Analysis of Pseudo-Symmetry in Protein Oligomers and its Correlation with Protein Dynamics

Kavya Shankar, Purdue University

Abstract

Symmetry is a feature which can be noticed almost anywhere around us. Animals exhibit bilateral symmetry whereas flowers show a rotational symmetry. Proteins are complex systems also exhibiting this property; however, there is a disturbance which prevents it from being perfectly symmetrical. Interestingly, homo-oligomers made of identical subunits are not exempt from this. In this research, we focused on protein homo-dimers and homo-trimers; we introduced off-symmetry (OS) to quantify how much a protein complex is off from perfect symmetry. We decomposed off-symmetry into two aspects which are structure index (SI) which measures structural difference and assembly index (AI) which measures assembly difference. We found in most cases, the major contributor to OS is SI in dimers and AI in trimers. During our research, we found the SI and in turn the 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.

Degree

M.S.

Advisors

Liu, Purdue University.

Subject Area

Biochemistry

COinS