The molecular properties and applications of Anthozoa fluorescent proteins and chromoproteins

Peroxisome Ca(2+) homeostasis in animal and plant cells

Ca(2+) homeostasis in peroxisomes has been an unsolved problem for many years. Recently novel probes to monitor Ca(2+) levels in the lumen of peroxisomes in living cells of both animal and plant cells have been developed. Here we discuss the contrasting results obtained in mammalian cells with chemiluminecsent (aequorin) and fluorescent (cameleon) probes targeted to peroxisomes. We briefly discuss the different characteristics of these probes and the possible pitfalls of the two approaches. We conclude that the contrasting results obtained with the two probes may reflect a heterogeneity among peroxisomes in mammalian cells. We also discuss the results obtained in plant peroxisomes. In particular we demonstrate that Ca(2+) increases in the cytoplasm are mirrored by similar rises of Ca(2+) concentration the lumen of peroxisomes. The increases in peroxisome Ca(2+) level results in the activation of a catalase isoform, CAT3. Other functional roles of peroxisomal Ca(2+) changes in plant physiology are briefly discussed.

Recovery of red fluorescent protein chromophore maturation deficiency through rational design

Red fluorescent proteins (RFPs) derived from organisms in the class Anthozoa have found widespread application as imaging tools in biological research. For most imaging experiments, RFPs that mature quickly to the red chromophore and produce little or no green chromophore are most useful. In this study, we used rational design to convert a yellow fluorescent mPlum mutant to a red-emitting RFP without reverting any of the mutations causing the maturation deficiency and without altering the red chromophore's covalent structure. We also created an optimized mPlum mutant (mPlum-E16P) that matures almost exclusively to the red chromophore. Analysis of the structure/function relationships in these proteins revealed two structural characteristics that are important for efficient red chromophore maturation in DsRed-derived RFPs. The first is the presence of a lysine residue at position 70 that is able to interact directly with the chromophore. The second is an absence of non-bonding interactions limiting the conformational flexibility at the peptide backbone that is oxidized during red chromophore formation. Satisfying or improving these structural features in other maturation-deficient RFPs may result in RFPs with faster and more complete maturation to the red chromophore.

Photoactivatable Fluorophores

Photoactivatable fluorophores switch from a nonemissive to an emissive state upon illumination at an activating wavelength and then emit after irradiation at an exciting wavelength. The interplay of such activation and excitation events can be exploited to switch fluorescence on in a defined region of space at a given interval of time. In turn, the spatiotemporal control of fluorescence translates into the opportunity to implement imaging and spectroscopic schemes that are not possible with conventional fluorophores. Specifically, photoactivatable fluorophores permit the monitoring of dynamic processes in real time as well as the reconstruction of images with subdiffraction resolution. These promising applications can have a significant impact on the characterization of the structures and functions of biomolecular systems. As a result, strategies to implement mechanisms for fluorescence photoactivation with synthetic fluorophores are particularly valuable. In fact, a number of versatile operating principles have already been identified to activate the fluorescence of numerous members of the main families of synthetic dyes. These methods are based on either the irreversible cleavage of covalent bonds or the reversible opening and closing of rings. This paper overviews the fundamental mechanisms that govern the behavior of these photoresponsive systems, illustrates structural designs for fluorescence photoactivation, and provides representative examples of photoactivatable fluorophores in actions.

Interpolated mechanics-molecular mechanics study of internal rotation dynamics of the chromophore unit in blue fluorescent protein and its variants

The excited state dynamics of the blue fluorescent protein (BFP) and its variants, azurite, EBFP1.2, and EBFP2.0, are studied using molecular dynamics (MD) simulations on potential energy surfaces (PESs) generated with the interpolated mechanics-molecular mechanics (IM/MM) scheme. This IM/MM strategy adopts the interpolated PES for an important area of the complex and the conventional force field for the remaining part. We focus on the internal rotation dynamics of the chromophore unit, which is directly related to its fluorescence property, and analyze the time evolutions of the nonrotated chromophore fractions based on trajectories over 10 μs of aggregate simulation time. The characteristics obtained from the calculated time progresses of the nonrotated chromophore fractions in BFP and other variants agree well with experimentally observed properties. The results show that the MD simulation with an IM/MM potential is an attractive approach for studying excited state dynamics of fluorescent proteins in consideration of its efficiency and reliability. We also attempt to investigate the detailed roles that the mutated residues play in delaying the excited state chromophore twisting and thus improving the fluorescence property, and discuss the contributions by the Coulombic and the steric interactions between the chromophore and the mutated residues.

