Site-directed spin label EPR studies of the structure and membrane interactions of the bacterial phospholipase ExoU.

Site-directed spin labeling (SDSL) has been invaluable in the analysis of protein structure and dynamics, and has been particularly useful in the study of membrane proteins. ExoU, an important virulence factor in infections, is a bacterial phospholipase A2 that functions at the membrane - aqueous interface. Using SDSL methodology developed in the Hubbell lab, we find that the region surrounding the catalytic site of ExoU is buried within the tertiary structure of the protein in the soluble, apoenzyme state, but shows a significant increase in dynamics upon membrane binding and activation by ubiquitin.

Mitigating gut microbial degradation of levodopa and enhancing brain dopamine: Implications in Parkinson's disease.

Parkinson's disease is managed using levodopa; however, as Parkinson's disease progresses, patients require increased doses of levodopa, which can cause undesirable side effects. Additionally, the oral bioavailability of levodopa decreases in Parkinson's disease patients due to the increased metabolism of levodopa to dopamine by gut bacteria, Enterococcus faecalis, resulting in decreased neuronal uptake and dopamine formation. Parkinson's disease patients have varying levels of these bacteria.

Characterization of the ExoU activation mechanism using EPR and integrative modeling.

ExoU, a type III secreted phospholipase effector of Pseudomonas aeruginosa, serves as a prototype to model large, dynamic, membrane-associated proteins. ExoU is synergistically activated by interactions with membrane lipids and ubiquitin. To dissect the activation mechanism, structural homology was used to identify an unstructured loop of approximately 20 residues in the ExoU amino acid sequence.

Rapid Simulation of Unprocessed DEER Decay Data for Protein Fold Prediction.

Despite advances in sampling and scoring strategies, Monte Carlo modeling methods still struggle to accurately predict de novo the structures of large proteins, membrane proteins, or proteins of complex topologies. Previous approaches have addressed these shortcomings by leveraging sparse distance data gathered using site-directed spin labeling and electron paramagnetic resonance spectroscopy to improve protein structure prediction and refinement outcomes. However, existing computational implementations entail compromises between coarse-grained models of the spin label that lower the resolution and explicit models that lead to resource-intense simulations.

Interactions of the effector ExoU from with short-chain phosphatidylinositides provide insights into ExoU targeting to host membranes.

is an opportunistic multidrug-resistant pathogen and a common cause of infection in cystic fibrosis and ventilator-associated pneumonia and in burn and wound patients. uses its type III secretion system to secrete various effector proteins directly into mammalian host cells. ExoU is a potent type III secretion system effector that, after secretion, localizes to the inner cytoplasmic membrane of eukaryotic cells, where it exerts its phospholipase A2 activity upon interacting with ubiquitin and/or ubiquitinated proteins.

Conformational Changes and Membrane Interaction of the Bacterial Phospholipase, ExoU: Characterization by Site-Directed Spin Labeling.

Numerous pathogenic bacteria produce proteins evolved to facilitate their survival and dissemination by modifying the host environment. These proteins, termed effectors, often play a significant role in determining the virulence of the infection. Consequently, bacterial effectors constitute an important class of targets for the development of novel antibiotics.

Identification of a ubiquitin-binding interface using Rosetta and DEER.

ExoU is a type III-secreted cytotoxin expressing A phospholipase activity when injected into eukaryotic target cells by the bacterium The enzymatic activity of ExoU is undetectable in vitro unless ubiquitin, a required cofactor, is added to the reaction. The role of ubiquitin in facilitating ExoU enzymatic activity is poorly understood but of significance for designing inhibitors to prevent tissue injury during infections with strains of producing this toxin. Most ubiquitin-binding proteins, including ExoU, demonstrate a low (micromolar) affinity for monoubiquitin (monoUb).

A Budding-Defective M2 Mutant Exhibits Reduced Membrane Interaction, Insensitivity to Cholesterol, and Perturbed Interdomain Coupling.

Influenza A M2 is a membrane-associated protein with a C-terminal amphipathic helix that plays a cholesterol-dependent role in viral budding. An M2 mutant with alanine substitutions in the C-terminal amphipathic helix is deficient in viral scission. With the goal of providing atomic-level understanding of how the wild-type protein functions, we used a multipronged site-directed spin labeling electron paramagnetic resonance spectroscopy (SDSL-EPR) approach to characterize the conformational properties of the alanine mutant.

