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First Pass at Supramolecular Structures
Published in Thomas M. Nordlund, Peter M. Hoffmann, Quantitative Understanding of Biosystems, 2019
Thomas M. Nordlund, Peter M. Hoffmann
Figure 6.25 shows a trimeric protein called Omp32 (outer membrane porin protein 32), which is an anion-selective porin, a protein that forms pores in membranes. The selectivity (anion/cation ratio) is about 20. This porin consists of a 16-stranded beta barrel with eight and seven loops or turns on either side of the membrane. A cluster of positively charged arginines (Arg 38, Arg 75, and Arg 133) determines the electrostatic field close to the constriction zone. The energy of the charged arginines is stabilized by a buried Glu amino acid (Glu 58), which strongly interacts with Arg 75 and Arg 38. A sulfate ion is bound to Arg 38 in the channel constriction zone in the X-ray–determined crystal structure of Figure 6.25. A small polypeptide of mass 5.8 kDa appears bound to Omp32 on one side, close to the axis of the trimer. Omp32 selectivity for relatively small anions is conferred by the Arg positive potential, which is not attenuated by negative charges inside the channel, and by a narrow constriction zone. This porin protein membrane “hole” is typical of OMP proteins found in various organisms.
Biosensors for Food Component Analysis
Published in C. Anandharamakrishnan, S. Parthasarathi, Food Nanotechnology, 2019
Praveena Bhatt, Monali Mukherjee, Uchangi Satyaprasad Akshath
In a previous work by one of the authors of this chapter (Padmaja et al., 2014; Figure 15.5), an immunosensor was designed to assess bovine mastitis by quantifying leukotoxin M/F′-PV (LukM/F′-PV), a potent neutrophil targeting a beta-barrel pore-forming toxin secreted by bovine strains of S. aureus. Initially, polyclonal antibodies to the recombinant LukF (rLukF) component of LukM/F′-PV were raised in chicken. They were functionalized to gold nanoparticles, and an immunoassay based on nanosurface energy transfer (NSET) was designed. In brief, rLukF was incubated with functionalized GNPs, and fluorescein isothiocyanate (FITC)-labeled secondary antibodies were added. The simultaneous fluorescence quenching was monitored as a function of toxin concentration. The method enabled detection of leukotoxin in the range of 100–0.1 ng ml−1 (LOD of 0.1 ng ml−1 and R2 = 0.9908). The suitability of the assay to detect toxins in spiked and field samples was also reported.
Advanced Light Microscopy Techniques
Published in Jay L. Nadeau, Introduction to Experimental Biophysics, 2017
These proteins are characterized by a chromophore formed in their beta-barrel structure. This chromophore shielding renders the photoswitching performance of FPs less sensitive to their nanoenvironment as compared to synthetic dyes. FPs used for PALM are either photoactivatable, photoconvertable, or photoswitchable. Photoactivatable and photoconvertable FPs undergo permanent structural changes upon UV activation, such as permanent breakage of their protein backbone. Therefore, in principle, one molecule should be imaged only once after the FP has been photoactivated or photoconverted. In practice, however, these probes have been shown to reversibly switch, which means that a single FP can yield several molecular localizations. This complicates experiments where quantitative molecular counting is required. Several studies have addressed this concern and developed methods to overcome this overcounting problem.
Biosynthesis of silver nanoparticles with adiantum capillus-veneris L leaf extract in the batch process and assessment of antibacterial activity
Published in Green Chemistry Letters and Reviews, 2018
Sariyeh Omidi, Sajjad Sedaghat, Kambiz Tahvildari, Pirouz Derakhshi, Fereshte Motiee
The maximum inhibition zone in a highly concentrated solution (stock AgNPs) is listed in Table 1. Also, the zone inhibition of two antibiotics Ciprofloxacin and Gentamicin was compared with AgNPs (52). AgNPs were as effective as Ciprofloxacin and Gentamicin. Also, silver not only have a close interaction with the surface of the membrane, but can also penetrate deep inside the bacteria. According to some studies, the antimicrobial activity of silver is relatively better against Gram-negative bacteria, compared to Gram-positive bacteria; this may be related to the thinner layer of peptidoglycans and beta barrel proteins (porins) in the cell wall structure (53). This mechanism is classified broadly as the direct effects of NPs on microbial cells. The cell wall becomes permeable to the extracellular medium as soon as the cell membrane is damaged, and bacterial cells become susceptible to damage (54).