Tryptophan-Centric Bioinformatics Identifies New Lasso Peptide Modifications

Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) defined by a macrolactam linkage between the N-terminus and the side chain of an internal aspartic acid or glutamic acid residue. Instead of adopting a branched-cyclic conformation, lasso peptides are "threaded", with the C-terminal tail passing through the macrocycle to present a kinetically trapped rotaxane conformation. The availability of enhanced bioinformatics methods has led to a significant increase in the number of secondary modifications found on lasso peptides. To uncover new ancillary modifications in a targeted manner, a bioinformatic strategy was developed to discover lasso peptides with modifications to tryptophan. This effort identified numerous putative lasso peptide biosynthetic gene clusters with core regions of the precursor peptides enriched in tryptophan. Parsing of these tryptophan (Trp)-rich biosynthetic gene clusters uncovered several putative ancillary modifying enzymes, including halogenases and dimethylallyltransferases expected to act upon Trp. Characterization of two gene products yielded a lasso peptide with two 5-Cl-Trp modifications (chlorolassin) and another bearing 5-dimethylallyl-Trp and 2,3-didehydro-Tyr modifications (wygwalassin). Bioinformatic analysis of the requisite halogenase and dimethylallyltransferase revealed numerous other putative Trp-modified lasso peptides that remain uncharacterized. We anticipate that the Trp-centric strategy reported herein may be useful in discovering ancillary modifications for other RiPP classes and, more generally, guide the functional prediction of enzymes that act on specific amino acids.

Bioinformatic prediction and experimental validation of RiPP recognition elements

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a family of natural products for which discovery efforts have rapidly grown over the past decade. There are currently 38 known RiPP classes encoded by prokaryotes. Half of the prokaryotic RiPP classes include a protein domain called the RiPP Recognition Element (RRE) for successful installation of post-translational modifications on a RiPP precursor peptide. In most cases, the RRE domain binds to the N-terminal "leader" region of the precursor peptide, facilitating enzymatic modification of the C-terminal "core" region. The prevalence of the RRE domain renders it a theoretically useful bioinformatic handle for class-independent RiPP discovery; however, first-in-class RiPPs have yet to be isolated and experimentally characterized using an RRE-centric strategy. Moreover, with most known RRE domains engaging their cognate precursor peptide(s) with high specificity and nanomolar affinity, evaluation of the residue-specific interactions that govern RRE:substrate complexation is a necessary first step to leveraging the RRE domain for various bioengineering applications. This chapter details protocols for developing custom bioinformatic models to predict and annotate RRE domains in a class-specific manner. Next, we outline methods for experimental validation of precursor peptide binding using fluorescence polarization binding assays and in vitro enzyme activity assays. We anticipate the methods herein will guide and enhance future critical analyses of the RRE domain, eventually enabling its future use as a customizable tool for molecular biology.

Nickel-Catalyzed Decarboxylative Arylation of Azoles with Perfluoro- and Nitrobenzoates

This manuscript describes a Ni-catalyzed method for the direct arylation of azoles using benzoates. Perfluorophenyl and 2-nitrobenzoates participate in these reactions to afford the corresponding products in modest to good yields. The efficiency of the arylations with perfluorobenzoates is highly dependent on both the degree and position of fluorine atoms in the benzoates.

Nickel-Mediated Synthesis of Isoindolinones at Room Temperature

This communication describes a method for the Ni(cod) 2-mediated intramolecular arylation of alkyl C-H bonds adjacent to the nitrogen atom in benzamide substrates. The transformation proceeds at room temperature and exhibits selectivity for functionalization of more substituted C-H bonds. The yields of the desired isoindolinone products are higher with benzamide substrates containing tertiary alkyl groups on the nitrogen atom than with those bearing primary or secondary alkyls. The results described herein suggest a mechanism involving radical intermediates for these reactions.

