Biliproteins and their Applications in Bioimaging

Central Composite Design for Optimization of Mitomycin C-Loaded Quantum Dots/Chitosan Nanoparticles as Drug Nanocarrier Vectors

Cancer is one of the most devastating diseases that leads to a high degree of mortality worldwide. Hence, extensive efforts have been devoted to the development of drug nanocarrier vectors as a potential new cancer treatment option. The main goal of this treatment is to deliver an anticancer medicine successfully and effectively to the patient's cells using non-toxic nanocarriers. Here, we present a drug delivery system to emphasize the optimization of an anticancer drug-loaded formulation using Mitomycin C (MMC) encapsulated in chitosan nanocarrier conjugated with a bioimaging fluorescence probe of Mn:ZnS quantum dots (MMC@CS-Mn:ZnS). Additionally, the Response Surface Methodology (RSM), which uses a quadratic model to forecast the behaviour of the nano-drug delivery system, was used to assess the optimization of encapsulation efficiency. In this investigation, the core points of the Central Composite Design (CCD) model were used with 20 runs and 6 replications. The encapsulation efficiency (EE%) was measured using UV-Vis spectroscopy at 362 nm. The highest EE% is 55.31 ± 3.09 under the optimum parameters of incubation time (105 min), concentration of MMC (0.875 mg/mL), and concentration of nanocarriers (5.0 mg/mL). Physicochemical characterizations for the nanocarriers were accessed using a nanosizer and field-emission scanning electron microscopy (FESEM). Three independent variables for the evaluation of the encapsulation efficiency were used, in which the incubation time, concentration of MMC, concentration of nanocarriers, and correlation for each variable were studied. Furthermore, the MMC drug release efficiency was carried out in four different solution pHs of 5.5, 6.0, 6.5, 7.0, and pH 7.5, and the highest cumulative drug release of 81.44% was obtained in a pH 5.5 release medium, followed by cumulative releases of 68.55%, 50.91%, 41.57%, and 32.45% in release mediums with pH 6.0, pH 6.5, pH 7.0, and pH 7.5. Subsequently, five distinct mathematical models-pseudo-first-order, pseudo-second-order, Hixson-Crowell, Korsmeyer-Peppas, and Higuchi kinetic models-were used to fit all of the drug release data. The Korsmeyers-Peppas model was found to fit it well, highlighting its importance for the log of cumulative drug release proportional to the log of time at the equilibrium state. The correlation coefficient value (R²) was obtained as 0.9527, 0.9735, 0.9670, 0.9754, and 0.9639 for the drug release in pH 5.5, pH 6.0, pH 6.5, pH 7.0, and pH 7.5, respectively. Overall, from the analysis, the as-synthesized MMC nanocarrier (MMC@CS-Mn:ZnS) synergistically elucidates the underlying efficient delivery of MMC and leverages the drug loading efficiency, and all these factors have the potential for the simultaneous curbing of non-muscle invasive bladder cancer reoccurrence and progression when applied to the real-time disease treatment.

Crystal structure of a far-red-sensing cyanobacteriochrome reveals an atypical bilin conformation and spectral tuning mechanism

Cyanobacteriochromes (CBCRs) are small, linear tetrapyrrole (bilin)-binding photoreceptors in the phytochrome superfamily that regulate diverse light-mediated adaptive processes in cyanobacteria. More spectrally diverse than canonical red/far-red-sensing phytochromes, CBCRs were thought to be restricted to sensing visible and near UV light until recently when several subfamilies with far-red-sensing representatives (frCBCRs) were discovered. Two of these frCBCRs subfamilies have been shown to incorporate bilin precursors with larger pi-conjugated chromophores, while the third frCBCR subfamily uses the same phycocyanobilin precursor found in the bulk of the known CBCRs. To elucidate the molecular basis of far-red light perception by this third frCBCR subfamily, we determined the crystal structure of the far-red-absorbing dark state of one such frCBCR Anacy_2551g3 from Anabaena cylindrica PCC 7122 which exhibits a reversible far-red/orange photocycle. Determined by room temperature serial crystallography and cryocrystallography, the refined 2.7-Å structure reveals an unusual all-Z,syn configuration of the phycocyanobilin (PCB) chromophore that is considerably less extended than those of previously characterized red-light sensors in the phytochrome superfamily. Based on structural and spectroscopic comparisons with other bilin-binding proteins together with site-directed mutagenesis data, our studies reveal protein-chromophore interactions that are critical for the atypical bathochromic shift. Based on these analyses, we propose that far-red absorption in Anacy_2551g3 is the result of the additive effect of two distinct red-shift mechanisms involving cationic bilin lactim tautomers stabilized by a constrained all-Z,syn conformation and specific interactions with a highly conserved anionic residue.

Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJ

We present a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics-statistical approach for the interpretation of nuclear magnetic resonance (NMR) chemical shift patterns in phycocyanobilin (PCB). These were originally associated with colour tuning upon photoproduct formation in red/green-absorbing cyanobacteriochrome AnPixJg2 and red/far-red-absorbing phytochrome Cph1Δ2. We pursue an indirect approach without computation of the absorption frequencies since the molecular geometry of cofactor and protein are not accurately known. Instead, we resort to a heuristic determination of the conjugation length in PCB through the experimental NMR chemical shift patterns, supported by quantum chemical calculations. We have found a characteristic correlation pattern of 13C chemical shifts to specific bond orders within the π-conjugated system, which rests on the relative position of carbon atoms with respect to electron-withdrawing groups and the polarisation of covalent bonds. We propose the inversion of this regioselective relationship using multivariate statistics and to apply it to the known experimental NMR chemical shifts in order to predict changes in the bond alternation pattern. Therefrom the extent of electronic conjugation, and eventually the change in absorption frequency, can be derived. In the process, the consultation of explicit mesomeric formulae plays an important role to qualitatively account for possible conjugation scenarios of the chromophore. While we are able to consistently associate the NMR chemical shifts with hypsochromic and bathochromic shifts in the Pg and Pfr, our approach represents an alternative method to increase the explanatory power of NMR spectroscopic data in proteins.

The Arabidopsis CRUMPLED LEAF protein, a homolog of the cyanobacterial bilin lyase, retains the bilin-binding pocket for a yet unknown function

The photosynthetic bacterial phycobiliprotein lyases, also called CpcT lyases, catalyze the biogenesis of phycobilisome, a light-harvesting antenna complex, through the covalent attachment of chromophores to the antenna proteins. The Arabidopsis CRUMPLED LEAF (CRL) protein is a homolog of the cyanobacterial CpcT lyase. Loss of CRL leads to multiple lesions, including localized foliar cell death, constitutive expression of stress-related nuclear genes, abnormal cell cycle, and impaired plastid division. Notwithstanding the apparent phenotypes, the function of CRL still remains elusive. To gain insight into the function of CRL, we examined whether CRL still retains the capacity to bind with the bacterial chromophore phycocyanobilin (PCB) and its plant analog phytochromobilin (PΦB). The revealed structure of the CpcT domain of CRL is comparable to that of the CpcT lyase, despite the low sequence identity. The subsequent in vitro biochemical assays found, as shown for the CpcT lyase, that PCB/PΦB binds to the CRL dimer. However, some mutant forms of CRL, substantially compromised in their bilin-binding ability, still restore the crl-induced multiple lesions. These results suggest that although CRL retains the bilin-binding pocket, it seems not functionally associated with the crl-induced multiple lesions.

CpeY is a phycoerythrobilin lyase for cysteine 82 of the phycoerythrin I α-subunit in marine Synechococcus

Marine Synechococcus are widespread in part because they are efficient at harvesting available light using their complex antenna, or phycobilisome, composed of multiple phycobiliproteins and bilin chromophores. Over 40% of Synechococcus strains are predicted to perform a type of chromatic acclimation that alters the ratio of two chromophores, green-light-absorbing phycoerythrobilin and blue-light-absorbing phycourobilin, to optimize light capture by phycoerythrin in the phycobilisome. Lyases are enzymes which catalyze the addition of bilin chromophores to specific cysteine residues on phycobiliproteins and are involved in chromatic acclimation. CpeY, a candidate lyase in the model strain Synechococcus sp. RS9916, added phycoerythrobilin to cysteine 82 of only the α subunit of phycoerythrin I (CpeA) in the presence or absence of the chaperone-like protein CpeZ in a recombinant protein expression system. These studies demonstrated that recombinant CpeY attaches phycoerythrobilin to as much as 72% of CpeA, making it one of the most efficient phycoerythrin lyases characterized to date. Phycobilisomes from a cpeY^- mutant showed a near native bilin composition in all light conditions except for a slight replacement of phycoerythrobilin by phycourobilin at CpeA cysteine 82. This demonstrates that CpeY is not involved in any chromatic acclimation-driven chromophore changes and suggests that the chromophore attached at cysteine 82 of CpeA in the cpeY^- mutant is ligated by an alternative phycoerythrobilin lyase. Although loss of CpeY does not greatly inhibit native phycobilisome assembly in vivo, the highly active recombinant CpeY can be used to generate large amounts of fluorescent CpeA for biotechnological uses.

