Recent advances in technology for measuring and manipulating cell signals

Alternative Strategy for Spectral Tuning of Flavin-Binding Fluorescent Proteins

iLOV is an engineered flavin-binding fluorescent protein (FbFP) with applications for in vivo cellular imaging. To expand the range of applications of FbFPs for multicolor imaging and FRET-based biosensing, it is desirable to understand how to modify their absorption and emission wavelengths (i.e., through spectral tuning). There is particular interest in developing FbFPs that absorb and emit light at longer wavelengths, which has proven challenging thus far. Existing spectral tuning strategies that do not involve chemical modification of the flavin cofactor have focused on placing positively charged amino acids near flavin's C4a and N5 atoms. Guided by previously reported electrostatic spectral tunning maps (ESTMs) of the flavin cofactor and by quantum mechanical/molecular mechanical (QM/MM) calculations reported in this work, we suggest an alternative strategy: placing a negatively charged amino acid near flavin's N1 atom. We predict that a single-point mutant, iLOV-Q430E, has a slightly red-shifted absorption and fluorescence maximum wavelength relative to iLOV. To validate our theoretical prediction, we experimentally expressed and purified iLOV-Q430E and measured its spectral properties. We found that the Q430E mutation results in a slight change in absorption and a 4-8 nm red shift in the fluorescence relative to iLOV, in good agreement with the computational predictions. Molecular dynamics simulations showed that the carboxylate side chain of the glutamate in iLOV-Q430E points away from the flavin cofactor, which leads to a future expectation that further red shifting may be achieved by bringing the side chain closer to the cofactor.

Implementation of a Practical Teaching Course on Protein Engineering

Simple Summary

Proteins are the workhorses of the cell. With different combinations of the 20 common amino acids and some modifications of these amino acids, proteins have evolved with a staggering array of new functions and capabilities due to Protein Engineering techniques. The practical course presented was offered to undergraduate bioengineering and chemical students at the Faculty of Engineering of the University of Porto (Portugal) and consists of sequential laboratory sessions to learn the basic skills related to the expression and purification of recombinant proteins in bacterial hosts. These experiments were successfully applied by students as all working groups were able to isolate a model recombinant protein (the enhanced green fluorescent protein) from a cell lysate containing a mixture of proteins and other biomolecules produced by an Escherichia coli strain and evaluate the performance of the extraction and purification procedures they learned.

Abstract

Protein Engineering is a highly evolved field of engineering aimed at developing proteins for specific industrial, medical, and research applications. Here, we present a practical teaching course to demonstrate fundamental techniques used to express, purify and analyze a recombinant protein produced in Escherichia coli—the enhanced green fluorescent protein (eGFP). The methodologies used for eGFP production were introduced sequentially over six laboratory sessions and included (i) bacterial growth, (ii) sonication (for cell lysis), (iii) affinity chromatography and dialysis (for eGFP purification), (iv) bicinchoninic acid (BCA) and fluorometry assays for total protein and eGFP quantification, respectively, and (v) sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for qualitative analysis. All groups were able to isolate the eGFP from the cell lysate with purity levels up to 72%. Additionally, a mass balance analysis performed by the students showed that eGFP yields up to 46% were achieved at the end of the purification process following the adopted procedures. A sensitivity analysis was performed to pinpoint the most critical steps of the downstream processing.

Development of a BRET2 Screening Assay Using β-Arrestin 2 Mutants

This study has focused on enhancing the signal generated from the interaction between a G-protein-coupled receptor (GPCR) and β-arrestin 2 (β-arr2), measured by the bioluminescence resonance energy transfer (BRET2) technology. Both class A (β2-adrenergic receptor [β2-AR]) and class B (neurokinin-type 1 receptor [NK1-R]) GPCRs, classified based on their internalization characteristics, have been analyzed. It was evaluated whether the BRET2 signal can be enhanced by using (1) β-arr2 phosphorylation-independent mutant (β-arr2 R169E) and (2) β-arr2 mutants deficient in their ability to interact with the components of the clathrin-coated vesicles (β-arr2 R393E, R395E and β-arr2 373 stop). For the class B receptor, there was no major difference in the agonist-promoted BRET2 signal when comparing results obtained with wild-type (wt) and mutant β-arr2. However, with the class A receptor, a more than 2-fold increase in the BRET2 signal was observed with β-arr2 mutants lacking the AP-2 or both AP-2 and clathrin binding sites. This set of data suggests that the inability of these β-arr2 mutants to interact with the components of the clathrin-coated vesicle probably prevents their rapid dissociation from the receptor, thus yielding an increased and more stable BRET2 signal. The β-arr2 R393E, R395E mutant also enhanced the signal window with other members of the GPCR family (neuropeptide Y type 2 receptor [NPY2-R] and TG1019 receptor) and was successfully applied in full-plate BRET2-based agonist and antagonist screening assays.

