Lipid-binding proteins: structure of the phospholipid ligands.
Dihedral angles are evaluated for the phospholipid ligands of the lipid-binding proteins found in the Protein Data Base (PDB). Phospholipid structures occur with a trans C1-C2 configuration of the glycerol backbone and oppositely extended chains, in addition to the gauche C1-C2 rotamers found in membranes. Headgroup conformations are not restricted to the single bent-down configuration and gauche-gauche configuration of the phosphodiester that is found in phospholipid crystals. Additionally, fully extended headgroups and orientations directed away from the lipid chains are found for phospholipids in the protein binding pockets. On average, the hydrocarbon chains of the protein-bound lipids are conformationally more disordered than in fluid bilayer membranes. However, much of this configurational disorder arises from energetically disallowed skew conformations. This suggests a configurational heterogeneity in the lipids at a single binding site: Eclipsed conformations occur also in some lipid headgroups and glycerol backbones. Stereochemical violations appear for some of the ester carboxyl groups of the protein-bound phospholipids in the PDB, and two glycerol backbones have the incorrect enantiomeric configuration.
Marsh
Derek
D
Max-Planck-Institut für biophysikalische Chemie, 37070 Göttingen, Germany. dmarsh@gwdg.de
D000818:Animals; D002352:Carrier Proteins / Q000737:chemistry*; D002462:Cell Membrane / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry; D019992:Databases as Topic; D029721:Drosophila Proteins; D000071438:Fatty Acid-Binding Protein 7; D050556:Fatty Acid-Binding Proteins; D005990:Glycerol / Q000737:chemistry; D006023:Glycoproteins / Q000737:chemistry; D006801:Humans; D008024:Ligands; D008051:Lipid Bilayers / Q000378:metabolism; D008055:Lipids / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008968:Molecular Conformation; D010741:Phospholipases A / Q000737:chemistry; D010743:Phospholipids / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D049128:Sphingolipid Activator Proteins; D014157:Transcription Factors / Q000737:chemistry; D025521:Tumor Suppressor Proteins
D002352:Carrier Proteins; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; C107608:FABP7 protein, human; D000071438:Fatty Acid-Binding Protein 7; D050556:Fatty Acid-Binding Proteins; D006023:Glycoproteins; D008024:Ligands; D008051:Lipid Bilayers; D008055:Lipids; D010743:Phospholipids; D049128:Sphingolipid Activator Proteins; D014157:Transcription Factors; D025521:Tumor Suppressor Proteins; C066030:USP protein, Drosophila; D010741:Phospholipases A; D005990:Glycerol