Development of a genetically encoded site-specific fluorescent sensor of human cardiac voltage-gated sodium channel inactivation

Genetic mutations perturbing inactivation of human cardiac voltage-gated sodium channels (VGSCs), specifically Nav1.5, can cause long QT syndrome type 3 (LQT3). LQT3 is a cardiac disorder in which patients experience syncope and ventricular tachyarrhythmia, and are thus predisposed to sudden cardiac death. Deeper understanding of the structural dynamics of VGSC inactivation is needed to inform treatment of and drug design for potentially life-threatening arrhythmias. A well supported hypothesis is that the VGSC inactivated state is stabilized by hydrophobic interactions between the inactivation gate and an unknown binding site potentially involving the underside of the channel pore, C-terminus (C-T), and auxiliary proteins. Despite advances in biophysical and structural characterization of VGSCs, the specific molecular components and timing of their interactions within the inactivation complex remain unclear. Fluorescence imaging approaches that connect conformational change with channel function in mammalian cells could provide much needed mechanistic insight on the structural dynamics of the VGSC inactivation complex. This thesis describes the development of a site-specific fluorescent unnatural amino acid (UAA) labeling and spectral imaging methodology to probe the cardiac VGSC, Nav1.5, inactivation complex in live mammalian cells. First, UAA mutagenesis experiments were performed to validate orthogonal synthetase-tRNA (aaRS-tRNA) technology for fluorescent labeling of intracellular and membrane proteins in mammalian cells. Next, towards investigating conformational dynamics and intramolecular interactions related to inactivation, the Nav1.5 inactivation gate was labeled with a single environmentally sensitive fluorescent UAA L-anap. While the function of L-anap labeled channels was altered, their function remained within pathophysiological range. Then, imaging of L-anap labeled Nav1.5 in mammalian cells afforded characterization of unique L-anap spectra at different sites in the inactivation gate. Finally, using potassium-depolarization (K-depolarization) as rough means of voltage control, L-anap spectral shifts demonstrated conformational changes between the closed and open-inactivated states, which depended on the presence of the distal C-T (DCT). Site-specific L-anap labeling of the inactivation gate combined with spectral imaging and K-depolarization affords a general imaging assay to directly monitor conformational rearrangements of the Nav1.5 inactivation gate in channels expressed in live mammalian cells. While interactions with the DCT are specifically probed, this general assay provides an opportunity to bring necessary unification of ideas about VGSC inactivation, as well as insight on outstanding questions of VGSC regulation

Genetic Code Expansion: A Brief History and Perspective

Since the establishment of site-specific mutagenesis of single amino acids to interrogate protein function in the 1970s, biochemists have sought to tailor protein structure in the native cell environment. Fine-tuning the chemical properties of proteins is an indispensable way to address fundamental mechanistic questions. Unnatural amino acids (UAAs) offer the possibility to expand beyond the 20 naturally occurring amino acids in most species and install new and useful chemical functions. Here, we review the literature about advances in UAA incorporation technology from chemoenzymatic aminoacylation of modified tRNAs to in vitro translation systems to genetic encoding of UAAs in the native cell environment and whole organisms. We discuss innovative applications of the UAA technology to challenges in bioengineering and medicine

Detection of Nav1.5 conformational change in mammalian cells using the non-canonical amino acid ANAP

Nav1.5 inactivation is necessary for healthy conduction of the cardiac action potential. Genetic mutations of Nav1.5 perturb inactivation and cause potentially fatal arrhythmias associated with long QT syndrome type 3. The exact structural dynamics of the inactivation complex is unknown. To sense inactivation gate conformational change in live mammalian cells, we incorporated the solvatochromic fluorescent non-canonical amino acid ANAP into single sites in the Nav1.5 inactivation gate. ANAP was incorporated in full-length and C-terminally truncated Nav1.5 channels using mammalian cell synthetase-tRNA technology. ANAP-incorporated channels were expressed in mammalian cells and they exhibited pathophysiological function. A spectral imaging potassium-depolarization assay was designed to detect ANAP emission shifts associated with Nav1.5 conformational change. Site-specific intracellular ANAP incorporation affords live-cell imaging and detection of Nav1.5 inactivation gate conformational change in mammalian cells

Ionic modulation of immune checkpoint proteins

Despite extensive basic and clinical research on immune checkpoint regulatory pathways, little is known about the effects of the ionic tumour microenvironment on immune checkpoint expression and function. We screened effects of ion channel modulating compounds on indoleamine-2',3'-dioxygenase (IDO1) activity. Here, we describe a mechanistic link between Na+/K+ ATPase inhibition by cardiac glycosides and activity of IDO1, a well-characterized immune checkpoint. IDO1 catalyses the rate-limitig step of tryptophan catabolim and inhibits the immune response to the tumour by local depletion of tryptophan, an amino acid essential for anabolic functions in cancer and T cells

In vivo biosensing via tissue-localizable near-infrared-fluorescent single-walled carbon nanotubes

