Design of fluorescent fusion protein probes

Application of FRET-Based Biosensor "ATeam" for Visualization of ATP Levels in the Mitochondrial Matrix of Living Mammalian Cells

Genetically encoded biosensors utilizing the Förster resonance energy transfer (FRET) are powerful tools for live cell imaging of various cellular processes. Our group has previously developed a series of FRET-based biosensors, named "ATeam," for visualization of ATP levels inside a single living cell. ATeam not only provides a window of insight into a single cell but also allows for visualization of ATP levels in mitochondrial matrix of a single living cell. This novel tool is able to monitor alterations in cellular ATP in response to various treatments in real time. Here we present a method for the evaluation of ATP levels in mitochondria in living cells by using ATeam. At the end of this chapter, an example of experimental results is described for a better understanding of the presented procedure.

Modular assembly of synthetic proteins that span the plasma membrane in mammalian cells

Background

To achieve synthetic control over how a cell responds to other cells or the extracellular environment, it is important to reliably engineer proteins that can traffic and span the plasma membrane. Using a modular approach to assemble proteins, we identified the minimum necessary components required to engineer such membrane-spanning proteins with predictable orientation in mammalian cells.

Results

While a transmembrane domain (TM) fused to the N-terminus of a protein is sufficient to traffic it to the endoplasmic reticulum (ER), an additional signal peptidase cleavage site downstream of this TM enhanced sorting out of the ER. Next, a second TM in the synthetic protein helped anchor and accumulate the membrane-spanning protein on the plasma membrane. The orientation of the components of the synthetic protein were determined through measuring intracellular Ca²⁺ signaling using the R-GECO biosensor and through measuring extracellular quenching of yellow fluorescent protein variants by saturating acidic and salt conditions.

Conclusions

This work forms the basis of engineering novel proteins that span the plasma membrane to potentially control intracellular responses to extracellular conditions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-016-0320-7) contains supplementary material, which is available to authorized users.

The spatiotemporal relationship between local Ca(2+) signaling and P2X2R-activated membrane blebbing

Mammalian P2X receptors (P2XRs), a family of seven ionotropic purinergic receptors, function as ion channels modulating diverse cellular processes such as secretion, apoptosis and proliferation in response to extracellular ATP. Previously, it was shown that upon ATP stimulus, the P2X7 receptor (a member of P2XR family) triggers plasma membrane (PM) blebbing in HEK293 cells. In this study, we demonstrate that this phenomenon extends to another member of the P2XR family-P2X2 receptor (P2X2R). Similar to P2X7 receptor, P2X2R blebbing is dependent on Ca(2+)-calmodulin and ROCK-I. To elucidate the spatiotemporal relationship between Ca(2+) signaling and blebbing, protein biosensors and switches were used to image and generate Ca(2+) signals, respectively, while observing PM blebbing in cells. Blebbing cannot be initiated by Ca(2+) influx from the endoplasmic reticulum or by Ca(2+) transport across the PM by other Ca(2+) channels. To trigger blebbing, it is necessary for Ca(2+) to enter specifically through the P2X2R. Lastly, a local Ca(2+) signal near a fragment that encodes the intracellular P2X2R C-terminus tail is sufficient to trigger blebbing.

Molecular Modeling of Fluorescent SERCA Biosensors

Molecular modeling and simulation are useful tools in structural biology, allowing the formulation of functional hypotheses and interpretation of spectroscopy experiments. Here, we describe a method to construct in silico models of a fluorescent fusion protein construct, where a cyan fluorescent protein (CFP) is linked to the actuator domain of the Sarco/Endoplasmic Reticulum Ca(2+)-ATPase (SERCA). This CFP-SERCA construct is a biosensor that can report on structural dynamics in the cytosolic headpiece of SERCA. Molecular modeling and FRET experiments allow us to generate new structural and mechanistic models that better describe the conformational landscape and regulation of SERCA. The methods described here can be applied to the creation of models for any fusion protein constructs and also describe the steps needed to simulate FRET results using molecular models.