Live cell imaging in live animals with fluorescent proteins

The discovery, cloning, and characterization of GFP and related proteins of many colors have enabled live cell imaging to an unprecedented extent and resolution. Essentially, any cellular process can be imaged with a fluorescent protein. These proteins serve as genetic reporters and therefore can be used to follow cellular processes over indefinite periods in vivo as well as in vitro. The brightness and specific spectra of fluorescent proteins allow them to be imaged in vivo, using specific filters, without interference from autofluorescence. This chapter describes the development of live imaging in live animals with subcellular resolution, emphasizing the study of in vivo cell biology of cancer growth, spread, and metastasis.

Isomerization mechanism of the HcRed fluorescent protein chromophore

To understand how the protein achieves fluorescence, the isomerization mechanism of the HcRed chromophore is studied both under vacuum and in the solvated red fluorescent protein. Quantum mechanical (QM) and quantum mechanical/molecular mechanical (QM/MM) methods are applied both for the ground and the first excited state. The photoinduced processes in the chromophore mainly involve torsions around the imidazolinone-bridge bond (τ) and the phenoxy-bridge bond (φ). Under vacuum, the isomerization of the cis-trans chromophore essentially proceeds by τ twisting, while the radiationless decay requires φ torsion. By contrast, the isomerization of the cis-trans chromophore in HcRed occurs via simultaneous τ and φ twisting. The protein environment significantly reduces the barrier of this hula twist motion compared with vacuum. The excited-state isomerization barrier via the φ rotation of the cis-coplanar conformer in HcRed is computed to be significantly higher than that of the trans-non-coplanar conformer. This is consistent with the experimental observation that the cis-coplanar-conformation of the chromophore is related to the fluorescent properties of HcRed, while the trans-non-planar conformation is weakly fluorescent or non-fluorescent. Our study shows how the protein modifies the isomerization mechanism, notably by interactions involving the nearby residue Ile197, which keeps the chromophore coplanar and blocks the twisting motion that leads to photoinduced radiationless decay.

Ultramarine, a chromoprotein acceptor for Förster resonance energy transfer

We have engineered a monomeric blue non-fluorescent chromoprotein called Ultramarine (fluorescence quantum yield, 0.001; ε _585nm, 64,000 M⁻¹. cm⁻¹) for use as a Förster resonance energy transfer acceptor for a number of different donor fluorescent proteins. We show its use for monitoring activation of caspase 3 in live cells using fluorescence lifetime imaging. Ultramarine has the potential to increase the number of cellular parameters that can be imaged simultaneously.

Flow cytometry of fluorescent proteins

Fluorescent proteins are now a critical tool in all areas of biomedical research. In this article, we review the techniques required to use fluorescent proteins for flow cytometry, concentrating specifically on the excitation and emission requirements for each protein, and the specific equipment required for optimal use.

An orange fluorescent protein with a large Stokes shift for single-excitation multicolor FCCS and FRET imaging

Multicolor imaging based on genetically encoded fluorescent proteins (FPs) is a powerful approach to study several dynamic processes in a live cell. We report a monomeric orange FP with a large Stokes shift (LSS), called LSSmOrange (excitation/emission at 437/572 nm), which fills up an existing spectral gap between the green-yellow and red LSSFPs. Brightness of LSSmOrange is five-fold larger than that of the brightest red LSSFP and similar to the green-yellow LSSFPs. LSSmOrange allows numerous multicolor applications using a single-excitation wavelength that was not possible before. Using LSSmOrange we developed four-color single-laser fluorescence cross-correlation spectroscopy, solely based on FPs. The quadruple cross-correlation combined with photon counting histogram techniques allowed quantitative single-molecule analysis of particles labeled with four FPs. LSSmOrange was further applied to simultaneously image two Förster resonance energy transfer pairs, one of which is the commonly used CFP-YFP pair, with a single-excitation laser line. The combination of LSSmOrange-mKate2 and CFP-YFP biosensors enabled imaging of apoptotic activity and calcium fluctuations in real time. The LSSmOrange mutagenesis, low-temperature, and isotope effect studies revealed a proton relay for the excited-state proton transfer responsible for the LSS phenotype.