Enjoy the Trip: Calcium in Mitochondria Back and Forth

In the last 5 years, most of the molecules that control mitochondrial Ca(2+) homeostasis have been finally identified. Mitochondrial Ca(2+) uptake is mediated by the Mitochondrial Calcium Uniporter (MCU) complex, a macromolecular structure that guarantees Ca(2+) accumulation inside mitochondrial matrix upon increases in cytosolic Ca(2+). Conversely, Ca(2+) release is under the control of the Na(+)/Ca(2+) exchanger, encoded by the NCLX gene, and of a H(+)/Ca(2+) antiporter, whose identity is still debated. The low affinity of the MCU complex, coupled to the activity of the efflux systems, protects cells from continuous futile cycles of Ca(2+) across the inner mitochondrial membrane and consequent massive energy dissipation. In this review, we discuss the basic principles that govern mitochondrial Ca(2+) homeostasis and the methods used to investigate the dynamics of Ca(2+) concentration within the organelles. We discuss the functional and structural role of the different molecules involved in mitochondrial Ca(2+) handling and their pathophysiological role.

Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches

Following the sequencing of the human genome and many other organisms, research on protein-coding genes and their functions (functional genomics) has intensified. Subsequently, with the observation that proteins are indeed the molecular effectors of most cellular processes, the discipline of proteomics was born. Clearly, proteins do not function as single entities but rather as a dynamic network of team players that have to communicate. Though genetic (yeast two-hybrid Y2H) and biochemical methods (co-immunoprecipitation Co-IP, affinity purification AP) were the methods of choice at the beginning of the study of protein-protein interactions (PPI), in more recent years there has been a shift towards proteomics-based methods and bioinformatics-based approaches. In this review, we first describe in depth PPIs and we make a strong case as to why unraveling the interactome is the next challenge in the field of proteomics. Furthermore, classical methods of investigation of PPIs and structure-based bioinformatics approaches are presented. The greatest emphasis is placed on proteomic methods, especially native techniques that were recently developed and that have been shown to be reliable. Finally, we point out the limitations of these methods and the need to set up a standard for the validation of PPI experiments.

Spinal interneurons providing input to the final common path during locomotion

As the nexus between the nervous system and the skeletomuscular system, motoneurons effect all behavior. As such, motoneuron activity must be well regulated so as to generate appropriately timed and graded muscular contractions. Accordingly, motoneurons receive a large number of both excitatory and inhibitory synaptic inputs from various peripheral and central sources. Many of these synaptic contacts arise from spinal interneurons, some of which belong to spinal networks responsible for the generation of locomotor activity. Although the complete definition of these networks remains elusive, it is known that the neural machinery necessary to generate the basic rhythm and pattern of locomotion is contained within the spinal cord. One approach to gaining insights into spinal locomotor networks is to describe those spinal interneurons that directly control the activity of motoneurons, so-called last-order interneurons. In this chapter, we briefly survey the different populations of last-order interneurons that have been identified using anatomical, physiological, and genetic methodologies. We discuss the possible roles of these identified last-order interneurons in generating locomotor activity, and in the process, identify particular criteria that may be useful in identifying putative last-order interneurons belonging to spinal locomotor networks.

