Relative stabilities of conserved and non-conserved structures in the ob-fold superfamily

International Journal of Molecular Sciences

Volumn 10, Issue 5, 2009, Pages 2412-2430

  Guardino, Kaitlyn M ^a   Sheftic, Sarah R ^a   Slattery, Robert E ^a   Alexandrescu, Andrei T ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Modularity; Protein dynamics; Protein folding; Structural genomics; Structure similarity

Indexed keywords

OLIGONUCLEOTIDE; OLIGOSACCHARIDE;

ARTICLE; BINDING AFFINITY; CALCULATION; CRYSTALLOGRAPHY; DENSITY; HYDROPHOBICITY; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE; SENSITIVITY ANALYSIS;

MODULARITY; PROTEIN DYNAMICS; PROTEIN FOLDING; STRUCTURAL GENOMICS; STRUCTURE SIMILARITY;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; OLIGONUCLEOTIDES; OLIGOSACCHARIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 67049154403     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms10052412     Document Type: Article

References (54)

1. Efimov, A.V. Structural trees for protein superfamilies. Proteins 1997, 28, 241-260.
2. Murzin, A.G. OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J. 1993, 12, 861-867.
3. Murzin, A.G.; Brenner, S.E.; Hubbard, T.; Chothia, C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 1995, 247, 536-540.
4. Orengo, C.A.; Jones, D.T.; Thornton, J.M. Protein superfamilies and domain superfolds. Nature 1994, 372, 631-634.
5. Taylor, W.R. A 'periodic table' for protein structures. Nature 2002, 416, 657-660.
6. Alexandrescu, A.T.; Gittis, A.G.; Abeygunawardana, C.; Shortle, D. NMR structure of a stable 'OB-fold' sub-domain isolated from staphylococcal nuclease. J. Mol. Biol. 1995, 250, 134-143.
7. Watson, E.; Matousek, W.M.; Irimies, E.L.; Alexandrescu, A.T. Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins. Biochemistry 2007, 46, 9484-9494.
8. Murzin, A.G. How far divergent evolution goes in proteins. Curr. Opin. Struct. Biol. 1998, 8, 380-387.
9. Bai, Y.; Sosnick, T.R.; Mayne, L.; Englander, S.W. Protein folding intermediates: native-state hydrogen exchange. Science 1995, 269, 192-197.
10. Jeng, M.F.; Englander, S.W. Stable submolecular folding units in a non-compact form of cytochrome c. J. Mol. Biol. 1991, 221, 1045-1061.
11. Lindorff-Larsen, K.; Rogen, P.; Paci, E.; Vendruscolo, M.; Dobson, C.M. Protein folding and the organization of the protein topology universe. Trends Biochem. Sci. 2005, 30, 13-19.
12. Wang, Y.; Alexandrescu, A.T.; Shortle, D. Initial studies of the equilibrium folding pathway of staphylococcal nuclease. Philos. Trans. R. Soc. Lond. B Biol. Sci. 1995, 348, 27-34.
13. Agrawal, V.; Kishan, K.V. OB-fold: growing bigger with functional consistency. Curr. Protein Pept. Sci. 2003, 4, 195-206.
14. Arcus, V. OB-fold domains: a snapshot of the evolution of sequence, structure and function. Curr. Opin. Struct. Biol. 2002, 12, 794-801.
15. Theobald, D.L.; Mitton-Fry, R.M.; Wuttke, D.S. Nucleic acid recognition by OB-fold proteins. Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 115-133.
16. Alexandrescu, A.T.; Jaravine, V.A.; Dames, S.A.; Lamour, F.P. NMR hydrogen exchange of the OB-fold protein LysN as a function of denaturant: the most conserved elements of structure are the most stable to unfolding. J. Mol. Biol. 1999, 289, 1041-1054.
