The green fluorescent protein (GFP) from jellyfish Aequorea victoria and homologues fluorescent proteins (FPs) from Anthozoa corals have become invaluable tools for cell imaging. Anthozoa FPs is available in colors and with features unlike those of GFP variants and, thus, provides powerful templates for new probes for molecular labeling and intracellular detection. Several Anthozoa FPs have been already developed into biotechnological tools. Nevertheless, the continuing progress in optical microscopy methods and fluorescence imaging approaches requires probes with new colors and photochemical properties. Two super-resolution fluorescence techniques, stimulated emission depletion (STED) fluorescence microscopy and photoactivated localization microscopy (PALM), have been recently developed. With the improvement of two-photon lasers, a deep-tissue intravital imaging in live animals has become widely available. However, enhanced monomeric FPs suitable for these imaging techniques exist in two colors only. Our analysis of the chromophore formation mechanisms in Anthozoa FPs suggest that fluorescent probes with novel spectral and photochemical features can be indeed designed. On the basis of existing monomeric FPs we plan to develop three new types of protein labels complementary to the available green and red probes. These include monomeric photoactivatable FPs (PA-FPs), which are initially dark but become fluorescent in Blue, Orange or Far-red regions upon irradiation with violet light (Aim 1);monomeric FPs with large Stokes shift (LSS) emission (LSSFPs), which absorb in cyan but fluoresce in Orange or Far-Red regions, and which we further plan to convert into photoactivatable LSS-FPs (Aim 2);and an enhanced monomeric Far-Red FP with improved brightness and further shifted towards far-red for efficient excitation using red lasers (Aim 3). We will apply directed molecular evolution techniques consisting of rational structure-based design and random mutagenesis of candidate proteins, followed by flow cytometry and multiwell plate screening. Moreover, screening methods utilizing two-photon excitation and single-molecule characterization will be developed to optimize photophysical properties of LSS-FPs for intravital imaging and of PA-FPs for PALM, respectively. We will correlate the mutagenesis process with spectral and photochemical changes, in order to gain insight into the molecular evolution of chromophore structures responsible for fluorescence properties and will apply these to the next rounds of molecular evolution. The fluorescent variants will be thoroughly characterized in vitro and as fusion tags in live cells, using a conventional fluorescence microscopy, as well as the super-resolution imaging techniques. The anticipated end result of the proposed research is a collection of molecular fluorescent tools with new fluorescent colors that will be as versatile as the respective green and red proteins. The resulting probes will expand the PA-FP technology to allow diffraction-limited or super-resolution PALM imaging of localization and dynamics of several intracellular proteins simultaneously. The enhanced FRFP and new LSSFPs, excitable with a single wavelength two-photon laser, will further advance the deep-tissue and multicolor intravital imaging approaches.

Public Health Relevance

The green fluorescent protein (GFP) from jellyfish and fluorescent proteins (FPs) from corals have become invaluable tools for microscopy of cells and tissues. Coral FPs are available in colors and with features unlike those of GFP variants. Several coral FPs have been already developed into biotechnological tools. However, continuing progress of microscopy methods and imaging approaches has been requiring genetically-encoded fluorescent probes with new properties. This project focuses on the development of three types of proteins that currently do not exist: blue, orange and far-red so called photoactivatable FPs;orange and far-red FPs with a large difference between absorbance and fluorescence wavelengths;and an enhanced bright monomeric far-red FP. The anticipated end result of the proposed project is a collection of molecular fluorescent probes with new fluorescent colors that will be as versatile as existing conventional green and red FPs. These new probes will expand the FP-technology to allow simultaneous detection of dynamics and interactions of more than two proteins in a single live cell. The planned photoactivatable FPs will provide more colors for super-resolution optical microscopy that enables 10-fold better spatial resolution than confocal imaging. The planned FPs with a large difference between absorbance and fluorescence will allow multicolor imaging with a single two-photon laser. The bright far-red FP will make a deep tissue imaging in living animals possible.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Enabling Bioanalytical and Imaging Technologies Study Section (EBIT)
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Lewis, Catherine D
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Albert Einstein College of Medicine
Anatomy/Cell Biology
Schools of Medicine
United States
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Pletnev, Sergei; Shcherbakova, Daria M; Subach, Oksana M et al. (2014) Orange fluorescent proteins: structural studies of LSSmOrange, PSmOrange and PSmOrange2. PLoS One 9:e99136
Piatkevich, Kiryl D; English, Brian P; Malashkevich, Vladimir N et al. (2014) Photoswitchable red fluorescent protein with a large Stokes shift. Chem Biol 21:1402-14
Shcherbakova, Daria M; Verkhusha, Vladislav V (2014) Chromophore chemistry of fluorescent proteins controlled by light. Curr Opin Chem Biol 20:60-8
Pletnev, Sergei; Subach, Fedor V; Verkhusha, Vladislav V et al. (2014) The rotational order-disorder structure of the reversibly photoswitchable red fluorescent protein rsTagRFP. Acta Crystallogr D Biol Crystallogr 70:31-9
Stepanenko, Olesya V; Stepanenko, Olga V; Kuznetsova, Irina M et al. (2014) Sensitivity of superfolder GFP to ionic agents. PLoS One 9:e110750
Krumholz, Arie; Shcherbakova, Daria M; Xia, Jun et al. (2014) Multicontrast photoacoustic in vivo imaging using near-infrared fluorescent proteins. Sci Rep 4:3939
Yao, Junjie; Shcherbakova, Daria M; Li, Chiye et al. (2014) Reversibly switchable fluorescence microscopy with enhanced resolution and image contrast. J Biomed Opt 19:086018
Nedosekin, Dmitry A; Verkhusha, Vladislav V; Melerzanov, Alexander V et al. (2014) In vivo photoswitchable flow cytometry for direct tracking of single circulating tumor cells. Chem Biol 21:792-801
Stepanenko, Olesya V; Bublikov, Grigory S; Stepanenko, Olga V et al. (2014) A knot in the protein structure - probing the near-infrared fluorescent protein iRFP designed from a bacterial phytochrome. FEBS J 281:2284-98
Shcherbakova, Daria M; Sengupta, Prabuddha; Lippincott-Schwartz, Jennifer et al. (2014) Photocontrollable fluorescent proteins for superresolution imaging. Annu Rev Biophys 43:303-29

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