@article{ye_williams_2014, title={Mapping a Ketosynthase:Acyl Carrier Protein Binding Interface via Unnatural Amino Acid-Mediated Photo-Cross-Linking}, volume={53}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi500936u}, DOI={10.1021/bi500936u}, abstractNote={Probing and interrogating protein interactions that involve acyl carrier proteins (ACP's) in fatty acid synthases and polyketide synthases are critical to understanding the molecular basis for the programmed assembly of complex natural products. Here, we have used unnatural amino acid mutagenesis to site specifically install photo-cross-linking functionality into acyl carrier proteins from diverse systems and the ketosynthase FabF from the Escherichia coli type II fatty acid synthase. Subsequently, a photo-cross-linking assay was employed to systematically probe the ability of FabF to interact with a broad panel of ACP's, illustrating the expected orthogonality of ACP:FabF interactions and the role of charged residues in helix II of the ACP. In addition, FabF residues involved in the binding interaction with the cognate carrier protein were identified via surface scanning mutagenesis and photo-cross-linking. Furthermore, the ability to install the photo-cross-linking amino acid at virtually any position allowed interrogation of the role that carrier protein acylation plays in determining the binding interface with FabF. A conserved carrier protein motif that includes the phosphopantetheinylation site was also shown to play an integral role in maintenance of the AcpP:FabF binding interaction. Our results provide unprecedented insight into the molecular details that describe the AcpP:FabF binding interface and demonstrate that unnatural amino acid based photo-cross-linking is a powerful tool for probing and interrogating protein interactions in complex biosynthetic systems.}, number={48}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={Ye, Zhixia and Williams, Gavin J.}, year={2014}, month={Nov}, pages={7494–7502} }
 @article{ye_musiol_weber_williams_2014, title={Reprogramming Acyl Carrier Protein Interactions of an Acyl-CoA Promiscuous trans-Acyltransferase}, volume={21}, ISSN={1074-5521}, url={http://dx.doi.org/10.1016/j.chembiol.2014.02.019}, DOI={10.1016/j.chembiol.2014.02.019}, abstractNote={Protein interactions between acyl carrier proteins (ACPs) and trans-acting acyltransferase domains (trans-ATs) are critical for regioselective extender unit installation by many polyketide synthases, yet little is known regarding the specificity of these interactions, particularly for trans-ATs with unusual extender unit specificities. Currently, the best-studied trans-AT with nonmalonyl specificity is KirCII from kirromycin biosynthesis. Here, we developed an assay to probe ACP interactions based on leveraging the extender unit promiscuity of KirCII. The assay allows us to identify residues on the ACP surface that contribute to specific recognition by KirCII. This information proved sufficient to modify a noncognate ACP from a different biosynthetic system to be a substrate for KirCII. The findings form a foundation for further understanding the specificity of trans-AT:ACP protein interactions and for engineering modular polyketide synthases to produce analogs.}, number={5}, journal={Chemistry & Biology}, publisher={Elsevier BV}, author={Ye, Zhixia and Musiol, Ewa M. and Weber, Tilmann and Williams, Gavin J.}, year={2014}, month={May}, pages={636–646} }
 @article{ye_bair_desai_williams_2011, title={A photocrosslinking assay for reporting protein interactions in polyketide and fatty acid synthases}, volume={7}, ISSN={1742-206X 1742-2051}, url={http://dx.doi.org/10.1039/c1mb05270e}, DOI={10.1039/c1mb05270e}, abstractNote={Understanding protein-protein interactions that occur between ACP and KS domains of polyketide synthases and fatty acid synthases is critical to improving the scope and efficiency of combinatorial biosynthesis efforts aimed at producing non-natural polyketides. Here, we report a facile strategy for rapidly reporting such ACP-KS interactions based on the incorporation of an amino acid with photocrosslinking functionality. Crucially, this photocrosslinking strategy can be applied to any polyketide or fatty acid synthase regardless of substrate specificity, and can be adapted to a high-throughput format for directed evolution studies.}, number={11}, journal={Molecular BioSystems}, publisher={Royal Society of Chemistry (RSC)}, author={Ye, Zhixia and Bair, Morgan and Desai, Hemant and Williams, Gavin J.}, year={2011}, pages={3152} }