Publications

2018

Genetically encodable bioluminescent system from fungi
A.A. Kotlobay, K.S. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L.G. Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L.I. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S. V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F.A. Kondrashov, I.V. Yampolsky
Proceedings of the National Academy of Sciences of the U.S.A, 2018, published online.

Luciferase of the Japanese syllid polychaete Odontosyllis umdecimdonta
D.T. Schultz, A.A. Kotlobay, R. Ziganshin, A. Bannikov, N.M. Markina, T.V. Chepurnyh, E.S. Shakhova, K. Palkina, S.H.D. Haddock, I.V. Yampolsky, Y. Oba.
Biochemical and Biophysical Research Communications, 2018, 502, 3, 318-323.

SypHer3s: genetically encoded fluorescent ratiometric probe with enhanced brightness and improved dynamic range
Y.G. Ermakova, V.V. Pak, Y.A. Bogdanova, A.A. Kotlobay, I.V. Yampolsky, A.G. Shokhina, A.S. Panova, R. Marygin, D.B. Staroverov, D.S. Bilan, H. Sies and V.V. Belousov.
Chemical Communications, 2018, 54, 2898-2901.

2017

Unveiling Structural Motions of a Highly Fluorescent Superphotoacid by Locking and Fluorinating the GFP Chromophore in Solution
Ch. Chen, W. Liu, M.S Baranov, N.S. Baleeva, I.V. Yampolsky, L. Zhu, Y. Wang, A. Shamir, K.M. Solntsev, Ch. Fang.
Journal of Physical Chemistry Letters, 2017, 8, 5921−5928.

Prolonged bioluminescence imaging in living cells and mice using novel pro-substrates for Renilla luciferase
M. Yuan, X. Ma, T. Jiang, Y. Gao, Y. Cui, Ch. Zhang, X. Yang, Y. Huang, L. Du, I. Yampolsky, M. Li.
Organic and Biomolecular Chemistry, 2017, 15, 10238-10244.

Hispidin-3-hydroxylase: a luciferin biosynthesis enzyme of glowing fungi
N. Markina, A. Gorokhovatsky, A. Kotlobay, K. Sarkisyan, Y. Mokrushina, I. Yampolsky.
The FEBS Journal, 2017, 284 (Suppl. 1) p. 106, P.1.1-010.

Fungal bioluminescence system: luciferin, luciferase and luciferin biosynthesis
I.V. Yampolsky.
The FEBS Journal, 2017, 284 (Suppl. 1) p. 189, P.1.3-027

New bioluminescent coelenterazine derivatives with various C-6 substitutions
T. Jiang, X. Yang, Y. Zhou, I. Yampolsky, L. Dua, M. Li.
Organic and Biomolecular Chemistry, 2017, 15, 7008-7018.

Synthetic Analogue of Fridericia Luciferin with Improved Spectral Properties
Osipova ZM.
Russian Journal of Bioorganic Chemistry, 2017, 43, 2, pp. 223–225.

Fucoxanthin production by heterokont microalgae
M. Petrushkina, E. Gusev, B. Sorokin, N. Zotko, A. Mamaeva, A. Filimonova, M. Kulikovskiy, Y. Maltsev, I. Yampolsky, E. Guglya, V. Vinokurov, Z. Namsaraev, D. Kuzmin.
Algal Research, 2017, 24A, 387–393.

Protein labeling for live cell fluorescence microscopy with a highly photostable renewable signal
N.G. Bozhanova, M.S. Baranov, N.V. Klementieva, K.S. Sarkisyan, A.S. Gavrikov, I.V. Yampolsky, E.V. Zagaynova, S. Lukyanov, K. Lukyanov, A.S. Mishin.
Chemical Science, 2017, 8, 7138–7142.

Identification of hispidin as a bioluminescent active compound and its recycling biosynthesis in the luminous fungal fruiting body
Y. Oba, Y. Suzuki, G.N.R. Martins, R.P. Carvalho, T.A. Pereira, H.E. Waldenmaier, Sh. Kanie, M. Naito, A.G. Oliveira, F.A. Dörr, E. Pinto, I.V. Yampolsky, C.V. Stevani.
Photochemical and Photobiological Science, 2017, 16, 1435-1440.

