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Lynch, S. R.

Publications and source records attributed to Lynch, S. R..

4 recordsLinked to original sources

Blocking oligomerization is the most viable strategy to inhibit STING

The anti-viral and anti-cancer STING innate immune pathway can exacerbate autoimmune and neurodegenerative diseases when aberrantly activated, emphasizing a key unmet need for STING pathway antagonists. However, no such inhibitors have advanced to the clinic because it remains unclear which mechanistic step(s) of human STING activation are crucial for potent and context-independent inhibition of downstream signaling. Here, we report that C91 palmitoylation, the mechanistic target of a potent tool compound, is not universally necessary for human STING signaling, making it a poor target for drug development. Instead, we discover that evolutionarily conserved C64 is basally palmitoylated and is crucial for preventing unproductive STING oligomerization in the absence of cGAMP stimulation. The effects of palmitoylation at C64 and C91 converge on the control of intra-dimer disulfide bond formation at C148. Importantly, we show for the first time that signaling-competent STING oligomers are composed of a mixture of two species: disulfide-linked STING dimers that stabilize the oligomer, and reduced STING dimers that are phosphorylated to actuate interferon signaling. Given this complex landscape and cell type specificity of palmitoylation modifications, we conclude that robust STING inhibitors must directly inhibit the oligomerization process. Taking inspiration from STINGs natural autoinhibitory mechanism, we identified an eight amino acid peptide that binds a defined pocket at the inter-dimer oligomerization interface as a proof-of-concept human STING inhibitor, setting the stage for future therapeutic development. SummaryWe report that functional STING oligomers require palmitoylation at cysteine 64 and some proportion of reduced dimers, and define the site of autoinhibition that can be targeted to disrupt STING oligomerization and activity.

biochemistry↗

Analysis of a "Split-and-Stuttering" Module of an Assembly Line Polyketide Synthase

Notwithstanding the "one-module-one-elongation-cycle" paradigm of assembly line polyketide synthases (PKSs), some PKSs harbor modules that iteratively elongate their substrates through a defined number of cycles. While some insights into module iteration, also referred to as "stuttering", have been derived through in vivo and in vitro analysis of a few PKS modules, a general understanding of the mechanistic principles underlying module iteration remains elusive. This report serves as the first interrogation of a stuttering module from a trans-AT subfamily PKS that is also naturally split across two polypeptides. Previous work has shown that Module 5 of the NOCAP (nocardiosis associated polyketide) synthase iterates precisely three times in the biosynthesis of its polyketide product, resulting in an all trans-configured triene moiety in the polyketide product. Here we describe the intrinsic catalytic properties of this NOCAP synthase module. Through complementary experiments in vitro and in E. coli, the "split-and-stuttering" module was shown to catalyze up to five elongation cycles, although its dehydratase domain ceased to function after three cycles. Unexpectedly, the central olefinic group of this truncated product had a cis configuration. Our findings set the stage for further in-depth analysis of a structurally and functionally unusual PKS module with contextual biosynthetic plasticity. TOC/Abstract Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/426894v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@150bdbforg.highwire.dtl.DTLVardef@1d958b6org.highwire.dtl.DTLVardef@4f19c7org.highwire.dtl.DTLVardef@1256656_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation

In this work, we describe the CRIMSON (CardiovasculaR Integrated Modelling and SimulatiON) software environment. CRIMSON provides a powerful, customizable and user-friendly system for performing three-dimensional and reduced-order computational haemodynamics studies via a pipeline which involves: 1) segmenting vascular structures from medical images; 2) constructing analytic arterial and venous geometric models; 3) performing finite element mesh generation; 4) designing, and 5) applying boundary conditions; 6) running incompressible Navier-Stokes simulations of blood flow with fluid-structure interaction capabilities; and 7) post-processing and visualizing the results, including velocity, pressure and wall shear stress fields. A key aim of CRIMSON is to create a software environment that makes powerful computational haemodynamics tools accessible to a wide audience, including clinicians and students, both within our research laboratories and throughout the community. The overall philosophy is to leverage best-in-class open source standards for medical image processing, parallel flow computation, geometric solid modelling, data assimilation, and mesh generation. It is actively used by researchers in Europe, North and South America, Asia, and Australia. It has been applied to numerous clinical problems; we illustrate applications of CRIMSON to real-world problems using examples ranging from pre-operative surgical planning to medical device design optimization. CRIMSON binaries for Microsoft Windows 10, documentation and example input files are freely available for download from www.crimson.software, and the source code with compilation instructions is available on GitHub https://github.com/carthurs/CRIMSONFlowsolver (CRIMSON Flowsolver) under the GPL v3.0 license, and https://github.com/carthurs/CRIMSONGUI (CRIMSON GUI), under the AGPL v3.0 license. Support is available on the CRIMSON Google Groups forum, located at https://groups.google.com/forum/#!forum/crimson-users.

bioengineering↗

Complete Reconstitution and Deorphanization of the 3 MDa NOCAP (NOCardiosis-Associated Polyketide) Synthase

Several Nocardia strains associated with nocardiosis, a potentially life-threatening disease, house a nonamodular assembly-line polyketide synthase (PKS) that presumably synthesizes an unknown natural product. Here, we report the discovery and structure elucidation of the NOCAP (NOCardiosis-Associated Polyketide) aglycone by first fully reconstituting the NOCAP synthase in vitro from purified protein components followed by heterologous expression in E. coli and spectroscopic analysis of the purified products. The NOCAP aglycone has an unprecedented structure comprised of a substituted resorcylaldehyde headgroup linked to a 15-carbon tail that harbors two conjugated all-trans trienes separated by a stereogenic hydroxyl group. This report is the first example of reconstituting a trans-acyltransferase assembly-line PKS either in vitro or in E. coli, and of using these approaches to "deorphanize" a complete assembly-line PKS identified via genomic sequencing. With the NOCAP aglycone in hand, the stage is set for understanding how this PKS and associated tailoring enzymes confer an advantage to their native hosts during human Nocardia infections.

biochemistry↗