Fluorescent proteins for FRET microscopy: monitoring protein interactions in living cells

The discovery and engineering of novel fluorescent proteins (FPs) from diverse organisms is yielding fluorophores with exceptional characteristics for live-cell imaging. In particular, the development of FPs for fluorescence (or Förster) resonance energy transfer (FRET) microscopy is providing important tools for monitoring dynamic protein interactions inside living cells. The increased interest in FRET microscopy has driven the development of many different methods to measure FRET. However, the interpretation of FRET measurements is complicated by several factors including the high fluorescence background, the potential for photoconversion artifacts and the relatively low dynamic range afforded by this technique. Here, we describe the advantages and disadvantages of four methods commonly used in FRET microscopy. We then discuss the selection of FPs for the different FRET methods, identifying the most useful FP candidates for FRET microscopy. The recent success in expanding the FP color palette offers the opportunity to explore new FRET pairs.

Coating gold particles with DNA (biolistics)

Imaging and reconstruction of developing neurons require cells that are labeled in a way that distinguishes them from their neighbors. This can be achieved with ballistic labeling, which refers to the delivery of a cell label by means of carrier particles (tungsten or gold) propelled from a pressurized gun. Ballistic delivery can reach many dispersed cells in one shot and can deploy a wide variety of cell markers to neurons in diverse preparations. The three most commonly used types of ballistic labels are carbocyanine dyes, dextran-conjugated fluorescent markers, and DNA plasmids. The primary advantage of ballistic labeling is that multiple dispersed cells can be labeled quickly in live or fixed tissue. This article describes a protocol for coating gold particles with plasmid DNA, which can be used to label developing ganglion cells in retinal flat mounts.

Screening reef corals for novel GFP-type fluorescent proteins by confocal imaging

The discovery of multicolored fluorescent proteins (FPs), in reef corals, that are close relatives of the green fluorescent protein (GFP) has led to what is now viewed as the second GFP revolution. Numerous GFP-type proteins, termed "reef FPs," have been cloned from reef organisms and many possess new colors, novel molecular characteristics, protein chemistry and many display unusual photophysical properties. Although some FPs have certain disadvantageous properties, such as the tendency to oligomerize or have slow maturation rates, reef FPs have been developed into versatile probes for cell biology and imaging applications. Screening of natural sources for novel GFP-type proteins continues to be valuable due to the need to expand the range of spectral colors, brightness, monomeric or dimeric states, faster maturation states, and photoactivity. Confocal imaging, coupled with microspectral detection, provides a rapid technique for in vivo characterization of FPs with desirable spectral and photoactive properties.

Fluorinated amino acids: compatibility with native protein structures and effects on protein-protein interactions

Fluorinated analogues of the canonical α-L-amino acids have gained widespread attention as building blocks that may endow peptides and proteins with advantageous biophysical, chemical and biological properties. This critical review covers the literature dealing with investigations of peptides and proteins containing fluorinated analogues of the canonical amino acids published over the course of the past decade including the late nineties. It focuses on side-chain fluorinated amino acids, the carbon backbone of which is identical to their natural analogues. Each class of amino acids--aliphatic, aromatic, charged and polar as well as proline--is presented in a separate section. General effects of fluorine on essential properties such as hydrophobicity, acidity/basicity and conformation of the specific side chains and the impact of these altered properties on stability, folding kinetics and activity of peptides and proteins are discussed (245 references).

PROTONATION STATES AND CONFORMATIONAL FLEXIBILITY OF THE RED FLUORESCENT PROTEIN CHROMOPHORE

Fluorescent proteins are important reporter molecules widely used in biotechnology and the biological sciences, generally. Their unusual spectrophotometric and fluorescence characteristics are controlled via protonation states of the chromophore, as for green fluorescent proteins (GFPs), and/or via cis–trans isomerization of the chromophore, as for red fluorescent proteins (RFPs). Here, we have performed both quantum mechanical calculations on substituted chromophores and structural comparisons of several RFPs (Rtms5, eqFP611, HcRed, and DsRed) and wild-type GFP. Our results indicate that the chromophore cis and trans isomers are comparably stable, and cis–trans isomerization has only a minor effect on electronic excitation. The chromophore is also found to exist in either the anionic or possibly zwitterionic protonation state. Structural comparisons of RFPs reveal that the conformation of the chromophore within a specific RFP is determined by only a few key residues, which could serve as mutation targets for engineering new fluorescent proteins for novel biotechnological applications.

