title: [Computer-aided molecular modeling and activity estimation for ligand screening with specific phage clone as the target].
abstract: To investigate the interaction between tumor necrosis factor alpha (TNF alpha) mimotopes and TNF alpha-binding peptides screened from random phage display peptide library with TNF alpha mimotopes displayed on phage clone as the target, the computational docking program AutoDock (with confirmation calculations using Discover) was used to predict and analyze the binding modes of LLT-18 (TNF alpha binding peptide, sequence EHMALTYPFRPP) with TNF alpha, after which LCS-7 (TNF alpha mimic phage clone, displayed positive sequence c-RRPAQSG-c) was docked to LLT-18 manually. The binding between LLT-18 and TNF alpha or LCS-7 was stabilized predominantly through electrostatic interaction and H-bond formation. The Arg residues in TNF alpha or LCS-7 were important for their interaction with LLT-18. For LLT-18, the key amino acid residues were Glu1, His2, Met3 and Tyr7. These results suggest the feasibility of screening ligand to single epitope with specific phage clone as the target, and of predicting the interaction between small peptides by computer-aided molecular modeling.
authors: Department of Immunology, Southern Medical University, Guangzhou 510515, China.
authors: Hai-Bo
authors: HB
authors: Luo
authors: Yuan-Dong
authors: YD
authors: Hu
authors: Bei-Yi
authors: BY
authors: Liu
authors: Song
authors: S
authors: Li
authors: Ning
authors: N
authors: Fu
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000911:Antibodies, Monoclonal / Q000276:immunology; D019921:Biotinylation; D003198:Computer Simulation; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D000939:Epitopes / Q000276:immunology; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry / Q000378:metabolism; D019151:Peptide Library; D011487:Protein Conformation; D012995:Solubility; D014409:Tumor Necrosis Factor-alpha / Q000737:chemistry / Q000276:immunology / Q000378:metabolism
chemical_list: D000911:Antibodies, Monoclonal; D000939:Epitopes; D008024:Ligands; D009842:Oligopeptides; D019151:Peptide Library; D014409:Tumor Necrosis Factor-alpha