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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. http://peds.oupjournals.org/cgi/content/full/14/8/533 Russell RB, Ponting CP. Protein fold irregularities that hinder sequence analysis. Curr Opin Struct Biol. 1998 Jun;8(3):364-71. http://www.ncbi.nlm.nih.gov/entrez/ query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9666333 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users