A stabilizing α/β-hydrophobic core greatly contributes to hyperthermostability of archaeal [P62A]Ssh10b

Biochemistry

Volumn 47, Issue 43, 2008, Pages 11212-11221

  Fang, Xianyang ^a   Cui, Qiu ^a   Tong, Yufeng ^a   Feng, Yingang ^a   Shan, Lu ^a   Huang, Li ^b   Wang, Jinfeng ^a  

^a INSTITUTE OF BIOPHYSICS   (China)

^b INSTITUTE OF MICROBIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES; HYDROGEN; HYDROGEN BONDS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACIDS; ORGANIC ACIDS; PYROLYSIS; STATISTICAL METHODS; SUGAR (SUCROSE);

AMIDE PROTONS; ARCHAEA; ARCHAEAL; BONDING INTERACTIONS; DATA ANALYSIS; ELEVATED TEMPERATURES; H/D EXCHANGES; HYDROPHOBIC; HYDROPHOBIC CORES; HYPERTHERMOPHILIC; HYPERTHERMOSTABILITY; INTERNAL MOTIONS; MESOPHILIC; MOLECULAR BASES; MULTIDIMENSIONAL NMR; MUTANT PROTEINS; SOLUTION STRUCTURES; SULFOLOBUS SHIBATAE; UNFOLDING PROCESSES;

HYDROPHOBICITY;

ALANINE; ASPARAGINE; DNA BINDING PROTEIN; LYSINE; PROLINE; SSH10B PROTEIN; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID SUBSTITUTION; ARTICLE; BETA SHEET; HYDROGEN BOND; NITROGEN NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTON TRANSPORT; THERMOSTABILITY;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; DIMERIZATION; DNA, ARCHAEAL; HEAT; HYDROGEN BONDING; HYDROPHOBICITY; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID; SULFOLOBUS; THERMODYNAMICS;

ARCHAEA; SULFOLOBUS SHIBATAE;

EID: 54849412555     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi8007593     Document Type: Article

References (42)

