Publications

2020

170. Leopold AV, Pletnev S, Verkhusha VV. Bacterial phytochrome as a scaffold for engineering of receptor tyrosine kinases controlled with near-infrared light. Journal of Molecular Biology 2020 Apr 14.

169. Redchuk TA, Karasev MM, Verkhusha PV, Donnelly SK, Hülsemann M, Virtanen J, Moore HM, Vartiainen MK, Hodgson L & Verkhusha VV. Optogenetic regulation of endogenous proteins. Nature Communications 2020, 11, 605.

168. Matlashov ME, Shcherbakova DM, Alvelid J, Baloban M, Pennacchietti F, Shemetov AA, Testa I, Verkhusha VV. A set of monomeric near-infrared fluorescent proteins for multicolor imaging across scales. Nature Communications 2020, 11, 239.

2019

167. Yang J, Li L, Shemetov AA, Lee S, Zhao Y, Liu Y, Shen Y, Li J, Oka Y, Verkhusha VV, Wang LV. Focusing light inside live tissue using reversibly switchable bacterial phytochrome as a genetically encoded photochromic guide star. Science Advances 2019, 1;5(12):eaay1211.

166. Leopold AV, Shcherbakova DM and Verkhusha VV. Fluorescent biosensors for neurotransmission and neuromodulation: engineering and applications. Frontiers Cell Neurosci. 2019, 13: 474.

165. Marcus J, Bejerano-Sagie M, Patterson N, Bagchi S, Verkhusha VV, Connolly D, Goldberg GL, Golden A, Sharma VP, Condeelis J, Montagna C. Septin 9 isoforms promote tumorigenesis in mammary epithelial cells by increasing migration and ECM degradation through metalloproteinase secretion at focal adhesions. Oncogene 2019, 38(30):5839-59.

164. Leopold AV, Chernov KG, Shemetov AA, Verkhusha VV. Neurotrophin receptor tyrosine kinases regulated with near-infrared light. Nature Communications 2019, 10(1):1129.

163. Karasev MM, Stepanenko OV, Rumyantsev KA, Turoverov KK, and Verkhusha VV. Near-Infrared Fluorescent Proteins and Their Applications. Biochemistry (Moscow) 2019, 84: S32-S50.

162. Buhrke D, Tavraz NN, Shcherbakova DM, Sauthof L, Moldenhauer M, Escobar FV, Verkhusha VV, Hildebrandt P, Friedrich T. Chromophore binding to two cysteines increases quantum yield of near-infrared fluorescent proteins. Scientific reports 2019, 9(1):1866.

161. Oliinyk OS, Shemetov AA, Pletnev S, Shcherbakova DM, Verkhusha VV. Smallest near-infrared fluorescent protein evolved from cyanobacteriochrome as versatile tag for spectral multiplexing. Nature Communications 2019, 10(1):279.

2018

160. Peng Q, Lu S, Shi Y, Pan Y, Limsakul P, Chernov AV, Qiu J, Chai X, Shi Y, Wang P, Ji Y. Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors. Proceedings of the National Academy of Sciences 2018, 115(50):E11681-90.

159. Kaberniuk AA, Mohr MA, Verkhusha VV, Snapp EL. moxMaple3: a Photoswitchable Fluorescent Protein for PALM and Protein Highlighting in Oxidizing Cellular Environments. Scientific reports 2018; 8(1):14738.

158. Liu W, Shcherbakova DM, Kurupassery N, Li Y, Zhou Q, Verkhusha VV, Yao J. Quad-mode functional and molecular photoacoustic microscopy. Scientific reports 2018, 8(1):11123.

157. Pennacchietti F, Serebrovskaya EO, Faro AR, Shemyakina II, Bozhanova NG, Kotlobay AA, Gurskaya NG, Bodén A, Dreier J, Chudakov DM, Lukyanov KA. Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy. Nature methods 2018, 15(8):601.

156. Liu W, Shcherbakova DM, Kurupassery N, Li Y, Zhou Q, Verkhusha VV, Yao J. Quad-mode functional and molecular photoacoustic microscopy. Scientific reports 2018, 8(1):11123.

155. Shcherbakova DM, Stepanenko OV, Turoverov KK, Verkhusha VV. Near-Infrared Fluorescent Proteins: Multiplexing and Optogenetics across Scales. Trends in Biotechnology 2018, 36(12): 1230-1243.

154. Li L, Shemetov AA, Baloban M, Hu P, Zhu L, Shcherbakova DM, Zhang R, Shi J, Yao J, Wang LV, Verkhusha VV. Small near-infrared photochromic protein for photoacoustic multi-contrast imaging and detection of protein interactions in vivo. Nature communications 2018, 9(1):2734.

153. Shcherbakova DM, Kaberniuk AA, Redchuk TA, Verkhusha VV. Engineering of Bacterial Phytochromes for Near-Infrared Imaging, Sensing and Light-Control in Mammals. Biophysical Journal 2018, 114(3):401a.

152. Redchuk TA, Karasev MM, Omelina ES, Verkhusha VV. Near‐Infrared Light‐Controlled Gene Expression and Protein Targeting in Neurons and Non‐neuronal Cells. ChemBioChem 2018, 19(12):1334-40.

151. Redchuk TA, Kaberniuk AA, Verkhusha VV. Near-infrared light-controlled systems for gene transcription regulation, protein targeting and spectral multiplexing. Nature Protocols 2018, 13: 1121-1136.

