title: Detailed comparison of two molecular models of the human CD40 ligand with an x-ray structure and critical assessment of model-based mutagenesis and residue mapping studies.
abstract: The interactions between the B cell receptor CD40 and its ligand on T cells are critical for the integrity of immune responses. The human CD40 ligand gp39, a tumor necrosis factor-like protein, has been the subject of intense efforts to identify the receptor-binding site and to analyze naturally occurring mutations that compromise gp39 function in vivo. These investigations relied heavily on molecular models of gp39, built in the presence of only approximately 25% sequence identity to tumor necrosis factor. The x-ray structure of gp39 has made it possible to assess modeling accuracy and to evaluate the results of model-based mutagenesis analyses. Although the models display local errors, their accuracy was sufficient to predict the CD40-binding site, to map natural mutations, and to rationalize their effects. One of five gp39 residues critical for CD40 binding was displaced in the models, and 1 of 21 point mutants was incorrectly classified. Factors most important for the reliability of the molecular models and their successful applications were valid sequence alignments and the focus of experimental studies on regions of high prediction confidence. Analysis of mutagenesis experiments correlated with anti-gp39 monoclonal antibody binding studies to assess the conformational integrity of mutant proteins.
authors.affiliation: MDS Panlabs, Computational Chemistry and Informatics, Bothell, Washington 98011-8805, USA. jbajorath@panlabs.com
authors.forename: J
authors.initials: J
authors.lastname: Bajorath
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D019013:CD40 Antigens / Q000378:metabolism; D023201:CD40 Ligand; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D006801:Humans; D008233:Lymphotoxin-alpha / Q000737:chemistry; D046911:Macromolecular Substances; D008562:Membrane Glycoproteins / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics*; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D017354:Point Mutation; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014409:Tumor Necrosis Factor-alpha / Q000737:chemistry
chemical_list: D019013:CD40 Antigens; D008233:Lymphotoxin-alpha; D046911:Macromolecular Substances; D008562:Membrane Glycoproteins; D011994:Recombinant Proteins; D014409:Tumor Necrosis Factor-alpha; D023201:CD40 Ligand