Genetically encoded probes for measurement of intracellular calcium

Small, fluorescent, calcium-sensing molecules have been enormously useful in mapping intracellular calcium signals in time and space, as chapters in this volume attest. Despite their widespread adoption and utility, they suffer some disadvantages. Genetically encoded calcium sensors that can be expressed inside cells by transfection or transgenesis are desirable. The last 10 years have been marked by a rapid evolution in the laboratory of genetically encoded calcium sensors both figuratively and literally, resulting in 11 distinct configurations of fluorescent proteins and their attendant calcium sensor modules. Here, the design logic and performance of this abundant collection of sensors and their in vitro and in vivo use and performance are described. Genetically encoded calcium sensors have proved valuable in the measurement of calcium concentration in cellular organelles, for the most part in single cells in vitro. Their success as quantitative calcium sensors in tissues in vitro and in vivo is qualified, but they have proved valuable in imaging the pattern of calcium signals within tissues in whole animals. Some branches of the calcium sensor evolutionary tree continue to evolve rapidly and the steady progress in optimizing sensor parameters leads to the certain hope that these drawbacks will eventually be overcome by further genetic engineering.

Modelling cellular signalling systems

Cell signalling pathways and networks are complex and often non-linear. Signalling pathways can be represented as systems of biochemical reactions that can be modelled using differential equations. Computational modelling of cell signalling pathways is emerging as a tool that facilitates mechanistic understanding of complex biological systems. Mathematical models are also used to generate predictions that may be tested experimentally. In the present chapter, the various steps involved in building models of cell signalling pathways are discussed. Depending on the nature of the process being modelled and the scale of the model, different mathematical formulations, ranging from stochastic representations to ordinary and partial differential equations are discussed. This is followed by a brief summary of some recent modelling successes and the state of future models.

Optical probes for molecular processes in live cells

In this review, I summarize the development over the past several years of fluorescent and/or bioluminescent indicators to pinpoint cellular processes in living cells. These processes involve second messengers, protein phosphorylations, protein-protein interactions, protein-ligand interactions, nuclear receptor-coregulator interactions, nucleocytoplasmic trafficking of functional proteins, and protein localization.

Optically switchable chelates: optical control and sensing of metal ions

This study introduces new concepts in the design, synthesis, and in vitro and in vivo characterization, manipulation, and imaging of organic chelates whose association with metal ions is rapidly and reversibly controlled by using light. Di- and tricarboxylic group bearing photochromes, nitrobenzospiropyran (nitroBIPS), undergo rapid and reversible, optically driven transitions between their spiro (SP) and fluorescent merocyanine (MC) states. The MC state of nitroBIPS-8-DA binds tightly to various metal ions resulting in specific shifts in absorption and fluorescence, and the dissociation constant for its Gadolinium complex in water is measured at approximately 5 microM. The metal-bound MC state is converted to the weaker-binding SP state with use of 543 nm light, while the SP to MC transition is complete with use of 365 or 720 nm (2-photon) light within several microseconds. Fluorescence imaging of the MC state of nitroBIPS-8-TriA was used to quantify the rate and efficiency of optical switching and to provide a real-time readout of the state of the optically switchable chelate within living cells.

Efficiency of resonance energy transfer in homo-oligomeric complexes of proteins

A theoretical model is proposed for the apparent efficiency of fluorescence (Förster) resonance energy transfer (FRET) in mixtures of free monomers and homo-oligomeric protein complexes of uniform size. The model takes into account possible pathways for transfer of optical excitations from single donors to multiple acceptors and from multiple donors (non-simultaneously) to single acceptors. This necessary departure from the standard theory has been suggested in the literature, but it has only been successfully implemented for a few particular cases, such as for particular geometries of the oligomers. The predictions of the present theoretical model differ significantly from those of the standard theory, with the exception of the case of dimers, for which agreement is observed. This model therefore provides new insights into the FRET behavior of oligomers comprising more than two monomers, and also suggests means for determining the size of oligomeric protein complexes as well as the proportion of associated and unassociated monomers.

"Turn-on" fluorescent sensor for the selective detection of zinc ion by a sterically-encumbered bipyridyl-based receptor

A sterically-encumbered 5,5'-distyryl-2,2'-bipyridyl derivative that enforces a 1:1 metal-to-ligand ratio acts as a selective turn-on sensor for Zn(2+) in THF.

Illuminating molecular processes in living cells

Lately, scientists have explored approaches to developing fluorescent and/or bioluminescent indicators to pinpoint cellular processes in single living cells. These analytical methods have become a key technology for visualizing and detecting what was otherwise unseen in live cells. The target signaling included second messengers, protein phosphorylations, protein-protein interactions, and protein localizations.