1. Grote, M., Dijk, J., and Reinhardt, R. (1986) Ribosomal and DNA binding proteins of the thermoacidophilic archaebacterium Sulfolobus acidocaldarius. Biochim. Biophys. Acta 873, 405-413.
2. Bell, S. D., Botting, C. H., Wardleworth, B. N., Jackson, S. P., and White, M. F. (2002) The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science 296, 148-151.
3. Forterre, P., Confalonieri, F., and Knapp, S. (1999) Identification of the gene encoding archeal-specific DNA-binding proteins of the Sac10b family. Mol. Microbiol. 32, 669-670.
4. Xue, H., Guo, R., Wen, Y., Liu, D., and Huang, L. (2000) An abundant DNA binding protein from the hyperthermophilic archaeon Sulfolobus shibatae affects DNA supercoiling in a temperature-dependent fashion. J. Bacteriol. 182, 3929-3933.
5. Zhao, K., Chai, X., and Marmorstein, R. (2003) Structure of a Sir2 substrate, Alba, reveals a mechanism for deacetylation-induced enhancement of DNA binding. J. Biol. Chem. 278, 26071-26077.
6. Chou, C. C., Lin, T. W., Chen, C. Y., and Wang, A. H. (2003) Crystal structure of the hyperthermophilic archaeal DNA-binding protein Sso10b2 at a resolution of 1.85 Angstroms. J. Bacteriol. 185, 4066-4073.
7. Wardleworth, B. N., Russell, R. J., Bell, S. D., Taylor, G. L., and White, M. F. (2002) Structure of Alba: an archaeal chromatin protein modulated by acetylation. Embo J. 21, 4654-4662.
8. Xu, S., Qin, S., and Pan, X. M. (2004) Thermal and conformational stability of Ssh10b protein from archaeon Sulfolobus shibattae. Biochem. J. 382, 433-440.
9. Tong, Y., Cui, Q., Feng, Y., Huang, L., and Wang, J. (2002) 1H, 15N, and 13C resonance assignments and secondary structure of the Ssh10b from hyperthermophilic archaeon Sulfolobus shibatae. J. Biomol. NMR 22, 385-386.
10. Cui, Q., Tong, Y., Xue, H., Huang, L., Feng, Y., and Wang, J. (2003) Two conformations of archaeal Ssh10b. The origin of its temperature-dependent interaction with DNA. J. Biol. Chem. 278, 51015-51022.
11. Maity, H., Maity, M., and Englander, S. W. (2004) How cytochrome c folds, and why: submolecular foldon units and their stepwise sequential stabilization. J. Mol. Biol. 343, 223-233.
12. Cavanagh, J. (1996) Protein NMR Spectroscopy: Principles and Practice, Academic Press, San Diego.
13. Vuister, G. W., and Bax, A. (1993) Quantitative J correlation: a new approach for measuring homonuclear three-bond J(HNH.alpha.) coupling constants in 15N-enriched proteins. J. Am. Chem. Soc. 115, 7772-7777.
14. Farrow, N. A., Muhandiram, R., Singer, A. U., Pascal, S. M., Kay, C. M., Gish, G., Shoelson, S. E., Pawson, T., Forman-Kay, J. D., and Kay, L. E. (1994) Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry 33, 5984-6003.
15. Markley, J. L., Bax, A., Arata, Y., Hilbers, C. W., Kaptein, R., Sykes, B. D., Wright, P. E., and Wuthrich, K. (1998) Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. J. Biomol. NMR 12, 1-23.
16. Nilges, M., and O'Donoghue, S. I. (1998) Ambiguous NOEs and automated NOE assignment. Prog. Nucl. Magn. Reson. Spectrosc. 32, 107-139.
17. Linge, J. P., O'Donoghue, S. I., and Nilges, M. (2001) Automated assignment of ambiguous nuclear overhauser effects with ARIA. Methods Enzymol. 339, 71-90.
18. Linge, J. P., Habeck, M., Rieping, W., and Nilges, M. (2003) ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 19, 315-316.
19. Nilges, M. (1993) A calculation strategy for the structure determination of symmetric dimers by 1H NMR. Proteins 17, 297-309.
20. Folmer, R. H., Hilbers, C. W., Konings, R. N., and Nilges, M. (1997) Floating stereospecific assignment revisited: application to an 18 kDa protein and comparison with J-coupling data. J. Biomol. NMR 9, 245-258.
21. Linge, J. P., and Nilges, M. (1999) Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation. J. Biomol. NMR 13, 51-59.
22. Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R., and Thornton, J. M. (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477-486.
23. Xie, T., Liu, D., Feng, Y., Shan, L., and Wang, J. (2007) Folding stability and cooperativity of the three forms of 1-110 residues fragment of staphylococcal nuclease. Biophys. J. 92, 2090-2107.
24. Dosset, P., Hus, J. C., Blackledge, M., and Marion, D. (2000) Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J. Biomol. NMR 16, 23-28.
25. Pawley, N. H., Wang, C., Koide, S., and Nicholson, L. K. (2001) An improved method for distinguishing between anisotropic tumbling and chemical exchange in analysis of 15N relaxation parameters. J. Biomol. NMR 20, 149-165.
26. Bai, Y., Milne, J. S., Mayne, L., and Englander, S. W. (1993) Primary structure effects on peptide group hydrogen exchange. Proteins 17, 75-86.
27. Bai, Y., Sosnick, T. R., Mayne, L., and Englander, S. W. (1995) Protein folding intermediates: native-state hydrogen exchange. Science 269, 192-197.
28. Connelly, G. P., Bai, Y., Jeng, M. F., and Englander, S. W. (1993) Isotope effects in peptide group hydrogen exchange. Proteins 17, 87-92.
29. Jaravine, V. A., Rathgeb-Szabo, K., and Alexandrescu, A. T. (2000) 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. 9, 290-301.
30. Bai, Y., Milne, J. S., Mayne, L., and Englander, S. W. (1994) Protein stability parameters measured by hydrogen exchange. Proteins 20, 4-14.
31. Chamberlain, A. K., Handel, T. M., and Marqusee, S. (1996) Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH. Nat. Struct. Biol. 3, 782-787.
32. Zeeb, M., Lipps, G., Lilie, H., and Balbach, J. (2004) Folding and Association of an Extremely Stable Dimeric Protein from Sulfolobus islandicus. J. Mol. Biol. 336, 227-240.
33. Cai, M., Gong, Y. X., Wen, L., and Krishnamoorthi, R. (2002) Correlation of binding-loop internal dynamics with stability and function in potato I inhibitor family: relative contributions of Arg(50) and Arg(52) in Cucurbita maxima trypsin inhibitor-V as studied by site-directed mutagenesis and NMR spectroscopy. Biochemistry 41, 9572-9579.
34. Wu, X., Oppermann, M., Berndt, K. D., Bergman, T., Jonvall, H., Knapp, S., and Oppermann, U. (2008) Thermal unfolding of the archaeal DNA and RNA binding protein Ssh10. Biochem. Biophy. Res. Commun. , doi:10.1016/j.bbrc.2008.06.030, in press.
35. Gouet, P., Robert, X., and Courcelle, E. (2003) ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 31, 3320-3323.
36. Wang, G., Guo, R., Bartlam, M., Yang, H., Xue, H., Liu, Y., Huang, L., and Rao, Z. (2003) Crystal structure of a DNA binding protein from the hyperthermophilic euryarchaeon Methanococcus jannaschii. Protein Sci. 12, 2815-2822.
37. Leone, M., Di Lello, P., Ohlenschlager, O., Pedone, E. M., Bartolucci, S., Rossi, M., Di Blasio, B., Pedone, C., Saviano, M., Isernia, C., and Fattorusso, R. (2004) Solution structure and backbone dynamics of the K18G/R82E Alicyclobacillus acidocaldarius thioredoxin mutant: a molecular analysis of its reduced thermal stability. Biochemistry 43, 6043-6058.
38. Jaenicke, R., and Bohm, G. (1998) The stability of proteins in extreme environments. Curr. Opin. Struct. Biol. 8, 738-748.
39. Yano, J. K., and Poulos, T. L. (2003) New understandings of thermostable and peizostable enzymes. Current Opin. Biotechnol. 14, 360-365.
40. Jaenicke, R. (2000) Do ultrastable proteins from hyperthermophiles have high or low conformational rigidity? Proc. Natl. Acad. Sci. U.S.A. 97, 2962-2964.
41. Zavodszky, P., Kardos, J., Svingor, and Petsko, G. A. (1998) Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins. Proc. Natl. Acad. Sci. U.S.A. 95, 7406-7411.
42. Elcock, A. H. (1998) The stability of salt bridges at high temperatures: implications for hyperthermophilic proteins. J. Mol. Biol. 284, 489-502.