Conformational dynamics of the membrane enzyme LspA upon antibiotic and substrate binding

Biophys J. 2022 Jun 7;121(11):2078-2083. doi: 10.1016/j.bpj.2022.04.038. Epub 2022 May 2.


Lipoprotein signal peptidase (LspA) is an aspartyl protease that cleaves the transmembrane helix signal peptide of lipoproteins as part of the lipoprotein-processing pathway. Members of this pathway are excellent targets for the development of antibiotic therapeutics because they are essential in Gram-negative bacteria, are important for virulence in Gram-positive bacteria, and may not develop antibiotic resistance. Here, we report the conformational dynamics of LspA in the apo state and bound to the antibiotic globomycin determined using molecular dynamics simulations and electron paramagnetic resonance. The periplasmic helix fluctuates on the nanosecond timescale and samples unique conformations in the different states. In the apo state, the dominant conformation is the most closed and occludes the charged active site from the lipid bilayer. With antibiotic bound there are multiple binding modes with the dominant conformation of the periplasmic helix in a more open conformation. The different conformations observed in both bound and apo states indicate a flexible and adaptable active site, which explains how LspA accommodates and processes such a variety of substrates.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, N.I.H., Extramural

MeSH terms

  • Anti-Bacterial Agents* / chemistry
  • Aspartic Acid Endopeptidases / metabolism
  • Bacterial Proteins* / metabolism
  • Catalytic Domain
  • Lipoproteins
  • Molecular Dynamics Simulation
  • Protein Conformation


  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Lipoproteins
  • Aspartic Acid Endopeptidases
  • signal peptidase II