150. Shcherbakova DM, Cammer NC, Huisman TM, Verkhusha VV, Hodgson L. Direct multiplex imaging and optogenetics of Rho GTPases enabled by near-infrared FRET. Nature Chem. Biol. 2018, 14: 591-600 

149. Leopold A.V., Chernov K.G. and Verkhusha V.V. Optogenetically controlled protein kinases for regulation of cellular signaling. Chem. Soc. Rev. 2018, 47(7), 2454-2484

2017

148. Piatkevich K.D., Suk H.-J., Kodandaramaiah S.B., Yoshida F., DeGennaro E.M., Drobizhev M., Hughes T.E., Desimone R., Boyden E.S. and Verkhusha V.V. Near-infrared fluorescence proteins engineered from bacterial photochromes in neuroimaging. Biophys. J. 2017, 113(10), 2299-2309.

147. Oliinyk O.S., Chernov K.G. and Verkhusha V.V. Bacterial phytochromes, cyanobacteriochromes and allophycocyanins as a source of near-infrared fluorescent probes. Intl. J. Mol. Sci. 2017, 18: 1691.

146. Zanca C., Villa G., Benitez J., Thorne A.H., Koga T., Verkhusha V.V., Mischel P., Cavenee W., and Furnari F. Glioblastoma cellular cross-talk converges on NF-κB to attenuate EGFR inhibitor sensitivity Genes & Development 2017, 31(12), 1212-1227.

145. Shemetov A.A., Oliinyk, O.S., and Verkhusha V.V. How to increase brightness of near-infrared fluorescent proteins in mammalian cells. Cell Chem. Biol. 2017, 24: 758–766.

144. Baloban M., Shcherbakova D.M., Pletnev S., Pletnev V.Z. Lagarias J.C., and Verkhusha V.V. Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies. Chem. Science 2017, 8: 4546-4557.

143. Chernov K.G., Redchuk T.A., Omelina E.S., and Verkhusha V.V. Near-infrared fluorescent proteins, biosensors and optogenetic tools engineered from phytochromes. Chem. Reviews 2017, 117: 6423-6446.

142. Chernov K.G., Neuvonen M., Brock I.I., Ikonen E.M., and Verkhusha V.V. Introducing inducible fluorescent split cholesterol oxidase to mammalian cells. J. Biol. Chem. 2017, 292: 8811-8822.

141. Redchuk T.A., Omelina E.S., Chernov K.G., and Verkhusha V.V. Near-infrared optogenetic pair for protein regulation and spectral multiplexing. Nature Chem. Biol. 2017, 13: 633-639.

140. Stepanenko O.V., Stepanenko O.V., Kuznetsova I.M., Shcherbakova D.M., Verkhusha V.V. and Turoverov K.K. Interaction of biliverdin chromophore with near-infrared fluorescent protein BphP1-FP engineered from bacterial phytochrome. Intl. J. Mol. Sci., 2017, 18: 1009.

139. Kaberniuk A.A., Morano N., Verkhusha V.V., and Snapp E.L. moxDendra2: an inert photoswitchable protein for oxidizing environments. Chem. Communications 2017, 53: 2106-2109. 

138. Stepanenko O.V., Bublikov G.S., Kuznetsova I.M., Verkhusha V.V., and Turoverov K.K. Stabilization of structure in near-infrared fluorescent proteins by binding of biliverdin chromophore. J. Mol. Struct. 2017, 1140: 22-31.

137. Fluegen G., Avivar-Valderas A., Wang Y., Padgen M.R., Williams J.K., Verkhusha V., Cheung J.F., Entenberg D., Castracane J., Keely P., Condeelis J., and Aguirre-Ghiso J. Phenotypic heterogeneity of disseminated tumour cells is preset by primary tumour hypoxic microenvironments. Nature Cell Biol. 2017, 19: 120-132.

2016

136. Lychagov V.V., Shemetov A.A., Jimenez R., and Verkhusha V.V. Microfluidic system for in-flow reversible photoswitching of near-infrared fluorescent proteins. Analytical Chemistry 2016, 88: 11821-11829.

135. Hontani Y., Shcherbakova D.M., Baloban M., Zhu J., Verkhusha V.V. and Kennis J.T.M. Bright blue-shifted fluorescent proteins with Cys in GAF domain engineered from bacterial phytochromes: fluorescence mechanisms and excited-state dynamics. Sci. Reports 2016, 6: 37362.

134. Rumyantsev K.A., Turoverov K.K., and Verkhusha V.V. Near-infrared bioluminescent proteins for two-color multimodal imaging. Sci. Reports 2016, 6: 36588.

133. Yao J., Kaberniuk A.A., Li L., Shcherbakova D.M., Zhang R., Wang L., Li G., Verkhusha V.V. and Wang L.H. Multiscale photoacoustic tomography using reversibly switchable bacterial phytochrome as a near-infrared photochromic probe. Nature Methods 2016, 13: 67-73.

132. Shcherbakova D.M., Baloban M., Emelyanov A.V., Brenowitz M., Guo P. and Verkhusha V.V. Bright monomeric near-infrared fluorescent proteins as tags and biosensors for multiscale imagingNature Communications 2016, 7: 12405.

131. Konold P.E., Yoon E., Lee J., Chapagain P.P., Gerstman B.S., Regmi C.K., Piatketvich K.D., Verkhusha V.V., Joo T. and Jimenez R.Fluorescence from multiple chromophore hydrogen-bonding states in the far-red protein TagRFP675J. Phys. Chem. Lett. 2016, 7: 3046-3051.

130. Kaberniuk A.A., Shemetov A.A. and Verkhusha V.V. A bacterial phytochrome-based optogenetic system controllable with near-infrared lightNature Methods 2016, 13: 591-597.

129. Champa D., Orlacchio A., Patel B., Ranieri M., Shemetov A.A., Verkhusha V.V., Cuervo A.M. and Cristofano A.D. Obatoclax kills anaplastic thyroid cancer cells by inducing lysosome neutralization and necrosisOncotarget 2016, 7: 34453-34471.

