[Chimera-users] circular permuation

Elaine Meng meng at cgl.ucsf.edu
Wed May 4 11:44:36 PDT 2005

Hi Bryan,
Several pairs of natural protein structures appear to be
related by circular permutation (and many sets have been
generated by artificial means).  Since these relationships
are known to exist, without specifying the mechanism,
it is useful for various programs to handle the situation.

However, you are correct: gene duplication is one of the
processes that might yield circularly permuted proteins.
However, it is not the only possibility.  Two proteins related
by circular permutation might have been generated by fusions
of two smaller parts that fused in the opposite order, for example.

Here are some reviews:

Uliel S, Fliess A, Unger R.
Naturally occurring circular permutations in proteins.
Protein Eng. 2001 Aug;14(8):533-42.

Russell RB, Ponting CP.
Protein fold irregularities that hinder sequence analysis.
Curr Opin Struct Biol. 1998 Jun;8(3):364-71.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Wednesday, May 4, 2005, at 11:23 AM, Bryan W. Lepore wrote:

> i want to test my understanding about the "circular permuation" during
> matching:  is this for proteins that result from gene duplication?
> -bryan
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