Synthesis of Panal Terpenoid Core
Baranov, M.S.; Kaskova, Z.M.; Gritсenko, R.; Postikova, S.G.; Ivashkin, P.E.; Kislukhin, A.A.; Moskvin, D.I.; Mineev, K.S.; Arseniev, A.S.; Labas, Y.A.; Yampolsky, I.V.
Synlett, 2017, 28, 583–588.

Mechanism and color modulation of fungal bioluminescence
Z. M. Kaskova, F. A. Dörr, V. N. Petushkov, K. V. Purtov, A. S. Tsarkova, N. S. Rodionova, K. S. Mineev, E. B. Guglya, A. Kotlobay, N. S. Baleeva, M. S. Baranov, A. S. Arseniev, J. I. Gitelson, S. Lukyanov, Y. Suzuki, S. Kanie, E. Pinto, P. Di Mascio, H. E. Waldenmaier, T. A. Pereira, R. P. Carvalho, A. G. Oliveira, Y. Oba, E. L. Bastos, C. V. Stevani, I. V. Yampolsky.
Science Advances, 2017, 3, e1602847.

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Selected Least Studied but not Forgotten Bioluminescent Systems
Y. Oba, C.V. Stevani, A.G. Oliveira, A.S. Tsarkova, T.V. Chepurnykh, I.V. Yampolsky.
Photochemistry and Photobiology, 2017, 93, 405–415.

Progress in the Study of Bioluminescent Earthworms
N.S. Rodionova, E. Rota, A.S. Tsarkova, V.N. Petushkov.
Photochemistry and Photobiology, 2017, 93, 416–428.

2016

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A Tale Of Two Luciferins: Fungal and Earthworm New 2 Bioluminescent Systems
A.S. Tsarkova, Z.M. Kaskova, I.V. Yampolsky.
Accounts of Chemical Research, 2016, 49,11, 2372–2380.

1001 Lights: Luciferins, Luciferases, Their Mechanisms of Action and Applications in Chemical Analysis, Biology and Medicine
Z.M. Kaskova, A.S. Tsarkova, I.V. Yampolsky.
Chemical Society Reviews, 2016, 45, 6048-6077.

Conformationally Locked GFP Chromophore Derivatives as Potential Fluorescent Sensors
N.S. Baleeva, I.V. Yampolsky, M.S. Baranov.
Russian Journal of Bioorganic Chemistry, 2016, 42 (4), 453–456.

Nambiscalarane, a novel sesterterpenoid comprising a furan ring, and other secondary metabolites from bioluminescent fungus Neonothopanus nambi
A.S. Tsarkova, M.A. Dubinnyi, M.S. Baranov, A.D. Oguienko, I.V. Yampolsky.
Mendeleev Communications, 2016, 26, 191–192.

Docking-guided identification of protein hosts for GFP chromophore-like ligands
N.V. Povarova, N.G. Bozhanova, K.S. Sarkisyan, R. Gritcenko, M.S. Baranov, I.V. Yampolsky, K. Lukyanov, A.S. Mishin.
Journal of Material Chemistry C, 2016, 4, 3036-3040.

2015

Bioinspired fluorescent dyes based on conformationally locked chromophore of fluorescent protein Kaede
N.S. Baleeva, K.A. Myannik, I.V. Yampolsky, M.S. Baranov.
European Journal of Organic Chemistry, 2015, 26, 5716–5721.

Fluorescence imaging using synthetic GFP chromophores
Ch.L. Walker, K.A. Lukyanov, I.V. Yampolsky, A.S. Mishin, A.S Bommarius, A.M. Duraj-Thatte, B. Azizi, L.M. Tolbert, K.M. Solntsev.
Current Opinions in Chemical Biology, 2015, 27, 64–74.

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The chemical basis of fungal bioluminescence
Purtov K.V., Petushkov V.N., Baranov M.S., Mineev K.S., Rodionova N.S., Kaskova Z.M., Tsarkova A.S., Petunin A.I., Bondar V.S., Rodicheva E.K., Medvedeva S.E., Oba Yuichi, Oba Yomiko, Arseniev A.S., Lukyanov S., Gitelson J.I., Yampolsky I.V.
Angewandte Chemie International Edition, 2015, 54, 8124–8128.