128. Stepanenko O.V., Baloban M., Bublikov G.S., Shcherbakova D.M., Stepanenko O.V., Turoverov K.K., Kuznetsova I.M. and Verkhusha V.V. Allosteric effects of chromophore interaction with dimeric near-infrared fluorescent proteins engineered from bacterial phytochromes. Scientific Reports 2016, 6: 18750. doi: 10.1038/srep18750

2015 

127. Rumyantsev K.A., Shcherbakova D.M., Zakharova N.I., Emelyanov A.V., Turoverov K.K. and Verkhusha V.V. Minimal domain of bacterial phytochrome required for chromophore binding and fluorescenceScientific Reports 2015, 5: 18348. doi: 10.1038/srep18348

126. 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 proteinsChemistry & Biology 2015, 22: 1540–1551. 

125. Yao J., Kaberniuk A.A., Li L., Shcherbakova D.M., Zhang R., Wang L., Li G., Verkhusha V.V. and Wang L.V. Multiscale photoacoustic tomography using reversibly switchable bacterial phytochrome as a near-infrared photochromic probeNature Methods 2015, in press (published online on Nov. 9). Co-first and co-senior authorship paper

124. Zhu J., Shcherbakova D.M., Hontani Y., Verkhusha V.V. and Kennis J.T.M. Ultrafast excited-state dynamics and fluorescence deactivation of near-infrared fluorescent proteins engineered from bacteriophytochromesScientific Reports 2015, 5: 12840. doi: 10.1038/srep12840. 

123. Costantini L.M., Baloban M., Markwardt M.L., Rizzo M., Guo F., Verkhusha V.V. and Snapp E.L. A palette of fluorescent proteins optimized for diverse cellular environmentsNature Communications 2015, 6: 7670 doi:10.1038/ncomms8670. 

122. Shcherbakova D.M., Baloban M. and Verkhusha V.V. Near-infrared fluorescent proteins engineered from bacterial phytochromesCurr. Opin. Chem. Biol. 2015, 27: 52–63. 

121. Shcherbakova D.M., Shemetov A.A., Kaberniuk A.A. and Verkhusha V.V.. Natural photoreceptors as a source of fluorescent proteins, biosensors, and optogenetic toolsAnnu. Rev. Biochem. 2015, 84: 519-550. 

120. Telford W.G., Shcherbakova D.M., Buschke D., Hawley T.S. and Verkhusha V.V.. Multiparametric flow cytometry using near-infrared fluorescent proteins engineered from bacterial phytochromesPLoS ONE 2015, 10: e0122342. doi:10.1371/journal.pone.0122342 

119. Rice W.L., Shcherbakova D.M., Verkhusha V.V. and Kumar A.T.N. In vivo tomographic imaging of deep-seated cancer using fluorescence lifetime contrastCancer Res. 2015, 75: 1236-1243 

2014 

118. Stepanenko Olesya V., Stepanenko Olga V., Kuznetsova I.M., Verkhusha V.V. and Turoverov K.K.  Sensitivity of superfolder GFP to ionic agentsPLoS ONE 2014, 9: e110750. doi:10.1371/journal.pone.0110750 

117. Piatkevich K.D., English B.P., Malashkevich V.N., Xiao H., Almo S.C., Singer R.H. and Verkhusha V.V.  Photoswitchable red fluorescent protein with a large Stokes shiftChemistry & Biology. 2014, 21: 1402-1414. 

116. Yao J., Shcherbakova D.M., Li C., Krumholz A., Lorca R.A., Reinl E., England S.K., Verkhusha V.V. and Wang L.V.  Reversibly switchable fluorescence microscopy with enhanced resolution and image contrastJ. Biomed. Opt. 2014, 19: 086018. 

115. Pletnev S., Shcherbakova D.M., Subach O.M., Pletneva N.V., Malashkevich V.N., Almo S.C., Dauter Z. and Verkhusha V.V.  Orange fluorescent proteins: structural studies of LSSmOrange, PSmOrange and PSmOrange2PLoS ONE 2014, 9: e99136. doi:10.1371/journal.pone.0099136

114. Nedosekin D.A., Verkhusha V.V. Melerzanov A.V., Zharov V.P. and Galanzha E.I.  In vivo photoswitchable flow cytometry for direct tracking of single circulating tumor cellsChemistry & Biology. 2014, 21: 792-801.

113. Denisova O.V., Söderholm S., Virtanen S., … Verkhusha V.V. and and Kainov D.E.  Akt inhibitor MK2206 prevents influenza pH1N1 virus infection in vitroAntimicrob. Agents Chemother. 2014, 58: 3689-3696

112. Shcherbakova D.M., Sengupta P., Lippincott-Schwartz J. and Verkhusha V.V. Photocontrollable fluorescent proteins for superresolution imagingAnnu. Rev. Biophys.2014, 43: 303-329.

111. Shcherbakova D.M. and Verkhusha V.V. Chromophore chemistry of fluorescent proteins controlled by lightCurr. Opin. Chem. Biol. 2014, 20: 60-68.

110. Stepanenko Olesya V., Bublikov G.S., Stepanenko Olga V., Shcherbakova D.M., Verkhusha V.V., Turoverov K.K. and Kuznetsova I.M. A knot in the protein structure – probing the near-infrared fluorescent protein iRFP designed from a bacterial phytochromeFEBS Journal. 2014, 281:2284-2298.

109. Krumholz A., Shcherbakova D.M., Xia, J., Wang L.V. and Verkhusha V.V. Multicontrast photoacoustic in vivo imaging using near-infrared fluorescent proteinsScientific Reports 2014, 4: 3939. doi:10.1038/srep03939

108. Pletnev S., Subach F.V., Verkhusha V.V. and Dauter Z. The rotational order-disorder structure of the reversibly photoswitchable red fluorescent protein rsTagRFPActa Crystallogr. D2014, 70: 31-39.

