Laboratory of genetically encoded molecular tools
Laboratory works on development of novel fluorescent tags and methods of fluorescence labeling of biological objects. The main focus is on the fluorescent proteins of GFP family, and also on other methods of noninvasive visualization of structures and processes in live cells. These methods are widely used in biomedical research enabling deciphering the molecular mechanisms of various normal and pathological phenomena and facilitating preclinical drug screening.
We are fully equipped for gene-engineering works, mammalian cell culture works, fluorescence and laser scanning confocal microscopy, and optical spectroscopy.
Laboratory collaborates with many groups of the Institute: Total Synthesis Lab on studying physic-chemical properties of fluorescent protein chromophores and developing novel methods of fluorescence labeling using their analogs; Molecular technologies laboratory on development of novel fluorescent sensors; Laboratory of X-ray study on analysis of 3D structure of fluorescent proteins and structure-guided changes of their spectral properties; Laboratory of molecular bases of embryogenesis on application of fluorescent tools for developmental studies.
Also, Laboratory collaborates with Institute of Biomedical Technologies (Nizhny Novgorod Medical State Academy) on novel methods of super-resolution fluorescence microscopy and on fluorescence imaging of mouse tumor models; Laboratory of Physical Biochemistry (A.N. Bach Institute of Biochemistry) on fluorescence lifetime imaging microscopy of biological models; Kyril Solntsev (Georgia Institute of Technology, Atlanta, GA) on ultrafast spectroscopy of fluorescent proteins; laboratory of Anna Krylov (University of Southern California, Los Angeles, CA) on studying physic-chemical processes in fluorescent proteins; laboratory of Vladislav Verkhusha (Albert Einstein College of Medicine, Bronx, NY) on development of novel fluorescent proteins; laboratory of Jens Meiler (Vanderbilt University, Nashville, TN) on computer modeling of fluorescent proteins.
Laboratory (Laboratory of Biophotonics in 2009-2020) was established in 2009 by branching out of the Laboratory of Molecular Technologies for Biology and Medicine headed by Sergey Lukyanov; our team is working with fluorescent proteins since 1999.
Novel fluorescent proteins
GFP and related fluorescent proteins are widely used as genetically encoded tags for visualization of proteins and cell populations in live systems. We use site-directed and random mutagenesis to create new variants of fluorescent proteins. This approach allows to generate proteins with usual spectral properties due to new chromophore structures or altered amino acid environment of the chromophore. In addition, we are working on improvement of fluorescent proteins characteristics such as brightness and photostability that are important for their practical applications.
Chudakov DM, et al. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol Rev. 2010, 90, 1103-63.
Pletnev VZ, et al. Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine. Acta Crystallogr D Biol Crystallogr. 2013, 69, 1850-60.
Sarkisyan KS, et al. Green fluorescent protein with anionic tryptophan-based chromophore and long fluorescence lifetime. Biophys J. 2015, 109, 380-9.
Mishin AS, et al. Novel uses of fluorescent proteins. Curr Opin Chem Biol. 2015, 27, 1-9.
Sarkisyan KS, et al. Local fitness landscape of the green fluorescent protein. Nature. 2016, 533, 397-401.
Bozhanova NG, et al. Yellow and Orange Fluorescent Proteins with Tryptophan-based Chromophores. ACS Chem Biol. 2017 Jul 21;12(7):1867-1873.
Povarova NV, et al. Functioning of Fluorescent Proteins in Aggregates in Anthozoa Species and in Recombinant Artificial Models. Int J Mol Sci. 2017 Jul 12;18(7). pii: E1503. doi: 10.3390/ijms18071503.
Bozhanova NG, et al. Protein labeling for live cell fluorescence microscopy with a highly photostable renewable signal. Chem. Sci., 2017, 8, 7138-7142.
Novel genetically encoded sensors
We are working on new fluorescent protein-based sensors for various regulatory activities, which enable quantitative visualization of the target events in live cells. For example, we recently developed ratiometric sensor for nonsense-mediated mRNA decay (NMD) and far-red sensor for caspase-3.
Gurskaya NG, et al. Analysis of alternative splicing of cassette exons at single-cell level using two fluorescent proteins. Nucleic Acids Res. 2012, 40, e57.
Pereverzev AP, et al. Method for quantitative analysis of nonsense-mediated mRNA decay at the single cell level. Sci Rep. 2015, 5, 7729.
Zlobovskaya OA, et al. Genetically encoded far-red fluorescent sensors for caspase-3 activity. Biotechniques. 2016, 60, 62-8.
