Analysis of pseudo-symmetry in protein oligomers and its correlation with protein dynamics

Abstract

Symmetry is a feature that can be noticed almost anywhere around us. Animals, for example, have bilateral symmetry whereas flowers have a rotational symmetry. Proteins are complex systems that also exhibit this property as a rule but there is a disturbance in it that prevents it from being perfectly symmetrical. Even homo-oligomers that are made of identical subunits are not exempt from this. In this paper, we focused on protein homo-dimers and homo-trimers and we introduced off-symmetry(OS) to quantify how much a protein complex is off from perfect symmetry. Furthermore, we decomposed off-symmetry into two aspects namely structure index (SI) that measures structural difference and assembly index (AI) that measures assembly difference. We found in most cases, the major contributor to OS is SI in dimers and AI in trimers. In addition, we found that the SI and in turn OS contributed by each residue is positively correlated with their B factors, which indicates that protein flexibility and mobility may contribute to the off-symmetry of protein oligomers.