Project description:Tripartite resistance nodulation and cell division multidrug efflux pumps span the periplasm and are major drivers of multidrug resistance among Gram-negative bacteria. Cations, such as Mg2+, become concentrated within the periplasm and, in contrast to the cytoplasm, it’s pH is sensitive to conditions outside the cell. Here, we reveal an interplay between Mg2+ and pH in modulating the structural dynamics of the periplasmic adaptor protein, AcrA, and its function within the prototypical AcrAB-TolC multidrug pump from Escherichia coli. In the absence of Mg2+, AcrA becomes increasingly plastic within acidic conditions, but when Mg2+ is bound this is ameliorated, resulting instead in domain specific organisation. We establish a unique histidine residue directs these dynamics and is essential for sustaining pump activity across acidic, neutral, and basic regimes. Overall, we propose Mg2+ conserves AcrA structural mobility to ensure optimal AcrAB-TolC function within rapid changing environments commonly faced during bacterial infection and colonization.
Project description:Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli, AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.
Project description:Hydrogen deuterium exchange mass spectrometry of HSL in the presence of artificial lipid droplets to analyze lipid droplets binding.
Project description:The tyrosine kinase domain (TKD) of the epidermal growth factor receptor (EGFR) activates via a unique mechanism of asymmetric dimerization with a partner EGFR TKD rather than a more typical mechanism of activation loop phosphorylation. There is an EGFR oncogenic variant found in patients in which the TKD region of EGFR has been duplicated, resulting in a construct in which two EGFR kinase domain are linked via a natural peptide linker (KDD). KDD is the best approximation of the natural process of EGFR kinase dimerization and activation as well as an example of bona fide oncogenic activation. We studied the structure, enzyme properties, and structural dynamics of KDD to gather insights into the EGFR kinase activation process and its oncogenicity.
Project description:Long RSH enzymes, Rel and RelA, are the master regulators of (p)ppGpp alarmone levels in bacteria. Their catalytic activity is governed by transitions between a compact, hydrolysis-competent (HDON) state and an elongated, synthesis-competent (SYNTHON) state. The equilibrium between these states is modulated by factors such as “starved” ribosomes and regulatory proteins DarB, EIIANTR, ACP and YtfK. Here, we identify and characterize camelid nanobodies that act as selective allosteric modulators by trapping Rel/RelA enzymes in distinct conformational states. Nanobodies that lock the TGS domain of RelA and prevent its activation by deacylated tRNA on starved ribosomes, strongly inhibit (p)ppGpp synthesis and suppress the virulence of E. coli in an animal model. Nb898 stabilizes Rel in the open SYNTHON state, enhancing synthesis activity while suppressing hydrolysis. Conversely, Nb585 traps Rel in a HDON conformation, strongly inhibiting alarmone synthesis while promoting (p)ppGpp hydrolysis. Structural and biochemical analyses reveal that nanobodies, like natural allosteric regulators, act by restricting the RSH enzyme’s conformational landscape. These findings establish nanobodies as powerful tools for dissecting RSH function and provide potential leads for developing protein-based RSH modulators.
Project description:Bacteria have evolved numerous biochemical processes that underpin their biology and pathogenesis. The small, non-enzymatic bacterial (Salmonella) effector SteE mediates kinase reprogramming, whereby the canonical serine/threonine host kinase GSK3 gains tyrosine-directed activity towards neosubstrates, promoting Salmonella virulence. Yet, both the mechanism behind the switch in GSK3’s activity and the diversity of this phenomenon remain to be determined. Here we show that kinase reprogramming of GSK3 is mediated by putative homologues from diverse Gram-negative pathogens. Next, we identify both the molecular basis of how SteE targets GSK3 and then uncover that the SteE-induced tyrosine activity conferred on GSK3 occurs by mimicry of an L/xGxP motif, previously shown to mediate GSK3 autophosphorylation on a tyrosine. Together, we demonstrate how a family of intrinsically disordered proteins mediate kinase reprogramming through the molecular mimicry of eukaryotic short linear motifs. With these advances comes the potential for the rationale design of synthetic reprogramming proteins
Project description:Harnessing the potential beneficial effects of kinase signalling through the generation of direct kinase activators remains an underexplored area of drug development. This also applies to the PI 3-kinase (PI3K) signalling pathway which has been extensively targeted by inhibitors for conditions with PI3K overactivation, such as cancer and immune dysregulation1-3. Here we report on the discovery of UCL-TRO-1938 (further referred to as 1938), a small molecule activator of the PI3Kα isoform, a critical effector of growth factor signalling. 1938 allosterically activates PI3Kα through a unique mechanism, by enhancing multiple steps of the PI3Kα catalytic cycle, and causes both local and global conformational changes in the PI3Kα structure. This compound is selective for PI3Ka over other PI3K isoforms and multiple protein and lipid kinases. It transiently activates PI3K signalling in all rodent and human cells tested, resulting in cellular responses such as proliferation and neurite outgrowth. In rodent models, acute treatment with 1938 provides cardioprotection from ischaemia reperfusion injury and, upon local administration, enhances nerve regeneration following nerve crush. This study identifies a unique chemical tool to directly probe PI3Kα signalling and a novel approach to modulate PI3K activity, widening the therapeutic potential of targeting these enzymes, through short-term activation for tissue protection and regeneration. Our findings illustrate the potential of activating kinases for therapeutic benefit, a currently largely untapped area of drug development.
