Finding an Average Core Structure: Application to the Globins

Russ B. Altman and Mark Gerstein

We present a procedure for automatically identifying from a set of aligned protein structures a subset of atoms with only a small amount of structural variation, i.e.. a core. We apply this procedure to the globin family of proteins. Based purely on the results of the procedure, we show that the globin fold can be divided into two parts. The part with greater structural variation consists of the residues near the heme (the helix and parts of the G and H helices), and the part with lesser structural variation (the core) forms structural framework similar to that of the repressor protein (A, B, and E helices and remainder of the and H helices). Such a division is consistent with many other structural and biochemical findings. In addition, we find further partitions within the core that may have biological significance. Finally, using the structural core of the globin family as a reference point, we have compared structural variation to sequence variation and shown that a core definition based on sequence conservation does not necessarily agree with one based on structural similarity.

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