Integrative Structure Modeling of the Core SPB

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Structural modeling of a macromolecular assembly is best cast as a computational optimization problem where information about the assembly is encoded into the scoring function used to evaluate candidate models. To this end, we are developing IMP, the Integrative Modeling Platform (9) (http://inteqrativemodelinq.orq/), an open source software package to construct spatial models of large macromolecular protein complexes by satisfaction of spatial restraints from a variety of experimental data. IMP was demonstrated by application to several complexes, including the Nuclear Pore Complex (4) and the 26S proteasome (11). We will use IMP inan iterative experimental and computational process to construct a pseudo-atomic resolution model of the Yeast Spindle Pole Body (SPB). The spatial restraints for model construction will be derived from the currently available data as well as new data generated in the proposed POl center. We will first improve, develop, and benchmark computational protocols for using crystallography, electron microscopy (EM), small angle X-ray scattering (SAXS), Forster resonance energy transfer (FRET) spectroscopy, and cross-linking data for integrative structure modeling ofthe SPB. Incompleteness, noise, and ambiguity in experimental data will be treated using an inference-based scoring function that will extract the maximum possible information from the data, following a Bayesian approach with minimal assumptions and approximations (13). Sampling all model structures consistent with the data is generally,a challenging problem, in part due to the rugged nature ofthe scoring function landscape and its many local minima. To this end, we will develop a sampling method that efficiently divides the complete set of degrees of freedom into potentially overiapping subsets, finds candidate' solutions for the subsets independently by traditional optimizers or enumeration, and then combines compatible solutions to obtain guaranteed best-scoring solutions for the whole system (15). Finally, we will apply these scoring and sampling methods to determine the pseudo-atomic structure of the SPB. PHS 398/