Project description:Hydrogen/deuterium exchange (HDX) methods for studying protein dynamics would benefit from millisecond-scale incubations to probe intrinsically disordered proteins, highly dynamic regions and conformation changes. Here we investigate droplet microfluidics for rapid mixing to trigger D2O labelling, uniform incubations and rapid droplet merging for acid quenching in advance of mass spectrometry. A surfactant-free merging approach combining expansion elements for synchronised droplet collision proved robust. The high diffusive flux of D2O and protons enable microsecond mixing to trigger and arrest D2O labelling, respectively, affording the possibility of single millisecond incubations. Droplet HDX processors were used to measure the fast uptake characteristics of a model peptide. Forward exchange measurements demonstrate D2O labelling to be the rate-limiting step, in essence defining 10 milliseconds as the minimum practical incubation time for proteins in typical physiological conditions. With the ability to access millisecond time scales the fast dynamics of calmodulin, a model of calcium-triggered allostery with rapid conformational switching, was investigated. At 10 milliseconds, we could observe significant deuterium uptake within the well-defined EF-hand motifs (Ca2+ binding sites). These findings demonstrate millisecond HDX enabled by droplet microfluidics allows areas of heightened plasticity to be detected within a stably folded protein. Associated dataset: PXD077479
Project description:Biased agonists targeting the α2A-adrenergic receptor (α2AAR) have therapeutic potential by preferentially engaging G protein signaling over β-arrestin pathways. Here, we used hydrogen-deuterium exchange mass spectrometry (HDX-MS) to compare α2AAR conformational dynamics across apo, agonist-bound, and GoA-coupled states. We analyzed HDX-MS changes induced by norepinephrine (NorEpi), the endogenous full agonist; dexmedetomidine (Dex), a clinically used full agonist that activates both Gi/o and β-arrestin signaling; and PS75, a Gi/o-biased partial agonist. By quantifying ligand-dependent differences in deuterium uptake and local dynamics, we aimed to define ligand-specific conformational ensembles. These findings provide mechanistic insight into partial agonism and suggest potential implications for biased signaling.
Project description:The enzyme glutamate decarboxylase (GAD) produces the neurotransmitter GABA, using pyridoxal-5’-phosphate. GAD exists as two isoforms, GAD65 and GAD67. Only GAD65 acts as a major autoantigen, with its autoantibodies frequently found in type 1 diabetes and other autoimmune diseases. Here we characterize the structure and dynamics of GAD65 and its interaction with the autoimmune polyendocrine syndrome type 2-associated autoantibody b96.11. Combining hydrogen-deuterium exchange mass spectrometry (HDX), X-ray crystallography, cryo-electron microscopy and computational approaches, we dissect the conformational dynamics of the inactive apo- and the active holo-forms of GAD65, as well as the structure of the GAD65-autoantibody complex. HDX reveals the local dynamics that accompany autoinactivation, with the catalytic loop playing a key role in promoting collective dynamics at the interface between CTD and PLP domains. In the GAD65-b96.11 complex, heavy chain CDRs dominate the interaction, with the relatively long CDRH3 at the interface centre and uniquely bridging the GAD65 dimer via extensive electrostatic interactions with the 260PEVKEK265 motif. The autoantibody bridges structural elements on GAD65 that contribute to conformational change in GAD65, thus connecting the unique and intrinsic conformational flexibility that governs the autoinactivation mechanism of the enzyme to its autoantigenicity. The intrinsic dynamics, rather than sequence differences within epitopes, appear to be responsible for the contrasting autoantigenicities of GAD65 and GAD67.