Peptide bond trans-cis isomerization and acylimine formation in chromophore maturation of the red fluorescent proteins

In red fluorescent proteins such as DsRed, an acylimine is formed from the Phe65-Gln66 linkage in GFP-like immature form, while it shows a cis configuration in its mature state. To date, the relationship between acylimine formation and trans-cis isomerization is still unresolved. We have calculated bond rotation profiles for mature and immature chromophores within the protein using our own n-layered integrated molecular orbital and molecular mechanism (ONIOM) approach. The results suggested that the isomerization is barrierless in acylimine formed in the mature state, suggesting that the acylimine formation precedes the trans-cis isomerization in DsRed chromophores. Further decomposition analysis of electrostatic contributions from individual residues has identified several residues and a specific water molecule which could play key roles in controlling the rate of the trans-cis isomerization of peptide bond in immature GFP-like protein. The results also highlight the importance of Gln66-like of tripeptide motif (chromophore) in the maturation of red fluorescent proteins. In view of the considerable interest in developing red fluorescent proteins for numerous biotechnological applications, these results should be useful for design of novel fluorescent proteins.

Plant organelle proteomics: collaborating for optimal cell function

Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.

Imaging intracellular pH in live cells with a genetically encoded red fluorescent protein sensor

Intracellular pH affects protein structure and function, and proton gradients underlie the function of organelles such as lysosomes and mitochondria. We engineered a genetically encoded pH sensor by mutagenesis of the red fluorescent protein mKeima, providing a new tool to image intracellular pH in live cells. This sensor, named pHRed, is the first ratiometric, single-protein red fluorescent sensor of pH. Fluorescence emission of pHRed peaks at 610 nm while exhibiting dual excitation peaks at 440 and 585 nm that can be used for ratiometric imaging. The intensity ratio responds with an apparent pK(a) of 6.6 and a >10-fold dynamic range. Furthermore, pHRed has a pH-responsive fluorescence lifetime that changes by ~0.4 ns over physiological pH values and can be monitored with single-wavelength two-photon excitation. After characterizing the sensor, we tested pHRed's ability to monitor intracellular pH by imaging energy-dependent changes in cytosolic and mitochondrial pH.

Crystallographic study of red fluorescent protein eqFP578 and its far-red variant Katushka reveals opposite pH-induced isomerization of chromophore

The wild type red fluorescent protein eqFP578 (from sea anemone Entacmaea quadricolor, λ(ex) = 552 nm, λ(em) = 578 nm) and its bright far-red fluorescent variant Katushka (λ(ex) = 588 nm, λ(em) = 635 nm) are characterized by the pronounced pH dependence of their fluorescence. The crystal structures of eqFP578f (eqFP578 with two point mutations improving the protein folding) and Katushka have been determined at the resolution ranging from 1.15 to 1.85 Å at two pH values, corresponding to low and high level of fluorescence. The observed extinguishing of fluorescence upon reducing pH in eqFP578f and Katushka has been shown to be accompanied by the opposite trans-cis and cis-trans chromophore isomerization, respectively. Asn143, Ser158, His197 and Ser143, Leu174, and Arg197 have been shown to stabilize the respective trans and cis fluorescent states of the chromophores in eqFP578f and Katushka at higher pH. The cis state has been suggested as being primarily responsible for the observed far-red shift of the emission maximum of Katushka relative to that of eqFP578f.

Superfolder GFP is fluorescent in oxidizing environments when targeted via the Sec translocon

The ability to study proteins in live cells using genetically encoded fluorescent proteins (FPs) has revolutionized cell biology (1-3). Researchers have created numerous FP biosensors and optimized FPs for specific organisms and subcellular environments in a rainbow of colors (4,5). However, expressing FPs in oxidizing environments such as the eukaryotic endoplasmic reticulum (ER) or the bacterial periplasm can impair folding, thereby preventing fluorescence (6,7). A substantial fraction of enhanced green fluorescent protein (EGFP) oligomerizes to form non-fluorescent mixed disulfides in the ER (6) and EGFP does not fluoresce in the periplasm when targeted via the SecYEG translocon (7). To overcome these obstacles, we exploited the highly efficient folding capability of superfolder GFP (sfGFP) (8). Here, we report sfGFP does not form disulfide-linked oligomers in the ER and maltose-binding protein (MBP) signal sequence (peri)-sfGFP (9) is brightly fluorescent in the periplasm of Escherichia coli. Thus, sfGFP represents an important research tool for studying resident proteins of oxidizing environments.

Stabilizing role of glutamic acid 222 in the structure of Enhanced Green Fluorescent Protein

Enhanced Green Fluorescent Protein (EGFP) is a variant of wild-type Green Fluorescent Protein from the jellyfish Aequorea victoria, whose mutations S65T and F64L increase brightness and folding efficiency. EGFP is extensively used in cell biology and biochemistry as a colocalization or expression reporter. Surprisingly, the structure of this very popular protein has not been determined yet. We report here its crystallographic structure at 1.5Å resolution which shows significant differences in the vicinity of residue 64 and of the chromophore. In particular, two conformations are observed for the key residue glutamic acid 222, in apparent contradiction with the single fluorescence lifetime of the protein. We then show that X-ray induced decarboxylation of Glu222 during diffraction data collection results in the disruption of a hydrogen-bond network near the chromophore. Using single-crystal microspectrophotometry, we demonstrate that this correlates with a significant loss of the fluorescence properties. We thus propose a mechanism of bleaching of the protein at low temperature. Taken together, these two sets of results highlight the stabilizing role of Glu222 to the chromophore cavity of EGFP.