17. Jaravine, V.A.; Rathgeb-Szabo, K.; Alexandrescu, A.T. Microscopic stability of cold shock protein A examined by NMR native state hydrogen exchange as a function of urea and trimethylamine N-oxide. Protein Sci. 2000, 9, 290-301.
18. Bahar, I.; Wallqvist, A.; Covell, D.G.; Jernigan, R.L. Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry 1998, 37, 1067-1075.
19. Shortle, D.; Stites, W.E.; Meeker, A.K. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry 1990, 29, 8033-8041.
20. Tartaglia, G.G.; Cavalli, A.; Vendruscolo, M. Prediction of local structural stabilities of proteins from their amino acid sequences. Structure 2007, 15, 139-143.
21. Andreeva, A.; Howorth, D.; Chandonia, J.M.; Brenner, S.E.; Hubbard, T.J.; Chothia, C.; Murzin, A.G. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 2008, 36, D419-D425.
22. Yang, L.W.; Liu, X.; Jursa, C.J.; Holliman, M.; Rader, A.J.; Karimi, H.A.; Bahar, I. iGNM: a database of protein functional motions based on Gaussian Network Model. Bioinformatics 2005, 21, 2978-2987.
23. Yang, L.W.; Rader, A.J.; Liu, X.; Jursa, C.J.; Chen, S.C.; Karimi, H.A.; Bahar, I. oGNM: online computation of structural dynamics using the Gaussian Network Model Nucleic Acids Res. 2006, 34, W24-W31.
24. Bahar, I.; Atilgan, A.R.; Erman, B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 1997, 2, 173-181.
25. Kabsch, W.; Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22, 2577-2637.
26. Alexandrescu, A.T.; Rathgeb-Szabo, K. An NMR investigation of solution aggregation reactions preceding the misassembly of acid-denatured cold shock protein A into fibrils. J. Mol. Biol. 1999, 291, 1191-1206.
27. Max, K.E.; Zeeb, M.; Bienert, R.; Balbach, J.; Heinemann, U. Common mode of DNA binding to cold shock domains. Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus. FEBS J. 2007, 274, 1265-1279.
28. Reichmann, L.; Winter, G. Novel folded protein domains generated by combinatorial shuffling of polypeptide segments. Proc. Natl. Acad. Sci. USA 2000, 97, 10068-10073.
29. Wang, Y.; Shortle, D. A dynamic bundle of four adjacent hydrophobic segments in the denatured state of staphylococcal nuclease. Protein Sci. 1996, 5, 1898-1906.
30. Gu, Z.; Zitzewitz, J.A.; Matthews, C.R. Mapping the Structure of Folding Cores in TIM Barrel Proteins by Hydrogen Exchange Mass Spectrometry: The Roles of Motif and Sequence for the Indole-3-glycerol Phosphate Synthase from Sulfolobus solfataricus. J. Mol. Biol. 2007, 368, 582-594.
31. Yuan, Z.; Bailey, T.L.; Teasdale, R.D. Prediction of protein B-factor profiles. Proteins 2005, 58, 905-912.
32. Yuan, Z.; Zhao, J.; Wang, Z.X. Flexibility analysis of enzyme active sites by crystallographic temperature factors. Protein Eng. 2003, 16, 109-114.
33. Kyte, J.; Doolittle, R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 1982, 157, 105-132.
34. Finkelstein, A.V.; Ptitsyn, O.B. Protein Physics: A Course of Lectures; Academic Press: Amsterdam, The Netherlands, 2002.
35. Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
36. Kuriyan, J.; Weis, W.I. Rigid protein motion as a model for crystallographic temperature factors. Proc. Natl. Acad. Sci. USA 1991, 88, 2773-2777.
37. Alexandrescu, A.T.; Jahnke, W.; Wiltscheck, R.; Blommers, M.J. Accretion of structure in staphylococcal nuclease: an 15N NMR relaxation study. J. Mol. Biol. 1996, 260, 570-587.
