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Proteins. 2015 Apr;83(4):722-34. doi: 10.1002/prot.24706. Epub 2015 Feb 6.

The near-symmetry of proteins.

Author information

1
Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel.

Abstract

The majority of protein oligomers form clusters which are nearly symmetric. Understanding of that imperfection, its origins, and perhaps also its advantages requires the conversion of the currently used vague qualitative descriptive language of the near-symmetry into an accurate quantitative measure that will allow to answer questions such as: "What is the degree of symmetry deviation of the protein?," "how do these deviations compare within a family of proteins?," and so on. We developed quantitative methods to answer this type of questions, which are capable of analyzing the whole protein, its backbone or selected portions of it, down to comparison of symmetry-related specific amino-acids, and which are capable of visualizing the various levels of symmetry deviations in the form of symmetry maps. We have applied these methods on an extensive list of homomers and heteromers and found that apparently all proteins never reach perfect symmetry. Strikingly, even homomeric protein clusters are never ideally symmetric. We also found that the main burden of symmetry distortion is on the amino-acids near the symmetry axis; that it is mainly the more hydrophilic amino-acids that take place in symmetry-distortive interactions; and more. The remarkable ability of heteromers to preserve near-symmetry, despite the different sequences, was also shown and analyzed. The comprehensive literature on the suggested advantages symmetric oligomerizations raises a yet-unsolved key question: If symmetry is so advantageous, why do proteins stop shy of perfect symmetry? Some tentative answers to be tested in further studies are suggested in a concluding outlook.

KEYWORDS:

CSM; near-symmetry; rotational symmetry; symmetric proteins; symmetry maps; symmetry measure

PMID:
25354765
DOI:
10.1002/prot.24706
[Indexed for MEDLINE]

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