107. Galanzha E.I., Nedosekin D.A., Sarimollaoglu M., Orza A.I., Biris A.S., Verkhusha V.V. and Zharov V.P. Photoacoustic and photothermal cytometry using photoswitchable proteins and nanoparticles with ultrasharp resonancesJ. Biophotonics 2014, 7: in press. doi: 10.1002/jbio.201300140.

 2013

106. Filonov G. S. and Verkhusha V.V. A near-infrared BiFC reporter for in vivo imaging of protein-protein interactionsChemistry & Biology 2013, 20: 1078-1086.

105. Hartwich T.M., Subach F.V., Cooley L., Verkhusha V.V. and Bewersdorf J. Determination of two-photon photoactivation rates of fluorescent proteinsPhys. Chem. Chem. Phys. 2013, 15: 14868-14872.

104. Piatkevich, K.D., Subach F.V. and Verkhusha V.V. Far-red light photoactivatable near-infrared fluorescent proteins engineered from a bacterial phytochrome. Nature Communications2013, 4: 2153 doi:10.1038/ncomms3153.

103. Shcherbakova D.M. and Verkhusha V.V. Near-infrared fluorescent proteins for multicolor in vivo imagingNature Methods 2013, 10: 751-754. 

102. Piatkevich K.D., Malashkevich V.N., Morozova K.S., Nemkovich N.A., Almo S.C. and Verkhusha V.V. Extended Stokes shift in fluorescent proteins: chromophore - protein interactions in a near-infrared TagRFP675 variantScientific Reports 2013, 3: 1847. doi:10.1038/srep01847. 

101. Piatkevich K.D., Subach F.V. and Verkhusha V.V. Engineering of bacterial phytochromes for near-infrared imaging, sensing, and light-control in mammalsChem. Soc. Rev. 2013,42:3441-3452. 

100. Stepanenko Olesya V., Stepanenko Olga V., Kuznetsova I.M., Verkhusha V.V. and Turoverov K.K. Beta-barrel scaffold of fluorescent proteins: folding, stability and role in chromophore formationInt. Rev. Cell Mol. Biol. 2013, 302: 221-278. 

99. Costantini L.M., Subach O.M., Jaureguiberry-bravo M., Verkhusha V.V. and Snapp E.L. Cysteineless non-glycosylated monomeric blue fluorescent protein, secBFP2, for studies in the eukaryotic secretory pathwayBiochem. Biophys. Res. Commun. 2013, 430: 1114–1119. 

2012

98. Telford W.G., Hawley T.,Subach F., Verkhusha V.V. and Hawley R.G. Flow cytometry of fluorescent proteinsMethods 2012, 56: 318-330. 

97. Stepanenko Olesya V. Stepanenko Olga V., Kuznetsova I.M., Shcherbakova D.M.,Verkhusha V.V. and Turoverov K.K. Distinct effects of guanidine thiocyanate on the structure of superfolder GFPPLoS ONE 2012, 7: e48809. doi: 10.1371/journal.pone.0048809.  

96 . Miyawaki A., Shcherbakova D.M. and Verkhusha V.V..Red fluorescent proteins: chromophore formation and cellular applicationsCurr. Opin. Struct. Biol. 2012, 22: 679-688. 

95. Salomonnson E., Mihalko L.A.,Verkhusha V.V. , Luker K.E. and Luker G.D. Cell-based and in vivo spectral analysis of fluorescent proteins for multiphoton microscopyJ. Biomed. Opt.2012, 17: 96001. 

94. Nedosekin D.A., Sarimollaoglu M., Galanzha E.I., Sawant R., Torchilin V.P.,Verkhusha V.V. , Ma J., Frank M.H., Biris A.S. and Zharov V.P. Synergy of photoacoustic and fluorescence flow cytometry of circulating cells with negative and positive contrastsJ. Biophotonics, 2013, 6: 425-434. 

93. Subach O.M., Entenberg D., Condeelis J.S. and Verkhusha V.V. A FRET-facilitated photoswitching using an orange fluorescent protein with the fast photoconversion kineticsJ. Am. Chem. Soc. 2012, 134: 14789-14799.

92. Shcherbakova D.M., Subach O.M. and Verkhusha V.V. Red fluorescent proteins: advanced imaging applications and future designAngew. Chem. Int. Ed. 2012, 51: 10724-10738.

91. Subach F.M. and Verkhusha V.V. Chromophore transformations in red fluorescent proteinsChemical Reviews 2012, 112: 4308-4327.

90. Shcherbakova D.M., Hink M.A., Joosen L., Gadella T.W.J. and Verkhusha V.V. An orange fluorescent protein with a large Stokes shift for single-excitation multicolor FCCS and FRET imagingJ. Am. Chem. Soc., 2012, 134: 7913-7923.

89. Pletnev S., Subach F.V., Dauter Z., Wlodawer A. and Verkhusha V.V. A structural basis for reversible photoswitching of absorbance spectra in red fluorescent protein rsTagRFPJ. Mol. Biol., 2012, 417: 144-151.

88. Bravaya K.B., Subach O.M., Verkhusha V.V. and Krylov A.I. Insight into the common mechanism of the chromophore formation in the red fluorescent proteins: the elusive blue intermediate revealedJ. Am. Chem. Soc. 2012, 134: 2807-2814.

87. Filonov G.S., Krumholz A., Xia J., Yao J., Wang L.V. and Verkhusha V.V. Deep-tissue photoacoustic tomography of a genetically encoded near-infrared fluorescent probeAngew. Chem. Int. Ed. 2012, 51: 1448-1451.

2011

86. Subach O.M, Cranfill P.J., Davidson W.M. and Verkhusha V.V. An enhanced monomeric blue fluorescent protein with the high chemical stability of the chromophorePLoS ONE 2011, 6: e28674. doi:10.1371/journal.pone.0028674 

85. Subach F.V., Piatkevich K.D. and Verkhusha V.V. Directed molecular evolution to design advanced red fluorescent proteinsNature Methods 2011, 8: 1019-1026.

