro, NCaMP7 showed positive response with an ΔF/F of 27 and high affinity (Kd of 125 nM) to calcium ions. NCaMP7 demonstrated a 1.7-fold higher brightness and similar calcium-association/dissociation dynamics compared to the standard GCaMP6s GECI in vitro. According to fluorescence recovery after photobleaching (FRAP) experiments, the NCaMP7 design partially prevented interactions of NCaMP7 with the intracellular environment. The NCaMP7 crystal structure was obtained at 1.75 Å resolution to uncover the molecular basis of its calcium ions sensitivity. The NCaMP7 indicator retained a high and fast response when expressed in cultured HeLa and neuronal cells. Finally, we successfully utilized the NCaMP7 indicator for in vivo visualization of grating-evoked and place-dependent neuronal activity in the visual cortex and the hippocampus of mice using a two-photon microscope and an NVista miniscope, respectively.
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Affiliation(s)
- Oksana M. Subach
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Vladimir P. Sotskov
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
| | - Viktor V. Plusnin
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Anna M. Gruzdeva
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
| | - Natalia V. Barykina
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Olga I. Ivashkina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Konstantin V. Anokhin
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Alena Y. Nikolaeva
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Dmitry A. Korzhenevskiy
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Anna V. Vlaskina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Vladimir A. Lazarenko
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia;
| | - Tatiana V. Rakitina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia;
| | - Anna M. Varizhuk
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (A.M.V.); (G.E.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Galina E. Pozmogova
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (A.M.V.); (G.E.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Oleg V. Podgorny
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia;
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- N.K. Koltzov Institute of Developmental Biology, RAS, Moscow 119334, Russia
| | - Kiryl D. Piatkevich
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (K.D.P.); (E.S.B.)
- School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Edward S. Boyden
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (K.D.P.); (E.S.B.)
| | - Fedor V. Subach
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Correspondence: ; Tel.: +07-499-196 7100-3389
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Petrenko DE, Mikhailova AG, Timofeev VI, Agapova YК, Karlinsky DM, Komolov AS, Korzhenevskiy DA, Vlaskina AV, Rumsh LD, Rakitina TV. Molecular dynamics complemented by site-directed mutagenesis reveals significant difference between the interdomain salt bridge networks stabilizing oligopeptidases B from bacteria and protozoa in their active conformations. J Biomol Struct Dyn 2019; 38:4868-4882. [PMID: 31724904 DOI: 10.1080/07391102.2019.1692694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Oligopeptidases B (OpdBs) are trypsin-like peptidases from protozoa and bacteria that belong to the prolyl oligopeptidase (POP) family. All POPs consist of C-terminal catalytic domain and N-terminal β-propeller domain and exist in two major conformations: closed (active), where the domains and residues of the catalytic triad are positioned close to each other, and open (non-active), where two domains and residues of the catalytic triad are separated. The interdomain interface, particularly, one of its salt bridges (SB1), plays a role in the transition between these two conformations. However, due to double amino acid substitution (E/R and R/Q), this functionally important SB1 is absent in γ-proteobacterial OpdBs including peptidase from Serratia proteamaculans (PSP). In this study, molecular dynamics was used to analyze inter- and intradomain interactions stabilizing PSP in the closed conformation, in which catalytic H652 is located close to other residues of the catalytic triad. The 3D models of either wild-type PSP or of mutant PSPs carrying activating mutations E125A and D649A in complexes with peptide-substrates were subjected to the analysis. The mechanism that regulates transition of H652 from active to non-active conformation upon domain separation in PSP and other γ-proteobacterial OpdB was proposed. The complex network of polar interactions within H652-loop/C-terminal α-helix and between these areas and β-propeller domain, established in silico, was in a good agreement with both previously published results on the effects of single-residue mutations and new data on the effects of the activating mutations on each other and on the low active mutant PSP-K655A.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dmitry E Petrenko
- National Research Center "Kurchatov Institute", Moscow, Russian Federation
| | - Anna G Mikhailova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir I Timofeev
- National Research Center "Kurchatov Institute", Moscow, Russian Federation.,Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russian Federation
| | - Yulia К Agapova
- National Research Center "Kurchatov Institute", Moscow, Russian Federation
| | - David M Karlinsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Aleksandr S Komolov
- National Research Center "Kurchatov Institute", Moscow, Russian Federation.,Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russian Federation
| | | | - Anna V Vlaskina