The use of bioluminescence resonance energy transfer for the study of therapeutic targets: application to tyrosine kinase receptors

During recent years, the bioluminescence resonance energy transfer (BRET) methodology has emerged as a powerful technique for the study of protein-protein interactions. This review focuses on recent work demonstrating the power of BRET for the study of tyrosine kinase receptors, using insulin and IGF-1 receptors as models. The authors show that BRET can be used to monitor ligand-induced conformational changes within homodimeric insulin and IGF-1 receptors, as well as heterodimeric insulin/IGF-1 hybrid receptors. BRET can also be used to study, in real time and in living cells, the interaction of tyrosine kinase receptors with cellular partners negatively or positively involved in the regulation of intracellular signalling (protein tyrosine phosphatases, molecular adaptors). In addition, BRET can be used to develop high-throughput screening assays for the search of molecules with therapeutic interest and could, therefore, constitute a valuable tool for laboratories involved in drug discovery.

It's cheap to be colorful. Anthozoans show a slow turnover of GFP-like proteins

Pigments homologous to the green fluorescent protein (GFP) contribute up to approximately 14% of the soluble protein content of many anthozoans. Maintenance of such high tissue levels poses a severe energetic penalty to the animals if protein turnover is fast. To address this as yet unexplored issue, we established that the irreversible green-to-red conversion of the GFP-like pigments from the reef corals Montastrea cavernosa (mcavRFP) and Lobophyllia hemprichii (EosFP) is driven by violet-blue radiation in vivo and in situ. In the absence of photoconverting light, we subsequently tracked degradation of the red-converted forms of the two proteins in coral tissue using in vivo spectroscopy and immunochemical detection of the post-translational peptide backbone modification. The pigments displayed surprisingly slow decay rates, characterized by half-lives of approximately 20 days. The slow turnover of GFP-like proteins implies that the associated energetic costs for being colorful are comparatively low. Moreover, high in vivo stability makes GFP-like proteins suitable for functions requiring high pigment concentrations, such as photoprotection.

Applications of combined spectral lifetime microscopy for biology

Live cell imaging has been greatly advanced by the recent development of new fluorescence microscopy-based methods such as multiphoton laser-scanning microscopy, which can noninvasively image deep into live specimens and generate images of extrinsic and intrinsic signals. Of recent interest has been the development of techniques that can harness properties of fluorescence, other than intensity, such as the emission spectrum and excited state lifetime of a fluorophore. Spectra can be used to discriminate between fluorophores, and lifetime can be used to report on the microenvironment of fluorophores. We describe a novel technique-combined spectral and lifetime imaging-which combines the benefits of multiphoton microscopy, spectral discrimination, and lifetime analysis and allows for the simultaneous collection of all three dimensions of data along with spatial and temporal information.

Expression and optical properties of green fluorescent protein expressed in different cellular environments

This study has investigated the expression of green fluorescent protein (GFP) variants in the cytosol and the endoplasmic reticulum (ER) of HeLa cells and evaluated the effects of the different cellular environments on the fluorescence properties of these GFP variants. Several GFP variants have been constructed by adding different N- or C-terminal signal sequences. These proteins were expressed and folded in distinct cellular compartments in HeLa cells. The localization of these GFP variants targeted to the endoplasmic recticulum was confirmed by the co-localization of DsRed2-ER as assessed by confocal microscopy. The addition of signal peptides targeting GFP variants to the ER or cytosol did not appear to alter the optical spectra of these GFP variants. However, the fluorescence intensity of these GFP variants in the ER was significantly less than that in the cytosol. Thus, the results clearly suggest that the cellular environment affects the formation and/or maturation of green fluorescence protein in vivo. These findings will be helpful in the future development and application of GFP technology aimed at investigating cellular functions performed in the ER and the cytosol.

A Steroid-Conjugated Contrast Agent for Magnetic Resonance Imaging of Cell Signaling

We have synthesized the first steroid hormone-MR contrast agent conjugate designed to track the cell signaling process upon binding to a gene switch system. The derivative has a high relaxivity and when tested in vitro is active as a progesterone antagonist (RU-486). By combining a transcriptional system and a noninvasive imaging technology, such as MRI, it would be a powerful tool to research the cell signaling pathway in vivo.