Novel mechanism of bioluminescence: oxidative decarboxylation of Fridericia luciferin
M.A. Dubinnyi, Z.M. Kaskova, N.S. Rodionova, M.S. Baranov, A.Y. Gorokhovatsky, A. Kotlobay, K.M. Solntsev, A.S. Tsarkova, V.N. Petushkov, I.V. Yampolsky.
Angewandte Chemie International Edition, 2015, 54, 7065 –7067.

Total synthesis of AsLn2 – a luciferin analogue from the Siberian bioluminescent earthworm Fridericia heliota
A.S. Tsarkova, M.A. Dubinnyi, M.S. Baranov, V.N. Petushkov, N.S. Rodionova, M.B. Zagudaylova, I.V. Yampolsky.
Mendeleev Communications, 2015, 25, 99-100.

Novel Peptide Chemistry in Terrestrial Animals: Natural Luciferin Analogues from the Bioluminescent Earthworm Fridericia heliota
M. A. Dubinnyi, A. S. Tsarkova, V. N. Petushkov, Z. M Kaskova, N. S. Rodionova, S. I. Kovalchuk, R. H. Ziganshin, M. S. Baranov, K. S. Mineev, I. V. Yampolsky.
Chemistry - A European Journal, 2015, 21, 3942 – 3947.

2014

Red-shifted fluorescent aminated derivatives of conformationally locked GFP chromophore
Baranov M.S., Solntsev K.M., Baleeva N.S., Mishin A.S., Lukyanov K.A., Yampolsky I.V.
Chemistry - A European Journal, 2014, 20, 41, 13234–13241.

A novel type of luciferin from Siberian luminous earthworm Fridericia heliota: structure elucidation by spectral studies and total synthesis
Petushkov V.N., Dubinnyi M.A., Tsarkova A.S., Rodionova N.S., Baranov M.S., Kublitski V.S., Shimomura O., Yampolsky I.V.
Angewandte Chemie International Edition, 2014, 53, 22, 5566–5568.

Ring-expanding rearrangement of 2-acyl-5-arylidene-3,5-dihydro-4H-imidazol-4-ones in synthesis of flutimide analogs
Baranov M.S., Fedyakina I.T., Shchelkanov M.Y., Yampolsky I.V.
Tetrahedron, 2014, 70, 3714-3719.

AsLn2, a luciferin-related modified tripeptide from the bioluminescent earthworm Fridericia heliota
V.N. Petushkov, M.A. Dubinnyi, N.S. Rodionova, K.D. Nadezhdin, S.M. Marques, J.C.G. Esteves da Silva, O.Shimomura, I.V. Yampolsky.
Tetrahedron Letters, 2014, 55, 463-465.

CompX, a luciferin-related tyrosine derivative from the bioluminescent earthworm Fridericia heliota. Structure elucidation and total synthesis
V.N. Petushkov, A.S. Tsarkova, M.A. Dubinnyi, N.S. Rodionova, S.M. Marques, J.C.G. Esteves da Silva, O. Shimomura, I. V. Yampolsky.
Tetrahedron Letters, 2014, 55, 460-462.

2013

Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine
V.Z. Pletnev, N.V. Pletneva, K.A. Lukyanov, E.A. Souslova, A.F. Fradkov, D.M. Chudakov, T. Chepurnykh, I.V. Yampolsky, A. Wlodawer, Z. Dauter, S. Pletnev.
Acta Crystallographica Section D, 2013, D69, 1850-1860.

Chemical introduction of the green fluorescence: imaging of cysteine cathepsins by an irreversibly locked GFP fluorophore
M. Frizler, I.V. Yampolsky, M.S. Baranov, M. Stirnberga, M. Gütschow.
Organic and Biomolecular Chemistry, 2013, 11, 5913.

Synthetic approach to GFP chromophore analogs from 3-azidocinnamates. Role of methyl rotors on the chromophore photophysics
M.S. Baranov, K.M. Solntsev, K.A. Lukyanov, I.V. Yampolsky.
Chemical Communications, 2013, 49, (51), 5778-5780.

Synthesis of the chromophores of fluorescent proteins and their analogs
Baranov M.S., Lukyanov K.A., Yampolsky I.V.
Russian Journal of Bioorganic Chemistry, 2013, 3, 223-244.