Sergeeva TF, et al. Relationship between intracellular pH, metabolic co-factors and caspase-3 activation in cancer cells during apoptosis. Biochim Biophys Acta. 2017, 1864(3):604-611.
Kost LA, Nikitin ES, Ivanova VO, Sung U, Putintseva EV, Chudakov DM, Balaban PM, Lukyanov KA, Bogdanov AM. Insertion of the voltage-sensitive domain into circularly permuted red fluorescent protein as a design for genetically encoded voltage sensor. PLoS One. 2017 Sep 1;12(9):e0184225.
Photoconversions of fluorescent proteins
Photoactivatable fluorescent proteins (PAFP) are used for tracking movements of proteins, organelles and cells in live systems, as well as for super-resolution fluorescence microscopy. Earlier, our team developed several PAFPs, such as KFP1, PS-CFP and Dendra, which were among the world's first members of this protein type. Currently, we continue to work on development of new PAFPs and PAFP-based techniques.
In 2009 we discovered oxidative photoconversion of green fluorescent proteins based on electron transfer from the chromophore to an external molecule of electron acceptor. We are studying mechanisms of this phenomenon and development of methods of its practical applications (for example, for enhancement of fluorescent protein photostability).
In collaboration with Nizhny Novgorod State Medical Academy we work on development of novel labels and methods of super-resolution fluorescence microscopy (PALM/STORM single molecule localization microscopy).
Chudakov DM, et al. Kindling fluorescent proteins for precise in vivo photolabeling. Nat Biotechnol. 2003, 21, 191-4.
Gurskaya NG, et al. Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light. Nat Biotechnol. 2006, 24, 461-5.
Bogdanov AM, et al. Green fluorescent proteins are light-induced electron donors. Nat Chem Biol. 2009, 5, 459-61.
Bogdanov AM, et al. Cell culture medium affects GFP photostability: a solution. Nat Methods. 2009, 6, 859-60.
Mamontova AV, et al. Influence of cell growth conditions and medium composition on EGFP photostability in live cells. Biotechniques. 2015, 58, 258-61.
Bogdanov AM, et al. Turning On and Off Photoinduced Electron Transfer in Fluorescent Proteins by π-Stacking, Halide Binding, and Tyr145 Mutations. J. Am. Chem. Soc. 2016, 138, 4807-4817.
Acharya A, et al. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev. 2017 Jan 25;117(2):758-795.
Klementieva NV, et al. Green-to-red primed conversion of Dendra2 using blue and red lasers. Chem Commun (Camb). 2016 Nov 18;52(89):13144-13146.
Klementieva NV, et al. Intrinsic blinking of red fluorescent proteins for super-resolution microscopy. Chem Commun (Camb). 2017 Jan 10;53(5):949-951.
Genetically encoded photosensitizers
Phototoxic fluorescent proteins (the first such protein, KillerRed, was developed by us in 2006) produce reactive oxygen species (ROS) upon light illumination. We are developing this optoginetic technology, which makes it possible to induce oxidative stress in target cell compartments, inactivate proteins and kill specific cell populations using light.
Bulina ME, et al. A genetically encoded photosensitizer. Nat Biotechnol. 2006, 24, 95-9.
Lukyanov KA, et al. Fluorescent proteins as light-inducible photochemical partners. Photochem Photobiol Sci. 2010, 9, 1301-6.
Serebrovskaya EO, et al. Phototoxic effects of lysosome-associated genetically encoded photosensitizer KillerRed. J Biomed Opt. 2014,19, 071403.
Sarkisyan KS, et al. KillerOrange, a Genetically Encoded Photosensitizer Activated by Blue and Green Light. PLoS One. 2015, 10, e0145287.
2002—2006. A panel of photoactivated fluorescent proteins with different types of light-induced spectral transitions was introduced: nonflourescent-to-red (KFP1), blue-to-green (PS-CFP), and green-to-red (Dendra). These newly developed instruments KFP1, PS-CFP and Dendra were applied for precise photolabeling of cells, cell organelles, and proteins and subsequent tracking of the labeled object. The new tools were also used for monitoring the target protein degradation in an individual cell in real time using fluorescence confocal microscopy.
2005—2006. The first genetically encoded photosensitizer was created. This phototoxic red fluorescent protein named KillerRed can be used for precise light-induced destruction of proteins and cell killing.
