A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins

Structure. 2015 Jan 6;23(1):34-43. doi: 10.1016/j.str.2014.11.011.

Abstract

In proteins, functional divergence involves mutations that modify structure and dynamics. Here we provide experimental evidence for an evolutionary mechanism driven solely by long-range dynamic motions without significant backbone adjustments, catalytic group rearrangements, or changes in subunit assembly. Crystallographic structures were determined for several reconstructed ancestral proteins belonging to a GFP class frequently employed in superresolution microscopy. Their chain flexibility was analyzed using molecular dynamics and perturbation response scanning. The green-to-red photoconvertible phenotype appears to have arisen from a common green ancestor by migration of a knob-like anchoring region away from the active site diagonally across the β barrel fold. The allosterically coupled mutational sites provide active site conformational mobility via epistasis. We propose that light-induced chromophore twisting is enhanced in a reverse-protonated subpopulation, activating internal acid-base chemistry and backbone cleavage to enlarge the chromophore. Dynamics-driven hinge migration may represent a more general platform for the evolution of novel enzyme activities.

Publication types

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

MeSH terms

  • Catalytic Domain / genetics
  • Color
  • Crystallography, X-Ray
  • Evolution, Molecular*
  • Fluorescence
  • Green Fluorescent Proteins / chemistry*
  • Green Fluorescent Proteins / genetics*
  • Luminescent Proteins / chemistry*
  • Luminescent Proteins / genetics*
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Motion
  • Mutation
  • Protein Folding*
  • Protein Stability
  • Protein Structure, Tertiary / genetics

Substances

  • Luminescent Proteins
  • red fluorescent protein
  • Green Fluorescent Proteins