Biosynthesis and mode of action of ribosomally synthesized and post-translationally modified antimicrobial peptides

One of the greatest sources of biologically active compounds is natural products. Often these compounds serve as platforms for the design and development of novel drugs and therapeutics. The overwhelming amount of genomic information acquired in recent years has revealed that ribosomally synthesized and post-translationally modified natural products are much more widespread than originally anticipated. Identified in nearly all forms of life, these natural products display incredible structural diversity and possess a wide range of biological functions that include antimicrobial, antiviral, anti-inflammatory, antitumor, and antiallodynic activities. The unique pathways taken to biosynthesize these compounds offer exciting opportunities for the bioengineering of these complex molecules. The studies described herein focus on both the mode of action and biosynthesis of antimicrobial peptides. In Chapter 2, it is demonstrated that haloduracin, a recently discovered two-peptide lantibiotic, possesses nanomolar antimicrobial activity against a panel of bacteria strains. The potency of haloduracin rivals that of nisin, an economically and therapeutically relevant lantibiotic, which can be attributed to a similar dual mode of action. Moreover, it was demonstrated that this lantibiotic of alkaliphile origin has better stability at physiological pH than nisin. The molecular target of haloduracin was identified as the cell wall peptidoglycan precursor lipid II. Through the in vitro biosynthesis of haloduracin, several analogues of Halα were prepared and evaluated for their ability to inhibit peptidoglycan biosynthesis as well as bacterial cell growth. In an effort to overcome the limitations of in vitro biosynthesis strategies, a novel strategy was developed resulting in a constitutively active lantibiotic synthetase enzyme. This methodology, described in Chapter 3, enabled the production of fully-modified lacticin 481 products with proteinogenic and non-proteinogenic amino acid substitutions. A number of lacticin 481 analogues were prepared and their antimicrobial activity and ability to bind lipid II was assessed. Moreover, site-directed mutagenesis of the constitutively active synthetase resulted in a kinase-like enzyme with the ability to phosphorylate a number of peptide substrates. The hunt for a lantibiotic synthetase enzyme responsible for installing the presumed dehydro amino acids and a thioether ring in the natural product sublancin, led to the identification and characterization of a unique post-translational modification. The studies described in Chapter 4, demonstrate that sublancin is not a lantibiotic, but rather an unusual S-linked glycopeptide. Its structure was revised based on extensive chemical, biochemical, and spectroscopic characterization. In addition to structural investigation, bioinformatic analysis of the sublancin gene cluster led to the identification of an S-glycosyltransferase predicted to be responsible for the post-translational modification of the sublancin precursor peptide. The unprecedented glycosyltransferase was reconstituted in vitro and demonstrated remarkable substrate promiscuity for both the NDP-sugar co-substrate as well as the precursor peptide itself. An in vitro method was developed for the production of sublancin and analogues which were subsequently evaluated in bioactivity assays. Finally, a number of putative biosynthetic gene clusters were identified that appear to harbor the necessary genes for production of an S-glycopeptide. An additional S-glycosyltransferase with more favorable intrinsic properties including better expression, stability, and solubility was reconstituted in vitro and demonstrated robust catalytic abilities.

Plasma diagnostics and ITO film deposition by RF-assisted closed-field dual magnetron system

Deposition of indium tin oxide (ITO) among various transparent conductive materials on flexible organic substrates has been intensively investigated among academics and industrials for a whole new array of imaginative optoelectronic products. One critical challenge coming with the organic materials is their poor thermal endurances, considering that the process currently used to produce industry-standard ITO usually involves relatively high substrate temperature in excess of 200°C and post-annealing. A lower processing temperature is thus demanded, among other desires of high deposition rate, large substrate area, good uniformity, and high quality of the deposited materials. For this purpose, we developed an RF-assisted closed-field dual magnetron sputtering system. The “prototype” system consists of a 3-inch unbalanced dual magnetron operated at a closed-field configuration. An RF coil was fabricated and placed between the two magnetron cathodes to initiate a secondary plasma. The concept is to increase the ionization faction with the RF enhancement and utilize the ion energy instead of thermal energy to facilitate the ITO film growth. The closed-field unbalanced magnetrons create a plasma in the intervening region rather than confine it near the target, thus achieving a large-area processing capability. An RF-compensated Langmuir probe was used to characterize and compare the plasmas in mirrored balanced and closed-field unbalanced magnetron configurations. The spatial distributions of the electron density ne and electron temperature Te were measured. The density profiles reflect the shapes of the plasma. Rather than intensively concentrated to the targets/cathodes in the balanced magnetrons, the plasma is more dispersive in the closed-field mode with a twice higher electron density in the substrate region. The RF assistance significantly enhances ne by one or two orders of magnitude higher. The effect of various other parameters, such as pressure, on the plasma was also studied. The ionization fractions of the sputtered atoms were measured using a gridded energy analyzer (GEA) combined with a quartz crystal microbalance (QCM). The presence of the RF plasma effectively increases the ITO ionization fraction to around 80% in both the balanced and closed-field unbalanced configurations. The ionization fraction also varies with pressure, maximizing at 5-10 mTorr. The study of the ionization not only facilitates understanding the plasma behaviors in the RF-assisted magnetron sputtering, but also provides a criterion for optimizing the film deposition process. ITO films were deposited on both glass and plastic (PET) substrates in the 3-inch RF-assisted closed-field magnetrons. The electrical resistivity and optical transmission transparency of the ITO films were measured. Appropriate RF assistance was shown to dramatically reduce the electrical resistivity. An ITO film with a resistivity of 1.2×10-3 Ω-cm and a visible light transmittance of 91% was obtained with a 225 W RF enhancement, while the substrate temperature was monitored as below 110°C. X-ray photoelectron spectroscopy (XPS) was employed to confirm the ITO film stoichiometry. The surface morphology of the ITO films and its effect on the film properties were studied using atomic force microscopy (AFM). The prototype of RF-assisted closed-field magnetron was further extended to a larger rectangular shaped dual magnetron in a flat panel display manufacturing system. Similar improvement of the ITO film conductivities by the auxiliary RF was observed on the large-area PET substrates. Meanwhile, significant deposition rates of 25-42 nm/min were achieved.