Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase

Journal of Molecular Biology

Volumn 257, Issue 5, 1996, Pages 1070-1087

  Thomas, Aline ^a   Field, Martin J ^a   Mouawad, Liliane ^b   Perahia, David ^b  

^a INSTITUT DE BIOLOGIE STRUCTURALE   (France)

^b UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

Allostery; Aspartate transcarbamylase; Low frequency modes; Normal mode analysis; Quaternary motions

Indexed keywords

ASPARTATE CARBAMOYLTRANSFERASE; PYRIMIDINE;

ALLOSTERISM; ARTICLE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN QUATERNARY STRUCTURE; PYRIMIDINE METABOLISM; RNA TRANSLATION;

ESCHERICHIA COLI;

EID: 0030004936     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0224     Document Type: Article

References (44)

1. Brooks, B. & Karplus, M. (1985). Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc. Natl Acad. Sci. USA, 82, 4995-4999.
2. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983). CHARMM: a program for macromolecular energy, minimization and dynamics calculations. J. Comput. Chem. 4, 187-217.
3. Brünger, A. T. & Karplus, M. (1988). Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins: Struct. Funct. Genet. 4, 148-156.
4. Case, D. A. (1994). Normal mode analysis of protein dynamics. Curr. Opin. Struct. Biol. 4, 285-290.
5. Cherfils, J., Vachette, P. & Janin, J. (1990). Modelling allosteric processes in E. coli aspartate transcarbamylase. Biochimie, 72, 617-624.
6. Dembowski, N. J. & Kantrowitz, E. R. (1994). The use of alanine scanning to determine the role of the N terminus of the regulatory chain in the heterotropic mechanism of Escherichia coli aspartate transcarbamoylase. Protein Eng. 7, 673-679.
7. De Staercke, C., Van Vliet, F., Xi, X. G., Swarupa Rani, C., Ladjimi, M., Jacobs, A., Triniolles, F., Hervé, G. & Cunin, R. (1995). Intramolecular transmission of the ATP regulatory signal in Escherichia coli aspartate transcarbamylase: specific involvment of a clustered set of amino acid interactions at an interface between regulatory and catalytic subunits. J. Mol. Biol. 246, 132-143.
8. Gerstein, M., Lesk, A. M. & Chothia, C. (1994). Structural mechanisms for domain movements in proteins. J. Mol. Biol. 33, 6739-6749.
9. Gibrat, J.-E & Gô, N. (1990). Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion. Proteins: Struct. Funct. Genet. 8, 258-279.
10. Go, N., Noguti, T. & Nishikawa, T. (1983). Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl Acad. Sci. USA, 80, 3696-3700.
11. Gouaux, J. E. & Lipscomb, W. N. (1989). Structural transitions in crystals of native aspartate carbamoyltransferase. Proc. Natl Acad. Sci. USA, 86, 845-848.
12. Gouaux, J. E., Krause, K. L. & Lipscomb, W. N. (1987). The catalytic mechanism of Escherichia coli aspartate carbamoyltransferase: a molecular modelling study Biochem. Biophys. Res. Commun. 142, 893-897.
13. Gouaux, J. E., Stevens, R. C. & Lipscomb, W. N. (1990). Crystal structures of aspartate carbamoyltransferase ligated with phosphonoacetamide, malonate, and CTP or ATP at 2.8 Å resolution and neutral pH. Biochemistry, 29, 7702-7715.
14. Guilbert, C., Pecorari, F., Perahia, D. & Mouawad, L. (1995). Low-frequency motions in phosphoglycerate kinase. A normal mode analysis. Comp. Phys. Commun., 91, 263-273.
15. Ikura, T. & Gô, N. (1993). Normal mode analysis of mouse epidermal growth factor: characterization of the harmonic motion. Proteins: Struct. Funct. Genet. 16, 423-436.
16. Kabsch, W. (1976). A solution for the best rotation to relate two sets of vectors. Acta Crystallog. sect. A, 32, 922-923.
17. Kabsch, W. (1978). A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallog. sect. A, 34, 827-828.
18. Ke, H. M., Lipscomb, W. N., Cho, Y. & Honzatko, R. B. (1988). Complex of N-phosphonoacetyl-1-aspartate with aspartate carbamoyltransferase. X-ray refinement, analysis of conformational changes and catalytic and allosteric mechanisms. J. Mol. Biol. 204, 725-747.
19. Kim, K. H., Pan, Z., Honzatko, R. B., Ke, H.-M. & Lipscomb, W. N. (1987). Structural asymmetry in the CTP-liganded form of aspartate carbamoyltransferase from Escherichia coli. J. Mol. Biol. 196, 853-875.
20. Kosman, R. P., Gouaux, J. E. & Lipscomb, W. N. (1993). Crystal structure of CTP-ligated T state aspartate transcarbamylase at 2.5 Å resolution: implications for ATCase mutants and the mechanism of negative cooperativity Proteins: Struct. Funct. Genet. 15, 147-176.
