Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins

Bioinformatics

Volumn 27, Issue 17, 2011, Pages 2368-2375

  Goncearenco, Alexander ^a   Berezovsky, Igor N ^a  

^a UNIVERSITY OF BERGEN   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE; ENZYME; METALLOPROTEIN;

ARTICLE; BIOLOGY; CHEMISTRY; METHODOLOGY; MOLECULAR EVOLUTION; PROTEOMICS; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; CYSTEINE; ENZYMES; EVOLUTION, MOLECULAR; METALLOPROTEINS; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN;

EID: 80051923523     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr396     Document Type: Article

References (49)

1. Altschul,S.F. et al. (1990) Basic local alignment search tool. J.Mol. Biol., 215, 403-410.
2. Atkinson,H.J. and Babbitt,P.C. (2009) An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PLoS Comput. Biol., 5, e1000541.
3. Bateman,A. et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32, D138-D141.
4. Benini,S. et al. (2000) Crystal structure of oxidized Bacillus pasteurii cytochrome c553 at 0.97-A resolution. Biochemistry, 39, 13115-13126.
5. Berezovsky,I.N. (2003)Discrete structure of van derWaals domains in globular proteins. Protein Eng., 16, 161-167.
6. Berezovsky,I.N. et al. (2000) Closed loops of nearly standard size: common basic element of protein structure. FEBS Lett., 466, 283-286.
7. Berezovsky,I.N. et al. (2003a) Protein sequences yield a proteomic code. J. Biomol. Struct. Dyn., 21, 317-325.
8. Berezovsky,I.N. et al. (2003b) Spelling protein structure. J. Biomol. Struct. Dyn., 21, 327-339.
9. Berezovsky,I.N. and Trifonov,E.N. (2001) Van der Waals locks: loop-n-lock structure of globular proteins. J. Mol. Biol., 307, 1419-1426.
10. Berndt,C. et al. (2008) Thioredoxins and glutaredoxins as facilitators of protein folding. Biochim. Biophys. Acta, 1783, 641-650.
11. Boal,A.K. et al. (2011) Structural basis for methyl transfer by a radical SAM enzyme. Science, 332, 1089-1092.
12. Cai,W. et al. (2004) Reconstruction of ancestral protein sequences and its applications. BMC Evol. Biol., 4, 33.
13. Chivers,P.T. et al. (1996) The CXXC motif: imperatives for the formation of native disulde bonds in the cell. EMBO J., 15, 2659-2667.
14. Chivers,P.T. et al. (1997) The CXXC motif: a rheostat in the active site. Biochemistry, 36, 4061-4066.
15. Davidson,A.L. et al. (2008) Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems. Microbiol. Mol. Biol. Rev., 72, 317-364.
16. de Gennes,P.G. (1990) Introduction to Polymer Dynamics. Cambridge University Press pp.17-26.
17. Dupont,C.L. et al. (2010) History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proc. Natl Acad. Sci. USA, 107, 10567-10572.
18. Fan,S.W. et al. (2009) Conformational changes in redox pairs of protein structures. Protein Sci., 18, 1745-1765.
19. Fomenko,D.E. and Gladyshev,V.N. (2003) Identity and functions of CxxC-derived motifs. Biochemistry, 42, 11214-11225.
20. Frey,P.A. et al. (2008) The radical SAM superfamily. Crit. Rev. Biochem. Mol. Biol., 43, 63-88.
21. Golovin,A. and Henrick,K. (2008) MSDmotif: exploring protein sites and motifs. BMC Bioinformatics, 9, 312.
22. Goncearenco,A. and Berezovsky,I.N. (2010) Prototypes of elementary functional loops unravel evolutionary connections between protein functions. Bioinformatics, 26, i497-i503.
23. Gutierrez,P. et al. (2004) Structure of the archaeal translation initiation factor aIF2 beta from Methanobacterium thermoautotrophicum: implications for translation initiation. Protein Sci., 13, 659-667.
24. Harms,M.J. and Thornton,J.W. (2010) Analyzing protein structure and function using ancestral gene reconstruction. Curr. Opin. Struct. Biol., 20, 360-366.
25. Holliday,G.L. et al. (2009) Understanding the functional roles of amino acid residues in enzyme catalysis. J. Mol. Biol., 390, 560-577.
26. Hopfner,K.P. et al. (2002) The Rad50 zinc-hook is a structure joiningMre11 complexes in DNA recombination and repair. Nature, 418, 562-566.
27. Hopfner,K.P. et al. (2001) Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase. Cell, 105, 473-485.
28. Iwasaki,T. (2010) Iron-sulfur world in aerobic and hyperthermoacidophilic archaea Sulfolobus. Archaea, 2010, 842639.
29. Johnson,D.C. et al. (2005) Structure, function, and formation of biological iron-sulfur clusters. Annu. Rev. Biochem., 74, 247-281.
30. Koonin,E.V. (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat. Rev. Microbiol., 1, 127-136.
31. Kullback,S. and Leibler,R.A. (1951) On information and sufciency. Ann. Math. Stat., 22, 142-143.
32. Li,W. and Godzik,A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
33. Lipkus,A.H. (1999)Aproof of the triangle inequality for the Tanimoto distance. J.Math. Chem., 26, 263-265.
34. Marchler-Bauer,A. et al. (2005) CDD: a Conserved Domain Database for protein classication. Nucleic Acids Res., 33, D192-D196.
35. Meyer,J. (2008) Iron-sulfur protein folds, iron-sulfur chemistry, and evolution. J. Biol. Inorg. Chem., 13, 157-170.
36. Min,J. et al. (2001) Crystal structure of a SIR2 homolog-NAD complex. Cell, 105, 269-279.
37. Mirkin,B.G. et al. (2003) Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol., 3,2.
38. Murtagh,F. (1984) Complexities of hierarchic clustering algorithms: the state of the art Comput., Stat. Q., 1, 101-113.
39. Murzin,A.G. et al. (1995) SCOP: a structural classication of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
40. Putilina,T. et al. (1999) The DHHC domain: a new highly conserved cysteine-richmotif. Mol. Cell. Biochem., 195, 219-226.
41. Quan,S. et al. (2007) The CXXC motif is more than a redox rheostat. J. Biol. Chem., 282, 28823-28833.
42. Shannon,P. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
43. Shoemaker,B.A. et al. (2010) Inferred biomolecular interaction server-a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Res., 38, D518-D524.
44. Sigrist,C.J. et al. (2010) PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res., 38, D161-D166.
45. Sokal,R.R. and Michener,C.D. (1958) A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin, 38, 1409-1438.
46. Trifonov,E.N. et al. (2001) Distinct stages of protein evolution as suggested by protein sequence analysis. J. Mol. Evol., 53, 394-401.
47. Waksman,G. et al. (1994) Crystal structure of Escherichia coli thioredoxin reductase rened at 2 A resolution. Implications for a large conformational change during catalysis. J. Mol. Biol., 236, 800-816.
48. Watanabe,S. et al. (2007) Crystal structures of [NiFe] hydrogenase maturation proteins HypC, HypD, and HypE: insights into cyanation reaction by thiol redox signaling. Mol. Cell, 27, 29-40.
49. Wilcox,D.E. et al. (2001) Oxidation of zinc-binding cysteine residues in transcription factor proteins. Antioxid Redox Signal, 3, 549-564.