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NMR‐based modeling and binding studies of a ternary complex between chicken liver bile acid binding protein and bile acids
Author(s) -
Tomaselli Simona,
Ragona Laura,
Zetta Lucia,
Assfalg Michael,
Ferranti Pasquale,
Longhi Renato,
Bonvin Alexandre M. J. J.,
Molinari Henriette
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21517
Subject(s) - ternary complex , cholic acid , chemistry , docking (animal) , chenodeoxycholic acid , bile acid , binding site , biochemistry , ligand (biochemistry) , stereochemistry , receptor , enzyme , medicine , nursing
Chicken liver bile acid binding protein (cL‐BABP) is involved in bile acid transport in the liver cytosol. A detailed study of the mechanism of binding and selectivity of bile acids binding proteins towards the physiological pool of bile salts is a key issue for the complete understanding of the role of these proteins and their involvement in cholesterol homeostasis. In the present study, we modeled the ternary complex of cL‐BABP with two molecules of bile salts using the data driven docking program HADDOCK on the basis of NMR and mass spectrometry data. Docking resulted in good 3D models, satisfying the majority of experimental restraints. The docking procedure represents a necessary step to help in the structure determination and in functional analysis of such systems, in view of the high complexity of the 3D structure determination of a ternary complex with two identical ligands. HADDOCK models show that residues involved in binding are mainly located in the C‐terminal end of the protein, with two loops, CD and EF, playing a major role in ligand binding. A spine, comprising polarresidues pointing toward the protein interior and involved in motion communication, has a prominent role in ligand interaction. The modeling approach has been complemented with NMR interaction and competition studies of cL‐BABP with chenodeoxycholic and cholic acids. A higher affinity for chenodeoxycholic acid was observed and a K d upper limit estimate was obtained. The binding is highly cooperative and no site selectivity was detected for the different bile salts, thus indicating that site selectivity and cooperativity are not correlated. Differences in physiological pathways and bile salt pools in different species is discussed in light of the binding results thus enlarging the body of knowledge of BABPs biological functions. Proteins 2007. © 2007 Wiley‐Liss, Inc.