"A smaller number of new protein folds are discovered each year despite the fact that the number of protein structures determined annually is increasing exponentially," Kim says. "This and other observations strongly suggests that the total number of protein folds is dramatically smaller than the number of genes."
The rationale behind this idea is that through the eons, proteins have selectively evolved into the architectural structures best-suited to do their specific jobs. These structures essentially stay the same for proteins from all three kingdoms of life -- bacteria, archaea, and eukarya - even though the DNA sequences encoding for a specific type of protein can wildly vary from the genome of one organism to another, and sometimes even within the same organism.
In the map created by Kim and his colleagues, elongated groups of fold distributions approximately corresponding to the four SCOP structural classifications can be clearly seen. These classifications, which are based on secondary structural compositions and topology are the "alpha" helices, "beta" strands, and two mixes of helices and strands, one called "alpha plus beta" and the other "alpha slash beta." The Berkeley map reveals that the first three groups share a common area of origin, possibly corresponding to small primordial proteins, while the "alpha slash beta" class of proteins does not emerge until much later in time.
"It is conceivable that, of the primordial peptides, those containing fragments with high helix and/or strand propensity found their way to fold into small alpha, beta, and alpha plus beta structures," Kim says. "The alpha slash beta fold structures do not appear until proteins of sufficient size rose through evolution and the formation of supersecondary structural units became possible."
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Contact: Lynn Yarris
lcyarris@lbl.gov
510-486-5375
DOE/Lawrence Berkeley National Laboratory
19-Feb-2003