title: Proteins: form and function.
abstract: An overwhelming array of structural variants has evolved from a comparatively small number of protein structural domains; 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. Protein function prediction strategies, both sequence and structure based, are also discussed and their associated strengths and weaknesses assessed.
authors.affiliation: Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland. roy.sleator@cit.ie
authors.forename: Roy D
authors.initials: RD
authors.lastname: Sleator
mesh_terms: D020816:Amino Acid Motifs; D030562:Databases, Protein; D020440:Gene Duplication; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000378:metabolism*; D020539:Sequence Analysis, Protein; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins
references.citation: Nature. 1983 Feb 24;301(5902):732-4
references.pmid: 6828156
references.citation: Cell Mol Life Sci. 2003 Dec;60(12):2637-50
references.pmid: 14685688
references.citation: J Mol Biol. 1988 Nov 20;204(2):417-33
references.pmid: 3221393
references.citation: J Mol Biol. 2001 Jul 6;310(2):311-25
references.pmid: 11428892
references.citation: J Mol Biol. 2002 Apr 26;318(2):595-608
references.pmid: 12051862
references.citation: Genome Res. 1998 Aug;8(8):779-90
references.pmid: 9724324
references.citation: Curr Opin Struct Biol. 2005 Jun;15(3):275-84
references.pmid: 15963890
references.citation: Trends Genet. 2003 Aug;19(8):415-7
references.pmid: 12902157
references.citation: Bioessays. 2006 Oct;28(10):973-8
references.pmid: 16998824
references.citation: Curr Opin Chem Biol. 2004 Feb;8(1):3-7
references.pmid: 15036149
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D380-6
references.pmid: 19036790
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D328-32
references.pmid: 18842637
references.citation: Sci Prog. 2010;93(Pt 1):1-6
references.pmid: 20222353
references.citation: Genome Res. 1999 Dec;9(12):1198-203
references.pmid: 10613842
references.citation: Arch Microbiol. 2010 Mar;192(3):151-5
references.pmid: 20127480
references.citation: Methods Mol Biol. 2009;563:241-58
references.pmid: 19597789
references.citation: J Mol Biol. 1994 Mar 4;236(4):1067-78
references.pmid: 8120887
references.citation: Novartis Found Symp. 2002;247:66-80; discussion 80-3, 84-90, 244-52
references.pmid: 12539950
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):400-2
references.pmid: 12520033
references.citation: J Struct Biol. 2001 May-Jun;134(2-3):232-45
references.pmid: 11551182
references.citation: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W582-5
references.pmid: 15215455
references.citation: Microbiology (Reading). 2009 Aug;155(Pt 8):2463-2475
references.pmid: 19542009
references.citation: Science. 2003 Jun 13;300(5626):1701-3
references.pmid: 12805536
references.citation: Structure. 2005 Apr;13(4):551-64
references.pmid: 15837194
references.citation: J Mol Biol. 2001 Apr 6;307(4):1113-43
references.pmid: 11286560
references.citation: Infect Immun. 2009 Nov;77(11):4895-904
references.pmid: 19737907
references.citation: EMBO J. 1986 Apr;5(4):823-6
references.pmid: 3709526
references.citation: Biochem J. 2009 Apr 1;419(1):15-28
references.pmid: 19272021
references.citation: BMC Bioinformatics. 2005 Oct 12;6:247
references.pmid: 16221304
references.citation: Genome Res. 2009 Aug;19(8):1393-403
references.pmid: 19443856
references.citation: Gut Pathog. 2010 Dec 10;2(1):20
references.pmid: 21143981
references.citation: Protein Sci. 1996 Jun;5(6):1001-13
references.pmid: 8762132
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W20-3
references.pmid: 16844992
references.citation: Protein Sci. 2003 Sep;12(9):1813-21
references.pmid: 12930981
references.citation: Cell Mol Life Sci. 2007 Oct;64(19-20):2505-11
references.pmid: 17611711
references.citation: Curr Opin Struct Biol. 1997 Jun;7(3):422-7
references.pmid: 9204286
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D245-9
references.pmid: 18003654
references.citation: Trends Biochem Sci. 2008 Sep;33(9):444-51
references.pmid: 18656364
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Genome Res. 2000 Apr;10(4):398-400
references.pmid: 10779480
references.citation: Gut Microbes. 2010 Mar;1(2):77-79
references.pmid: 21326913
references.citation: Appl Environ Microbiol. 2003 Jan;69(1):1-9
references.pmid: 12513970
references.citation: Protein Eng. 2001 Aug;14(8):533-42
references.pmid: 11579221
references.citation: Biol Chem. 1996 Jul-Aug;377(7-8):447-54
references.pmid: 8922278
references.citation: J Mol Biol. 1997 May 16;268(4):779-99
references.pmid: 9175860
references.citation: J Biol Chem. 1999 Sep 17;274(38):27047-55
references.pmid: 10480918
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):228-30
references.pmid: 10592233
references.citation: Math Biosci. 2005 Feb;193(2):223-34
references.pmid: 15748731
references.citation: Protein Sci. 1998 Apr;7(4):848-59
references.pmid: 9568892
references.citation: Nature. 2000 Jun 15;405(6788):823-6
references.pmid: 10866208
references.citation: Lett Appl Microbiol. 2008 Nov;47(5):361-6
references.pmid: 19146522
references.citation: Curr Opin Struct Biol. 1996 Jun;6(3):377-85
references.pmid: 8804824
references.citation: Amino Acids. 2008 Oct;35(3):517-30
references.pmid: 18427717
references.citation: J Struct Funct Genomics. 2003;4(2-3):167-77
references.pmid: 14649301
references.citation: Brief Bioinform. 2006 Sep;7(3):225-42
references.pmid: 16772267
references.citation: Genome Biol. 2005;6(1):R7
references.pmid: 15642099
references.citation: Biochemistry. 1998 Apr 14;37(15):5107-17
references.pmid: 9548741