Conjugated polymer-based fluorescence turn-on sensor for nitric oxide

A turn-on fluorescent sensor for NO (g) in solution was synthesized using a bipyridyl-substituted poly(p-phenylene vinylene) derivative (CP1) as the sensory scaffold. The action of NO (g) upon the CP1-Cu(II) complex reduces it to the CP1-Cu(I) complex with a concomitant 2.8-fold increase in emission intensity. The reagent is selective for NO (g) versus other biological reactive nitrogen species, except for nitroxyl, and has a detection sensitivity limit of 6.3 nM. [structure: see text]

Genetically encoded optical probes for imaging cellular signaling pathways

The intracellular signaling can be monitored in vivo in living cells by genetically encoded intracellular fluorescent and bioluminescent probes or indicators, which include second messengers, protein phosphorylation, protein conformational changes, protein-protein interactions, and protein localizations. These probes are of general use not only for fundamental biological studies, but also for assay and screening of possible pharmaceutical or toxic chemicals that inhibit or facilitate cellular signaling pathways. In this review, two examples of such indicators were briefly introduced. First, a genetically encoded fluorescent indicator was described for the detection and characterization of estrogen agonists and antagonists. The indicator was named SCCoR (single cell-coactivator recruitment). The high sensitivity of the present indicator made it possible to distinguish between estrogen strong and weak agonists in a dose-dependent fashion, immediately after adding a ligand to live cells. Discrimination of agonists from antagonists was efficiently achieved using the indicator. The approach described here can be applied to develop biosensors for other hormone receptors as well. Another example herein is a genetically encoded bioluminescent indicator for monitoring the nuclear trafficking of target proteins in vitro and in vivo. We demonstrated quantitative cell-based in vitro sensing of ligand-induced translocation of androgen receptor, which allowed high-throughput screening of exo- and endogenous agonists and antagonists. Furthermore, the indicator enabled noninvasive in vivo imaging of the androgen receptor translocation in the brains of living mice with a charge-coupled device imaging system. These rapid and quantitative analyses in vitro and in vivo provide a wide variety of applications for screening pharmacological or toxicological compounds and testing them in living animals.

Green and red fluorescent proteins: photo- and thermally induced dynamics probed by site-selective spectroscopy and hole burning

The cloning and expression of autofluorescent proteins in living matter, combined with modern imaging techniques, have thoroughly changed the world of bioscience. In particular, such proteins are widely used as genetically encoded labels to track the movement of proteins as reporters of cellular signals and to study protein-protein interactions by fluorescence resonance energy transfer (FRET). Their optical properties, however, are complex and it is important to understand these for the correct interpretation of imaging data and for the design of new fluorescent mutants. In this Minireview we start with a short survey of the field and then focus on the photo- and thermally induced dynamics of green and red fluorescent proteins. In particular, we show how fluorescence line narrowing and high-resolution spectral hole burning at low temperatures can be used to unravel the photophysics and photochemistry and shed light on the intricate electronic structure of these proteins.

In vivo incorporation of an alkyne into proteins in Escherichia coli

Using a genetic selection we identified mutants of the M. janaschii tyrosyl-tRNA synthetase that selectively charge an amber suppressor tRNA with para-propargyloxyphenylalanine in Escherichia coli. These evolved tRNA-synthetase pairs were used to site-specifically incorporate an alkynyl group into a protein, which was subsequently conjugated with fluorescent dyes by a [3+2]-cycloaddition reaction under mild reaction conditions.

Guiding neuronal growth cones using Ca2+ signals

Pathfinding by growing axons in the developing or regenerating nervous system is guided by gradients of molecular guidance cues. The neuronal growth cone, located at the ends of axons, uses surface receptors to sense these cues and to transduce guidance information to cellular machinery that mediates growth and turning responses. Cytoplasmic Ca2+ signals have key roles in regulating this motility. Global growth cone Ca2+ signals can regulate cytoskeletal elements and membrane dynamics to control elongation, whereas Ca2+ signals localized to one side of the growth cone can cause asymmetric activation of effector enzymes to steer the growth cone. Modulating Ca2+ levels in the growth cone might overcome inhibitory signals that normally prevent regeneration in the central nervous system.