Development of a new bimodal imaging methodology: a combination of fluorescence microscopy and high-resolution secondary ion mass spectrometry

In this paper, we present a new experimental methodology to combine mass spectrometry (NanoSIMS) with fluorescence microscopy to provide subcellular information on the location of small molecules in cultured cells. We demonstrate this by comparing the distribution of 5-bromo-2-deoxyuridine in the same cells given by both NanoSIMS analysis and by fluorescence immunohistochemistry. Fiducial markers in the substrates ensured that the images formed by SIMS mapping of bromine ions could be co-registered exactly with images from fluorescence microscopy. The NanoSIMS was shown to faithfully reproduce the information from fluorescence microscopy, but at a much higher spatial resolution. We then show preliminary SIMS images on the distribution of ATN-224, a therapeutic copper chelator for which there is no fluorescent marker, co-registered with conventional Lysotracker and Hoechst stains on the same cells.

Spectroscopic detection improves multi-color quantification in fluorescence tomography

Simultaneous detection of several biological processes in vivo is a common requirement in biomedical and biological applications, and in order to address this issue the use of multiple fluorophores is usually the method of choice. Existing methodologies however, do not provide quantitative feedback of multiple fluorophore concentrations in small animals in vivo when their spectra overlap, especially when imaging the whole body in 3D. Here we present an approach where a spectroscopic module has been implemented into a custom-built Fluorescence Molecular Tomography (FMT) system. In contrast with other multispectral approaches, this multimodal imaging system is capable of recording the fluorescence spectra from each illumination point during a tomographic measurement. In situ spectral information can thus be extracted and used to improve the separation of overlapping signals associated with different fluorophores. The results of this new approach tested on both in vitro and in vivo experiments are presented, proving that accurate recovery of fluorophore concentrations can be obtained from multispectral tomography data even in the presence of high autofluorescence.

Use of RNAlater in fluorescence-activated cell sorting (FACS) reduces the fluorescence from GFP but not from DsRed

Background

Flow cytometry utilizes signals from fluorescent markers to separate targeted cell populations for gene expression studies. However, the stress of the FACS process could change normal gene expression profiles. RNAlater could be used to stop such changes in original gene expression profiles through its ability to denature RNase and other proteins. The normal conformational structure of fluorescent proteins must be maintained in order to fluoresce. Whether or not RNAlater would affect signals from different types of intrinsic fluorescent proteins is crucial to its use in flow cytometry; this question has not been investigated in detail.

Findings

To address this question, we analyzed the effect of RNAlater on fluorescence intensity of GFP, YFP, DsRed and small fluorescent molecules attached to secondary antibodies (Cy2 and Texas-Red) when used in flow cytometry. FACS results were confirmed with fluorescence microscopy. Our results showed that exposure of YFP and GFP containing cells to RNAlater reduces the intensity of their fluorescence to such an extent that separation of such labeled cells is difficult if not impossible. In contrast, signals from DsRed2, Cy2 and Texas-Red were not affected by RNAlater treatment. In addition, the background fluorescence and clumping of dissociated cells are altered by RNAlater treatment.

Conclusions

When considering gene expression studies using cell sorting with RNAlater, DsRed is the fluorescent protein of choice while GFP/YFP have severe limitations because of their reduced fluorescence. It is necessary to examine the effects of RNAlater on signals from fluorescent markers and the physical properties (e.g., clumping) of the cells before considering its use in cell sorting.

Fluorescent proteins as light-inducible photochemical partners

Green Fluorescent Protein (GFP) and other related fluorescent proteins are generally used as genetically encoded, chemically inert labels in vivo. This review focuses on the emerging application of fluorescent proteins as light-inducible intracellular photochemical partners. The first example of a chemically active GFP-like protein was the phototoxic red fluorescent protein KillerRed, which can be used for precise light-induced killing of cells, protein inactivation, and studying reactive oxygen species signaling in different cellular compartments. Moreover, recent studies revealed that various GFPs can act as light-induced electron donors in photochemical reactions with biologically relevant electron acceptors. These findings have important implications for practical uses of fluorescent proteins as well as for our understanding of the evolution and biology of this protein family.