21. Kraulis, P. J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24, 946-950.
22. Kuriyan, J. & Weis, W. I. (1991). Rigid protein motion as a model for crystallographic temperature factors. Proc. Natl Acad. Sci. USA, 88, 2773-2777.
23. Lipscomb, W. N. (1992). Activity and regulation in aspartate transcarbamylase. Proc. Robert A. Welch Foundation Conference Chem. Res. 36, 103-143.
24. Lipscomb, W. N. (1994). Aspartate transcarbamylase from Escherichia coli: activity and regulation. Advan. Enzymol. Rel. Areas Mol. Biol. (USA), 68, 67-151.
25. Loncharich, R. J. & Brooks, B. R. (1989). The effects of truncating long-range forces on protein dynamics. Proteins: Struct. Funct. Genet. 6, 32-45.
26. Mouawad, L. & Perahia, D. (1993). Diagonalization in a mixed basis: a method to compute low-frequency normal modes for large macromolecules. Biopolymers, 33, 599-611.
27. Mouawad, L., Desmadril, M., Perahia, D., Yon, J. M. & Brochon, J.-C. (1990). The effects of ligands on the conformation of phosphoglycerate kinase: fluorescence anisotropy decay and theoretical interpretation. Biopolymers, 30, 1151-1160.
28. Nakamura, S. & Doi, J. (1994). Dynamics of transfer RNAs analyzed by normal mode calculation. Nucl. Acids Res. 22, 514-521.
29. Perahia, D. & Mouawad, L. (1995). Computation of low-frequency normal modes in macromolecules. Comput. Chem. 19, 241-246.
30. Perutz, M. F. (1989). Mechanisms of cooperativity and allosteric regulation in proteins. Quart. Rev. Biophys. 22, 139-236.
31. Schachman, H. K. (1993). Aspartate transcarbamoylase. Curr. Opin. Strut. Biol. 3, 960-967.
32. Seno, Y. & Gô, N. (1990). Deoxymyoglobin studied by the conformational normal mode analysis. J. Mol. Biol. 216, 95-109.
33. Simonson, T. & Perahia, D. (1992). Normal modes of symmetric protein assemblies. Application to the tobacco mosaic virus protein disk. Biophys. J. 61, 410-427.
34. Steinbach, P. J. & Brooks, B. R. (1994). New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comp. Chem. 15, 667-683.
35. Stevens, R. C. & Lipscomb, W. N. (1992). A molecular mechanism for pyrimidine and purine control of aspartate transcarbamylase. Proc. Natl Acad. Sci. USA, 89, 5281-5285.
36. Stevens, R. C., Chook, Y. M., Cho, C. Y., Lipscomb, W. N. & Kantrowitz, E. R. (1991). Escherichia coli aspartate carbamoyltransferase: the probing of crystal structure analysis via site-specific mutagenesis. Protein Eng. 4, 391-408.
37. Tanner, J. J., Smith, P. E. & Krause, K. L. (1993). Molecular dynamics simulations and rigid body (TLS) analysis of aspartate carbamoyltransferase: evidence for an uncoupled R state. Protein Sci. 2, 927-935.
38. Tirion, M. M. & ben-Avraham, D. (1993). Normal mode analysis of G-actin. J. Mol. Biol. 230, 186-195.
39. Van Vliet, F., Xi, X. G., Ladjimi, M. M., De Staerke, C., De Wannemaecker, B., Jacobs, A., Cherfils, J., Hervé, G. & Cunin, R. (1991). The heterotropic interactions in aspartate transcarbamylase turning allosteric ATP activation into inhibition as a consequence of a single tyrosine to phenylalanine mutation. Proc. Natl Acad. Sci. USA, 88, 9180-9183.
40. Wente, S. R. & Schachman, H. K. (1991). Different amino acid substitutions at the same position in the nucleotide-binding site of aspartate transcarbamoylase have diverse effects on the allosteric properties of the enzyme. J. Biol. Chem. 266, 20833-20839.
41. Wilson, E. B. Jr, Decius, J. C. & Cross, P. C. (1955). Molecular Vibrations, Dover Publications, New York.
42. Xi, X. G. (1993). Relations structure-fonction impliquées dans les propriétés de régulation de l'aspartate transcarbamylase. Regards sur la Biochimie, 3, 20-32.
43. Xi, X. G., Van Vliet, F., Ladjimi, M. M., De Wannemaecker, B., De Staerke, C., Glansdorff, N., Piérard, A., Jacobs, Cunin, R. & Hervé, G. (1991). Heterotropic interactions in Escherichia coli aspartate transcarbamylase. Subunit interfaces involved in CTP inhibition and ATP activation. J. Mol. Biol. 220, 789-799.
44. Xi, X. G., De Staerke, C., Van Vliet, F., Triniolles, F., Jacobs, A., Stas, P. P., Ladjimi, M., Simon, V., Cunin, R. & Hervé, G. (1994). The activation of Escherichia coli aspartate transcarbamylase by ATP Specific involvment of helix H2′ at the hydrophobic interface between the two domains of the regulatory chains. J. Mol. Biol. 242, 139-149.