Tertiary and quaternary conformational changes in aspartate transcarbamylase: A normal mode study

Proteins: Structure, Function and Genetics

Volumn 34, Issue 1, 1999, Pages 96-112

  Thomas, Aline ^a   Hinsen, Konrad ^a   Field, Martin J ^a   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 and tertiary motions

Indexed keywords

ASPARTATE CARBAMOYLTRANSFERASE;

ALLOSTERISM; ARTICLE; ENZYME CONFORMATION; ENZYME MECHANISM; ESCHERICHIA COLI; PRIORITY JOURNAL; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; PYRIMIDINE SYNTHESIS;

ALLOSTERIC SITE; ASPARTATE CARBAMOYLTRANSFERASE; CARBAMYL PHOSPHATE; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; ZINC;

EID: 0032932341     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990101)34:1<96::AID-PROT8>3.0.CO;2-0     Document Type: Article

References (56)

1. Thomas A, Field MJ, Mouawad L, Perahia D. Analysis of the low-frequency modes of the T-state of aspartate transcarbamylase. J Mol Biol 1996;257:1070-1087.
2. Thomas A, Field MJ, Perahia D. Analysis of the low-frequency modes of the R state of aspartate transcarbamylase and a comparison with the T state modes. J Mol Biol 1996;261:490-506.
3. Lipscomb WN. Activity and regulation in aspartate transcarbamylases. Proc. Robert A. Welch Found. Conf Chem Res 1992;36:103-143.
4. Lipscomb WN. Aspartate transcarbamylase from Escherichia coli: Activity and regulation. Adv Enzymol Relat Areas Mol Biol (U.S.A.) 1994;68:67-151.
5. Schachman HK. Aspartate transcarbamoylase. Curr Opin Struct Biol 1993;3:960-967.
6. Kim KH, Pan Z, Honzatko RB, Ke H-M, Lipscomb WN. Structural asymmetry in the CTP-liganded form of aspartate carbamoyltransferase from Escherichia coli. J Mol Biol 1987;196:853-875.
7. Gouaux JE, Stevens RC, Lipscomb WN. Crystal structures of aspartate carbamoyltransferase ligated with phosphonoacetamide, malonate, and CTP or ATP at 2.8 Å resolution and neutral pH. Biochemistry 1990;29:7702-7715.
8. Fetler L, Vachette P, Hervé G, Ladjimi MM. Unlike quaternary structure transition, the tertiary structure change of the 240s loop in allosteric aspartate transcarbamoylase requires active site saturation by substrate for completion. Biochemistry 1995;34: 15654-15660.
9. Collins KD, Stark GR. Aspartate transcarbamylase. Studies of the catalytic subunit by ultraviolet difference. J Biol Chem 1969;244: 1869-1877.
10. Griffin JH, Rosenbusch JP, Weber KK, Blout ER. Conformational changes in aspartate transcarbamylase. I. Studies of ligand binding and of subunit interactions by circular dichroim spectroscopy. J Biol Chem 1972;247:6482-6490.
11. Stevens RC, Lipscomb WN. A molecular mechanism for pyrimidine and purine control of aspartate transcarbamylase. Proc Natl Acad Sci USA 1992;89:5281-5285.
12. Stevens RC, Chook YM, Cho CY, Lipscomb WN, Kantrowitz ER. Escherichia coli aspartate carbamoyltransferase: The probing of crystal structure analysis via site-specific mutagenesis. Protein Eng 1991;4:391-408.
13. Lee BH, Ley BW, Kantrowitz ER, O'Leary MH, Wedler FC. Domain closure in the catalytic chains of Escherichia coli aspartate transcarbamoylase influences the kinetic mechanism. J Biol Chem 1995;270:15620-15627.
14. Newton CJ, Kantrowitz E. Importance of domain closure for homotropic cooperativity in Escherichia coli aspartate transcarbamylase. Biochemistry 1990;29:1444-1451.
15. Eisenstein E, Markby DW, Schachman HK. Heterotropic effectors promote a global conformational change in aspartate transcarbamoylase. Biochemistry 1990;29:3724-3731.
16. Svergun DI, Barberato C, Koch MHJ, Fetler L, Vachette P. Large differences are observed between the crystal and solution quaternary structures of allosteric aspartate transcarbamylase in the R state. Proteins 1997;27:110-117.
17. Tanner JJ, Smith PE, Krause KL. Molecular dynamics simulations and rigid body (TLS) analysis of aspartate carbamoyltransferase: Evidence for an uncoupled R state. Protein Sci 1993;2:927-935.
18. Case DA. Normal mode analysis of protein dynamics. Curr Opin Struct Biol 1994;4:285-290.
19. Gibrat J-F, Gô N. Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion. Proteins 1990;8:258-279.
20. Mouawad L, Perahia D. Motions in hemoglobin studied by normal mode analysis and energy minimization: Evidence for the existence of tertiary T-like, quaternary R-like intermediate structures. J Mol Biol 1996;258:393-410.
21. Faure P, Micu A, Perahia D, Doucet J, Smith JC, Benoit JP. Correlated intramolecular motions and diffuse X-ray scattering in lysozyme. Struct Biol 1994;1:124-128.
22. Lamy AV, Souaille M, Smith JC. Simulation evidence for experimentally detectable low-temperature vibrational inhomogeneity in a globular protein. Biopolymers 1996;39:471-478.
23. Perutz MF. Mechanisms of cooperativity and allosteric regulation in proteins. Q Rev Biophys 1989;22:139-236.
24. Kosman RP, Gouaux JE, Lipscomb WN. 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 1993;15:147-176.
