Highly efficient site-specific protein modification using tyrosinase from Streptomyces avermitilis: Structural insight.

Tyrosinase-mediated protein conjugation has recently drawn attention as a site-specific protein modification tool under mild conditions. However, the tyrosinases reported to date act only on extremely exposed tyrosine residues, which limits where the target tyrosine can be located. Herein, we report a tyrosinase from Streptomyces avermitilis (SaTYR), that exhibits a much higher activity against tyrosine residues on the protein surface than other tyrosinases. We determined the crystal structure of SaTYR and revealed that the enzyme has a relatively flat and shallow substrate-binding pocket to accommodate a protein substrate. We demonstrated SaTYR-mediated fluorescence dye tagging and PEGylation of a surface tyrosine residue that was unreacted by other tyrosinases with an approximately 95.2 % conjugation yield in 1 h. We also present a structural rationale that considers the steric hindrance from adjacent residues and surrounding structures along with the extent of solvent exposure of residues, as necessary when determining the optimal positions for introducing target tyrosine residues in SaTYR-mediated protein modification. The study demonstrated that the novel tyrosinase, SaTYR, extends the scope of tyrosinase-mediated protein modification, and we propose that site-specific tyrosine conjugation using SaTYR is a promising strategy for protein bioconjugation in various applications.

Arteriovenous Metabolomics to Measure In Vivo Metabolite Exchange in Brown Adipose Tissue.

Brown adipose tissue (BAT) plays a crucial role in regulating metabolic homeostasis through a unique energy expenditure process known as non-shivering thermogenesis. To achieve this, BAT utilizes a diverse menu of circulating nutrients to support its high metabolic demand. Additionally, BAT secretes metabolite-derived bioactive factors that can serve as either metabolic fuels or signaling molecules, facilitating BAT-mediated intratissue and/or intertissue communication. This suggests that BAT actively participates in systemic metabolite exchange, an interesting feature that is beginning to be explored. Here, we introduce a protocol for in vivo mouse-level optimized BAT arteriovenous metabolomics. The protocol focuses on relevant methods for thermogenic stimulations and an arteriovenous blood sampling technique using Sulzer's vein, which selectively drains interscapular BAT-derived venous blood and systemic arterial blood. Next, a gas chromatography-based metabolomics protocol using those blood samples is demonstrated. The use of this technique should expand the understanding of BAT-regulated metabolite exchange at the inter-organ level by measuring the net uptake and release of metabolites by BAT.

The role of immunomodulatory metabolites in shaping the inflammatory response of macrophages.

Macrophage activation has long been implicated in a myriad of human pathophysiology, particularly in the context of the dysregulated capacities of an unleashing intracellular or/and extracellular inflammatory response. A growing number of studies have functionally coupled the macrophages' inflammatory capacities with dynamic metabolic reprogramming which occurs during activation, albeit the results have been mostly interpreted through classic metabolism point of view; macrophages take advantage of the rewired metabolism as a source of energy and for biosynthetic precursors. However, a specific subset of metabolic products, namely immune-modulatory metabolites, has recently emerged as significant regulatory signals which control inflammatory responses in macrophages and the relevant extracellular milieu. In this review, we introduce recently highlighted immuno-modulatory metabolites, with the aim of understanding their physiological and pathological relevance in the macrophage inflammatory response. [BMB Reports 2022; 55(11): 519-527].

Generation of a recombinant antibody for sensitive detection of Pseudomonas aeruginosa.

Pseudomonas aeruginosa (P. aeruginosa) is a major pathogen that causes nosocomial infections and often exhibits antibiotic resistance. Therefore, the development of an accurate method for detecting P. aeruginosa is required to control P. aeruginosa-related outbreaks. In this study, we established an enzyme-linked immunosorbent assay method for the sensitive detection of three P. aeruginosa strains, UCBPP PA14, ATCC 27853, and multidrug-resistant ATCC BAA-2108. We produced a recombinant antibody (rAb) against P. aeruginosa V-antigen (PcrV), which is a needle tip protein of the type III secretion system of P. aeruginosa using mammalian cells with high yield and purity, and confirmed its P. aeruginosa binding efficiency. The rAb was paired with commercial anti-P. aeruginosa Ab for a sandwich ELISA, resulting in an antigen-concentration-dependent response with a limit of detection value of 230 CFU/mL. These results suggest that the rAb produced herein can be used for the sensitive detection of P. aeruginosa with a wide range of applications in clinical diagnosis and point-of-care testing.

Trap column-based intact mass spectrometry for rapid and accurate evaluation of protein molecular weight.

The determination of the molecular weight (MW) of a protein using high-resolution mass spectrometry (MS) is a crucial tool used to confirm whether the protein was correctly expressed and adequately purified. However, a non-volatile buffer is normally used for protein purification and storage. Therefore, a pre-treatment step using ultrafiltration (UF) is required to exchange the buffer with a volatile buffer prior to the introduction of the protein sample into the MS equipment. This pre-treatment step is time-consuming. In this study, a trap column-based pre-treatment method applied in a nano-LC system was developed for rapid and convenient analysis of the MW of proteins. First, the trap column system was compared with the conventional UF treatment system and non-treatment system using bovine serum albumin. Subsequently, the trap column system was applied to analyze the MW of commercially available and lab-synthesized recombinant proteins. The intensity of the base peak and signal-to-noise ratio of the trap column-based pre-treated protein were higher than those of the UF-treated protein. Moreover, the entire automated procedure of the trap column-based system was conducted within 20 min, which confirms its use in versatile and accurate protein identification.

