Structure of the complex between phosphorylated substrates and the SCF beta-TrCP ubiquitin ligase receptor: a combined NMR, molecular modeling, and docking approach.
The binding of phosphorylated peptides to the receptor plays a major role in many basic cellular processes in a variety of pathological states. Human beta-TrCP is a key component of a recently characterized E3 ubiquitin ligase complex that regulates protein degradation through the ubiquitin-dependent proteasome pathway. Docking studies were carried out to explore the structural requirements for the beta-TrCP substrates. Docking studies were performed on the bound conformation of the phosphorylated peptides determined by NMR, whereas the beta-TrCP structure was derived by X-ray from Protein Data Bank. After the docking calculation, during which the peptides were conformationally restrained, the complex presented herein was analyzed in terms of ligand-protein interactions and properties of contacting surfaces. The structural requirements for phosphorylated substrates in interaction with beta-TrCP were explored and compared with experimental data from TRNOESY and STD NMR results. The analysis revealed that the bend of the peptide structures, which is indispensable for beta-TrCP recognition, aligns two charged phosphate groups and a central hydrophobic group in a favorable arrangement that leads to the burial of the peptide surface in the binding cleft upon complexation. Through docking simulations, we have identified different specific binding pockets of beta-TrCP according to the ligand in interaction. These data should be valuable in the rational design of a ligand to be used in therapeutic approaches.
Evrard-Todeschi
Nathalie
N
Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Universite Paris Descartes, UMR 8601-CNRS, 45 rue des Saint-Peres, 75006 Paris, France.
Pons
Julien
J
Gharbi-Benarous
Josyane
J
Bertho
Gildas
G
Benarous
Richard
R
Girault
Jean-Pierre
JP
D000595:Amino Acid Sequence; D020134:Catalytic Domain; D003198:Computer Simulation; D016384:Consensus Sequence; D018360:Crystallography, X-Ray; D006801:Humans; D066298:In Vitro Techniques; D008024:Ligands; D046911:Macromolecular Substances / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D010455:Peptides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010766:Phosphorylation; D044843:SKP Cullin F-Box Protein Ligases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity; D051176:beta Catenin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
D008024:Ligands; D046911:Macromolecular Substances; D010455:Peptides; D051176:beta Catenin; D044843:SKP Cullin F-Box Protein Ligases