Effects of Membrane and Biological Target on the Structural and Allosteric Properties of Recoverin: A Computational Approach

Int J Mol Sci. 2019 Oct 10;20(20):5009. doi: 10.3390/ijms20205009.

Abstract

Recoverin (Rec) is a prototypical calcium sensor protein primarily expressed in the vertebrate retina. The binding of two Ca2+ ions to the functional EF-hand motifs induces the extrusion of a myristoyl group that increases the affinity of Rec for the membrane and leads to the formation of a complex with rhodopsin kinase (GRK1). Here, unbiased all-atom molecular dynamics simulations were performed to monitor the spontaneous insertion of the myristoyl group into a model multicomponent biological membrane for both isolated Rec and for its complex with a peptide from the GRK1 target. It was found that the functional membrane anchoring of the myristoyl group is triggered by persistent electrostatic protein-membrane interactions. In particular, salt bridges between Arg43, Arg46 and polar heads of phosphatidylserine lipids are necessary to enhance the myristoyl hydrophobic packing in the Rec-GRK1 assembly. The long-distance communication between Ca2+-binding EF-hands and residues at the interface with GRK1 is significantly influenced by the presence of the membrane, which leads to dramatic changes in the connectivity of amino acids mediating the highest number of persistent interactions (hubs). In conclusion, specific membrane composition and allosteric interactions are both necessary for the correct assembly and dynamics of functional Rec-GRK1 complex.

Keywords: molecular dynamics; myristoyl switch; phototransduction; protein structure networks; recoverin; rhodopsin kinase.

MeSH terms

  • Allosteric Site
  • Calcium-Binding Proteins
  • Computational Biology
  • Eye Proteins / chemistry
  • G-Protein-Coupled Receptor Kinase 1 / chemistry*
  • G-Protein-Coupled Receptor Kinase 1 / metabolism*
  • Hydrophobic and Hydrophilic Interactions
  • Light Signal Transduction
  • Membrane Proteins / chemistry*
  • Membrane Proteins / metabolism*
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Myristic Acids
  • Nerve Tissue Proteins / chemistry
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Domains and Motifs
  • Recoverin / chemistry*
  • Recoverin / metabolism*
  • Sequence Analysis, Protein

Substances

  • Calcium-Binding Proteins
  • Eye Proteins
  • Membrane Proteins
  • Myristic Acids
  • Nerve Tissue Proteins
  • Recoverin
  • G-Protein-Coupled Receptor Kinase 1
  • GRK1 protein, human