title: Potential of mean force for Syrian hamster prion epitope protein--monoclonal fab 3f4 antibody interaction studies.
abstract: Simulating antigen-antibody interactions are crucial for understanding antigen-antibody associations in immunology. To shed further light on this question, we study a dissociation of the Syrian hamster prion epitope protein-fab 3f4 antibody complex structure. The stretching, that is, the distance between the center of mass of the prion epitope protein and the fab 3f4 antibody, has been studied using potential of mean force (PMF) calculations based on molecular dynamics (MD) and the implicit water model. For the complex structure, there are four important intermediates, U-shaped groove on the antibodies, and two inter-protein molecular hydrogen bonds in the stretching process. Use of our simulations may help in understanding the binding mechanics of the complex structure, and thus of significance in the design of antibodies against prion disease.
authors.affiliation: National Center for High-performance Computing, Hsin-Shi, Tainan County, Taiwan, ROC.
authors.forename: Yeng-Tseng
authors.initials: YT
authors.lastname: Wang
authors.forename: Zhi-Yuan
authors.initials: ZY
authors.lastname: Su
authors.forename: Jun-Min
authors.initials: JM
authors.lastname: Liao
authors.forename: Cheng-Lung
authors.initials: CL
authors.lastname: Chen
mesh_terms: D000818:Animals; D000911:Antibodies, Monoclonal / Q000737:chemistry* / Q000276:immunology*; D000936:Antigen-Antibody Complex / Q000737:chemistry* / Q000276:immunology*; D003198:Computer Simulation; D006224:Cricetinae; D000939:Epitopes / Q000737:chemistry / Q000276:immunology; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry / Q000276:immunology; D018448:Models, Immunological; D008958:Models, Molecular; D011328:Prions / Q000737:chemistry* / Q000276:immunology*; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D000911:Antibodies, Monoclonal; D000936:Antigen-Antibody Complex; D000939:Epitopes; D007140:Immunoglobulin Fab Fragments; D011328:Prions