Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy.
The fundamental event in biological assembly is association of two biological macromolecules. Here we present a successful, accurate ab initio prediction of the binding of uncomplexed lysozyme to the HyHel5 antibody. The prediction combines pseudo Brownian Monte Carlo minimization with a biased-probability global side-chain placement procedure. It was effected in an all-atom representation, with ECEPP/2 potentials complemented with the surface energy, side-chain entropy and electrostatic polarization free energy. The near-native solution found was surprisingly close to the crystallographic structure (root-mean-square deviation of 1.57 A for all backbone atoms of lysozyme) and had a considerably lower energy (by 20 kcal mol-1) than any other solution.
Totrov
M
M
European Molecular Biology Laboratory, Heidelberg, Germany.
Abagyan
R
R
D000818:Animals; D000936:Antigen-Antibody Complex / Q000737:chemistry*; D001665:Binding Sites; D004563:Electrochemistry; D008958:Models, Molecular; D009010:Monte Carlo Method; D009113:Muramidase / Q000737:chemistry* / Q000276:immunology*; D011487:Protein Conformation; D013816:Thermodynamics
D000936:Antigen-Antibody Complex; D009113:Muramidase