Controlled photochemical release of nitric oxide from O2-substituted diazeniumdiolates

Diazeniumdiolates are a well-established class of nitric oxide (NO) donors that have been employed in a wide variety of biochemical and pharmacological investigations. To provide a means of targeting NO release, photosensitive precursors to diazeniumdiolates have been developed and are reviewed here. After a brief description of diazeniumdiolate chemistry and the potential uses of photosensitive precursors to NO, three different classes of phototriggered diazeniumdiolates are discussed: 2-nitrobenzyl derivatives, meta-substituted benzyl derivatives, and naphthylmethyl and naphthylallyl derivatives. In addition, the photochemistry of diazeniumdiolate salts themselves is covered.

Advances in high content screening for drug discovery

Cell-based target validation, secondary screening, lead optimization, and structure-activity relationships have been recast with the advent of HCS. Prior to HCS, a computational approach to the characterization of the functions of specific target proteins and other cellular constituents, along with whole-cell functions employing fluorescence cell-based assays and microscopy, required extensive interaction among the researcher, instrumentation, and software tools. Early HCS platforms were instrument-centric and addressed the need to interface fully automated fluorescence microscopy, plate-handling automation, and seamless image analysis. HCS has since evolved into an integrated solution for accelerated drug discovery by encompassing the workflow components of assay and reagent design, robust instrumentation for automated fixed-end-point and live cell kinetic analysis, generalized and specific BioApplication software (Cellomics, Pittsburgh, PA) modules that produce information on drug responses from cell image data, and informatics/bioinformatics solutions that build knowledge from this information while providing a means to globalize HCS throughout an entire organization. This review communicates how these recent advances are incorporated into the drug discovery workflow by presenting a real-world use case.

Store-operated calcium channels: how do we measure them, and why do we care?

A major mechanism whereby calcium entry into cells is regulated is the store-operated or capacitative calcium entry pathway. In this article, two basic issues are discussed: (i) the methods investigators use to measure store-operated entry, and (ii) the role played by the store-operated pathway in responses to hormones and neurotransmitters under physiological conditions. The two topics are considered together because they are closely interrelated; as we begin to ask questions about calcium movements at low concentrations of agonists, the technology to measure these movements becomes increasing challenging.

G-protein coupled receptor oligomerization in neuroendocrine pathways

Protein-protein interactions are fundamental processes for many biological systems including those involving the superfamily of G-protein coupled receptors (GPCRs). A growing body of biochemical and functional evidence supports the existence of GPCR-GPCR homo- and hetero-oligomers. In particular, hetero-oligomers can display pharmacological and functional properties distinct from those of the homodimer or oligomer thus adding another level of complexity to how GPCRs are activated, signal and traffick in the cell. Dimerization may also play a role in influencing the activity of agonists and antagonists. We are only beginning to unravel how and why such complexes are formed, the functional implications of which will have an enormous impact on GPCR biology. Future research that studies GPCRs as dimeric or oligomeric complexes will enhance not only our understanding of GPCRs in cellular function but will also be critical for novel drug design and improved treatment of the vast array of GPCR-related conditions.

Adding amino acids with novel reactivity to the genetic code of Saccharomyces cerevisiae

Using a novel genetic selection, we have identified a series of mutants of the E. coli tyrosyl-tRNA synthetase that selectively charge an amber suppressor tRNA with p-(propargyloxy)phenylalanine and p-azidophenylalanine in yeast. These evolved tRNA-synthetase pairs can be used to site-specifically label proteins with functional groups orthogonal to normal biological chemistries. As an example, we have shown that proteins containing these amino acids can be efficiently bioconjugated with small organic molecules by a [3 + 2] cycloaddition reaction that is mild enough for the manipulation of biological samples.