- National Research Center "Kurchatov Institute", Moscow, Russian Federation
| | - Lev D Rumsh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatiana V Rakitina
- National Research Center "Kurchatov Institute", Moscow, Russian Federation.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
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Timofeev VI, Altukhov DA, Talyzina AA, Agapova YK, Vlaskina AV, Korzhenevskiy DA, Kleymenov SY, Bocharov EV, Rakitina TV. Structural plasticity and thermal stability of the histone-like protein from Spiroplasma melliferum are due to phenylalanine insertions into the conservative scaffold. J Biomol Struct Dyn 2017; 36:4392-4404. [PMID: 29283021 DOI: 10.1080/07391102.2017.1417162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The histone-like (HU) protein is one of the major nucleoid-associated proteins of the bacterial nucleoid, which shares high sequence and structural similarity with IHF but differs from the latter in DNA-specificity. Here, we perform an analysis of structural-dynamic properties of HU protein from Spiroplasma melliferum and compare its behavior in solution to that of another mycoplasmal HU from Mycoplasma gallisepticum. The high-resolution heteronuclear NMR spectroscopy was coupled with molecular-dynamics study and comparative analysis of thermal denaturation of both mycoplasmal HU proteins. We suggest that stacking interactions in two aromatic clusters in the HUSpm dimeric interface determine not only high thermal stability of the protein, but also its structural plasticity experimentally observed as slow conformational exchange. One of these two centers of stacking interactions is highly conserved among the known HU and IHF proteins. Second aromatic core described recently in IHFs and IHF-like proteins is considered as a discriminating feature of IHFs. We performed an electromobility shift assay to confirm high affinities of HUSpm to both normal and distorted dsDNA, which are the characteristics of HU protein. MD simulations of HUSpm with alanine mutations of the residues forming the non-conserved aromatic cluster demonstrate its role in dimer stabilization, as both partial and complete distortion of the cluster enhances local flexibility of HUSpm.
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Affiliation(s)
- Vladimir I Timofeev
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,b Federal Scientific Research Center 'Crystallography and Photonics' RAS , Leninskii pr., 59, Moscow 119333 , Russian Federation
| | - Dmitry A Altukhov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna A Talyzina
- c Moscow Institute of Physics and Technology , Institutskiy per., 9, Dolgoprudny, Moscow Region 141700 , Russian Federation
| | - Yulia K Agapova
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna V Vlaskina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Dmitry A Korzhenevskiy
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Sergey Yu Kleymenov
- d Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences , Leninsky Prospekt. 33, bld. 2, Moscow 119071 , Russian Federation.,e Russian Academy of Sciences, Koltzov Institute of Developmental Biology , ul. Vavilova, 26, Moscow 119334 , Russian Federation
| | - Eduard V Bocharov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,f Shemyakin&Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
| | - Tatiana V Rakitina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,f Shemyakin&Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
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Mikhailova AG, Rakitina TV, Timofeev VI, Karlinsky DM, Korzhenevskiy DA, Agapova YК, Vlaskina AV, Ovchinnikova MV, Gorlenko VA, Rumsh LD. Activity modulation of the oligopeptidase B from Serratia proteamaculans by site-directed mutagenesis of amino acid residues surrounding catalytic triad histidine. Biochimie 2017; 139:125-136. [DOI: 10.1016/j.biochi.2017.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 11/16/2022]
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Altukhov DA, Talyzina AA, Agapova YK, Vlaskina AV, Korzhenevskiy DA, Bocharov EV, Rakitina TV, Timofeev VI, Popov VO. Enhanced conformational flexibility of the histone-like (HU) protein from Mycoplasma gallisepticum. J Biomol Struct Dyn 2016; 36:45-53. [PMID: 27884082 DOI: 10.1080/07391102.2016.1264893] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The histone-like (HU) protein is one of the major nucleoid-associated proteins involved in DNA supercoiling and compaction into bacterial nucleoid as well as in all DNA-dependent transactions. This small positively charged dimeric protein binds DNA in a non-sequence specific manner promoting DNA super-structures. The majority of HU proteins are highly conserved among bacteria; however, HU protein from Mycoplasma gallisepticum (HUMgal) has multiple amino acid substitutions in the most conserved regions, which are believed to contribute to its specificity to DNA targets unusual for canonical HU proteins. In this work, we studied the structural dynamic properties of the HUMgal dimer by NMR spectroscopy and MD simulations. The obtained all-atom model displays compliance with the NMR data and confirms the heterogeneous backbone flexibility of HUMgal. We found that HUMgal, being folded into a dimeric conformation typical for HU proteins, has a labile α-helical body with protruded β-stranded arms forming DNA-binding domain that are highly flexible in the absence of DNA. The amino acid substitutions in conserved regions of the protein are likely to affect the conformational lability of the HUMgal dimer that can be responsible for complex functional behavior of HUMgal in vivo, e.g. facilitating its spatial adaptation to non-canonical DNA-targets.