Salpingectomy improves the pregnancy rate in in-vitro fertilization patients with hydrosalpinx

The objective of this study was to assess the impact on pregnancy outcome of excising hydrosalpinx(ges) in patients with repeated in-vitro fertilization (IVF) failures. A group of 15 patients who had previously undergone failed IVF attempts and had unilateral or bilateral hydrosalpinx was subjected to an operative laparoscopy with excision of the affected tube(s). Of these, 10 patients underwent a unilateral salpingectomy and five had a bilateral salpingectomy. Stimulated cycles of IVF and/or cryo-thaw cycles were then carried out post-salpingectomy and the results were compared to those of pre-salpingectomy cycles. There was no statistically significant difference between the number of mature eggs retrieved, peak oestradiol concentrations, number of days to human chorionic gonadotrophin administration, or number of pre-zygotes frozen in the stimulated cycles pre- versus post-salpingectomy. Pre-salpingectomy, 15 patients underwent 38 stimulated cycles and eight patients underwent 14 cycles with cryopreserved-thawed embryos, achieving one pregnancy from a fresh transfer that resulted in a miscarriage. Post-salpingectomy, eight patients underwent 12 stimulated cycles, achieving five clinical pregnancies (two miscarriages and three ongoing pregnancies, i.e. either delivered or a pregnancy > or = 20 weeks), and nine patients underwent 10 cycles with cryopreserved-thawed embryos, achieving four clinical pregnancies (one miscarriage and three ongoing). We conclude that excision of hydrosalpinx(ges) improves the pregnancy potential after IVF, and that new and repeat IVF patients should be counselled accordingly.

Adipose tissue deposition in sleep apnea

To determine whether adipose tissue is deposited in the neck adjacent to the upper airway in patients with obstructive sleep apnea (OSA), we studied 21 subjects with OSA and nine without OSA using magnetic resonance imaging with a T-1 weighted spin echo sequence and polysomnography. We observed that patients with OSA had a larger volume of adipose tissue adjacent to their upper airway than did subjects without OSA.

Pharyngeal fat in obstructive sleep apnea

Although most patients with obstructive sleep apnea (OSA) are obese, it is not known how obesity contributes to airway collapse during sleep. The purpose of this study was to determine whether the volume of adipose tissue adjacent to the pharyngeal airway in humans is related to the degree of OSA. We studied 30 subjects, nine without OSA and 21 with OSA; two subjects were studied before and after weight loss. Adipose tissue was detected with magnetic resonance imaging using T1-weighted spin echo sequences. The volume of adipose tissue adjacent to the upper airway was determined by measuring the volume of all pixels in the intensity range of adipose tissue within the region bounded by the ramus of the mandible, the spine, the anterior border of the soft palate, and the hard palate. Polysomnography was performed with conventional techniques. All subjects had a collection of adipose tissue adjacent to the upper airway; the volume of this adipose tissue correlated with the number of apneas plus hypopneas per hour of sleep (r = 0.59, p < 0.001). Both patients who lost weight and had fewer apneas and hypopneas had a marked decrease in the pharyngeal adipose tissue volume. We conclude that adipose tissue is deposited adjacent to the pharyngeal airway in patients with OSA and that the volume of this tissue is related to the presence and degree of OSA.

Mandible enclosure of upper airway and weight in obstructive sleep apnea

Although anatomic lesions and obesity can produce obstructive sleep apnea (OSA), most subjects with OSA have no recognizable anatomic lesion. We hypothesized that the occurrence of OSA is related to the size of the region enclosed by the mandible and the degree of obesity. We studied 30 subjects with a range of OSA and obesity with magnetic resonance imaging (MRI). MRI was performed with T-1 weighted sequences. Nocturnal polysomnography was performed in all subjects. Univariate regression analysis indicated there was a significant correlation between the number of apneas and hypopneas per hour of sleep (AH/h) and (1) the area enclosed by the mandible ramus (AMR1) (r = 0.48, p < 0.01) and (2) the distance from the teeth to the posterior mandible ramus (r = 0.39, p < 0.05). Stepwise multiple regression analysis indicated that weight, AMR1, and height explained 69% of the variance of AH/h (r2 = 0.69). We conclude that the occurrence of OSA in these subjects is related to the size of the region enclosed by the mandible as well as to their weight.