Fluorescent proteins and their applications in imaging living cells and tissues

Green fluorescent protein (GFP) from the jellyfish Aequorea victoria and its homologs from diverse marine animals are widely used as universal genetically encoded fluorescent labels. Many laboratories have focused their efforts on identification and development of fluorescent proteins with novel characteristics and enhanced properties, resulting in a powerful toolkit for visualization of structural organization and dynamic processes in living cells and organisms. The diversity of currently available fluorescent proteins covers nearly the entire visible spectrum, providing numerous alternative possibilities for multicolor labeling and studies of protein interactions. Photoactivatable fluorescent proteins enable tracking of photolabeled molecules and cells in space and time and can also be used for super-resolution imaging. Genetically encoded sensors make it possible to monitor the activity of enzymes and the concentrations of various analytes. Fast-maturing fluorescent proteins, cell clocks, and timers further expand the options for real time studies in living tissues. Here we focus on the structure, evolution, and function of GFP-like proteins and their numerous applications for in vivo imaging, with particular attention to recent techniques.

Structural evidence for a dehydrated intermediate in green fluorescent protein chromophore biosynthesis

The acGFPL is the first-identified member of a novel, colorless and non-fluorescent group of green fluorescent protein (GFP)-like proteins. Its mutant aceGFP, with Gly replacing the invariant catalytic Glu-222, demonstrates a relatively fast maturation rate and bright green fluorescence (lambda(ex) = 480 nm, lambda(em) = 505 nm). The reverse G222E single mutation in aceGFP results in the immature, colorless variant aceGFP-G222E, which undergoes irreversible photoconversion to a green fluorescent state under UV light exposure. Here we present a high resolution crystallographic study of aceGFP and aceGFP-G222E in the immature and UV-photoconverted states. A unique and striking feature of the colorless aceGFP-G222E structure is the chromophore in the trapped intermediate state, where cyclization of the protein backbone has occurred, but Tyr-66 still stays in the native, non-oxidized form, with C(alpha) and C(beta) atoms in the sp(3) hybridization. This experimentally observed immature aceGFP-G222E structure, characterized by the non-coplanar arrangement of the imidazolone and phenolic rings, has been attributed to one of the intermediate states in the GFP chromophore biosynthesis. The UV irradiation (lambda = 250-300 nm) of aceGFP-G222E drives the chromophore maturation further to a green fluorescent state, characterized by the conventional coplanar bicyclic structure with the oxidized double Tyr-66 C(alpha)=C(beta) bond and the conjugated system of pi-electrons. Structure-based site-directed mutagenesis has revealed a critical role of the proximal Tyr-220 in the observed effects. In particular, an alternative reaction pathway via Tyr-220 rather than conventional wild type Glu-222 has been proposed for aceGFP maturation.

A new bright green-emitting fluorescent protein--engineered monomeric and dimeric forms

Fluorescent proteins have become essential tools in molecular and biological applications. Here, we present a novel fluorescent protein isolated from warm water coral, Cyphastrea microphthalma. The protein, which we named vivid Verde fluorescent protein (VFP), matures readily at 37 degrees C and emits bright green light. Further characterizations revealed that VFP has a tendency to form dimers. By creating a homology model of VFP, based on the structure of the red fluorescent protein, DsRed, we were able to make mutations that alter the protein's oligomerization state. We present two proteins, mVFP and mVFP1, that are both exclusively monomeric, and one protein, dVFP, which is dimeric. We characterized the spectroscopic properties of VFP and its variants in comparison with enhanced green fluorescent protein (EGFP), a widely used variant of GFP. All the VFP variants are at least twice as bright as EGFP. Finally, we demonstrated the effectiveness of the VFP variants in both in vitro and in vivo detection applications.

QM/MM studies of structural and energetic properties of the far-red fluorescent protein HcRed

