Title: A generative angular model of protein structure evolution
Authors: Michael Golden - University of Oxford (United Kingdom) [presenting]
Eduardo Garcia-Portugues - Carlos III University of Madrid (Spain)
Michael Sorensen - University of Copenhagen (Denmark)
Kanti Mardia - Leeds University (United Kingdom)
Thomas Hamelryck - University of Copenhagen (Denmark)
Jotun Hein - University of Oxford (United Kingdom)
Abstract: Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a generative, evolutionary model of protein structure and sequence that is valid on a local length scale. The model concerns the local dependencies between sequence and structure evolution in a pair of homologous proteins. The evolutionary trajectory between the two structures in the protein pair is treated as a random walk in dihedral angle space, which is modelled using a novel angular diffusion process on the two-dimensional torus. Coupling sequence and structure evolution in our model allows for modelling both `smooth' conformational changes and `catastrophic' conformational jumps, conditioned on the amino acid changes. The model has interpretable parameters and is comparatively more realistic than previous stochastic models, providing new insights into the relationship between sequence and structure evolution. For example, using the trained model we were able to identify an apparent sequence-structure evolutionary motif present in a large number of homologous protein pairs. The generative nature of our model enables us to evaluate its validity and its ability to simulate and infer aspects of protein evolution conditioned on an amino acid sequence, a related amino acid sequence, a related structure or any combination thereof.