Single-walled carbon nanotubes are particularly attractive for biomedical applications, because they exhibit a fluorescent signal in a spectral region where there is minimal interference from biological media. Although single-walled carbon nanotubes have been used as highly sensitive detectors for various compounds, their use as in vivo biomarkers requires the simultaneous optimization of various parameters, including biocompatibility, molecular recognition, high fluorescence quantum efficiency and signal transduction. Here we show that a polyethylene glycol ligated copolymer stabilizes near-infrared-fluorescent single-walled carbon nanotubes sensors in solution, enabling intravenous injection into mice and the selective detection of local nitric oxide concentration with a detection limit of 1 µM. The half-life for liver retention is 4 h, with sensors clearing the lungs within 2 h after injection, thus avoiding a dominant route of in vivo nanotoxicology. After localization within the liver, it is possible to follow the transient inflammation using nitric oxide as a marker and signalling molecule. To this end, we also report a spatial-spectral imaging algorithm to deconvolute fluorescence intensity and spatial information from measurements. Finally, we demonstrate that alginate-encapsulated single-walled carbon nanotubes can function as implantable inflammation sensors for nitric oxide detection, with no intrinsic immune reactivity or other adverse response for more than 400 days.National Institutes of Health (U.S.) (T32 Training Grant in Environmental Toxicology ES007020)National Cancer Institute (U.S.) (Grant P01 CA26731)National Institute of Environmental Health Sciences (Grant P30 ES002109)Arnold and Mabel Beckman Foundation (Young Investigator Award)National Science Foundation (U.S.). Presidential Early Career Award for Scientists and EngineersScientific and Technological Research Council of Turkey (TUBITAK 2211 Research Fellowship Programme)Scientific and Technological Research Council of Turkey (TUBITAK 2214 Research Fellowship Programme)Middle East Technical University. Faculty Development ProgrammeSanofi Aventis (Firm) (Biomedical Innovation Grant

Inhibition of the Na+/K+-ATPase by cardiac glycosides suppresses expression of the IDO1 immune checkpoint in cancer cells by reducing STAT1 activation

Despite extensive basic and clinical research on immune checkpoint regulatory pathways, little is known about the effects of the ionic tumor microenvironment on immune checkpoint expression and function. Here we describe a mechanistic link between Na+/K+-ATPase (NKA) inhibition and activity of the immune checkpoint protein indoleamine-pyrrole 2',3'-dioxygenase 1 (IDO1). We found that IDO1 was necessary and sufficient for production of kynurenine, a downstream tryptophan metabolite, in cancer cells. Based on this, we developed a spectrophotometric assay to screen a library of 31 model ion transport-targeting compounds for potential effects on IDO1 function in A549 lung and MDA-MB-231 breast cancer cells. This screen revealed that the cardiac glycosides ouabain and digoxin inhibited kynurenine production at concentrations that did not affect cell survival. Furthermore, NKA inhibition by ouabain and digoxin resulted in increased intracellular Na+ levels and downregulation of IDO1 mRNA and protein levels, which was consistent with the reduction in kynurenine levels. Additionally, knockdown of ATP1A1, the ɑ1 subunit of the NKA and target of cardiac glycosides, increased Na+ levels to a lesser extent than cardiac glycoside treatment, and did not affect IDO1 expression. However, ATP1A1 knockdown significantly enhanced the effect of cardiac glycosides on IDO1 expression and kynurenine production. Mechanistically, we show that cardiac glycoside treatment resulted in curtailing the length of phosphorylation-mediated stabilization of STAT1, a transcriptional regulator of IDO1 expression, an effect enhanced by ATP1A1 knockdown. Overall, our findings reveal cross-talk between ionic modulation via cardiac glycosides and immune checkpoint protein expression in cancer cells with broad mechanistic and clinical implications

Molecular recognition using corona phase complexes made of synthetic polymers adsorbed on carbon nanotubes.

Understanding molecular recognition is of fundamental importance in applications such as therapeutics, chemical catalysis and sensor design. The most common recognition motifs involve biological macromolecules such as antibodies and aptamers. The key to biorecognition consists of a unique three-dimensional structure formed by a folded and constrained bioheteropolymer that creates a binding pocket, or an interface, able to recognize a specific molecule. Here, we show that synthetic heteropolymers, once constrained onto a single-walled carbon nanotube by chemical adsorption, also form a new corona phase that exhibits highly selective recognition for specific molecules. To prove the generality of this phenomenon, we report three examples of heteropolymer-nanotube recognition complexes for riboflavin, L-thyroxine and oestradiol. In each case, the recognition was predicted using a two-dimensional thermodynamic model of surface interactions in which the dissociation constants can be tuned by perturbing the chemical structure of the heteropolymer. Moreover, these complexes can be used as new types of spatiotemporal sensors based on modulation of the carbon nanotube photoemission in the near-infrared, as we show by tracking riboflavin diffusion in murine macrophages

Molecular recognition using corona phase complexes made of synthetic polymers adsorbed on carbon nanotubes

Understanding mol. recognition is of fundamental importance in applications such as therapeutics, chem. catalysis and sensor design. The most common recognition motifs involve biol. macromols. such as antibodies and aptamers. The key to biorecognition consists of a unique three-dimensional structure formed by a folded and constrained bioheteropolymer that creates a binding pocket, or an interface, able to recognize a specific mol. Here, we show that synthetic heteropolymers, once constrained onto a single-walled carbon nanotube by chem. adsorption, also form a new corona phase that exhibits highly selective recognition for specific mols. To prove the generality of this phenomenon, we report three examples of heteropolymer-nanotube recognition complexes for riboflavin, L-thyroxine and oestradiol. In each case, the recognition was predicted using a two-dimensional thermodn. model of surface interactions in which the dissocn. consts. can be tuned by perturbing the chem. structure of the heteropolymer. Moreover, these complexes can be used as new types of spatiotemporal sensors based on modulation of the carbon nanotube photoemission in the near-IR, as we show by tracking riboflavin diffusion in murine macrophages. [on SciFinder(R)