Delta98Delta, a minimalist model of antiparallel beta-sheet proteins based on intestinal fatty acid binding protein

Protein Sci. 2009 Apr;18(4):735-46. doi: 10.1002/pro.71.

Abstract

The design of beta-barrels has always been a formidable challenge for de novo protein design. For instance, a persistent problem is posed by the intrinsic tendency to associate given by free edges. From the opposite standpoint provided by the redesign of natural motifs, we believe that the intestinal fatty acid binding protein (IFABP) framework allows room for intervention, giving rise to abridged forms from which lessons on beta-barrel architecture and stability could be learned. In this context, Delta98Delta (encompassing residues 29-126 of IFABP) emerges as a monomeric variant that folds properly, retaining functional activity, despite lacking extensive stretches involved in the closure of the beta-barrel. Spectroscopic probes (fluorescence and circular dichroism) support the existence of a form preserving the essential determinants of the parent structure, albeit endowed with enhanced flexibility. Chemical and physical perturbants reveal cooperative unfolding transitions, with evidence of significant population of intermediate species in equilibrium, structurally akin to those transiently observed in IFABP. The recognition by the natural ligand oleic acid exerts a mild stabilizing effect, being of a greater magnitude than that found for IFABP. In summary, Delta98Delta adopts a monomeric state with a compact core and a loose periphery, thus pointing to the nonintuitive notion that the integrity of the beta-barrel can indeed be compromised with no consequence on the ability to attain a native-like and functional fold.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Circular Dichroism
  • Escherichia coli / genetics
  • Fatty Acid-Binding Proteins / chemistry*
  • Fatty Acid-Binding Proteins / genetics*
  • Fatty Acid-Binding Proteins / metabolism
  • Ligands
  • Models, Molecular
  • Oleic Acid / metabolism
  • Protein Binding
  • Protein Conformation
  • Protein Folding*
  • Protein Stability
  • Rats
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Spectrometry, Fluorescence
  • Temperature

Substances

  • Fatty Acid-Binding Proteins
  • Ligands
  • Recombinant Proteins
  • Oleic Acid