2005—2007. A panel of improved fluorescent proteins for practical applications was created using the methods of directed molecular evolution. Particularly, there were obtained red and far-red fluorescent proteins, exceeding all known analogs in brightness. Bright far-red fluorescent proteins open up new prospects in whole-body fluorescent imaging technology.
2005—2008. First syntheses of chromophores of red fluorescent proteins (asFP595, Kaede, zFP538) and their structural analogs were performed. This work revealed various aspects of structure-properties relationship in this group of chromophores and allowed to propose promising amino-acid substitutions in fluorescent proteins to obtain variants with novel spectral properties.
Genetically encoded sensor for poly-ADP-ribose
Poly-(ADP-ribosyl)-ation (PARylation) is a reversible post-translational modification of proteins and DNA that plays important role in various cellular processes such as DNA damage response, replication, transcription, and cell death. Here we designed the first fully genetically encoded fluorescent sensor for poly-(ADP-ribose) (PAR) based on Förster Resonance Energy Transfer (FRET).
RNF146 E3 ubiquitin ligase WWE domain, which recognizes iso-ADP-ribose internal PAR-specific structural unit, was used as a PAR-targeting module. The sensor consisted of cyan Turquoise2 and yellow Venus fluorescent proteins, each in fusion with WWE domain. This bipartite sensor named sPARroW (sensor for PAR relying on WWE) enabled monitoring of PAR accumulation and depletion in live mammalian cells in response to different stimuli, namely hydrogen peroxide treatment, UV irradiation and hyperthermia.
The versatility of possible readouts (translocation vs. ratiometric FRET imaging vs. FLIM-FRET imaging) makes it readily applicable in various biological models and microscopy setups.
- (2020). Genetically Encoded Fluorescent Sensor for Poly-ADP-Ribose. Int J Mol Sci 21 (14), 1–11
Structure-functional relation of the red fluorescent biomarker FusionRed
In collaboration with Laboratory of X-ray study
Red fluorescent protein FusionRed is highly effective low toxic monomeric biomarker and it is widely used for tagging the biological objects in live cells and tissues. Its crystal structure has been determined at ultra high resolution 1.09 Å. The presence of two alternative pathways of post-translational protein modification with the formation of a mature chromophore (~ 60%) and an intact chromophore-forming triad (~ 40%) was revealed. The structurally based mutation of the Cys158 residue (which stabilizes the immature form due to the H-bond) by a bulky hydrophobic Leu residue led to 100% maturation of the chromophore.
- (2020). Two independent routes of post-translational chemistry in fluorescent protein FusionRed. Int J Biol Macromol 155, 551–559
K/E-coils: fluorescent protein labeling and Protein-PAINT nanoscopy
In collaboration with Group of molecular tags for optical nanoscopy
Heterodimerization of K/E-coils was applied for fluorescent labeling of proteins in living cells for the first time.
One of the specially selected α-helices (K or E) serves as a tag for the target protein, and the other is fused with a genetically encoded fluorescent protein. Due to the reversible interaction of K and E-helices, the target protein structure is highlighted, and the continuous exchange of fluorescent proteins in the complex increases the resistance to photobleaching by order of magnitude.
The small size of the labels (only 2-3 kDa) preserves the native dynamics of the studied proteins. Also, this method makes it possible to observe proteins almost immediately after their synthesis.
The most perspective was applying K/E-coils for Protein-PAINT – super-resolution localization microscopy based on reversibly binding labels. The continuous exchange of fluorescent proteins between the target cell structure and the cytoplasmic pool ensures a consistently high labeling density even during prolonged imaging. With the help of K/E-coils, for the first time, it was possible to implement the concept of Protein-PAINT nanoscopy using solely genetically encoded reporters.
- (2020). Highly photostable fluorescent labeling of proteins in live cells using exchangeable coiled coils heterodimerization. Cell Mol Life Sci 77 (21), 4429–4440
Photoswitchable red fluorescent proteins for nanoscopy of live cells
In collaboration with Laboratory of immunosequencing methods
We developed new reversibly photoswitchable red fluorescent proteins based on FusionRed. These proteins, rsFusionRed1, 2 and 3, can be switched OFF and ON and by orange and green light, respectively. This photoswitching behavior allows to avoid illumination by phototoxic violet and blue light, which is commonly used for other photoswitchable proteins. Due to high brightness, high photostability, rapid photoswitching and low phototoxic excitation wavelengths rsFusionReds represent excellent tags for nanoscale imaging of living cells.
