The thermostability of DNA-binding protein HU from mesophilic, thermophilic, and extreme thermophilic bacteria

Extremophiles

Volumn 6, Issue 1, 2002, Pages 21-31

  Christodoulou, Evangelos ^a   Vorgias, Constantinos E ^a  

^a UNIVERSITY OF ATHENS   (Greece)

Author keywords

CD spectroscopy; DNA binding protein HU; Mutations; Thermostability

Indexed keywords

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; GEOBACILLUS STEAROTHERMOPHILUS; THERMOTOGA MARITIMA;

BACTERIAL PROTEIN; DNA BINDING PROTEIN; HISTONE LIKE PROTEIN HU, BACTERIA; HISTONE-LIKE PROTEIN HU, BACTERIA; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ARTICLE; BACILLUS SUBTILIS; BACTERIUM; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; DRUG STABILITY; GENETICS; GEOBACILLUS STEAROTHERMOPHILUS; MOLECULAR GENETICS; MUTATION; PHYSIOLOGY; PROTEIN CONFORMATION; PROTEIN DENATURATION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; TEMPERATURE; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BACILLUS STEAROTHERMOPHILUS; BACILLUS SUBTILIS; BACTERIA; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DNA-BINDING PROTEINS; DRUG STABILITY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN CONFORMATION; PROTEIN DENATURATION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; TEMPERATURE; THERMODYNAMICS; TRANSCRIPTION FACTORS;

EID: 0036482260     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s007920100235     Document Type: Article

References (53)

