Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity
mediaposted on 2021-11-08, 20:36 authored by Sabahuddin Ahmad, Christoph Heinrich Strunk, Stephan N. Schott-Verdugo, Karl-Erich Jaeger, Filip Kovacic, Holger Gohlke
PlaF 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 have 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 (FA) products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by FA-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.
product feedback regulationexperimentally demonstrated plabulky tryptophan residuesatom molecular dynamicssubstrate access mechanismidentify access pathwaysgpls preferably entermonomer transition followedfavorable free energypseudomonas aeruginosa concordant1 subnatural gpl substratesmd simulations suggestsubstrates accesssn pseudomonas aeruginosaenergy computationsconfigurational freechain gplsaccess tunnelsubstrates reachgpl substratestunnel blockagetriggered dimerizationstructural featuresremained elusivemay acthuman pathogenfindings opendistinct tunneldimerization interfacecombined unbiasedcatalytic centerbound phospholipaseacyl chainactive site