Solution Structures Of Flexible Proteins Investigated By Computer Simulations Combined With Small-angle X-ray Scattering Data

Structure elucidation of large biomolecules comprised flexible unstructured regions has always been a challenging problem in structural biology. Flexibility between domains within a multi-domain protein is often critical for its biological function. A flexible multi-domain protein in solution should be represented by an ensemble of structures since it is often in equilibrium among multiple conformations with different domain orientations. Employed any high-resolution experimental technique, such as X-ray crystallography and nuclear magnetic resonance, determining structural ensemble of a multi-domain protein is generally more difficult than solving the structures of individual domains. Small-angle X-ray scattering (SAXS) is an efficient technique which can describe the size and shape of the flexible small proteins or large complexes.Recently, a notion of "integrative structural biology" has been proposed, which combines the complementary high and low resolution data as well as takes advantage of the easily integrated computational methods, to determine the protein structure and characterize its flexibility. Computer simulations, such as atomistic molecular dynamics simulations, rigid body modeling and coarse-grained simulations, is a powerful tool in studying biomolecule. It is playing more and more important roles in combining structural data in various resolution.In this work, we try to determine the structural ensemble of a multi-domain protein by integrating high-resolution structural information from NMR and low-resolution structural information from small-angle X-ray scattering and atomistic molecular dynamics simulations. The two tandem WW domains connected by a flexible linker from the formin binding protein21, is investigated. Extensive MD simulations at the time scale of microseconds are performed in order to adequately sample different conformations of the protein, and then these typical conformations are selected out of the MD trajectories to form structural ensembles that would be optimal to reproduce the experimental SAXS data. According to the structural ensembles, this two-domain protein is able to take either compact or extended conformations. The molecular mechanism of such conformational transitions is also revealed by analyzing the MD data.We also use the computational methods like atomistic molecular dynamics simulations and coarse-grained simulations integrating structural information from X-ray crystallography and SAXS to investigate the solution structural ensemble of the CAP-SH3ab complexed with Vinculin peptide. The result shows that the coarse-grained simulations are more effective in conformation sampling than the atomistic molecular dynamics simulations, and it is better to represent the solution CAP-SH3ab:vin857complex as an ensemble instead of any single dominant conformation.