84. Stepanenko Olesya V., Stepanenko Olga V., Shcherbakova D.M., Kuznetsova I.M., Turoverov K.K., and Verkhusha V.V. Modern fluorescent proteins: from chromophore formation to novel intracellular applicationsBioTechniques. 2011, 51: 313-327.

83. Gunewardene M.S., Subach F.V., Gould T.J., Penoncello G.P., Gudheti M.V., Verkhusha V.V. and Hess S.T. Superresolution imaging of multiple fluorescent proteins with highly overlapping emission spectra in living cellsBiophys. J. 2011, 101: 1522-1528. 

82. Entenberg D., Wyckoff J., Gligorijevic B., Roussos E., Verkhusha V.V. Pollard J.W. and Condeelis J. Setup and use of a two-laser multiphoton microscope for multichannel intravital fluorescence imagingNature Protocols. 2011, 6: 1500-1520. 

81. Subach O.M., Patterson G.H., Ting L.-M., Wang Y., Condeelis J.S. and Verkhusha V.V. A photoswitchable orange-to-far-red fluorescent protein, PSmOrangeNature Methods. 2011, 8: 771-777. 

80. Filonov G.S., Piatkevich K.D., Ting L.-M., Zhang J., Kim K. and Verkhusha V.V. Bright and stable near infra-red fluorescent protein for in vivo imagingNature Biotechnology. 2011, 29: 757-761. 

79. Stepanenko O.V., Fonin A.V., Stepanenko O.V., Morozova K.M., Verkhusha V.V., Kuznetsova I.M., Turoverov K.K., Staiano M. and D'Auria S. New insight in protein-ligand interactions. 2. Stability and properties of two mutant forms of the d-galactose/d-glucose-binding protein from E. coliJ. Phys. Chem. B. 2011, 115: 9022-9032.  

78. Koga H., Martinez-Vicente M., Macian F., Verkhusha V.V. and Cuervo A.M. A photoconvertible fluorescent reporter to track chaperone-mediated autophagyNature Communications. 2011, 2: 386 doi: 10.1038/ncomms1393. 

77. Gudkov D.A., Lyagin I.V., Verkhusha V.V. and Efremenko E.N. Hybrid proteins with organophosphorous hydrolase activity and fluorescence of deGFP4 proteinMoscow Univ. Chem. Bull., 2011, 66: 92–98. 

76. Piatkevich K.D. and Verkhusha V.V. Guide to red fluorescent proteins and biosensors for flow cytometry.Methods Cell Biol., 2011, 104: 431-461.

75. Wu B., Piatkevich K.D., Lionnet T., Singer R.H., and Verkhusha V.V. Modern fluorescent proteins and imaging technologies to study gene expression, nuclear localization, and dynamicsCurr. Opin. Cell Biol., 2011, 23: 310-317.

2010

74. Stepanenko O.V., Kuznetsova I.M., Kuznetsova I.M., Verkhusha V.V., Staiano M.,D’Auria S., and Turoverov K.K. Denaturation of proteins with beta-barrel topology induced by guanidine hydrochlorideSpectrosc. Int. J. , 2010, 24: 367-373. 

73. Piatkevich K.D., Malashkevich V.N., Almo S.C., and Verkhusha V.V. Engineering ESPT pathways based on structural analysis of LSSmKate red fluorescent proteins with large Stokes shiftJ. Am. Chem. Soc. 2010, 132: 10762–10770.

72. Subach F.V., Zhang L., Gadella T.W.J., Gurskaya N.G., Lukyanov K.A., and Verkhusha V.V.Red fluorescent protein with reversibly photoswitchable absorbance for photochromic FRETChemistry & Biology (Cell press). 2010, 17: 745-755.

71. Morozova K.S., Piatkevich K.D., Gould T.G., Zhang J., Bewersdorf J., and Verkhusha V.V.Far-Red fluorescent protein excitable with red lasers for flow cytometry and super-resolution STED nanoscopyBiophys. J. 2010, 99: L13-L15.

70. Piatkevich K.D., Efremenko E.N., Verkhusha V.V., and Varfolomeev S.D. Red fluorescent proteins and their propertiesRuss. Chem. Rev. 2010, 79: 243-258.

69. Subach F.M., Patterson G.H., Renz M., Lippincott-Schwartz J., and Verkhusha V.V. Bright monomeric photoactivatable red fluorescent protein for two-color super-resolution sptPALM of live cellsJ. Am. Chem. Soc. 2010, 132: 6481-6491.

68. Subach O.M., Malashkevich V.N., Zencheck W.D., Morozova K.S., Piatkevich K.D., Almo S.C., and Verkhusha V.V. Structural characterization of acylimine-containing blue and red chromophores in mTagBFP and TagRFP fluorescent proteinsChemistry & Biology (Cell press).2010, 17: 333-341.

67. Piatkevich K.D., Hulit J., Subach O.M., Wu B., Abdulla A., Segall J.E., and Verkhusha V.V.Monomeric red fluorescent proteins with a large Stokes shift. Proc. Natl. Acad. Sci. USA 2010, 107: 5369-5374.

66. Pletnev S., Subach F.V., Dauter Z., Wlodawer A., and Verkhusha V.V. Understanding blue-to-red conversion in monomeric fluorescent timers and hydrolytic degradation of their chromophoresJ. Am. Chem. Soc. 2010, 132: 2243-2253.

65. Piatkevich K.D. and Verkhusha V.V. Advances in engineering of fluorescent proteins and photoactivatable proteins with red emission. Curr. Opin. Chem. Biol. 2010, 14: 23-29.

