Figure 2. A schematic representation of the evolutionary processes that result in conservation patterns of amino acids. For a given family of folds, e.g., immunoglobulin (Ig) fold in this diagram, there are several alternative minima (3) in the hypothetical free energy landscape in the sequence space as a function of the "evolutionary" reaction coordinate (e.g., time). Each of these minima are formed by mutations in protein sequences at some typical time scales, to, that do not alter the protein's thermodynamically and/or kinetically important sites, forming families of homologous proteins. Transitions from one minimum to another occur at time scales, T=To exp(AG/ 7) where AG is the free energy barrier separating one family of homologous proteins from another. At time scale X mutations occur that would alter several amino acids at the important sites of the proteins in such a way that the protein properties are not compromised. At time scale X the family of analogs is formed. In three minima we present three families ofhomologs (1TEN, 1FNF, and 1CFB) each comprised of sue homologous proteins. We show 8 positions in the aligned proteins: from 18 to 28. It can be observed that at position 4 (marked by blocks) in each of the families presented in the diagram amino acids are conserved within each family ofhomologs, but vary between these families. This position corresponds to position 21 in Ig fold alignment (to 1TEN) and is conserved.

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