Journal Article

FZJ-2021-04293

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity

Ahmad, S.FZJ* ; Strunk, C. H. ; Schott, S.FZJ* ; Jaeger, K.-E.FZJ* ; Kovacic, F. (Corresponding author)FZJ* ; Gohlke, H. (Corresponding author)FZJ*

2021
American Chemical Society Washington, DC

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Please use a persistent id in citations: http://hdl.handle.net/2128/29086  doi:10.1021/acs.jcim.1c00973

Abstract: 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.

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Contributing Institute(s):

1. Bioinformatik (IBG-4)
2. Jülich Supercomputing Center (JSC)
3. John von Neumann - Institut für Computing (NIC)
4. Strukturbiochemie (IBI-7)
5. Institut für Molekulare Enzymtechnologie (HHUD) (IMET)

Research Program(s):

1. 2171 - Biological and environmental resources for sustainable use (POF4-217) (POF4-217)
2. 5111 - Domain-Specific Simulation & Data Life Cycle Labs (SDLs) and Research Groups (POF4-511) (POF4-511)
3. Forschergruppe Gohlke (hkf7_20200501) (hkf7_20200501)
4. DFG project 267205415 - SFB 1208: Identität und Dynamik von Membransystemen - von Molekülen bis zu zellulären Funktionen (267205415) (267205415)

Appears in the scientific report 2021

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Database coverage:
; ; Clarivate Analytics Master Journal List ; Current Contents - Physical, Chemical and Earth Sciences ; Essential Science Indicators ; IF < 5 ; JCR ; Nationallizenz ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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