My research interest is engineering of advanced genetically encoded tools for neuroscience. I believe that new tools based on near-infrared fluorescent proteins and optogenetics are needed for a leap in technology to allow large-scale and deep-tissue studies. In our work, we apply directed molecular evolution to natural photoreceptors and existing engineered protein modules. The evolution includes rational and random mutagenesis, systematic variation of protein modules and custom-designed screening and selection strategies. We perform the whole cycle of probe development, from the rational design based on structural and biochemical data, evolution and optimization in bacteria, mammalian cell lines and primary neuronal culture, to in vivo testing and validation of the best probes in living mice.

1. Matlashov M.E.*, Shcherbakova D.M.*, Alvelid J., Baloban M., Pennacchietti F., Shemetov A.A., Testa I., Verkhusha V.V. A set of monomeric near-infrared fluorescent proteins for multicolor imaging across scales. Nature Communications 2020, 11: 239* Equal contribution.
2. Oliinyk O.S., Shemetov A.A., Pletnev S., Shcherbakova, D.M. and Verkhusha V.V. miRFP670nano: a smallmonomeric near-infrared fluorescent protein designed from cyanobacteriochrome. Nature Communications 2019, 10: 279.
3. Shcherbakova D.M., Stepanenko O.V., Turoverov K.K. and Verkhusha V.V. Near-Infrared Fluorescent Proteins: Multiplexing and Optogenetics across Scales. Trends Biotechnol. (Cell press) 2018, 36:1230-1243
4. Li L., Shemetov A.A., Baloban M., Hu P., Zhu L., Shcherbakova D.M., Zhang R., Shi J., Yao J., Wang L.V. and Verkhusha V.V. Small near-infrared photochromic protein for photoacousticmulti-contrast imaging and detection of protein interactions invivo. Nature Communications 2018, 9: 2734.
5. Shcherbakova D.M., Cox-Cammer N., Huisman T., Verkhusha V.V. and Hodgson L. Direct multiplex imaging and optogenetics of Rho GTPases enabled by near-infrared FRET. Nature Chemical Biology 2018, 14: 591-600.
6. Baloban M., *Shcherbakova D.M., * Pletnev S., Pletnev V.Z. Lagarias J.C., and Verkhusha V.V. Designing brighter near-infrared fluorescent proteins: insightsfrom structural and biochemical studies. Chemical Science 2017, 8: 4546-4557. *Equal contribution.
7. Hontani Y., Shcherbakova D.M., Baloban M., Zhu J., Verkhusha V.V. and Kennis J.T.Brightblue-shifted fluorescent bacterial phytochromes with Cys in GAF domain: fluorescence mechanisms and excited-state dynamics. Sci. Reports (Nature press) 2016, 6:37362.
8. Shcherbakova D.M., Baloban M., Emelyanov A., Brenowitz M., Guo P. and Verkhusha V.V.Brightmonomeric near-infrared fluorescent proteins as tags and biosensors for multiscale imaging. Nature Communications 2016, 7:12405.
9. Yao J., Kaberniuk A.A., Li L., Shcherbakova D.M., Zhang R., Wang L., Li G., Verkhusha V.V. and Wang L.V. Multi-scale photoacoustic tomography using reversibly switchable bacterial phytochrome as a near-infrared photochromic probe. Nature Methods 2016, 13:67-73.
10. Rumyantsev K.A., Shcherbakova D.M., Zakharova N.I., Emelyanov A.V., Turoverov K.K. and Verkhusha V.V. Minimal domain ofbacterial phytochrome required for chromophore binding and fluorescence. Sci. Reports (Nature press) 2015, 5: 18348.
11. Shcherbakova D.M., Baloban M., Pletnev S., Malashkevich V.N., Xiao H., Dauter Z., and Verkhusha V.V. Molecular basis of spectral diversity in near-infrared phytochrome-based fluorescent proteins. Chem. Biol. (Cell press) 2015, 22: 1540-1551.
12. Zhu J., Shcherbakova D.M.,Verkhusha V.V., and Kennis J.T. Ultrafas texcited-state dynamics and fluorescence deactivation of near-infrared fluorescent proteins engineered from bacteriophytochromes. Sci. Reports (Nature press) 2015, 5: 12840.
13. Shcherbakova D.M., Baloban M., and Verkhusha V.V. Near-infrared fluorescent proteins engineered from bacterial phytochromes. Curr. Opin. Chem. Biol. 2015, 27: 52-63
14. Shcherbakova, D.M., ShemetovA.A., KaberniukA.A., and Verkhusha V.V. Natural photoreceptors as a source of fluorescent proteins, biosensors and optogenetic tools. Annu. Rev. Biochem. 2015, 84: 519-550.
15. Rice W.L., Shcherbakova, D.M., Verkhusha V.V., and Kumar A.T. Whole-body tomographic fluorescence lifetime imaging using near infra-red fluorescent proteins. Cancer Research 2015, 75: 1236-1243.
16. Shcherbakova, D.M., SenguptaP., Lippincott-SchwartzJ., and Verkhusha V.V. Photocontrollable fluorescent proteins for superresolution imaging. Annu. Rev. Biophys. 2014, 43: 303-329.
17. Shcherbakova D.M. and Verkhusha V.V. Chromophore chemistry of fluorescent proteins controlled by light. Curr. Opin. Chem. Biol. 2014, 20: 60-68.
18. Krumholz A.*, Shcherbakova, D.M.*, Xia, J., WangL.V. and Verkhusha V.V. Multicontrast photoa cousticinvivo imaging using near-infrared fluorescent proteins. Sci. Reports (Nature press) 2014, 4: 3939. *Equal contribution.
19. Shcherbakova D.M. and Verkhusha V.V. Near-infrared fluorescent proteins for multicolor in vivo imaging. Nature Methods 2013, 10: 751-754.
20. Miyawaki A., Shcherbakova D.M. and Verkhusha V.V. Red fluorescent proteins: chromophore formation and cellular applications. Curr. Opin. Struct. Biol. 2012, 22: 679-688.
21. Shcherbakova, D.M., Subach, O.M., and Verkhusha, V.V.Red fluorescent proteins: Advanced imaging applications and future design. Angew. Chem. Int.Ed. 2012, 51:10724-10738.
22. Shcherbakova, D.M., Hink, M.A., Joosen, L., Gadella, T.W., and Verkhusha, V.V. An orange fluorescent protein with a large Stokes shift for single-excitation multicolor FCCS and FRET imaging. J. Am. Chem. Soc. 2012, 134: 7913-7923.