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Affiliation(s)
- Dmitry A Altukhov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna A Talyzina
- b Moscow Institute of Physics and Technology , Institutskiy per., 9, Dolgoprudny, Moscow Region 141700 , Russian Federation
| | - Yulia K Agapova
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna V Vlaskina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Dmitry A Korzhenevskiy
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Eduard V Bocharov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,c Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
| | - Tatiana V Rakitina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,c Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
| | - Vladimir I Timofeev
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,d Federal Scientific Research Center 'Crystallography and Photonics' RAS , Leninskii pr., 59, Moscow 119333 , Russian Federation
| | - Vladimir O Popov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,e Bach Institute of Biochemistry , Research Center of Biotechnology of the Russian Academy of Sciences , Leninsky Prospekt. 33, bld. 2, Moscow 119071 , Russian Federation
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Vasil'eva SV, Strel'tsova DA, Vlaskina AV, Mikoian VD, Vanin AF. [The sources of inorganic sulfur in the process of cluster protein Fnr[4Fe-4S]2+ reconstruction in Escherichia coli cells cultivated with NO-donating agents]. Biofizika 2012; 57:247-252. [PMID: 22594280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Dinitrosyl iron complexes (DNICs) with thiol ligands--binuclear and mononuclear--inhibited aidB gene expression in E. coli cells. This process is due to the nitrosylation of the active center in iron-sulfur protein Fnr [4Fe-4S]2+ by low-molecular DNICs. The next step is transformation of the above DNICs into the DNICs with the thiol groups in the apo-form of Fnr protein. These nitrosylated proteins are characterized by the EPR signal with g perpendicular = 2.04 and g parallel 1 = 2,014. An addition of sulfur containing L-Cys or N-A-L-Cys as well as Na2S to the cells lead to the increasing in the aidB gene expression simultaneously with an appearance of the EPR signal with g perpendicular = 2.04 and g parallel = 2.02 as the characteristics of the DNICs with persulfide (R-S-S-) ligands. We suppose that the recovery of the aidB gene activity was due to the accumulation of inorganic sulfur in the cells and reconstruction of the active center in Fnr[4Fe-4S]2+. It appears that the above process is the function of L-cysteine-desulfurase protein which repaired the active center of Fnr[4Fe-4S]2+ protein using the sulfur from L-Cys or N-A-L-Cys after its deacetylation. On the other side the ions of inorganic sulfur being reacted with SH-groups led to the transformation of DNIC with thiol ligands into the persulfides. Na2S was the most potent activator of the aidB gene expression in our experiments.
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Webb TR, Jiang L, Sviridov S, Venegas RE, Vlaskina AV, McGrath D, Tucker J, Wang J, Deschenes A, Li R. Application of a novel design paradigm to generate general nonpeptide combinatorial templates mimicking beta-turns: synthesis of ligands for melanocortin receptors. ACTA ACUST UNITED AC 2007; 9:704-10. [PMID: 17429950 DOI: 10.1021/cc0601581] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the further application of a novel approach to template and ligand design by the synthesis of agonists of the melanocortin receptor. This design method uses the conserved structural data from the three-dimensional conformations of beta-turn peptides to design rigid nonpeptide templates that mimic the orientation of the main chain C-alpha atoms in a peptide beta-turn. We report details on a new synthesis of derivatives of template 1 that are useful for the synthesis of exploratory libraries. The utility of this technique is further exemplified by several iterative rounds of high-throughput synthesis and screening, which result in new partially optimized nonpeptide agonists for several melanocortin receptors.
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Affiliation(s)
- Thomas R Webb
- ChemBridge Research Labs, Inc., ChemBridge Corporation, 16981 Via Tazon, San Diego, California 92127, USA.
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