The far-red fluorescent protein HcRed was investigated using molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Three models of HcRed (anionic chromophore) were considered, differing in the protonation states of nearby Glu residues (A: Glu214 and Glu146 both protonated; B: Glu214 protonated and Glu146 deprotonated; C: Glu214 and Glu146 both deprotonated). SCC-DFTB/MM MD simulations of model B yield good agreement with the available crystallographic data at ambient pH. Bond lengths in the QM region are well reproduced, with a root mean square (rms) deviation between experimental and average MD data of 0.079 A; the chromophore is almost co-planar, which is consistent with experimental observation; and the five hydrogen bonds involving the chromophore are conserved. QM/MM geometry optimizations were performed on representative snapshot structures from the MD simulations for each model. They confirm the structural features observed in the MD simulations. According to the DFT(B3LYP)/MM results, the cis-conformation of the chromophore is more stable than the trans-form by 9.1-12.9 kcal mol(-1) in model B, and by 12.4-19.9 kcal mol(-1) in model C, consistent with the experimental preference for the cis-isomer. However, in model A when both Glu214 and Glu146 are protonated, the stability is inverted with the trans-form being favored. The different protonation states of the titratable active-site residues Glu214 and Glu146 thus critically influence the manner in which the relative stability and degree of planarity of the cis- and trans-conformers vary with pH. Coupled with the known correlation of chromophore conformation with fluorescence efficiency, this work provides a detailed structural basis for the observed phenomenon that red fluorescent proteins such as HcRed, mKate and Rtms5 show bright fluorescence at high pH.

Red-shifted voltage-sensitive fluorescent proteins

Electrical signals generated by nerve cells provide the basis of brain function. Whereas single or small numbers of cells are easily accessible using microelectrode recording techniques, less invasive optogenetic methods with spectral properties optimized for in vivo imaging are required for elucidating the operation mechanisms of neuronal circuits composed of large numbers of neurons originating from heterogeneous populations. To this end, we generated and characterized a series of genetically encoded voltage-sensitive fluorescent proteins by molecular fusion of the voltage-sensing domain of Ci-VSP (Ciona intestinalis voltage sensor-containing phosphatase) to red-shifted fluorescent protein operands. We show how these indicator proteins convert voltage-dependent structural rearrangements into a modulation of fluorescence output and demonstrate their applicability for optical recording of individual or simultaneous electrical signals in cultured hippocampal neurons at single-cell resolution without temporal averaging.

Structural basis for phototoxicity of the genetically encoded photosensitizer KillerRed

KillerRed is the only known fluorescent protein that demonstrates notable phototoxicity, exceeding that of the other green and red fluorescent proteins by at least 1,000-fold. KillerRed could serve as an instrument to inactivate target proteins or to kill cell populations in photodynamic therapy. However, the nature of KillerRed phototoxicity has remained unclear, impeding the development of more phototoxic variants. Here we present the results of a high resolution crystallographic study of KillerRed in the active fluorescent and in the photobleached non-fluorescent states. A unique and striking feature of the structure is a water-filled channel reaching the chromophore area from the end cap of the beta-barrel that is probably one of the key structural features responsible for phototoxicity. A study of the structure-function relationship of KillerRed, supported by structure-based, site-directed mutagenesis, has also revealed the key residues most likely responsible for the phototoxic effect. In particular, Glu(68) and Ser(119), located adjacent to the chromophore, have been assigned as the primary trigger of the reaction chain.

In vivo stable tumor-specific painting in various colors using dehalogenase-based protein-tag fluorescent ligands

In vivo fluorescence cancer imaging is an important tool in understanding tumor growth and therapeutic monitoring and can be performed either with endogenously produced fluorescent proteins or with exogenously introduced fluorescent probes bound to targeting molecules. However, endogenous fluorescence proteins cannot be altered after transfection, thus requiring rederivation of cell lines for each desired color, while exogenously targeted fluorescence probes are limited by the heterogeneous expression of naturally occurring cellular targets. In this study, we adapted the dehalogenase-based protein-Tag (HaloTag) system to in vivo cancer imaging, by introducing highly expressed HaloTag receptors (HaloTagR) in cancer cells coupled with a range of externally injected fluorophore-conjugated dehalogenase-reactive reactive linkers. Tumor nodules arising from a single transfected cell line were stably labeled with fluorescence varying in emission spectra from green to near-infrared. After establishing and validating a SHIN3 cell line stably transfected with HaloTagR (HaloTagR-SHIN3), in vivo spectral fluorescence imaging studies were performed in live animals using a peritoneal dissemination model. The tumor nodules arising from HaloTagR-SHIN3 could be successfully labeled by four different fluorophore-conjugated HaloTag-ligands each emitting light at different wavelengths. These fluorophores could be alternated on serial imaging sessions permitting assessment of interval growth. Fluorescence was retained in histological specimens after fixation. Thus, this tagging system proves versatile both for in vivo and in vitro imaging without requiring modification of the underlying cell line. Thus, this strategy can overcome some of the limitations associated with the use of endogenous fluorescent proteins and exogenous targeted optical agents in current use.