An efficient synthetic approach to fluorescent oxazole-4-carboxylate derivatives
Baranov M.S., Lukyanov K.A., IvashkinP.E., Yampolsky I.V.
Synthetic Communications, 2013, 43, 17, 2337-2342.

Novel condensations of nitroacetic esters with aromatic aldehydes leading to 5-hydroxy-1,2-oxazin-6-ones
Baranov M.S., Yampolsky I.V.
Tetrahedron Letters, 2013, 54, 7, 628-629.

2012

Unusual transformations of anthranilic acid imidazolides
Baranov M.S., Yampolsky I.V.
Chemistry of Heterocyclic Compounds, 2012, 1108-1110.

Tryptophan-based chromophore in fluorescent proteins can be anionic
Sarkisyan, K.S.; Yampolsky, I.V.; Solntsev, K.M.; et al.
Scientific reports, 2012, 2, 608.

Conformationally locked chromophores as a model of excited state proton transfer in fluorescent proteins
Baranov M.S., Lukyanov K.A., Borissova A.O., Shamir J., Kosenkov D., Slipchenko L.V., Tolbert L.M., Yampolsky I.V., Solntsev K.M.
Journal of the American Chemical Society, 2012, 134, 6025-6032.

2011 and earlier

Synthesis of Biosynthetic Precursors of Chromophores of Red Fluorescent Proteins
P.E. Ivashkin, K.A. Lukyanov, I.V. Yampolsky.
Russian Journal of Bioorganic Chemistry, 2011, 37, 411–420.

A Synthetic GFP-like Chromophore Undergoes Base-Catalyzed Autoxidation into Acylimine Red Form
Ivashkin PE, Lukyanov KA, Lukyanov S, et al.
Journal of Organic Chemistry, 2011, 76, 8, 2782-2791.

Synthesis and Properties of Chromophores of Fluorescent Proteins
P.E. Ivashkin, I.V. Yampolsky, K.A. Lukyanov.
Russian Journal of Bioorganic Chemistry, 2009, 35, 6, 652–669.

Synthesis and Spectral and Chemical Properties of the Yellow Fluorescent Protein zFP538 Chromophore
Yampolsky I.V., Balashova T.A., Lukyanov K.A.
Biochemistry, 2009, 48, 33, 8077-8082.

Green fluorescent proteins are light-induced electron donors
Bogdanov A.M., Mishin A.S., Yampolsky I.V., et al.
Nature Chemical Biology, 2009, 5, 7, 459-461.

Synthesis and properties of the red chromophore of the green-to-red photoconvertible fluorescent protein Kaede and its analogs
Yampolsky I.V., Kislukhin A.A., Amatov T.T., et al.
Bioorganic Chemistry, 2008, 36, 1-3, 96-104.

The first mutant of the Aequorea victoria green fluorescent protein that forms a red chromophore
Mishin A.S., Subach F.V., Yampolsky I.V., et al.
Biochemistry, 2008, 47, 16, 4666-4673.

Structural basis for the fast maturation of Arthropoda green fluorescent protein.
Evdokimov AG, Pokross ME, Egorov NS, et al.
EMBO reports, 2006,7,10, 1006-1012.

Synthesis and properties of the chromophore of the asFP595 Chromoprotein from Anemonia sulcata
Yampolsky I.V., Remington S.J., Martynov V.I., et al.
Biochemistry, 2005, 44, 15, 5788-5793.

New class of blue animal pigments based on Frizzled and Kringle protein domains
Bulina M.E., Lukyanov K.A., Yampolsky I.V., et al.
Journal of Biological Chemistry, 2004, 279, 42, 43367-43370.

Allylboration of functionalized isoquinolines
Pastukhov F.V., Yampolsky I.V., Bubnov Y.N.
Journal of Organometallic Chemistry, 2002, 657, 1-2, 123-128.

Allylic boron and zinc derivatives in synthesis and transformations of nitrogen heterocycles
Bubnov Y.N., Klimkina E.V., Zhun' I.V., F. V. Pastukhov, I. V. Yampolsky.
Pure and Applied Chemistry, 2000, 72, 9, 1641-1644.

A convenient synthesis of 2,2-diallylated nitrogen heterocycles by allylboration of lactams
Bubnov Y.N., Pastukhov F.V., Yampolsky I.V.
European Journal of Organic Chemistry, 2000, 8, 1503-1505.