Protein structure and dynamics using cross-linking mass spectrometry

To understand the function of macromolecules in the cells, we need to describe their structures and dynamics. However, no experimental method is universally applicable for direct structure determination. Integrative modeling is often used to characterize the structures of complexes by relying on multiple types of input information. The individual proteins or domains are determined by x-ray crystallography or modeled by comparative modeling and cross-links are used to assemble the subunits.

We have developed two novel computational methods that rely on cross-links for determination of structure and dynamics, respectively. The main challenge in integrative modeling of complexes is sampling the complete ensemble of models consistent with the input information. Due to the large system size, the sampling is often necessarily stochastic and does not guarantee obtaining a complete ensemble. Our deterministic method uses pairwise protein-protein docking to assemble the complexes in an hierarchical manner. We apply the method to assemble the yeast chromatin remodeling complex (RSC) which consists of 17 proteins.

A single structure often does not satisfy a large fraction of the cross-links due to conformational heterogeneity of the protein. The challenge is to determine the multi-state models (two or more conformations) starting from a single input structure, a list of flexible residues, and a list of cross-links. The second method addresses this problem. We sample the input structure by exploring the space of the main-chain dihedral angles in user-defined residues and enumerate the multi-state models that are consistent with the cross-links. We successfully applied the method on several systems.