Browsing by Author "Schott-Verdugo, Stephan"
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Item MD simulation data for: "Molecular Mechanisms Underlying Medium-Chain Free Fatty Acid-regulated Activity of the Phospholipase PlaF from Pseudomonas aeruginosa"(N/A, 2023-11) Gentile, Rocco; Schott-Verdugo, Stephan; Gohlke, HolgerPlaF is a membrane-bound phospholipase A1 from P. aeruginosa that is involved in remodeling membrane glycerophospholipids (GPLs) and modulation of virulence-associated signaling and metabolic pathways. Previously, we identified the role of medium-chain free fatty acids (FFA) in inhibiting PlaF activity and promoting homodimerization, yet the underlying molecular mechanism remained elusive. Here, we used unbiased and biased molecular dynamics simulations and free energy computations to assess how PlaF interacts with FFAs localized in the water milieu surrounding the bilayer or within the bilayer, and how these interactions regulate PlaF activity. Medium-chain FFAs localized in the upper bilayer leaflet can stabilize inactive dimeric PlaF, likely through interactions with charged surface residues as experimentally validated. Potential of mean force (PMF) computations indicate that membrane-bound FFAs may facilitate the activation of monomeric PlaF by lowering the activation barrier of changing into a tilted, active configuration. We estimated that the coupled equilibria of PlaF monomerization-dimerization and tilting at the physiological concentration of PlaF lead to the majority of PlaF forming inactive dimers when in a cell membrane loaded with decanoic acid (C10). This is in agreement with a suggested in vivo product feedback loop and GC-MS profiling results indicating that PlaF catalyzes the release of C10 from P. aeruginosa membranes. Additionally, we found that C10 in the water milieu can access the catalytic site of active monomeric PlaF, contributing to the competitive component of C10-mediated PlaF inhibition. Our study provides mechanistic insights into how medium-chain FFA may regulate the activity of PlaF, a potential bacterial drug target.Item Simulation data for "Substrate access mechanism in a novel membrane-bound phospholipase A of Pseudomonas aeruginosa concordant with specificity and regioselectivity"(N/A, 2021-07-12) Ahmad, Sabahuddin; Strunk, Christoph; Schott-Verdugo, Stephan; Jaeger, Karl-Erich; Kovacic, Filip; Gohlke, HolgerPlaF is a cytoplasmic membrane-bound phospholipase A1 from Pseudomonas aeruginosa that alters the membrane glycerophospholipid (GPL) composition and fosters the virulence of this human pathogen. PlaF activity is regulated by a dimer-to-monomer transition followed by tilting of the monomer in the membrane. However, how substrates reach the active site and how the characteristics of the active site tunnels determine the activity, specificity, and regioselectivity of PlaF for natural GPL substrates has remained elusive. Here, we combined unbiased and biased all-atom molecular dynamics (MD) simulations and configurational free energy computations to identify access pathways of GPL substrates to the catalytic center of PlaF. Our results map out a distinct tunnel through which substrates access the catalytic center. PlaF variants with bulky tryptophan residues in this tunnel revealed decreased catalysis rates due to tunnel blockage. The MD simulations suggest that GPLs preferably enter the active site with the sn-1 acyl chain first, which agrees with the experimentally demonstrated PLA1 activity of PlaF. We propose that the acyl chain-length specificity of PlaF is determined by the structural features of the access tunnel, which results in favorable free energy of binding of medium-chain GPLs. The suggested egress route conveys fatty acid products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by fatty acid-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.Item TopProperty dataset(N/A, 2021-07-07) Mulnaes, Daniel; Schott-Verdugo, Stephan; Koenig, Filip; Gohlke, HolgerTransmembrane proteins (TMPs) are critical components of cellular life. However, due to experimental challenges, the number of experimentally resolved TMP structures is severely underrepresented in databases compared to their cellular abundance. Prediction of (per-residue) features such as transmembrane topology, membrane exposure, secondary structure, and solvent accessibility can be a useful starting point for experimental design or protein structure prediction, but often requires different computational tools for different features or types of proteins. We present TopProperty, a meta-predictor that predicts all of these features for TMPs or globular proteins. TopProperty predictions are robust, especially for proteins with few sequence homologs, and significantly better than the evaluated state-of-the-art primary predictors on all quality metrics. TopProperty eliminates the need for protein type- or feature-tailored tools, specifically for TMPs. TopProperty is freely available as web server and standalone at https://cpclab.uni-duesseldorf.de/topsuite/.