1. Aitken A, Rouvière-Yaniv J (1979) Amino and carboxy terminal sequences of the DNA-binding protein HU from the cyanobacterium synechocystis PCC6701 (ATCC2710). Biochem Biophys Res Commun 91:461-467
2. Alber T, Dao-pin S, Wilson K, Wozniak JA, Cook SP, Matthews BW (1987) Contributions of hydrogen bonds of Thr 157 to the thermodynamic stability of phage T4 lysozyme. Nature (Lond) 330:41-46
3. Argos P, Rossman MG, Grau UM, Zuber H, Frank KG, Tratschin JD (1979) Thermal stability and protein structure. Biochemistry 18:5698-5703
4. Bennell D, Bouvier SE, Hardy LW, Poteete AR (1991) Systematic mutation of bacteriophage T4 lysozyme. J Mol Biol 222:67-88
5. Boelens R, Vis H, Vorgias CE, Wilson KS, Kaptein R (1996) Structure and dynamics of the DNA binding protein HU from Bacillus stearothermophilus by NMR spectroscopy. Biopolymers 40:553-559
6. Bradford M (1976) A rapid and sensitive method for the determination of microgram quantities of protein utilising the principle of protein dye binding. Anal Biochem 72:248-254
7. Christodoulou E, Vorgias CE (1998) Cloning, overproduction, purification and crystallisation of the DNA binding protein HU from the hyperthermophilic eubacterium Thermotoga maritima. Acta Crystallogr D 54:1043-1045
8. Drlica K, Rouviere-Yaniv J (1987) Histonelike proteins of bacteria. Microbiol Rev 51:301-319
9. Eijsink VGH, Dijkstra BW, Vriend G, van der Zee J, Veltman OR, van der Vinne B, van den Burg B, Kempe S, Venema G (1992) The effect of cavity-filling mutations on the thermostability of Bacillus stearothermophilus neutral protease. Prot Eng 5:421-426
10. Fersht AR, Serrano L (1993) Principles of protein stability derived from protein engineering experiments. Curr Opin Struct Biol 3:75-83
11. Frömmel C, Sander C (1989) Thermitase, a thermostable subtilisin: comparison of predicted and experimental structures and the molecular cause of thermostability. Proteins 5:22-37
12. Gill CS, von Hippel PH (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem 182:319-326
13. Horovitz A, Serrano L, Avron B, Bycroft M, Fersht AR (1990) Strength and co-operativity of contributions of surface salt bridges to protein stability. J Mol Biol 216:1031-1044
14. Hosaka H, Nakagawa A, Tanaka I, Harata N, Sano K, Kimura M, Yao M, Wakatsuki S (1997) Ribosomal protein S7: a new RNA-binding motif with structural similarities to a DNA architectural factor. Structure 5:1199-1208
15. Ishikawa K, Kimura S, Kanaya S, Morikawa K, Nakamura H (1993) Structural study of mutants of Escherichia coli ribonuclease HI with enhanced thermostability. Prot Eng 6:85-91
16. Karpusas M, Baase WA, Matsumura M, Matthews BW (1989) Hydrophobic packing in T4 lysozyme probed by cavity-filling mutants. Proc Natl Acad Sci USA 86:8237-8241
17. Kawamura S, Kakuta Y, Tanaka I, Hikichi K, Kuhara S, Yamasaki N, Kimura M (1996) Glycine-15 in the bend between two α-helices can explain the thermostability of DNA binding protein HU from Bacillus stearothermophilus. Biochemistry 35:1195-1200
18. Kawamura S, Tanaka I, Yamasaki N, Kimura M (1997) Contribution of a salt bridge to the thermostability of DNA binding protein HU from Bacillus stearothermophilus determined by site-directed mutagenesis. J Biochem (Tokyo) 121:448-455
19. Kawamura S, Abe Y, Ueda T, Masumoto K, Imoto T, Yamasaki N, Kimura M (1998) Investigation of the structural basis for thermostability of DNA-binding protein HU from Bacillus stearothermophilus. J Biol Chem 273:19982-19987
20. Kelly CA, Nishiyama M, Ohnishi Y, Beppu T, Birktoft JJ (1993) Determinants of protein thermostability observed in the 1.9-Å crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus. Biochemistry 32:3913-3922
21. Kimura S, Nakamura H, Hashimoto T, Oobatake M, Kanaya S (1992) Stabilisation of Escherichia coli ribonuclease HI by strategic replacement of amino acid residues with those from the thermophilic counterpart. J Biol Chem 267:21535-21542
22. Korolev S, Nayal M, Barnes WM, Di Cera E, Waksman G (1995) Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5 Å resolution: structural basis for thermostability. Proc Natl Acad Sci USA 92:9264-9268
23. Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature (Lond) 227:680-685
24. Lowry OH, Rosebrough NJ, Farr AL, Rendall RJ (1951) Protein measurement with the Folin phenol reagent. J Biol Chem 193:265-275
25. Maras B, Consalvi V, Chiaraluce R, Politi L, De Rosa M, Bossa F, Scandurra R, Barra D (1992) The protein sequence of glutamate dehydrogenase from Sulfolobus solfataricus, a thermoacidophilic archaebacterium. Eur J Biochem 203:81-87
26. Matthews B (1995) Studies on protein stability with T4 lysozyme. In: Eisenberg DS, Richards FM (eds) Advances in protein chemistry. Academic, New York
27. Matthews BW (1993) Structural and genetic analysis of protein folding and stability. Curr Opin Struct Biol 3:589-593
28. Matthews BW, Nicholson H, Becktel W (1987) Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc Natl Acad Sci USA 84:6663-6667
29. Menendez-Arias L, Argos P (1989) Engineering protein thermal stability. Sequence statistics point to residue substitutions in α-helices. J Mol Biol 206:397-406
30. Nosoh Y, Sekiguchi T (1990) Protein engineering for thermostability. Trends Biotechnol 8:16-20
31. Pace CN, Vajdos F, Fee L, Grimsley G, Gray T (1995) How to measure and predict the molar absorption coefficient of a protein. Protein Sci 4:2411-2423
32. Pace NC (1990) Conformational stability of globular proteins. Trends Biotechnol 8:93-98
33. Pace NC, Scholtz M (1997) Measuring the conformational stability. In Creighton TE (ed) Protein structure: a practical approach. IRL Oxford Press, Oxford
34. Padas PM, Wilson KS, Vorgias CE (1992) DNA binding protein from mesophilic and thermophilic Bacilli: cloning, overexpression and purification. Gene (Amst) 117:39-44
35. Querol E, Perz-Pons JA, Mozo-Villarias A (1996) Analysis of protein conformational characteristics related to thermostability. Protein Eng 9:265-271
36. Rice PA, Yang SW, Mizuuchi K, Nash H (1996) Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 87:1295-1306
37. Russel RJM, Taylor GL (1995) Engineering thermostability: lessons from thermophilic proteins. Curr Opin Biotechnol 6:370-374
38. Russell RJM, Hough DW, Danson MJ, Taylor GL (1994) The crystal structure of citrate synthase from the thermophilic archaeon, Thermoplasma acidophilum. Structure 2:1157-1167
39. Sali D, Bycroft M, Fersht AR (1991) Surface electrostatic interactions contribute little of stability of barnase. J Mol Biol 220:779-788
40. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
41. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467
42. Sauer RT, Lim WA (1992) Muational analysis of protein stability. Curr Opin Struct Biol 2:46-51
43. Serrano L, Horovitz A, Avron B, Bycroft M, Fersht AR (1990) Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles. Biochemistry 29:9343-9352
44. Studier FW, Rosenberg AH, Dunn JJ, Dubendorff JW (1990) Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol 185:60-89
45. Tanaka I, Appell K, Dijk J, White SW, Wilson KS (1984) 3-Å resolution structure of a protein with histone-like properties in prokaryotes. Nature (Lond) 310:376-381
46. Vis H, Mariani M, Vorgias CE, Wilson KS, Kaptein R, Boelens R (1995) Solution structure of the HU protein from Bacillus stearothermophilus. J Mol Biol 254:692-703
47. Vis H, Heinemann U, Dobson CM, Robinson CV (1998) Detection of a monomeric intermediate associated with dimerisation of protein HU by mass spectrometry. J Am Chem Soc 120:6427-6428
48. Vogt G, Woell S, Argos P (1997) Protein thermal stability, hydrogen bonds, and ion pairs. J Mol Biol 269:631-643
49. Vorgias CE, Antranikian G (2000) Glycosyl hydrolases from extremophiles. In Doyle (ed) Glycomicrobiology. Kluwer, New York
50. White SW, Appelt K, Wilson KS, Tanaka I (1989) A protein structural motif that bends DNA. Proteins 5:281-288
51. White SW, Wilson KS, Appelt K, Tanaka I (1999) The high-resolution structure of DNA-binding protein HU from Bacillus stearothermophilus. Acta Crystallogr D55:801-809
52. Wilson KS, Vorgias CE, Tanaka I, White SW, Kimura M (1990) The thermostability of DNA-binding protein HU from bacilli. Protein Eng 4:11-22
53. Yip KSP, Stillman TJ, Britton KL, Artymiuk PJ, Baker PJ, Sedelnikova SE, Engel PC, Pasquo A, Chiaraluce R, Consalvi V, Scandurra R, Rice DW (1995) The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures. Structure 3:1147-1158