2009

64. Subach F.V., Malashkevich V.N., Zencheck W.D., Xiao H., Filonov G.S., Almo S.C., and Verkhusha V.V. Photoactivation mechanism of PAmCherry based on crystal structures of the protein in the dark and fluorescent statesProc. Natl. Acad. Sci. USA 2009, 106: 21097-21102.  

63. Pletnev S., Morozova K.S., Verkhusha V.V., and Dauter Z. Rotational order-disorder structure of fluorescent protein FP480. Acta Crystallogr. D 2009, 65: 906-912.

62. He J., Vora M., Haney R.M., Filonov G.S., Musselman C.A., Burd C.G., Kutateladze A.G., Verkhusha V.V., Stahelin R.V., and Kutateladze T.G. Membrane insertion of the FYVE domain is modulated by pH. Proteins. 2009, 76: 852-860.

61. Bogdanov A.M., Mishin A.S., Yampolsky I.V., Belousov V.V., Chudakov D.M., Subach F.V., Verkhusha V.V., Lukyanov S., and Lukyanov K.A. Green fluorescent proteins are light-induced electron donorsNature Chemical Biology. 2009, 5: 459-461.

60. Shcherbo D., Murphy C.S., Ermakova G.V., Solovieva E.A., Chepurnykh T.V., Shcheglov A.S., Verkhusha V.V., Pletnev V.Z., Hazelwood K.L., Roche P.M., Lukyanov S., Zaraisky A.G., Davidson M.W., and Chudakov D.M. Far-red fluorescent tags for protein imaging in living tissuesBiochem. J. 2009, 418: 567-574.

59. Gould T.J., Verkhusha V.V., and Hess S.T. Imaging biological structures with fluorescence photoactivation localization microscopyNature Protocols2009, 4: 291-308.

58. Subach F.V., Patterson G.H., Manley S., Gillette J.M., Lippincott-Schwartz J., and Verkhusha V.V. Photoactivatable mCherry for high-resolution two-color fluorescence microscopyNature Methods. 2009, 6: 153-159.

57. Telford W.G., Subach F.V., and Verkhusha V.V. Supercontinuum white light lasers for flow cytometryCytometry2009, 75A: 450-459.

56. Subach F.V., Subach O.M., Gundorov I.S., Morozova K.S., Piatkevich K.D., Cuervo A.M., and Verkhusha V.V. Monomeric fluorescent timers that change color from blue to red report on cellular trafficking. Nature Chemical Biology2009, 5: 118-126.

2008

55. Lyagin I., Gudkov D., Verkhusha V., and Efremenko E. Genetic construct encoding the biosynthesis of N-His6-e-pHluorins-OPH in E.coli cells. In book: Chemical and Biochemical Physics, Kinetics and Thermodynamics: New Perspectives. (Scott P.E., Zaikov G.E., and Kablov V.F., Eds.), 2008, 83-90. Nova Science Publishers, NY, ISBN 1-60456-024-X.

54. Gould T.J., Gunewardene M.S., Gudheti M.V., Verkhusha V.V., Yin S.R., Gosse J.A., and Hess S.T. Nanoscale imaging of molecular positions and anisotropiesNature Methods. 2008,5: 1027-1030.

53. Kedrin D., Gligorijevic B., Wyckoff J., Verkhusha V.V., Condeelis J., Segall J.E., and van Rheenen J. Intravital imaging of metastatic behavior through a mammary imaging windowNature Methods. 2008, 5: 1019-1021.

52. Stepanenko O.V., Verkhusha V.V., Kuznetsova I.M., Uversky V.N., and Turoverov К.К. Fluorescent proteins as biomarkers and biosensors: throwing color lights on molecular and cellular processesCurr. Protein Pept. Sci. 2008, 9: 338-369.

51. Subach O.M., Gundorov I.S., Yoshimura M., Subach F.V., Zhang J., Grüenwald G., Souslova E.A., Chudakov D.M., and Verkhusha V.V. Conversion of red fluorescent protein into a bright blue probeChemistry & Biology (Cell press). 2008, 15: 1116-1124.

50. Stepanenko O.V., Verkhusha V.V., Shavlovsky M.M., Kuznetsova I.M., Uversky V.N., and Turoverov K.K. Understanding the role of Arg96 in structure and stability of green fluorescent proteinProteins. 2008, 73: 539-551.

49. He J., Haney R.M., Vora M., Verkhusha V.V., Stahelin R.V., and Kutateladze T.G. Molecular mechanism of membrane targeting by the GRP1 PH domainJ. Lipid Res. 2008, 49, 1807-1815.

48. Pena P.V., Hom R.A., Hung T., Lin H., Kuo A.J., Wong R.P.C., Subach O.M., Champagne K.S., Zhao R., Verkhusha V.V., Li G., Gozani O., and Kutateladze T.G. Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor. J. Mol. Biol. 2008, 380: 303-312.

47. Kapoor V., Karpov V., Linton C., Subach F.V., Verkhusha V.V., and Telford W.G. Solid state yellow and orange lasers for flow cytometryCytometry. 2008, 73A: 570-577.

46. Mishin A.S., Subach F.V., Yampolsky I.V., King W., Lukyanov K.A., and Verkhusha V.V.* The first mutant of the Aequorea victoria green fluorescent protein that forms a red chromophoreBiochemsitry. 2008, 47: 4666-4673. *Corresponding author

2007

45. Stepanenko O.V., Verkhusha V.V., Kuznetsova I.M., and Turoverov K.K. Fluorescent proteins: physical-chemical properties and application in cell biologyCytology2007, 49, 395-420.

44. Hom R.A, Vora M., Regner M., Subach O.M., Cho W., Verkhusha V.V., Stahelin R.V., and Kutateladze T.G. pH-dependent binding of the epsin ENTH domain and the AP180 ANTH domain to PI(4,5)P2-containing bilayersJ. Mol. Biol. 2007, 373, 412-423.

