This program investigates the role of protein-protein interactions in natural product modular synthases, a group of biosynthetic enzymes of three types: polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), and fatty acid synthase (FAS). Many of these natural products serve as anti-cancer agents or antibiotics, while others are pathogenic toxins. Recent evidence indicates that protein-protein interactions between the carrier protein domain and catalytic partner proteins of these pathways are key to proper catalysis and processivity. These critical interactions are transient in nature and remain largely uncharacterized. We have developed tools that allow synthetic modification of carrier protein domains, and here we leverage these tools to increase the lifetime of these protein-protein interactions using substrate mimics and covalent cross-linking inhibitors. These tools will allow us to visualize the molecular details by which carrier proteins bind tethered substrates prior to catalysis and how they interact with cognate catalytic partners. Through these studies, we intend to gain a more complete understanding of the molecular interactions of these catalytic events. We will develop new crosslinking probes to trap carrier proteins and their catalytic partners into their bound state. Subsequent structural studies through analysis of solution phase NMR spectra and X-ray crystallography will be used to visualize the crosslinked species. In addition, NMR titration experiments in the presence of partner proteins will further allow us to accurately pinpoint the residues involved in substrate sequestration and protein-protein interaction. We will further validate our findings through site-directed mutagenesis, crosslinking studies, and other biophysical methods. Finally, we will use molecular dynamics computation along with the data from structural biology to design a novel metabolic pathway through modification of protein-protein interactions between a FAS and NRPS pathway. A deeper understanding of these protein-protein interactions and how to control them will affect emerging fields in drug discovery. Using these tools to guide new interactions will enable combinatorial biosynthesis of new pharmacophores, while new drug targets may be discovered through abrogating these interactions in pathogen biosynthesis.

Public Health Relevance

Secondary metabolites including natural products continue to provide vital clinical entries for a wide range of human ailments. In this continuation, we develop new tools to understand how interactions between enzymes guide the natural product biosynthesis. These studies provide an important next step for drug discovery, and hence benefit human health, by enabling manipulation of these pathways to enable access new therapeutic leads and the biosynthetic systems that make them.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function A Study Section (MSFA)
Program Officer
Bond, Michelle Rueffer
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University of California, San Diego
Schools of Arts and Sciences
La Jolla
United States
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Chen, Aochiu; Re, Rebecca N; Burkart, Michael D (2018) Type II fatty acid and polyketide synthases: deciphering protein-protein and protein-substrate interactions. Nat Prod Rep 35:1029-1045
Sarria, Stephen; Bartholow, Thomas G; Verga, Adam et al. (2018) Matching Protein Interfaces for Improved Medium-Chain Fatty Acid Production. ACS Synth Biol 7:1179-1187
Barajas, Jesus F; Shakya, Gaurav; Moreno, Gabriel et al. (2017) Polyketide mimetics yield structural and mechanistic insights into product template domain function in nonreducing polyketide synthases. Proc Natl Acad Sci U S A 114:E4142-E4148
Dick, Benjamin L; Patel, Ashay; McCammon, J Andrew et al. (2017) Effect of donor atom identity on metal-binding pharmacophore coordination. J Biol Inorg Chem 22:605-613
Finzel, Kara; Beld, Joris; Burkart, Michael D et al. (2017) Utilizing Mechanistic Cross-Linking Technology to Study Protein-Protein Interactions: An Experiment Designed for an Undergraduate Biochemistry Lab. J Chem Educ 94:375-379
Jaremko, Matt J; Lee, D John; Patel, Ashay et al. (2017) Manipulating Protein-Protein Interactions in Nonribosomal Peptide Synthetase Type II Peptidyl Carrier Proteins. Biochemistry 56:5269-5273
Vickery, Christopher R; La Clair, James J; Burkart, Michael D et al. (2016) Harvesting the biosynthetic machineries that cultivate a variety of indispensable plant natural products. Curr Opin Chem Biol 31:66-73
Mindrebo, Jeffrey T; Nartey, Charisse M; Seto, Yoshiya et al. (2016) Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom. Curr Opin Struct Biol 41:233-246
McCulloch, Ian P; La Clair, James J; Jaremko, Matt J et al. (2016) Fluorescent Mechanism-Based Probe for Aerobic Flavin-Dependent Enzyme Activity. Chembiochem 17:1598-601
Rivera Jr, Heriberto; Dhar, Sachin; La Clair, James J et al. (2016) An unusual intramolecular trans-amidation. Tetrahedron 72:3605-3608

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