Structure and Dynamics of Type III Secretion Effector Protein ExoU As determined by SDSL-EPR Spectroscopy in Conjunction with De Novo Protein Folding.

ExoU is a 74 kDa cytotoxin that undergoes substantial conformational changes as part of its function, that is, it has multiple thermodynamically stable conformations that interchange depending on its environment. Such flexible proteins pose unique challenges to structural biology: (1) not only is it often difficult to determine structures by X-ray crystallography for all biologically relevant conformations because of the flat energy landscape (2) but also experimental conditions can easily perturb the biologically relevant conformation. The first challenge can be overcome by applying orthogonal structural biology techniques that are capable of observing alternative, biologically relevant conformations.

Cooperative Substrate-Cofactor Interactions and Membrane Localization of the Bacterial Phospholipase A (PLA) Enzyme, ExoU.

The ExoU type III secretion enzyme is a potent phospholipase A secreted by the Gram-negative opportunistic pathogen, Activation of phospholipase activity is induced by protein-protein interactions with ubiquitin in the cytosol of a targeted eukaryotic cell, leading to destruction of host cell membranes. Previous work in our laboratory suggested that conformational changes within a C-terminal domain of the toxin might be involved in the activation mechanism. In this study, we use site-directed spin-labeling electron paramagnetic resonance spectroscopy to investigate conformational changes in a C-terminal four-helical bundle region of ExoU as it interacts with lipid substrates and ubiquitin, and to examine the localization of this domain with respect to the lipid bilayer.

Cholesterol-Dependent Conformational Exchange of the C-Terminal Domain of the Influenza A M2 Protein.

The C-terminal amphipathic helix of the influenza A M2 protein plays a critical cholesterol-dependent role in viral budding. To provide atomic-level detail on the impact cholesterol has on the conformation of M2 protein, we spin-labeled sites right before and within the C-terminal amphipathic helix of the M2 protein. We studied the spin-labeled M2 proteins in membranes both with and without cholesterol.

Ubiquitin activates patatin-like phospholipases from multiple bacterial species.

Phospholipase A2 enzymes are ubiquitously distributed throughout the prokaryotic and eukaryotic kingdoms and are utilized in a wide array of cellular processes and physiological and immunological responses. Several patatin-like phospholipase homologs of ExoU from Pseudomonas aeruginosa were selected on the premise that ubiquitin activation of this class of bacterial enzymes was a conserved process. We found that ubiquitin activated all phospholipases tested in both in vitro and in vivo assays via a conserved serine-aspartate catalytic dyad.

Disruption of LptA oligomerization and affinity of the LptA-LptC interaction.

The lipopolysaccharide (LPS)-rich outer membrane (OM) is a unique feature of Gram-negative bacteria, and LPS transport across the inner membrane (IM) and through the periplasm is essential to the biogenesis and maintenance of the OM. LPS is transported across the periplasm to the outer leaflet of the OM by the LPS transport (Lpt) system, which in Escherichia coli is comprised of seven recently identified proteins, including LptA, LptC, LptDE, and LptFGB2 . Structures of the periplasmic protein LptA and the soluble portion of the membrane-associated protein LptC have been solved and show these two proteins to be highly structurally homologous with unique folds.

Identification of the major ubiquitin-binding domain of the Pseudomonas aeruginosa ExoU A2 phospholipase.

Numerous Gram-negative bacterial pathogens use type III secretion systems to deliver effector molecules into the cytoplasm of a host cell. Many of these effectors have evolved to manipulate the host ubiquitin system to alter host cell physiology or the location, stability, or function of the effector itself. ExoU is a potent A2 phospholipase used by Pseudomonas aeruginosa to destroy membranes of infected cells.

Ubiquitin and ubiquitin-modified proteins activate the Pseudomonas aeruginosa T3SS cytotoxin, ExoU.

Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that possesses a type III secretion system (T3SS) critical for evading innate immunity and establishing acute infections in compromised patients. Our research has focused on the structure-activity relationships of ExoU, the most toxic and destructive type III effector produced by P. aeruginosa.

Membrane fluidity profiles as deduced by saturation-recovery EPR measurements of spin-lattice relaxation times of spin labels.

There are no easily obtainable EPR spectral parameters for lipid spin labels that describe profiles of membrane fluidity. The order parameter, which is most often used as a measure of membrane fluidity, describes the amplitude of wobbling motion of alkyl chains relative to the membrane normal and does not contain explicitly time or velocity. Thus, this parameter can be considered as nondynamic.

