Water-mediated recognition of simple alkyl chains by heart-type fatty-acid-binding protein

Angew Chem Int Ed Engl. 2015 Jan 26;54(5):1508-11. doi: 10.1002/anie.201409830. Epub 2014 Dec 9.


Long-chain fatty acids (FAs) with low water solubility require fatty-acid-binding proteins (FABPs) to transport them from cytoplasm to the mitochondria for energy production. However, the precise mechanism by which these proteins recognize the various lengths of simple alkyl chains of FAs with similar high affinity remains unknown. To address this question, we employed a newly developed calorimetric method for comprehensively evaluating the affinity of FAs, sub-Angstrom X-ray crystallography to accurately determine their 3D structure, and energy calculations of the coexisting water molecules using the computer program WaterMap. Our results clearly showed that the heart-type FABP (FABP3) preferentially incorporates a U-shaped FA of C10-C18 using a lipid-compatible water cluster, and excludes longer FAs using a chain-length-limiting water cluster. These mechanisms could help us gain a general understanding of how proteins recognize diverse lipids with different chain lengths.

Keywords: fatty acids; molecular dynamics; molecular evolution; structural biology; water clusters.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Calorimetry
  • Crystallography, X-Ray
  • Fatty Acid Binding Protein 3
  • Fatty Acid-Binding Proteins / chemistry
  • Fatty Acid-Binding Proteins / metabolism*
  • Fatty Acids / chemistry
  • Fatty Acids / metabolism
  • Humans
  • Molecular Dynamics Simulation
  • Myocardium / metabolism*
  • Protein Structure, Tertiary
  • Thermodynamics
  • Water / chemistry
  • Water / metabolism*


  • FABP3 protein, human
  • Fatty Acid Binding Protein 3
  • Fatty Acid-Binding Proteins
  • Fatty Acids
  • Water