High-resolution voxelation mapping of human and rodent brain gene expression

Voxelation allows high-throughput acquisition of multiple volumetric images of brain gene expression, similar to those obtained from biomedical imaging systems. To obtain these images, the method employs analysis of spatially registered voxels (cubes). For creation of high-resolution maps using voxelation, relatively small voxel sizes are necessary and instruments will be required for semiautomated harvesting of such voxels. Here, we describe two devices that allow spatially registered harvesting of voxels from the human and rodent brain, giving linear resolutions of 3.3 and 1 mm, respectively. Gene expression patterns obtained using these devices showed good agreement with known expression patterns. The voxelation instruments and their future iterations represent a valuable approach to the genome scale acquisition of gene expression patterns in the human and rodent brain.

Confocal ratiometric voltage imaging of cultured human keratinocytes reveals layer-specific responses to ATP

Recent evidence suggests that changes in membrane potential influence the proliferation and differentiation of keratinocytes. To further elucidate the role of changes in membrane potential for their biological fate, the electrical behavior of keratinocytes needs to be studied under complex conditions such as multilayered cultures. However, electrophysiological recordings from cells in the various layers of a complex culture would be extremely difficult. Given the high spatial resolution of confocal imaging and the availability of novel voltage-sensitive dyes, we combined these methods in an attempt to develop a viable alternative for recording membrane potentials in more complex tissue systems. As a first step, we used confocal ratiometric imaging of fluorescence resonance energy transfer (FRET)-based voltage-sensitive dyes. We then validated this approach by comparing the optically recorded voltage signals in HaCaT keratinocytes with the electrophysiological signals obtained by whole cell recordings of the same preparation. We demonstrate 1) that optical recordings allow precise multisite measurements of voltage changes evoked by the extracellular signaling molecules ATP and bradykinin and 2) that responsiveness to ATP differs in various layers of cultured keratinocytes.

Single-cell kinase assays: opening a window onto cell behavior

Recent advances in analytical techniques have made the performance of biochemical assays on individual mammalian cells possible. Of particular interest is the ability to measure the activation of kinases, enzymes with critical roles in virtually every aspect of cell physiology. Single-cell kinase assays promise to deliver a newfound understanding of the molecular mechanisms responsible for cellular control and behavior by revealing the dynamic nature of signal transduction networks in living cells. A recent exciting development is the potential to perform assays of multiple kinases simultaneously in a single cell.

Complexity of calcium signaling in synaptic spines

Long-term potentiation and long-term depression are thought to be cellular mechanisms contributing to learning and memory. Although the physiological phenomena have been well characterized, little consensus of their underlying molecular mechanisms has emerged. One reason for this may be the under-appreciated complexity of the signaling pathways that can arise if key signaling molecules are discretely localized within the synapse. Recent findings suggest an unanticipated degree of structural organization at the synapse, and improved methods in cellular imaging of living tissue have provided much-needed information about the intracellular dynamics of Ca(2+), thought to be critical for both LTP and LTD. In this review, we briefly summarize some of these developments, and show that a more complete understanding of cellular signaling depends on the successful integration of traditional biochemistry and molecular biology with the spatial and temporal details of synaptic ultrastructure. Biophysically realistic computer simulations can have an important role in bridging these disciplines.

Applications of novel resonance energy transfer techniques to study dynamic hormone receptor interactions in living cells

Many aspects of hormone receptor function that are crucial for controlling signal transduction of endocrine pathways can be monitored more accurately with the use of non-invasive, live cell resonance energy transfer (RET) techniques. Fluorescent RET (FRET), and its variation, bioluminescent RET (BRET), can be used to assess the real-time responses to specific hormonal stimuli, whilst preserving the cellular protein network, compartmentalization and spatial arrangement. Both FRET and BRET can be readily adapted to the study of membrane proteins. Here, we focus on their applications to the analysis of interactions involving the superfamily of hormone G-protein-coupled receptors. RET is also emerging as a significant tool for the determination of protein function in general. Such techniques will undoubtedly be of value in determining the functional identities of the vast array of proteins that are encoded by the human genome.

The use of resonance energy transfer in high-throughput screening: BRET versus FRET

Bioluminescence resonance energy transfer has developed in recent years as a new technique to study protein-protein interactions. Protein partners of interest are tagged with either luciferase or green fluorescent protein (GFP). Non-radiative energy transfer between the excited luciferase and the GFP permits the study of spatial relationships between the two partners. This technique constitutes an important tool for the study of the functional activity of different types of receptors, and can be used in sensitive, homogenous high-throughput screening assays.