Induced conformational changes in the activation of the Pseudomonas aeruginosa type III toxin, ExoU.

ExoU is a 74-kDa, water-soluble toxin injected directly into mammalian cells through the type III secretion system of the opportunistic pathogen, Pseudomonas aeruginosa. Previous studies have shown that ExoU is a Ca(2+)-independent phospholipase that requires a eukaryotic protein cofactor. One protein capable of activating ExoU and serving as a required cofactor was identified by biochemical and proteomic methods as superoxide dismutase (SOD1).

Effects of D-Lysine Substitutions on the Activity and Selectivity of Antimicrobial Peptide CM15.

Despite their potent antimicrobial activity, the usefulness of antimicrobial peptides (AMPs) as antibiotics has been limited by their toxicity to eukaryotic cells and a lack of stability . In the present study we examined the effects of introducing D-lysine residues into a 15-residue hybrid AMP containing residues 1-7 of cecropin A and residues 2-9 of melittin (designated CM15). Diastereomeric analogs of CM15 containing between two and five D-lysine substitutions were evaluated for their antimicrobial activity, lysis of human erythrocytes, toxicity to murine macrophages, ability to disrupt cell membranes, and protease stability.

Physical properties of lipid bilayers from EPR spin labeling and their influence on chemical reactions in a membrane environment.

The influence of a variety of microenvironmental factors on the inherent reactivity of membrane-located reagents is poorly understood. A goal of this review is to provide detailed profiles of membrane properties, including hydrophobicity, oxygen and nitric oxide solubility and diffusion rates, bilayer penetration of metal ions and metal-ion complexes, and membrane order and fluidity, that can be obtained with EPR spin-labeling methods. These properties can drastically vary with membrane composition, membrane depth, and membrane domain formation, influencing the fate of chemical reactions that occur in a lipid bilayer environment.

Lysine-enriched cecropin-mellitin antimicrobial peptides with enhanced selectivity.

Lysine-enriched analogs of the cecropin-mellitin hybrid peptide, CA(1-7) M(2-9) (designated CM15), designed with optimized amphipathicity, retained antimicrobial activities similar to that of wild-type CM15 and had substantially reduced levels of hemolytic activity and cytotoxicity toward cultured macrophages, resulting in enhanced selectivity. These lysine-enriched analogs provide templates for improved CM15 peptide or peptidomimetic antibiotics.

Methods and applications of site-directed spin labeling EPR spectroscopy.

Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy has emerged as a well-established method that can provide specific information on the location and environment of an individual residue within large and complex protein structures. The SDSL technique involves introducing a cysteine residue at the site of interest and then covalently labeling with a sulfhydryl-specific spin label containing a stable free radical, which is used as the EPR-detectable probe. SDSL directly probes the local environment, structure, and proximity of individual residues, and is often greatly advantageous over techniques that give global information on protein structure and changes.

Membrane insertion and bilayer perturbation by antimicrobial peptide CM15.

Antimicrobial peptides (AMPs) are an important component of innate immunity and have generated considerable interest as a potential new class of antibiotic. The biological activity of AMPs is strongly influenced by peptide-membrane interactions; however, for many of these peptides the molecular details of how they disrupt and/or translocate across target membranes are not known. CM15 is a linear, synthetic hybrid AMP composed of the first seven residues of the cecropin A and residues 2-9 of the bee venom peptide mellitin.

Identification of superoxide dismutase as a cofactor for the pseudomonas type III toxin, ExoU.

Pseudomonas aeruginosa is an opportunistic pathogen that uses a type III secretion system and four effector proteins to avoid innate immune responses. ExoS, ExoT, ExoY, and ExoU all possess enzymatic activities that disrupt host cellular physiology and prevent bacterial clearance by host defense mechanisms. The specificity of these toxins for eukaryotic cells depends on the presence of substrate targets and eukaryotic cofactors responsible for effector activation.

Osmoprotection of bacterial cells from toxicity caused by antimicrobial hybrid peptide CM15.

Antimicrobial peptides exist ubiquitously as a host defense system in a broad range of species, including insects, amphibians, and mammals. The binding of these peptides is followed by the disruption of cytoplasmic membranes, leading to bacterial cell death; however, the precise mechanism of membrane destruction has remained controversial. In this study, we have examined the mechanism of action for the antimicrobial peptide, CM15 (KWKLFKKIGAVLKVL), a chimeric peptide of cecropin and mellitin.