Structural role of a buried salt bridge in the 434 repressor DNA-binding domain

Journal of Molecular Biology

Volumn 264, Issue 5, 1996, Pages 1002-1012

  Pervushin, Konstantin ^a   Billeter, Martin ^a   Siegal, Gregg ^a,b   Wüthrich, Kurt ^a  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

434 repressor; Helix turn helix motif; Interior salt bridge; NMR structure; Site directed mutagenesis

Indexed keywords

ARGININE; DNA BINDING PROTEIN; GLUTAMIC ACID; HELIX LOOP HELIX PROTEIN; METHIONINE; MUTANT PROTEIN;

ALPHA HELIX; AMINO ACID SUBSTITUTION; AMINO TERMINAL SEQUENCE; ARTICLE; CHEMICAL BOND; CRYSTAL STRUCTURE; EUKARYOTE; HYDROGEN BOND; MOLECULAR STABILITY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PH; PKA; PRIORITY JOURNAL; PROKARYOTE; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 0030596082     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0692     Document Type: Article

References (46)

1. Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne, M. & Harrison, S. C. (1988). Recognition of a DNA operator by the represser of phage 434. A view at high resolution. Science, 242, 899-892.
2. Anderson, D. E., Becktel, W. J. & Dahlquist, F. W. (1990). pH-induced denaturation of proteins: a single salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme. Biochemistry, 29, 2403-2408.
3. Anil-Kumar, Ernst, R. R. & Wüthrich, K. (1980). A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem. Biophys. Res. Commun. 95, 1-6.
4. Barlow, D. J. & Thornton, J. M. (1983). Ion-pairs in proteins. J. Mol. Biol. 168, 867-885.
5. Bartels, C, Xia, T., Billeter, M., Güntert. P. & Wüthrich, K. (1995). The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR, 5, 1-10.
6. 1H nuclear magnetic resonance spectra. Computation of sterically allowed proton-proton distances and statistical analysis of proton-proton distances in single crystal protein conformations. J. Mol. Biol. 155, 321-346.
7. Billeter, M., Kline, A. D., Braun, W., Huber, R. & Wüthrich, K. (1989). Comparison of the high-resolution structures of the α-amylase inhibitor Tendamistat determined by nuclear magnetic resonance in solution and by X-ray diffraction in single crystals. J. Mol. Biol. 206, 677-687.
8. Billeter, M., Schaumann, Th., Braun, W. & Wüthrich, K. (1990). Restrained energy refinement with two different algorithms and force fields of the structure of the α-amylase inhibitor Tendamistat determined by NMR in solution. Biopolymers, 29, 695-706.
9. Bodenhausen, G. & Ruben, D. J. (1980). Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy. Chem. Phys. Letters, 69, 185-189.
10. Brennan, R. G. & Matthews, B. W. (1989). The helix-turn-helix DNA binding motif. J. Biol. Chem. 264, 1903-1906.
11. 1H-NMR titration shifts for studies of polypeptide conformation. Biopolymers, 18, 299-311.
12. Dao-pin, S., Anderson, D. E., Baase, W. A., Dahlquist, F. W. & Matthews, B. W. (1991). Structural and thermodynamic consequences of burying a charged residue within the hydrophobic core of T4 lysozyme. Biochemistry, 30, 11521-11529.
13. Dill, K. A. (1990). Dominant forces in protein folding. Biochemistry, 29, 7133-7155.
14. Dötsch, V., Wider, G., Siegal, G. & Wüthrich, K. (1995). Salt-stabilized globular protein structure in 7 M aqueous urea solution. FEBS Letters, 372, 288-290.
15. Fersht, A. D. (1972). Conformational equilibria in α- and δ-chymotrypsin. The energetics and importance of the salt bridge. J. Mol. Biol. 64, 497-509.
16. Fesik, S. W. & Zuiderweg, E. P. R. (1988). Heteronuclear three-dimensional NMR spectroscopy. A strategy for the simplification of homonuclear two-dimensional NMR spectra. J. Magn. Reson. 78, 588-593.
17. Griesinger, C, Sørensen, O. W. & Ernst, R. R. (1985). Two-dimensional correlation of connected NMR transitions. J. Am. Chem. Soc. 107, 6394-6396.
18. 1H spin system identification in macromolecules. J. Am. Chem. Soc. 110, 7870-7872.
