"http://www.pnas.org/cgi/content/abstract/0606239103v1" [Broken] on limitations in the apparent evolution of proteins in living things: Evolution of protein structural classes and protein sequence families ( protein fold classes | common structural ancestor | evolutionary age | protein structure universe ) In-Geol Choi * and Sung-Hou Kim * In protein structure space, protein structures cluster into four elongated regions when mapped based solely on similarity among the 3D structures. These four regions correspond to the four major classes of present-day proteins defined by the contents of secondary structure types and their topological arrangement. Evolution of and restriction to these four classes suggest that, in most cases, the evolution of genes may have been constrained or selected to those genetic changes that results in structurally stable proteins occupying one of the four "allowed" regions of the protein structure space, "structural selection," an important component of natural selection in gene evolution. Our studies on tracing the "common structural ancestor" for each protein sequence family of known structure suggest that: (i) recently emerged proteins belong mostly to three classes; (ii) the proteins that emerged earlier evolved to gain a new class; and (iii) the proteins that emerged earliest evolved to become the present-day proteins in the four major classes, with the fourth-class proteins becoming the most dominant population. Furthermore, our studies also show that not all present-day proteins evolved from one single set of proteins in the last common ancestral organism, but new common ancestral proteins were "born" at different evolutionary times, not traceable to one or two ancestral proteins: "the multiple birth model" for the evolution of protein sequence families. *Physical Biosciences Division, Lawrence Berkeley National Laboratory, and Department of Chemistry, University of California, Berkeley, CA 94720 Contributed by Sung-Hou Kim, July 30, 2006 Link courtesy of "http://johnhawks.net/weblog/reviews/evolution/constraints/protein_universe_choi_kim_2006.html" [Broken] Apparently a trade-off between complexity and stability of protein structures has drifted in the complexity direction as evolution has progressed. Could this be due to the use of temporary "throw-away" proteins by complex organism while older, simpler ones "don't get their proteins they have their proteins" (parodying a joke about old-line blue-blooded Boston ladies and their hats).