25. Brünger AT, Karplus M. Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison. Proteins 1998;4:148-156.
26. Zanotti G, Monaco HL, Foote J. Structure of the inhibitor of aspartate transcarbamylase N-(phosphonoacetyl)-L aspartate. J Am Chem Soc 1984;106:7900-7904.
27. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization and dynamics calculations. J Comp Chem 1983;4: 187-217.
28. Loncharich RJ, Brooks BR. The effects of truncating long-range forces on protein dynamics. Proteins 1989;6:32-45.
29. Steinbach PJ, Brooks BR. New spherical-cutoff methods for long-range forces in macromolecular simulation. J Comp Chem 1994;15:667-683.
30. Mouawad L, Perahia D. Motions in hemoglobin studied by normal mode analysis and energy minimizations. Evidence for the existence of tertiary T-like, quaternary R-like intermediate structures. J Mol Biol 1996;258:393-410.
31. Mouawad L, Perahia D. Diagonalization in a mixed basis: A method to compute low-frequency normal modes for lage macromolecules. Biopolymers 1993;33:599-611.
32. Perahia D, Mouawad L. Computation of low-frequency normal modes in macromolecules: Improvements to the method of diagonalization in a mixed basis set. Application to hemoglobin. Comput Chem 1995;19:241-246.
33. Guilbert C, Pecorari F, Perahia D, Mouawad L. Low frequency motions in phosphoglycerate kinase. A normal mode analysis. Chem Phys 1996;204:327-336.
34. Wilson EB, Jr, Decius JC, Cross PC. "Molecular Vibrations." New York: Dover Publications, 1955.
35. Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr 1976;A32:922-923.
36. Kabsch W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr 1978;A34:827-828.
37. Hinsen K. The molecular modeling toolkit: A case study of a large scientific application in Python. Proceedings of the 6th International Python Conference, 1997.
38. Gô N, Noguti T, Nishikawa T. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc Natl Acad Sci USA 1983;80:3696-3700.
39. ben-Avraham D, Tirion MM. Dynamic and elastic properties of F-actin: A normal modes analysis. Biophys J 1995;68:1231-1245.
40. Hayward S, Kitao A, Berendsen HJC. Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 1997;27:425-437.
41. Nichols WL, Rose G, Eyck LFT, Zimm BH. Rigid domains in protein: An algorithmic approach to their identification. Proteins 1995;23:38-48.
42. Islam SA, Luo J, Sternberg MJ. Identification and analysis of domains in proteins. Protein Eng 1995;8:513-525.
43. Wriggers W, Schulten K. Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins 1997;29:1-14.
44. Arnold GE, Ornstein RL. Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: Cytochrome P450BM-3. Biophys J 1997;73:1147-1159.
45. Van Vliet F, Xi XG, Ladjimi MM, et al. 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 1991;88:9180-9183.
46. Xi XG, Van Vliet F, Ladjimi MM, et al. Heterotropic interactions in Escherichia coli aspartate transcarbamylase. Subunit interfaces involved in CTP inhibition and ATP activation. J Mol Biol 1991;220:789-799.
47. Xi XG, De Staerke C, Van Vliet F, et al. The activation of Escherichia coli aspartate transcarbamylase by ATP. Specific involvement of helix H2′ at the hydrophobic interface between the two domains of the regulatory chains. J Mol Biol 1994;242:139-149.
48. Gerstein M, Lesk AM, Chothia C. Structural mechanisms for domain movements in proteins. J Mol Biol 1994;33:6739-6749.
49. Stebbins JW, Robertson DE, Roberts MF, Stevens RC, Lipscomb WN, Kantrowitz ER. Arginine 54 in the active site of Escherichia coli aspartate transcarbamoylase is critical for catalysis: A site-specific mutagenesis, NMR, and X-ray crystallographic study. Protein Sci 1992;1:1435-1446.
50. Ladjimi MM, Middleton SA, Kellher KS, Kantrowitz ER. Relationship between domain closure and binding, catalysis and regulation in E. coli aspartate transcarbamylase. Biochemistry 1988;27: 268-276.
51. Tauc P, Keiser RT, Kantrowitz ER, Vachette P. Glu-50 in the catalytic chain of Escherichia coli aspartate transcarbamoylase plays a crucial role in the stability of the R quaternary structure. Protein Sci 1994;3:1998-2004.
52. Baker DP, Fetler L, Vachette P, Kantrowitz ER. The allosteric activator ATP induces a substrate-dependent alteration of the quaternary structure of a mutant aspartate transcabamoylase impaired in active site closure. Protein Sci 1996;5:2276-2286.
53. Aucoin JM, Pishko EJ, Baker DP, Kantrowitz ER. Engineered complementation in Escherichia coli aspartate transcarbamoylase. J Biol Chem 1996;47:29865-29868.
54. Oberoi H, Trikha J, Yuan X, Allewell NM. Identification and analysis of long-range electrostatic effects in proteins by computer modeling: Aspartate transcarbamylase. Proteins 1996;25:300-314.
55. Ke HM, Lipscomb WN, Cho Y, Honzatko RB. Complex of N-phosphonoacetyl-1-aspartate with aspartate transcarbamylase. X-ray refinement, analysis of conformational changes and catalytic and allosteric mechanisms. J Mol Biol 1988;204:725-747.
56. Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallog 1991;24: 946-950.