19. Güntert, P. & Wüthrich, K. (1991). Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. j. Biomol. NMR, 1, 447-456.
20. 1H NMR assignment and their impact on the precision of protein structure determination in solution. J. Am. Chem. Soc. III, 3997-4004.
21. Güntert, P., Braun, W. & Wüthrich, K. (1991). Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217, 517-530.
22. Güntert, P., Dötsch, V., Wider, G. & Wüthrich, K. (1992). Processing of multi-dimensional NMR data with the new software PROSA. J. Biomol. NMR, 2, 619-629.
23. Güntert, P., Berndt, K. D. & Wüthrich, K. (1993). The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination. J. Biomol. NMR, 3, 601-606.
24. Hendsch, Z. S. & Tidor, B. (1994). Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 3, 211-226.
25. Koradi, R., Billeter, M. & Wüthrich, K. (1996). MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55.
26. Levitt, M. (1983). Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol. 170, 723-764.
27. Luginbühl, P., Güntert, P., Billeter, M. & Wüthrich, K. (1996). The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules. J. Biomol. NMR, 8, 136-146.
28. Marion, D., Ikura, K., Tschudin, R. & Bax, A. (1989a). Rapid recording of 2D NMR spectra without phase cycling, application to the study of hydrogen exchange in proteins. J. Magn. Reson. 85, 393-399.
29. 15N-labelled proteins. J. Am. Chem. Soc. 111, 1515-1517.
30. Mondragon, A., Subbiah, S., Almo, S. C., Drottar, M. & Harrison, S. C. (1989). Structure of the amino-terminal domain of phage 434 represser at 2.0 Å resolution. J. Mol. Biol. 205, 189-201.
31. αβ in the basic pancreatic trypsin inhibitor measured by two-dimensional J-resolved NMR spectroscopy. Eur. J. Biochem. 115, 653-657.
32. Neri, D., Billeter, M. & Wüthrich, K. (1992a). Determination of the nuclear magnetic resonance solution structure of the DNA-binding domain (residues 1 to 69) of the 434 represser and comparison with the X-ray crystal structure. J. Mol. Biol. 223, 743-767.
33. Neri, D., Billeter, M., Wider, G. & Wüthrich, K. (1992b). NMR determination of residual structure in ureadenatured protein, the 434 repressor. Science, 257, 1559-1563.
34. 1H NMR spectra of proteins via double quantum filtering. Biochem. Biophys. Res. Commun. 117, 479-485.
35. Rashin, A. A. & Honig, B. (1984). On the environment of ionizable groups in globular proteins. J. Mol. Biol. 173, 515-521.
36. Richmond, T. J. (1984). Solvent-accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. J. Mol. Biol. 178, 63-89.
37. Saudek, V., Piotto, M. & Sklenar, V. (1994). WATERGATE, Water suppression by gradient-tailored excitation. Bruker. Report, 140, 6-9.
38. Serrano, L., Kellis, J. T. Jr, Matouschek P. C. A. & Fersht, A. R. (1992). The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J. Mol. Biol. 224, 783-804.
39. Szyperski, T., Güntert, P., Otting, G. & Wüthrich, K. (1992). Determination of scalar coupling constants by inverse Fourier transformation of in-phase multiplets. J. Magn. Reson. 99, 552-560.
40. Szyperski, T., Antuch, W. P., Schick, M., Betz, A., Stone, S. R. & Wüthrich, K. (1994). Transient hydrogen bonds identified on the surface of the NMR solution structure of Hirudin. Biochemistry, 93, 9303-9310.
41. 1H nuclear magnetic resonance spectra. Basic pancreatic trypsin inhibitor. J. Mol. Biol. 155, 347-366.
42. 1H NMR spectroscopy of proteins. Biochem. Biophys. Res. Commun. 113, 854-860.
43. Waldburger, C. D., Schildbach, J. F. & Sauer, R. T. (1995). Are salt bridges important for protein stability and conformational specificity? Nature. Struct. Biol. 2, 122-128.
44. Weiner, S. J., Kollman, P. A., Nguyen, D. T. & Case, D. A. (1986). An all atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7, 230-252.
45. Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids, Wiley, New York.
46. Wüthrich, K., Billeter, M. & Braun, W. (1983). Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance. J. Mol. Biol. 169, 949-961 .