title: Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies.
abstract: BACKGROUND
  How antibodies recognize and bind to antigens can not be totally explained by rigid shape and electrostatic complimentarity models. Alternatively, pre-existing equilibrium hypothesis states that the native state of an antibody is not defined by a single rigid conformation but instead with an ensemble of similar conformations that co-exist at equilibrium. Antigens bind to one of the preferred conformations making this conformation more abundant shifting the equilibrium.
  
  
  RESULTS
  Here, two antibodies, a germline antibody of 36-65 Fab and a monoclonal antibody, SPE7 are studied in detail to elucidate the mechanism of antibody-antigen recognition and to understand how a single antibody recognizes different antigens. An elastic network model, Anisotropic Network Model (ANM) is used in the calculations. Pre-existing equilibrium is not restricted to apply to antibodies. Intrinsic fluctuations of eight proteins, from different classes of proteins, such as enzymes, binding and transport proteins are investigated to test the suitability of the method. The intrinsic fluctuations are compared with the experimentally observed ligand induced conformational changes of these proteins. The results show that the intrinsic fluctuations obtained by theoretical methods correlate with structural changes observed when a ligand is bound to the protein. The decomposition of the total fluctuations serves to identify the different individual modes of motion, ranging from the most cooperative ones involving the overall structure, to the most localized ones.
  
  
  CONCLUSIONS
  Results suggest that the pre-equilibrium concept holds for antibodies and the promiscuity of antibodies can also be explained this hypothesis: a limited number of conformational states driven by intrinsic motions of an antibody might be adequate to bind to different antigens.
authors.affiliation: Koc University, Center for Computational Biology and Bioinformatics and College of Engineering, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey. okeskin@ku.edu.tr
authors.forename: Ozlem
authors.initials: O
authors.lastname: Keskin
mesh_terms: D000906:Antibodies / Q000737:chemistry* / Q000378:metabolism*; D000941:Antigens / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D008024:Ligands; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013696:Temperature
chemical_list: D000906:Antibodies; D000941:Antigens; D008024:Ligands