On identifying collective displacements in apo-proteins that reveal eventual binding pathways

PLoS Comput Biol. 2019 Jan 15;15(1):e1006665. doi: 10.1371/journal.pcbi.1006665. eCollection 2019 Jan.

Abstract

Binding of small molecules to proteins often involves large conformational changes in the latter, which open up pathways to the binding site. Observing and pinpointing these rare events in large scale, all-atom, computations of specific protein-ligand complexes, is expensive and to a great extent serendipitous. Further, relevant collective variables which characterise specific binding or un-binding scenarios are still difficult to identify despite the large body of work on the subject. Here, we show that possible primary and secondary binding pathways can be discovered from short simulations of the apo-protein without waiting for an actual binding event to occur. We use a projection formalism, introduced earlier to study deformation in solids, to analyse local atomic displacements into two mutually orthogonal subspaces-those which are "affine" i.e. expressible as a homogeneous deformation of the native structure, and those which are not. The susceptibility to non-affine displacements among the various residues in the apo- protein is then shown to correlate with typical binding pathways and sites crucial for allosteric modifications. We validate our observation with all-atom computations of three proteins, T4-Lysozyme, Src kinase and Cytochrome P450.

MeSH terms

  • Animals
  • Computational Biology / methods
  • Ligands
  • Molecular Dynamics Simulation
  • Protein Binding
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / metabolism*

Substances

  • Ligands
  • Proteins

Grant support

The authors received no specific funding for this work.