Abstract
In membrane proteins, symmetry and pseudosymmetry often have functional or evolutionary implications. However, available symmetry detection methods have not been tested systematically on this class of proteins because of the lack of an appropriate benchmark set. Here we present MemSTATS, a publicly available benchmark set of both quaternary- and internal-symmetries in membrane protein structures. The symmetries are described in terms of order, repeated elements, and orientation of the axis with respect to the membrane plane. Moreover, using MemSTATS, we compare the performance of four widely used symmetry detection algorithms and highlight specific challenges and areas for improvement in the future.
Highlights
Membrane proteins are encoded by around one third of a given genome [1,2,3] and play key roles in transmission of information and chemicals such as neurotransmitters into the cell
These symmetries are often intimately associated with the folding and function of membrane proteins and a systematic study of symmetry should provide a framework for a broader understanding of the mechanistic principles and evolutionary development of this important class of proteins
Investigations of the applicability of existing symmetry detection algorithms to membrane proteins are hampered by the lack of a reference benchmark that can be used to evaluate the performance of the detection methods
Summary
Membrane proteins are encoded by around one third of a given genome [1,2,3] and play key roles in transmission of information and chemicals such as neurotransmitters into the cell. Sophisticated algorithms exist that detect repeated structural elements in proteins [4,5], there has been limited effort to investigate their applicability to membrane proteins.
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