Molecular Replacement for Multi-Domain Structures Using Packing Models

Molecular replacement (MR) is frequently used to obtain phase information for a unit cell packed with a macromolecule of unknown structure. The goal of MR searches is to place a homologous/similar molecule in the unit cell so as to maximize the correlation with x-ray diffraction data. MR software packages typically perform rotation and translation searches separately. This works quite well for single-domain proteins. However, for multi-domain structures and complexes, computational requirements can become prohibitive and the desired peaks can become hidden in a noisy landscape. The main contribution of our approach is that computationally expensive MR searches in continuous configuration space are replaced by a search on a relatively small discrete set of candidate packing arrangements of a multi-rigid-body model. These candidate arrangements are generated by collision detections on a coarse grid in the configuration space first. The list of feasible arrangements is short because packing constraints together with unit cell symmetry and geometry impose strong constraints. After computing Patterson correlations of the collision-free arrangements, an even shorter list can be obtained using the 10 candidates with highest correlations. In numerical trials, we found that a candidate from the feasible set is usually similar to the arrangement of the target structure within the unit cell. To further improve the accuracy, a Rapidly-exploring Random Tree (RRT) can be applied in the neighborhood of this packing arrangement. Our approach is demonstrated with multi-domain models in silico for 3D, with ellipsoids representing both the domains of the model and target structures. Configurations are defined by sets of angles between the ellipsoids. Our results show that an approximate configuration can be found with mean absolute error (MAE) less than 5 degrees.