Programming membrane fusion and subsequent apoptosis into mammalian cells

By the delivery of specific natural or engineered proteins, mammalian cells can be programmed to perform increasingly sophisticated and useful functions. Here, we introduce a set of proteins that has potential value in cell-based therapies by programming a cell to target tumor cells. First, the delivery of VSV-G (vesicular stomatitis virus glycoprotein) allowed the cell to undergo membrane fusion with adjacent cells to form syncytia (i.e., a multinucleated cell) in conditions of low pH typically occurring at a tumor site. The formation of syncytia caused the clustering of nuclei along with an integration of the microtubule network and ER. Interestingly, the formation of syncytia between cells that are dynamically blebbing, a mode of migration preferred during tumor metastasis, resulted in the loss of these morphology changes. Lastly, the codelivery of VSV-G with L57R (an engineered photoactivated caspase-7) allowed cells to undergo low pH-dependent membrane fusion followed by blue light-dependent apoptosis. In cell-based therapies, the clearance of syncytia between tumor cells might further trigger an immune response against the tumor.

Engineered regulation of lysozyme by the SH3-CB1 binding interaction

The ability to design proteins with desired properties by using protein structural information will allow us to create high-value therapeutic and diagnostic products. Using the protein structures of lambda lysozyme and the SH3 domain of human Crk, we designed a synthetic protein switch that controls the activity of lysozyme by sterically hindering its active cleft through the binding of SH3 to its CB1 peptide-binding partner. First, several fusion protein designs with lysozyme and CB1 were modeled to determine the one with greatest steric effect in the presence of SH3. Next, the selected fusion protein was created and tested in vitro. In the absence of SH3, the lysozyme-CB1 fusion protein functioned normally. In the presence of SH3, the lysozyme activity was inhibited and with the addition of excess CB1 peptides to compete for SH3 binding, the lysozyme activity was restored. Lastly, this structure-based strategy can be used to engineer synthetic regulation by peptide-domain-binding interfaces into a variety of proteins.

Parts-based assembly of synthetic transmembrane proteins in mammalian cells

Transmembrane proteins span cellular membranes such as the plasma membrane and endoplasmic reticulum (ER) membrane to mediate inter- and intracellular interactions. An N-terminal signal peptide and transmembrane helices facilitate recruitment to the ER and integration into the membrane, respectively. Using a parts-based assembly approach in this study, we confirm that the minimum requirement to create a transmembrane protein is indeed only a transmembrane helix (TM). When transfected in mammalian cells, our fusion proteins in the schematic form X-TM-Y were localized to vesicles, the golgi apparatus, the nuclear envelope, or the endoplasmic reticulum, consistent with ER targeting. Further studies to determine orientation showed that X was facing the cytoplasm, and Y the lumen. Lastly, in our fusion proteins with an N-terminal TM, the TM effectively reversed the orientation of X and Y. This knowledge can be applied to the parts-based engineering of synthetic transmembrane proteins with varied functions and biological applications.

Effects of rapamycin-induced oligomerization of parvalbumin, Stim1 and Orai1 in puncta formation

Elevations of cytosolic Ca2+ from the endoplasmic reticulum (ER) regulate a diverse range of cellular processes. When these luminal stores become depleted, the transmembrane ER protein Stim1 oligomerizes and translocates within the ER membrane to puncta junctions to couple with Orai1 channels, activating store-operated calcium entry (SOCE). Stim1 oligomerization and puncta formation have generally been associated with its luminal domains, however, studies have implicated that the cytoplasmic domains may contribute to this oligomerization. Studies have also suggested that intermediate or regulating elements may be required to fine-tune puncta formation and activation of SOCE. Here we made fusion proteins of Stim1 and Orai1 with FRB and FKBP12 domains that associate in the presence of rapamycin. Rapamycin-induced coupling of Stim1 to Stim1, Orai1 to Orai1 and Stim1 to Orai1 was found to be insufficient for puncta formation. Rapamycin was then used to recruit the cytosolic Ca2+ buffer protein parvalbumin (Pav) to Stim1 in order to buffer the local cytosolic Ca2+ near the ER membrane. Interestingly, Pav buffering near the ER caused puncta formation that was indistinguishable from those caused by thapsigargin. Our results suggest that Stim1 oligomerization and puncta formation may be additionally regulated either by local Ca2+ levels near the ER membrane or by as yet unidentified Ca2+-dependent proteins interacting with the cytoplasmic domains of Stim1.