From a comparatively small number of protein structural domains a staggering array of structural variants has evolved which has, in turn, facilitated an expanse of functional derivatives. Herein I review the primary mechanisms which have contributed to the vastness of our existing, and expanding, protein repertoires.
ChothiaC., and GoughJ. (2009) Genomic and structural aspects of protein evolution. Biochem. J., 419, 15–28.
2.
BrennerS.E., HubbardT., MurzinA., and ChothiaC. (1995) Gene duplications in H. influenzae. Nature, 378, 140.
3.
TeichmannS.A., ParkJ., and ChothiaC. (1998) Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl. Acad. Sci. USA, 95, 14658–14663.
4.
VolffJ.N., and BrosiusJ. (2007) Modern genomes with retro-look: retro-transposed elements, retroposition and the origin of new genes. Genome Dyn., 3, 175–190.
5.
WilsonD., PethicaR., ZhouY., TalbotC., VogelC., MaderaM., ChothiaC., and GoughJ. (2009) SUPERFAMILY–sophisticated comparative genomics, data mining, visualization and phylogeny. Nucl. Acids Res., 37, D380–386.
6.
BlanchetotA., WilsonV., WoodD., and JeffreysA.J. (1983) The seal myoglobin gene: an unusually long globin gene. Nature, 301, 732–734.
7.
MooreA.D., BjorklundA.K., EkmanD., Bornberg-BauerE., and ElofssonA. (2008) Arrangements in the modular evolution of proteins. Trends Biochem. Sci., 33, 444–451.
8.
LonghiS., CzjzekM., LamzinV., NicolasA., and CambillauC. (1997) Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereo-chemical analysis. J. Mol. Biol., 268, 779–799.
9.
ChenJ.C., MierckeL.J., KrucinskiJ., StarrJ.R., SaenzG., WangX., SpilburgC.A., LangeL.G., EllsworthJ.L., and StroudR.M. (1998) Structure of bovine pancreatic cholesterol esterase at 1.6 A: novel structural features involved in lipase activation. Biochemistry, 37, 5107–5117.
10.
GersteinM., SonnhammerE.L., and ChothiaC. (1994) Volume changes in protein evolution. J. Mol. Biol., 236, 1067–1078.
11.
ChothiaC., and LeskA.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J., 5, 823–826.
12.
KawashimaT., KawashimaS., TanakaC., MuraiM., YonedaM., PutnumN.H., RokhsarD.S., KanehisaM., SatohN., and WadaH. (2009) Domain shuffling and the evolution of vertebrates. Genome Res. (in press).
13.
VogelC., and MoreaV. (2006) Duplication, divergence and formation of novel protein topologies. Bioessays, 28, 973–978.
14.
LindqvistY., and SchneiderG. (1997) Circular permutations of natural protein sequences: structural evidence. Curr. Opin. Struct. Biol., 7, 422–427.
15.
LoW.C., LeeC.C., LeeC.Y., and LyuP.C. (2009) CPDB: a database of circular permutation in proteins. Nucl. Acids Res., 37, D328–332.
16.
HeinemannU., AyJ., GaiserO., MullerJ.J., and PonnuswamyM.N. (1996) Enzymology and folding of natural and engineered bacterial beta-glucanases studied by X-ray crystallography. Biol. Chem., 377, 447–454.
17.
ChuV., FreitagS., Le TrongI., StenkampR.E., and StaytonP.S. (1998) Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-biotin system. Protein Sci., 7, 848–859.
18.
ToddA.E., OrengoC.A., and ThorntonJ.M. (2001) Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol., 307, 1113–1143.
19.
WyckoffT.J., and RaetzC.R. (1999) The active site of Escherichia coli UDP-N-acetylglucosamine acyltransferase. Chemical modification and site-directed mutagenesis. J. Biol. Chem., 274, 27047–27055.
20.
YoonS.I., JonesB.C., LogsdonN.J., and WalterM.R. (2005) Same structure, different function crystal structure of the Epstein-Barr virus IL-10 bound to the soluble IL-10R1 chain. Structure, 13, 551–564.
21.
ApicG., GoughJ., and TeichmannS.A. (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol., 310, 311–325.
22.
ChothiaC., GoughJ., VogelC., and TeichmannS.A. (2003) Evolution of the protein repertoire. Science, 300, 1701–1703.
23.
SleatorR.D., ShortallC., and HillC. (2008) Metagenomics. Lett. Appl. Microbiol., 47, 361–366.
