Direct conversion of cytochrome c spectral shifts to fluorescence using photochromic FRET

Genetically Encoded Fluorescent Probe for Detection of Heme-Induced Conformational Changes in Cytochrome c

Cytochrome c (Cytc) is a key redox protein for energy metabolism and apoptosis in cells. The activation of Cytc is composed of several steps, including its transfer to the mitochondrial membrane, binding to cytochrome c heme lyase (CCHL) and covalent attachment to heme. The spectroscopic methods are often applied to study the structural changes of Cytc. However, they require the isolation of Cytc from cells and have limited availability under physiological conditions. Despite recent studies to elucidate the tightly regulated folding mechanism of Cytc, the role of these events and their association with different conformational states remain elusive. Here, we provide a genetically encoded fluorescence method that allows monitoring of the conformational changes of Cytc upon binding to heme and CCHL. Cerulean and Venus fluorescent proteins attached at the N and C terminals of Cytc can be used to determine its unfolded, intermediate, and native states by measuring FRET amplitude. We found that the noncovalent interaction of heme in the absence of CCHL induced a shift in the FRET signal, indicating the formation of a partially folded state. The higher concentration of heme and coexpression of CCHL gave rise to the recovery of Cytc native structure. We also found that Cytc was weakly associated with CCHL in the absence of heme. As a result, a FRET-based fluorescence approach was demonstrated to elucidate the mechanism of heme-induced Cytc conformational changes with spatiotemporal resolution and can be applied to study its interaction with small molecules and other protein partners in living cells.

Transient absorption spectroscopy and imaging of redox in muscle mitochondria

Mitochondrial redox is an important indicator of cell metabolism and health, with implications in cancer, diabetes, aging, neurodegenerative diseases, and mitochondrial disease. The most common method to observe redox of individual cells and mitochondria is through fluorescence of NADH and FAD+, endogenous cofactors serve as electron transport inputs to the mitochondrial respiratory chain. Yet this leaves out redox within the respiratory chain itself. To a degree, the missing information can be filled in by exogenous fluorophores, but at the risk of disturbed mitochondrial permeability and respiration. Here we show that variations in respiratory chain redox can be detected up by visible-wavelength transient absorption microscopy (TAM). In TAM, the selection of pump and probe wavelengths can provide multiphoton imaging contrast between non-fluorescent molecules. Here, we applied TAM with a pump at 520nm and probe at 450nm, 490nm, and 620nm to elicit redox contrast from mitochondrial respiratory chain hemeproteins. Experiments were performed with reduced and oxidized preparations of isolated mitochondria and whole muscle fibers, using mitochondrial fuels (malate, pyruvate, and succinate) to set up physiologically relevant oxidation levels. TAM images of muscle fibers were analyzed with multivariate curve resolution (MCR), revealing that the response at 620nm probe provides the best redox contrast and the most consistent response between whole cells and isolated mitochondria.

Biological Stimuli-Induced Phase Transition of a Synthesized Block Copolymer: Preferential Interactions between PNIPAM-b-PNVCL and Heme Proteins

The beguiling world of functional polymers is dominated by thermoresponsive polymers with unique structural and molecular attributes. Limited work has been reported on the protein-induced conformational transition of block copolymers; furthermore, the literature lacks a clear understanding of the influence of proteins on the phase behavior of thermoresponsive copolymers. Herein, we have synthesized poly(N-isopropylacrylamide)-b-poly(N-vinylcaprolactam) (PNIPAM-b-PNVCL) by RAFT polymerization using N-isopropylacrylamide and N-vinylcaprolactam. Furthermore, using various biophysical techniques, we have explored the effect of cytochrome c (Cyt c), myoglobin (Mb), and hemoglobin (Hb) with varying concentrations on the aggregation behavior of PNIPAM-b-PNVCL. Absorption and steady-state fluorescence spectroscopy measurements were performed at room temperature to examine the copolymerization effect on fluorescent probe binding and biomolecular interactions between PNIPAM-b-PNVCL and proteins. Furthermore, temperature-dependent fluorescence spectroscopy and dynamic light scattering studies were performed to get deeper insights into the lower critical solution temperature (LCST) of PNIPAM-b-PNVCL. Small-angle neutron scattering (SANS) was also employed to understand the copolymer behavior in the presence of heme proteins. With the incorporation of proteins to PNIPAM-b-PNVCL aqueous solution, LCST has been varied to different extents owing to the preferential, molecular, and noncovalent interactions between PNIPAM-b-PNVCL and proteins. The present study can pave new insights between heme proteins and block copolymer interactions, which will help design biomimetic surfaces and aid in the strategic fabrication of copolymer-protein bioconjugates.

Comprehensive Insight into the Protein-Surface Biomolecular Interactions on a Smart Material: Complex Formation between Poly(N-vinyl Caprolactam) and Heme Protein

Proteins are naturally occurring biopolymers that exhibit a wide range of functional applications. Meticulous knowledge about biomolecular interactions between polymeric biomaterials and body fluids or proteins is essential for designing biospecific surfaces and understanding protein-polymer interactions beyond existing limitations. In this regard, we studied the comparative effect of heme proteins such as cytochrome c, myoglobin, and hemoglobin on the phase behavior of poly(N-vinyl caprolactam) (PVCL) aqueous solution and demonstrated various biomolecular interactions in the polymer-protein complex with the aid of various biophysical techniques. Absorption spectroscopy, steady-state fluorescence spectroscopy, Fourier transform infrared spectroscopy, dynamic light scattering studies, laser Raman spectroscopy, field emission scanning electron microscopy, and transmission electron microscopy were carried out at room temperature to examine the changes in absorbance, fluorescence intensity, molecular interactions, particle size, agglomeration behavior, and surface morphologies. Furthermore, differential scanning calorimetry studies were also performed to analyze conformational changes, coil to globule transition, and phase behavior in the presence of proteins. With the addition of heme proteins, the lower critical solution temperature of PVCL increases toward higher temperature. The present study may help in designing smart biomaterials and stimulate more novel concepts in polymer-protein interactions. It also helps in the development of a biomimetic polymer for "smart" applications such as pulsatile drug release systems and controlled bioadhesion by temperature-mediated hydrophilic/hydrophobic switching.

Development of heme protein based oxygen sensing indicators

Oxygen is essential for aerobic life and is required for various oxygen-dependent biochemical reactions. In addition, oxygen plays important roles in multiple intracellular signaling pathways. Thus, to investigate oxygen homeostasis in living cells, we developed a genetically encoded oxygen sensor protein using the oxygen sensor domain of bacterial phosphodiesterase direct oxygen sensor protein (DosP), which was connected to yellow fluorescence protein (YFP) using an optimized antiparallel coiled-coil linker. The resulting ANA-Y (Anaerobic/aerobic sensing yellow fluorescence protein) was highly sensitive to oxygen and had a half saturation concentration of 18 μM. The ANA-Y reacts with dissolved oxygen within 10 s and the resulting increases in fluorescence are reversed with decreases in oxygen concentrations. This sensitivity of the ANA-Y enabled direct determinations of initial photosynthetic oxygen production by cyanobacteria. ANA-Y exhibits reversible fluorescence change of donor YFP following reversible absorbance change of acceptor DosH, and the operating mechanism of this ANA-Y could be used to develop various protein sensor probes for intracellular signaling molecules using natural sensor proteins.