Generation of Recombinant Antibodies in HEK293F Cells for the Detection of Staphylococcus aureus.

Staphylococcus aureus is a major resistant pathogen in clinical practice. Due to the increasing number of infections, rapid and sensitive detection of antibiotic-resistant S. aureus as well as antibiotic-sensitive S. aureus is important for the prevention and control of infectious diseases. In this study, we produced recombinant antibodies against S. aureus from mammalian human embryonic kidney 293 Freestyle cells with high yield and purity. These recombinant antibodies showed high binding affinity and low detection limit in both indirect and sandwich enzyme-linked immunosorbent assays for the detection of methicillin-resistant S. aureus and methicillin-sensitive S. aureus. These results suggest that the recombinant antibodies produced herein can be used for the accurate detection of S. aureus with a wild range of applications in medical diagnosis, food safety, and drug discovery.

Enhanced Thermoelectric Conversion Efficiency of CVD Graphene with Reduced Grain Sizes.

The grain size of CVD (Chemical Vapor Deposition) graphene was controlled by changing the precursor gas flow rates, operation temperature, and chamber pressure. Graphene of average grain sizes of 4.1 µm, 2.2 µm, and 0.5 µm was synthesized in high quality and full coverage. The possibility to tailor the thermoelectric conversion characteristics of graphene has been exhibited by examining the grain size effect on the three elementary thermal and electrical properties of σ, S, and k. Electrical conductivity (σ) and Seebeck coefficients (S) were measured in a vacuum for supported graphene on SiO2/Si FET (Field Effect Transistor) substrates so that the charge carrier density could be changed by applying a gate voltage (VG). Mobility (µ) values of 529, 459, and 314 cm²/V·s for holes and 1042, 745, and 490 cm²/V·s for electrons for the three grain sizes of 4.1 µm, 2.2 µm, and 0.5 µm, respectively, were obtained from the slopes of the measured σ vs. VG graphs. The power factor (PF), the electrical portion of the thermoelectric figure of merit (ZT), decreased by about one half as the grain size was decreased, while the thermal conductivity (k) decreased by one quarter for the same grain decrease. Finally, the resulting ZT increased more than two times when the grain size was reduced from 4.1 µm to 0.5 µm.

In-Plane Thermal Conductivity of Polycrystalline Chemical Vapor Deposition Graphene with Controlled Grain Sizes.

Manipulation of the chemical vapor deposition graphene synthesis conditions, such as operating P, T, heating/cooling time intervals, and precursor gas concentration ratios (CH4/H2), allowed for synthesis of polycrystalline single-layered graphene with controlled grain sizes. The graphene samples were then suspended on 8 µm diameter patterned holes on a silicon-nitride (Si3N4) substrate, and the in-plane thermal conductivities k(T) for 320 K < T < 510 K were measured to be 2660-1230, 1890-1020, and 680-340 W/m·K for average grain sizes of 4.1, 2.2, and 0.5 µm, respectively, using an opto-thermal Raman technique. Fitting of these data by a simple linear chain model of polycrystalline thermal transport determined k = 5500-1980 W/m·K for single-crystal graphene for the same temperature range above; thus, significant reduction of k was achieved when the grain size was decreased from infinite down to 0.5 µm. Furthermore, detailed elaborations were performed to assess the measurement reliability of k by addressing the hole-edge boundary condition, and the air-convection/radiation losses from the graphene surface.

How to reliably determine the complex refractive index (RI) of graphene by using two independent measurement constraints.

Reliable determination of the complex refractive index (RI) of graphene inherently requires two independent measurement realizations for two independent unknowns of the real (nG) and imaginary (kG) components, i.e., RI = nG + i kG. Thus, any single set of measurement realization provides only one constraint that is insufficient to uniquely determine the complex RI of graphene. Tandem uses of two independent measurement techniques, namely the surface plasmon resonance (SPR) angle detection and the attenuated total reflection (ATR) intensity measurement, allow for the unique determination of the complex RI of CVD-synthesized graphene. The presently measured graphene RI is determined to be 2.65 + 1.27i for the E-field oscillating parallel to graphene at 634 nm wavelength, with variations for different numbers of L (1, 3 and 5) remaining within ±3%. Thus, our demonstration results for the specified wavelength serve as an impetus to suggest the need for two independent measurement techniques in determining both the real and imaginary RI values for graphene. Additional efforts have been made to characterize graphene layers using the density function theory (DFT): this calculation provides RIG = 2.71 + 1.41i.

Wetting and evaporative aggregation of nanofluid droplets on CVD-synthesized hydrophobic graphene surfaces.

The wetting and evaporative aggregation of alumina nanofluids (Al2O3) are examined for CVD-synthesized graphene-coated (GC) surfaces that are known as strongly hydrophobic (θcontact ≈ 90°). Our findings are compared to those associated with a hydrophilic cover glass (CG) substrate (θcontact ≈ 45°). The nanofluidic self-assemblies on the GC substrate are elaborately characterized in terms of the droplet wetting/crack formation, the particle migration time over the evaporative time (CR), the Derjaguin-Landau-Verwey-Overbeek forces (FDLVO), and the relative thermal conductivity (KR). The GC substrate forms relatively thicker and larger cracks and requires a longer evaporation time. Both the GC and CG substrates share approximately the same time constant CR, which suggests the formation of coffee-ring patterns for both substrates. The GC shows negative FDLVO, which implies a repulsive force between the nanoparticles and the substrate, and the CG shows a positive FDLVO of attraction. Furthermore, a more than 3 order of magnitude larger thermal conductivity of GC compared to that of CG drives significantly different particle/fluid motions near the drop edge areas between the two substrates.