- (2018). Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy. Nat Methods 15 (8), 601–604
A method of protein labeling in live cells based on fluorogen and fluorogen-binding protein
In collaboration with Laboratory of Chemistry of Metabolic Pathways,  Group of synthetic biology,  Group of chemistry of heterocyclic compounds
We developed a new method of target protein labeling called Protein-PAINT. This method is based on reversible binding of a protein domain with a fluorogenic dye that leads to a strong increase in fluorescence intensity. Using computer molecular docking we engineered three mutants of bacterial lipocalin Blc with different affinities to the fluorogen. It was shown that the fluorogen enters live cell quickly and stains target proteins fused with the Blc mutants. The new method ensures an order of magnitude higher photostability of the fluorescence signal in comparison with fluorescent proteins. Protein-PAINT also enables prolonged super-resolution fluorescence microscopy of living cells in both single molecule detection and stimulated emission depletion regimes.
- (2017). Protein labeling for live cell fluorescence microscopy with a highly photostable renewable signal. Chem Sci 8 (10), 7138–7142
Deep structure-functional analysis of amino acid substitutions on photophysical properties of green fluorescent proteins
In collaboration with Group of synthetic biology
A so called “fitness landscape” was for the first time experimentally probed at the whole protein level using GFP as a model. A unique approach developed in this work enabled to correlate a function (fluorescence) with amino acid sequence of several tens of thousands of random mutants, revealing a number of negative and positive epistatic interactions between substitutions. Characterization of the GFP fitness landscape allows for computer prediction of properties of new mutants of fluorescent proteins. It also has important implications for several fields including molecular evolution and protein design.
Using calculations of the possible electron transfer pathways from excited GFP chromophore to external molecules and further experimental verification of these hypotheses, we constructed mutants with blocked electron transfer pathway and correspondingly increased photostability. This strategy may represent a new approach toward enhancing photostability of fluorescent proteins.
Figure. (A) Scheme of GFP fitness landscape derived from analysis of 51000 mutants. The GFP sequence arranged in a circle, each column representing one amino acid site. In the first circle, the colour intensity of the squares indicates the brightness of a single mutation at the corresponding site relative to the wild type, shown in the centre. Sites with positive and negative epistatic interactions between pairs of mutations are connected by green and black lines, respectively. In circles further away from the centre, representing genotypes with multiple mutations, the fraction of the column coloured green (black) represents the fraction of genotypes corresponding to high (low) fluorescence among all assayed genotypes with a mutation at that site. (B) Electron transfer in GFP. Upper panel – scheme of calculated pathway of electron transfer from the chromophore to external acceptor molecule via tyrosine-145 as an intermediate electron acceptor. Bottom panel – photobleaching curves of EGFP and its mutants in the presence of oxidant in the medium, showing a dramatic enhancement of photostability due to blocking the electron transfer pathway.
- (2016). Local fitness landscape of the green fluorescent protein. Nature 533 (7603), 397–401
- (2016). Turning on and off Photoinduced Electron Transfer in Fluorescent Proteins by π-Stacking, Halide Binding, and Tyr145 Mutations. J Am Chem Soc 138 (14), 4807–4817
- (2017). Photoinduced chemistry in fluorescent proteins: Curse or blessing? Chem Rev 117 (2), 758–795
Method for analysis of nonsense-mediated mRNA decay in the single live cells using fluorescent proteins
Nonsense-mediated mRNA decay (NMD) is an evolutionary conserved mechanism of recognition and degradation of transcripts with a premature stop-codon. Recent studies demonstrated that NMD plays an important role in global regulation of gene expression. We developed novel reporter of NMD activity based on fluorescent proteins. It enables quantitative analysis of NMD activity at the level of single live cells (this cannot be done by any other known method of NMD analysis). Using our NMD reporter, we revealed strong differences of NMD activity between mammalian cell lines. Also, a phenomenon of significant heterogeneity of NMD activity within some cell lines was observed for the first time. In particular, subpopulations of cells with high and low NMD activity were detected in HEK293, Jurkat, and HaCaT cells. Our method opens new possibilities to decipher mechanisms of NMD regulation as well as to study consequences of low NMD activity on gene expression patterns and cell physiology.
- (2015). Differences of Nonsense-Mediated mRNA Degradation Activity in Mammalian Cell Lines Revealed by a Fluorescence Reporter. Bioorg Khim 41 (5), 587–591
- (2015). Novel uses of fluorescent proteins. Curr Opin Chem Biol 27, 1–9
- (2015). Method for quantitative analysis of nonsense-mediated mRNA decay at the single cell level. Sci Rep 5, 7729