Evolution of protein complexity: The blue copper-containing oxidases and related proteins |
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Authors: | Lars G Rydén Lois T Hunt |
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Institution: | (1) Department of Biochemistry, Uppsala University, Uppsala Biomedical Center, Box 576, 751 23 Uppsala, Sweden;(2) National Biomedical Research Foundation, Georgetown University Medical Center, 3900 Reservoir Road, NW, 20007 Washington DC, USA |
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Abstract: | Summary The blue copper proteins and their relatives have been compared by sequence alignments, by comparison of three-dimensional
structures, and by construction of phylogenetic trees. The group contains proteins varying in size from 100 residues to over
2,300 residues in a single chain, containing from zero to nine copper atoms, and with a broad variation in function ranging
from electron carrier proteins and oxidases to the blood coagulation factors V and VIII. Difference matrices show the sequence
difference to be over 90% for many pairs in the group, yet alignment scores and other evidence suggest that they all evolved
from a common ancestor. We have attempted to delineate how this evolution took place and in particular to define the mechanisms
by which these proteins acquired an ever-increasing complexity in structure and function. We find evidence for six such mechanisms
in this group of proteins: domain enlargement, in which a single domain increases in size from about 100 residues up to 210;
domain duplication, which allows for a size increase from about 170 to about 1,000 residues; segment elongation, in which
a small segment undergoes multiple successive duplications that can increase the chain size 50-fold; domain recruitment, in
which a domain coded elsewhere in the genome is added on to the peptide chain; subunit formation, to form multisubunit proteins;
and glycosylation, which in some cases doubles the size of the protein molecule. Size increase allows for the evolution of
new catalytic properties, in particular the oxidase function, and for the formation of coagulation factors with multiple interaction
sites and regulatory properties. The blood coagulation system is examined as an example in which a system of interacting proteins
evolved by successive duplications of larger parts of the genome. The evolution of size, functionality, and diversity is compared
with the general question of increase in size and complexity in biology. |
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Keywords: | Blue copper proteins Blue oxidases Coagulation factors Discoidins Domain evolution Evolutionary mechanisms Phylogeny |
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