Synthesis and spectral and chemical properties of the yellow fluorescent protein zFP538 chromophore

Members of the green fluorescent protein (GFP) family become chromophoric through a unique pathway based on autocatalytic modifications of their amino acid residues. The yellow fluorescent protein zFP538 from the button polyp Zoanthus possesses unique spectral characteristics that are intermediate between those of the green and orange-red fluorescent proteins. In this study, we used chemical synthesis to resolve conflicting data from crystallographic and biochemical analyses of the zFP538 chromophore structure. We synthesized 2-(5-amino-1-oxopentyl)-5-(4-hydroxybenzylidene)-3-methyl-3,5-dihydro-4H-imidazol-4-one (5), which can spontaneously react intramolecularly to form cyclic imine (7). Compound 7 represents the native chromophore structure reported in the crystallographic study. We have also discovered an unusual isomerization of a 2-acylimidazolone to a 2,6-diketopiperazine derivative. The zFP538 chromophore is a complex system with intriguing chemical and spectral behavior, properties that have led to discrepancies in the interpretation of its structure. Our study supports the findings of previous crystallographic work, which postulated a cyclic imine chromophore structure within the native zFP538 protein, and also provides an explanation for experimental results obtained in the biochemical characterization of zFP538-derived chromopeptides.

The 559-to-600 nm shift observed in red fluorescent protein eqFP611 is attributed to cis-trans isomerization of the chromophore in an anionic protein pocket

Fluorescent proteins are commonly used as molecular labels, noninvasive markers of gene expression, and reporters of environmental conditions in live cells. We investigate the structural and spectroscopic properties of the chromophore of a far-red fluorescent protein eqFP611. Both the cis and trans isomers of the chromophore are examined within the protein for which both anionic and neutral states of protonation are considered. Spectroscopic properties are examined using time-dependent density functional theory (TDDFT), employing the B3LYP, PBE and B3PW91 density functionals. Intermolecular and long-range contributions to the structure and spectroscopy were treated using the own n-layered integrated molecular orbital and molecular mechanics (ONIOM) approach. The results indicated that the chromophore before excitation is in an anionic, protonated state, with the long-range contributions inducing a blue shift in the absorption and fluorescence maxima of the chromophore. Moreover, the calculated changes of the lowest pi-pi* excitation energy upon isomerization match the observed shift from 559 to 600 nm in the absorption maximum of the system following prolonged irradiation. Furthermore, decomposition analysis of the electrostatic contributions from individual residues indicated that the interactions from four residues Arg92, Lys67, Glu145, and His197 to the chromophore play a key role in the absorption and fluorescence spectra of eqFP611, suggesting that mutations at these sites should provide very useful mechanistic information.

The fluorescent protein palette: tools for cellular imaging

This critical review provides an overview of the continually expanding family of fluorescent proteins (FPs) that have become essential tools for studies of cell biology and physiology. Here, we describe the characteristics of the genetically encoded fluorescent markers that now span the visible spectrum from deep blue to deep red. We identify some of the novel FPs that have unusual characteristics that make them useful reporters of the dynamic behaviors of proteins inside cells, and describe how many different optical methods can be combined with the FPs to provide quantitative measurements in living systems (227 references).

Structure, dynamics and optical properties of fluorescent proteins: perspectives for marker development

GFP-like proteins, originally cloned from marine animals, are genetically encoded fluorescence markers that have become indispensable tools for the life sciences. The search for GFP-like proteins with novel and improved properties is still ongoing, however, driven by the persistent need for advanced and specialized fluorescence labels for cellular imaging. Overall, the structures of these proteins are similar, but considerable variations have been found in the covalent structures and stereochemistry of the fluorophore, which govern essential optical properties such as the absorption/emission wavelengths. Moreover, as the fluorophore-enclosing cavity forms its solvation shell, it can also have a significant effect on the absorption/emission wavelengths and the brightness of the fluorophore. Most exciting are recent developments of photoactivatable fluorescence markers which change their color and/or intensity upon irradiation with light of specific wavelengths. A detailed understanding of the structure and dynamics of GFP-like proteins greatly aids in the rational engineering of advanced fluorescence marker proteins. Herein, we review our present knowledge of the structural diversity of GFP-like proteins and discuss how structure and dynamics govern their optical properties, with an emphasis on red fluorescent proteins.

Green fluorescent proteins are light-induced electron donors

Proteins of the green fluorescent protein (GFP) family are well known owing to their unique biochemistry and extensive use as in vivo markers. We discovered that GFPs of diverse origins can act as light-induced electron donors in photochemical reactions with various electron acceptors, including biologically relevant ones. Moreover, via green-to-red GFP photoconversion, this process can be observed in living cells without additional treatment.