38. Feng, W.; Tejero, R.; Zimmerman, D.E.; Inouye, M.; Montelione, G.T. Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding site. Biochemistry 1998, 37, 10881-10896.
39. Zeeb, M.; Max, K.E.; Weininger, U.; Low, C.; Sticht, H.; Balbach, J. Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution. Nucleic Acids Res. 2006, 34, 4561-4571.
40. Aramini, J.M.; Huang, Y.J.; Cort, J.R.; Goldsmith-Fischman, S.; Xiao, R.; Shih, L.Y.; Ho, C.K.; Liu, J.; Rost, B.; Honig, B.; Kennedy, M.A.; Acton, T.B.; Montelione, G.T. Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Protein Sci. 2003, 12, 2823-2830.
41. Williamson, R.A.; Panagiotidou, P.; Mott, J.D.; Howard, M.J. Dynamic characterisation of the netrin-like domain of human type 1 procollagen C-proteinase enhancer and comparison to the Nterminal domain of tissue inhibitor of metalloproteinases (TIMP). Mol. Biosyst. 2008, 4, 417-425.
42. Li, W.; Hoffman, D.W. Structure and dynamics of translation initiation factor aIF-1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy. Protein Sci. 2001, 10, 2426-2438.
43. Enggist, E.; Thony-Meyer, L.; Guntert, P.; Pervushin, K. NMR structure of the heme chaperone CcmE reveals a novel functional motif. Structure 2002, 10, 1551-1557.
44. Schubert, M.; Edge, R.E.; Lario, P.; Cook, M.A.; Strynadka, N.C.; Mackie, G.A.; McIntosh, L.P. Structural characterization of the RNase E S1 domain and identification of its oligonucleotidebinding and dimerization interfaces. J. Mol. Biol. 2004, 341, 37-54.
45. Gao, G.; Semenchenko, V.; Arumugam, S.; Van Doren, S.R. Tissue inhibitor of metalloproteinases-1 undergoes microsecond to millisecond motions at sites of matrix metalloproteinase-induced fit. J. Mol. Biol. 2000, 301, 537-552.
46. Mitton-Fry, R.M.; Anderson, E.M.; Theobald, D.L.; Glustrom, L.W.; Wuttke, D.S. Structural basis for telomeric single-stranded DNA recognition by yeast Cdc13. J. Mol. Biol. 2004, 338, 241-255.
47. Wu, B.; Arumugam, S.; Gao, G.; Lee, G.I.; Semenchenko, V.; Huang, W.; Brew, K.; Van Doren, S.R. NMR structure of tissue inhibitor of metalloproteinases-1 implicates localized induced fit in recognition of matrix metalloproteinases. J. Mol. Biol. 2000, 295, 257-268.
48. Battiste, J.L.; Pestova, T.V.; Hellen, C.U.; Wagner, G. The eIF1A solution structure reveals a large RNA-binding surface important for scanning function. Mol. Cell 2000, 5, 109-119.
49. Perl, D.; Schmid, F.X. Electrostatic stabilization of a thermophilic cold shock protein. J. Mol. Biol. 2001, 313, 343-357.
50. Swindells, M.B.; Orengo, C.A.; Jones, D.T.; Hutchinson, E.G.; Thornton, J.M. Contemporary approaches to protein structure classification. Bioessays 1998, 20, 884-891.
51. Laskowski, R.A.; Chistyakov, V.V.; Thornton, J.M. PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res. 2005, 33, D266-D 268.
52. DeLano, W.L. The PyMOL Molecular Graphics System; DeLano Scientific: San Carlos, CA, USA, 2002.
53. Hobohm, U.; Sander, C. Enlarged representative set of protein structures. Protein Sci. 1994, 3, 522-524.
54. Gasteiger, E.; Hoogland, C.; Gattiker, A.; Duvaud, S.; Wilkins, M.R.; Appel, R.D.; Bairoch, A. Protein Identification and Analysis Tools on the ExPASy Server; Humana Press: Totowa, NJ, USA, 2005.