43. Kapoor V., Subach F.V., Kozlov V.G., Grudinin A., Verkhusha V.V., and Telford W.G. New lasers for flow cytometry: filling the gapsNature Methods. 2007, 4, 678-679.

42. Nevzglyadova O.V., Artemov A.V., Zenin V.V., Verkhusha V.V., Shavlovsky M.M., Povarova O.I., Stepanenko O.V., Kuznetsova I.M., and Turoverov K.K. Expression of recombinant actin 5C from Drosophila in the methylotrophic yeast Pichia pastorisCell Tissue Biol2007, 1, 248-258.

2006

41. Pena P.V., Davrazou F., Shi X., Walter K., Verkhusha V.V., Gozani O., Zhao R., and Kutateladze T.G. Molecular mechanism of histone H3K4Me3 recognition by plant homeodomain of ING2Nature. 2006, 442, 100-103.

40. Gurskaya N.G., Verkhusha V.V., Shcheglov A.S., Staroverov D.B., Chepurnykh T.V., Fradkov A.F., Lukyanov S., and Lukyanov K.A. Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue lightNature Biotechnol. 2006, 24: 461-465.

2005

39. Lukyanov K.A., Chudakov D.M., Lukyanov S., and Verkhusha V.V.* Photoactivatable fluorescent proteinsNature Rev. Mol. Cell Biol. 2005, 6: 885-891. *Corresponding author

38. Lee S.A., Eyeson R., Cheever M.L., Geng J., Verkhusha V.V., Burd C., Overduin M., and Kutateladze T.G. Targeting of the FYVE domain to endosomal membranes is regulated by a histidine switchProc. Natl. Acad. Sci. USA. 2005, 102, 13052-13057.

37. Stepanenko O.V., Verkhusha V.V., Shavlovsky M.M., Aleinikova T.D., Uversky V.N., Kuznetsova I.M., and Turoverov K.K. The role of quaternary structure in fluorescent protein stabilityCytology2005, 47, 1017-1027.

36. Verkhusha V.V.,* and Sorkin A. Conversion of the monomeric red fluorescent protein into a photoactivatable probeChemistry & Biology (Cell press). 2005, 12, 279-285.*Corresponding author

2004

35. Stepanenko O.V., Verkhusha V.V., Kazakov V.I., Shavlovsky M.M., Kuznetsova I.M., Uversky V.N., and Turoverov K.K. Comparative studies on the structure and stability of fluorescent proteins EGFP, zFP506, mRFP1, dimer2 and DsRedBiochemistry. 2004, 43, 14913-14923.

34. Galperin E.#, Verkhusha V.V.,# and Sorkin A. Three-chromophore FRET microscopy to analyze multiprotein interactions in living cellsNature Methods. 2004, 1, 209-217. #Co-first author

33. Chudakov D.M.#, Verkhusha V.V.#, Staroverov D.B., Lukyanov S., and Lukyanov K.A. Photo-switchable fluorescent label for protein trackingNature Biotechnol. 2004, 22, 1435-1439. #Co-first author

32. Verkhusha V.V., Chudakov D.M., Gurskaya N.G., Lukyanov S., and Lukyanov K.A. Common pathway for the red chromophore formation in the fluorescent proteins and chromoproteinsChemistry & Biology (Cell press).2004, 11, 845-854.

31. Verkhusha V.V.*, and Lukyanov K.A. The molecular properties and applications of Anthozoa fluorescent proteins and chromoproteinsNature Biotechnol. 2004, 22, 289-296. *Corresponding author

2003

30. Verkhusha V.V.*, Pozhitkov A.E., Smirnov S.A., Borst J.W., van Hoek A., Klyachko N.L., Levashov A.V., and Visser A.J. Effect of high pressure and reversed micelles on the fluorescent proteinsBiochim. Biophys. Acta. 2003, 1622, 192-195. *Corresponding author

29. Verkhusha V.V.*, Kuznetsova I.M., Stepanenko O.V., Zaraisky A.G., Shavlovsky M.M., Turoverov K.K., and Uversky V.N. High stability of Discosoma DsRed as compared to Aequorea EGFPBiochemistry. 2003, 42, 7879-7884. *Corresponding author

28. Bulina M.E.#, Verkhusha V.V.#, Staroverov D.B., Chudakov D.M., and Lukyanov K.A. Heterooligomeric tagging diminishes non-specific aggregation of target proteins fused with Anthozoa fluorescent proteinsBiochem. J. 2003, 371, 109-114. #Co-first author

27. Verkhusha V.V., Shavlovsky M.M., Nevzglyadova O.V., Gaivoronsky A.A., Artemov A.V., Stepanenko O.V., Kuznetsova I.M., and Turoverov K.K. Expression of recombinant GFP-actin fusion protein in the methylotrophic yeast P.pastorisFEMS Yeast Res. 2003, 3, 105-111.

26. Verkhusha V.V.*, Matz M.V., Sakurai T., and Lukyanov K.A. GFP-like fluorescent proteins and chromoproteins of class Anthozoa. In book: Protein Structures: Kaleidoscope of Structural Properties and Functions. (Uversky V.N, Ed.). 2003, 405-439. Research Signpost Publishers. ISBN 81-7736-1775. *Corresponding author

2002

25. Kuznetsova I.M., Stepanenko O.V., Stepanenko O.V., Povarova O.I., Biktashev A.G, Verkhusha V.V., Shavlovsky M.M., and Turoverov K.K. The place of inactivated actin and its kinetic predecessor in actin folding-unfoldingBiochemistry. 2002, 41, 13127-13132.

24. Fradkov A.F., Verkhusha V.V., Staroverov D.B., Bulina M.E., Yanushevich Y.G., Martynov V.I., Lukyanov S., and Lukyanov K.A. Far-red fluorescent tag for protein labellingBiochem. J. 2002, 368, 17-21.

