MONTE-CARLO DOCKING WITH UBIQUITIN

The development of general strategies for the performance of docking s imulations is prerequisite to the exploitation of this powerful comput ational method. Comprehensive strategies can only be derived from dock ing experiences with a diverse array of biological systems, and we hav e chosen the ubiquitin/diubiquitin system as a learning tool for this process. Using our multiple-start Monte Carlo docking method, we have reconstructed the known structure of diubiquitin from its two halves a s well as from two copies of the uncomplexed monomer. For both of thes e cases, our relatively simple potential function ranked the correct s olution among the lowest energy configurations. In the experiments inv olving the ubiquitin monomer, various structural modifications were ma de to compensate for the lack of flexibility and for the lack of a cov alent bond in the modeled interaction. Potentially flexible regions co uld be identified using available biochemical and structural informati on. A systematic conformational search ruled out the possibility that the required covalent bond could be formed in one family of low-energy configurations, which was distant from the observed dimer configurati on. A variety of analyses was performed on the low-energy dockings obt ained in the experiment involving structurally modified ubiquitin. Cha racterization of the size and chemical nature of the interface surface s was a powerful adjunct to our potential function, enabling us to dis tinguish more accurately between correct and incorrect dockings. Calcu lations with the structure of tetraubiquitin indicated that the dimer configuration in this molecule is much less favorable than that observ ed in the diubiquitin structure, for a simple monomer-monomer pair. Ba sed on the analysis of our results, we draw conclusions regarding some of the approximations involved in our simulations, the use of diverse chemical and biochemical information in experimental design and the a nalysis of docking results, as well as possible modifications to our d ocking protocol.