Category Archives: Uncategorized

Matthew and Jib’s paper is published in Biochemistry

This paper characterizes the amide ligases in peptidyl nucleoside antifungal biosynthesis and demonstrates that the cryptic phosphorylation retains until the last step of these pathways. Cryptic phosphorylation is a mechanism recently identified in these pathways and emerging in other nucleoside and aminoglycoside pathways. The results provide further insights into the crytpic phosphorylation in natural product biosynthesis in general.

Haoran won the best poster award in Southeast Enzymes Conference

Haoran received the best poster award in the 11th Annual Southeast Enzymes Conference (SEC) held virtually in April. He presented his work on the mechanism of MoaA radical SAM enzyme catalysis. He combined enzyme kinetics, EPR, and DFT calculation to obtain insights into the mechanism of rate acceleration of MoaA-catalyzed radical C-C bond formation. A part of his work was published in JACS in 2020. Congratulations, Haoran.

Lydia joined the lab

Lydia Li, a first-year biochemistry student, joined our lab.  She will be working on the Moco project. Welcome, Lydia!

Abhi’s protocol paper on glucan synthase assay is published online

In this protocol paper, we describe details of the GS assay protocol that we originally published in the 2020 Biochemistry paper.  The assay is based on size-exclusion chromatography under the basic condition that 1,3-beta-D-glucan is soluble. This approach allows quantitative determination of the amount and the length of glucan produced by yeast GS. In our Biochemistry 2020 paper, we used this assay to study the mechanism of GS catalysis and inhibition.

Matthew successfully defended his PhD dissertation

Matthew successfully defended his Ph.D. dissertation about the mechanism of peptidyl nucleoside antifungal antibiotic biosynthesis. He discovered cryptic phosphorylation during the PN biosynthesis and characterized all the downstream enzymes in the pathway. He also demonstrated the generality of this cryptic phosphorylation in other antifungal nucleoside pathways. Please see his NCB paper for details. Congratulations!!

Matthew and Jib’s work is published online in Nature Chemical Biology

In this paper, we report the discovery of cryptic phosphorylation essential for the biosynthesis of nikkomycin and polyoxin class of antifungal peptidyl nucleoside natural products. Nikkomycins and polyoxins are an important class of antifungals currently used as agricultural fungicides and are clinically investigated to treat invasive fungal infections in humans. However, their biosynthesis has long remained poorly characterized. Our discovery of the cryptic phosphorylation allowed the characterization of all the downstream steps in these pathways and revealed a divergent mechanism of structurally related antifungal nucleosides. Furthermore, our study suggests that the cryptic phosphorylation is conserved in many other nucleoside biosynthetic pathways.  Congratulations, Matthew and Jib!

Our Comprehensive Natural Products reviews are published online

We contributed two reviews to the latest edition of the Comprehensive Natural Products III.  The first review entitled “Biosynthesis and Mode of Action of Antifungal Pepetidyl Nucleoside Natural Products” was written with Mathew as the first author and comprehensively summarized the current state of our understanding in the mode of action and biosynthesis of antifungal peptidyl nucleosides (PNs).  PNs are represented by nikkomycins and polyoxins that have been used as agricultural fungicides or investigated as novel antifungals against invasive fungal infections. In the past ~15 years, there have been a significant advancement in our understanding of their biosynthesis, which could facilitate the future development of these compounds into clinically useful drugs.

The second review entitled “Radical-Mediated Carbon Skeleton Formation in Natural Products and Cofactor Biosynthesis” summarizes an emerging group of radical SAM enzymes that catalyze carbon skeleton formations in natural products and cofactor biosynthesis with particular focus on the mechanism of radical quenching. These enzymes play key roles in their biosynthetic pathways, and thus their functional and mechanistic characterizations are critical for the understanding of the pathways. The review highlights the as yet poorly understood mechanisms of radical quenching that provide diversity in their reactivities.

Haoran and Edward’s work on MoaA is published online in JACS

Haoran and Edward’s work on the catalytic mechanism of MoaA was published in JACS. MoaA catalyzes the first step in the molybdenum cofactor biosynthesis; a unique radical cyclization of guanosine 5’-triphosphate. In this work, Edward initially found an accumulation of a unique radical species, 5′-deoxyadenos-4′-yl radical, and Haoran kinetically characterized it and came up with the mechanistic model, which revealed the rate constants of the radical cyclization step for the first time. Moreover, Haoran initiated a collaboration with Pan Zhang in the Weitao Yang lab in the Chemistry Department to demonstrate that MoaA accelerates the radical C-C bond formation by 6-9 orders of magnitudes by constraining the radical conformation and stabilizing the transition state by the Arg17 residue. Together, the study revealed the first evidence that a radical SAM enzyme accelerates radical chemistry using its unique active site environment. The study also revealed the function of Arg17 whose mutation is known to cause Moco deficiency disease in humans. Congratulations to everyone.

Abhi successfully defended his PhD dissertation

Abhi successfully defended his PhD dissertation.  He studied the mechanism of 1,3-beta-D-glucan synthase by developing a novel SEC assay for glucan length determination and chain length terminators. A part of his work has been published in Biochemistry. Congratulations, Dr. Abhi!

Dr. Ogasawara visited Duke to give a seminar

Dr. Ogasawara visited Duke to give a seminar about his studies on peptide natural product biosynthesis. We had a group meeting with him and had a very insightful discussion. It was great to have you here, and we look forward to more interactions in the future! Dr. Ogasawara is an assistant professor at Hokkaido University and the 2018 recipient of the award for young researchers from Japan Society for Bioscience, Biotechnology, and Agrochemistry.