23. Turoverov K.K., Verkhusha V.V., Shavlovsky M.M., Biktashev A.G., Povarova O.I., and Kuznetsova I.M. Kinetics of actin unfolding induced by guanidine hydrochlorideBiochemistry.2002, 41, 1014-1019.

2001

22. Verkhusha V.V.*, Akovbian N.A., Efremenko E.N., Varfolomeyev S.D., and Vrzheshch P.V. The kinetic analysis of maturation and denaturation of DsRed, a coral-derived red fluorescent proteinBiochemistry (Mosc)2001, 66, 342-1351. *Corresponding author

21. Verkhusha V.V.*, Otsuna H., Awasaki T., Oda H., Tsukita S., and Ito K. An enhanced mutant of red fluorescent protein DsRed for double labeling and developmental timer of neural fiber bundle formationJ. Biol. Chem. 2001, 276, 29621­29624. *Corresponding author

1990 - 2000

20. Vrzheshch P.V.#, Abovikyan N.A., Varfolomeyev S.D., and Verkhusha V.V. # Denaturation and partial renaturation of a tightly tetramerized DsRed protein under mildly acidic conditionsFEBS Letters. 2000, 487, 203-208. #Co-first author

19. Varfolomeyev, S.D., Efremenko, A.I., Verkhusha, V.V., and Vrzheshch, P.V. Synthetic amino acid analogues in cells and proteins. Moscow Univ. Chem. Bull. 2000, 41, 352-354.

18. Verkhusha V.V.*, Tsukita S., and Oda H. Analysis of cytoskeleton dynamics and cell migration in Drosophila ovaries using GFP-actin and E-cadherin-GFP fusion moleculesProc. SPIE. 1999, 3604, 130-139. *Corresponding author  

17. Verkhusha V.V.*, Tsukita S., and Oda H. Actin dynamics in lamellipodia of migrating border cells in the Drosophila ovaries revealed by a GFP-actin fusion proteinFEBS Letters. 1999,445, 395-401. *Corresponding author

16. Potanin A.A., Verkhusha V.V., and Muller V.M. Disaggregation of particles with biospecific interactions in shear flowJ. Coll. Interface Sci. 1997, 188, 251-256.

15. Potanin A.A., Verkhusha V.V., and Muller V.M. Aggregate breakage of particles with biospecific interaction in a shear flow. Colloid J. 1996, 58, 355-362.

14. Takikawa O., Oku T., lto N., Ushio Y., Yamamoto N., Yoneda Y., Tsuji J., Sanchez-Bueno A., Verkhusha V.V., and Yoshida R. Multiple expression of Ly-6C and accumulation of Ly-6C pre-mRNA in activated macrophages involved in rejection of an allografted tumorBiochem. Biophys. Res. Commun. 1996, 226, 247-253.

13. Sanchez-Bueno A., Verkhusha V.V., Takikawa O., Tanaka Y., and Yoshida R. Interferon-gamma dependent expression of inducible nitric oxide synthase, interleukin-12 and interferon-g-inducing factor in macrophages elicited by allografted tumor cellsBiochem. Biophys. Res. Commun. 1996, 224, 555-563.

12. Verkhusha V.V.*, Staroverov V.M., and Vrzheshch P.V. Model of cell adhesive interaction in liquid flow. Membr. Cell. Biol. 1995, 8, 455-470. *Corresponding author  

11. Potanin A.A., Verkhusha V.V., Belokoneva O.S., and Wiegel F.W. Kinetics of ligand binding to a cluster of membrane-associated receptorsEur. Biophys. J. 1994, 23, 197-205.

10. Potanin A.A., Verkhusha V.V., Vrzheshch P.V., and Muller V.M. Theory of adhesion interaction of biological cells in liquid flow: influence of cell deformation on coagulation. Colloid J. 1994, 56, 365-369.

9. Potanin A.A., Verkhusha V.V., Vrzheshch P.V., and Muller V.M. Theory of adhesion interaction of biological cells in liquid flow: undeformed cells. Colloid J. 1994, 56, 356-364.

8. Verkhusha V.V.*, Lebedev E.S., Vrzheshch P.V., and Muller V.M. Experimental investigation of aggregation of platelets and latex immunoconjugates in shear flow. Colloid J. 1994, 56, 269-279. *Corresponding author  

7. Verkhusha V.V.*, Staroverov V.M., and Vrzheshch P.V. Model for cell adhesion in the flow of liquid. Biol. Membranes. 1994, 11, 437-450. *Corresponding author  

6. Verkhusha V.V.*, Smorodin V.E., and Vrzheshch P.V. Model of bioaerosol adhesion interactions in respiratory tracts. J. Aerosol Sci. 1993, 24, S433-S434. *Corresponding author  

5. Potanin A.A., Verkhusha V.V., Vrzheshch P.V. Coagulation of particles in shear flow: applications to biological cellsJ. Coll. Interface Sci. 1993, 160, 405-418.

4. Verkhusha V.V., Vrzheshch P.V., Staroverov V.M., and Varfolomeyev S.D. Cell-cell adhesion in shear flow. J. Chem. Biochem. Kinetics. 1992, 2, 135-153.

3. Verkhusha V.V., Vrzheshch P.V., and Varfolomeyev S.D. Mathematical approaches for kinetics of blood platelet aggregation. Proc. USSR Acad. Med. Sci. 1991, 10, 20-28.

2. Vrzheshch P.V., Verkhusha V.V., and Varfolomeyev S.D. Rate equation for platelets aggregation. Biophysics (Mosc). 1990, 35, 637-641.

1. Vrzheshch P.V., Verkhusha V.V., and Varfolomeyev S.D. Kinetic analysis of blood platelets aggregation. Proc. USSR Acad. Sci. 1990, 313, 726-729.