Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network

Sci Rep. 2018 Sep 10;8(1):13540. doi: 10.1038/s41598-018-31422-5.

Abstract

Given the tight relation between protein structure and function, we present a set of methods to analyze protein topology, implemented in the VLDP program, relying on Laguerre space partitions built from series of molecular dynamics snapshots. The Laguerre partition specifies inter-atomic contacts, formalized in graphs. The deduced properties are the existence and count of water aggregates, possible passage ways and constrictions, the structure, connectivity, stability and depth of the water network. As a test-case, the membrane protein FepA is investigated in its full environment, yielding a more precise description of the protein surface. Inside FepA, the solvent splits into isolated clusters and an intricate network connecting both sides of the lipid bilayer. The network is dynamic, connections set on and off, occasionally substantially relocating traversing paths. Subtle differences are detected between two forms of FepA, ligand-free and complexed with its natural iron carrier, the enterobactin. The complexed form has more constricted and more centered openings in the upper part whereas, in the lower part, constriction is released: two main channels between the plug and barrel lead directly to the periplasm. Reliability, precision and the variety of topological features are the main interest of the method.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Outer Membrane Proteins / chemistry*
  • Carrier Proteins / chemistry*
  • Enterobactin / chemistry
  • Molecular Dynamics Simulation*
  • Protein Stability
  • Protein Structure, Secondary*
  • Receptors, Cell Surface / chemistry*
  • Structure-Activity Relationship
  • Water / chemistry

Substances

  • Bacterial Outer Membrane Proteins
  • Carrier Proteins
  • Receptors, Cell Surface
  • enterobactin receptor
  • Water
  • Enterobactin