The contribution of halogen atoms to protein-ligand interactions.
The three-dimensional structure of para-fluoro-D-phenylalanine (PFF) in its complex with the zinc protease carboxypeptidase A (CPA) has been determined at 2.0 A resolution by X-ray crystallographic methods. The structure reveals that the para-fluorobenzyl side chain of the inhibitor is buried in the S'1 hydrophobic pocket of the enzyme. Intriguingly, this ligand molecule inhibits CPA better than its amino acid analogues D-phenylalanine (D-Phe) and D-tyrosine (D-Tyr) by factors of 4 and 5, respectively. Moreover, the para-fluoro derivative is a better inhibitor than para-chloro- or para-bromo-D-phenylalanine by nearly a factor of 50. This result is consistent with binding enhancements realized in other protein complexes involving halogenated ligand molecules, regardless of whether the carbon-halogen group of the ligand makes specific polar interactions or non-specific hydrophobic interactions with its protein host. In the CPA-PFF complex, the fluorine atom of PFF does not make any direct polar contact with the enzyme, and the contact surface area of the protein-ligand interface is only slightly greater, although more hydrophobic, than that of D-Phe and D-Tyr. Therefore, we conclude that the slight binding enhancement measured for PFF relative to D-Phe and D-Tyr arises predominantly from increasing the hydrophobic character of the protein-ligand interface, and not solely from increasing the degree of protein-ligand contact.
Ippolito
J A
JA
Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323.
Christianson
D W
DW
D002268:Carboxypeptidases / Q000737:chemistry / Q000378:metabolism*; D043422:Carboxypeptidases A; D006219:Halogens / Q000737:chemistry*; D008024:Ligands; D014961:X-Ray Diffraction; D010135:p-Fluorophenylalanine / Q000737:chemistry / Q000378:metabolism*
D006219:Halogens; D008024:Ligands; D010135:p-Fluorophenylalanine; D002268:Carboxypeptidases; D043422:Carboxypeptidases A