High-quality quantum dots for multiplexed bioimaging: A critical review

Bioimaging done using two or more fluorophores possessing different emission wavelengths can be termed as a multicolor/multiplexed bioimaging technique. Traditionally, images are captured sequentially using multiple fluorophores having specific excitation and emission. For this purpose, multifunctional nanoprobes, such as organic fluorophores, metallic nanoparticles, semiconductor quantum dots, and carbon dots (CDs) are used. Among these fluorophores, quantum dots (QDs) have emerged as an ideal probe for multiplexed bioimaging due to their unique property of size tunable emission. However, the usage of quantum dots in bioimaging is limited due to their toxicity. Furthermore, the reproducibility of optical properties is cynical. These desirable properties, along with enhancement in quantum efficiency, photostability, fluorescence lifetime, etc. can be achieved by stringent control over synthesis parameters. This review summarizes the desirable properties and synthesis methods of such superior QDs followed by their application in multiplexed imaging.

Repurposing a photosynthetic antenna protein as a super-resolution microscopy label

Techniques such as Stochastic Optical Reconstruction Microscopy (STORM) and Structured Illumination Microscopy (SIM) have increased the achievable resolution of optical imaging, but few fluorescent proteins are suitable for super-resolution microscopy, particularly in the far-red and near-infrared emission range. Here we demonstrate the applicability of CpcA, a subunit of the photosynthetic antenna complex in cyanobacteria, for STORM and SIM imaging. The periodicity and width of fabricated nanoarrays of CpcA, with a covalently attached phycoerythrobilin (PEB) or phycocyanobilin (PCB) chromophore, matched the lines in reconstructed STORM images. SIM and STORM reconstructions of Escherichia coli cells harbouring CpcA-labelled cytochrome bd ₁ ubiquinol oxidase in the cytoplasmic membrane show that CpcA-PEB and CpcA-PCB are suitable for super-resolution imaging in vivo. The stability, ease of production, small size and brightness of CpcA-PEB and CpcA-PCB demonstrate the potential of this largely unexplored protein family as novel probes for super-resolution microscopy.

Conformational control of cofactors in nature - the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles

Tetrapyrrole-containing proteins are one of the most fundamental classes of enzymes in nature and it remains an open question to give a chemical rationale for the multitude of biological reactions that can be catalyzed by these pigment-protein complexes. There are many fundamental processes where the same (i.e., chemically identical) porphyrin cofactor is involved in chemically quite distinct reactions. For example, heme is the active cofactor for oxygen transport and storage (hemoglobin, myoglobin) and for the incorporation of molecular oxygen in organic substrates (cytochrome P450). It is involved in the terminal oxidation (cytochrome c oxidase) and the metabolism of H2O2 (catalases and peroxidases) and catalyzes various electron transfer reactions in cytochromes. Likewise, in photosynthesis the same chlorophyll cofactor may function as a reaction center pigment (charge separation) or as an accessory pigment (exciton transfer) in light harvesting complexes (e.g., chlorophyll a). Whilst differences in the apoprotein sequences alone cannot explain the often drastic differences in physicochemical properties encountered for the same cofactor in diverse protein complexes, a critical factor for all biological functions must be the close structural interplay between bound cofactors and the respective apoprotein in addition to factors such as hydrogen bonding or electronic effects. Here, we explore how nature can use the same chemical molecule as a cofactor for chemically distinct reactions using the concept of conformational flexibility of tetrapyrroles. The multifaceted roles of tetrapyrroles are discussed in the context of the current knowledge on distorted porphyrins. Contemporary analytical methods now allow a more quantitative look at cofactors in protein complexes and the development of the field is illustrated by case studies on hemeproteins and photosynthetic complexes. Specific tetrapyrrole conformations are now used to prepare bioengineered designer proteins with specific catalytic or photochemical properties.