Engineering the hCRBPII Domain-Swapped Dimer into a New Class of Protein Switches

J Am Chem Soc. 2019 Oct 30;141(43):17125-17132. doi: 10.1021/jacs.9b04664. Epub 2019 Oct 16.

Abstract

Protein conformational switches or allosteric proteins play a key role in the regulation of many essential biological pathways. Nonetheless, the implementation of protein conformational switches in protein design applications has proven challenging, with only a few known examples that are not derivatives of naturally occurring allosteric systems. We have discovered that the domain-swapped (DS) dimer of hCRBPII undergoes a large and robust conformational change upon retinal binding, making it a potentially powerful template for the design of protein conformational switches. Atomic resolution structures of the apo- and holo-forms illuminate a simple, mechanical movement involving sterically driven torsion angle flipping of two residues that drive the motion. We further demonstrate that the conformational "readout" can be altered by addition of cross-domain disulfide bonds, also visualized at atomic resolution. Finally, as a proof of principle, we have created an allosteric metal binding site in the DS dimer, where ligand binding results in a reversible 5-fold loss of metal binding affinity. The high resolution structure of the metal-bound variant illustrates a well-formed metal binding site at the interface of the two domains of the DS dimer and confirms the design strategy for allosteric regulation.

Publication types

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

MeSH terms

  • Allosteric Regulation
  • Binding Sites
  • Circular Dichroism
  • Crystallography, X-Ray
  • Disulfides / chemistry
  • Ligands
  • Metals / metabolism
  • Models, Molecular
  • Mutation
  • Protein Domains
  • Protein Engineering / methods*
  • Protein Multimerization
  • Retinol-Binding Proteins, Cellular / chemistry*
  • Retinol-Binding Proteins, Cellular / genetics
  • Retinol-Binding Proteins, Cellular / metabolism*
  • Threonine / genetics
  • Tyrosine / genetics
  • Zinc / metabolism

Substances

  • Disulfides
  • Ligands
  • Metals
  • RBP2 protein, human
  • Retinol-Binding Proteins, Cellular
  • Threonine
  • Tyrosine
  • Zinc