An extended sampling of the configurational space of HPr from E. coli

Proteins: Structure, Function and Genetics

Volumn 26, Issue 3, 1996, Pages 314-322

  De Groot, B L ^a   Amadei, A ^a   Scheek, R M ^a   Van Nuland, N A J ^b   Berendsen, H J C ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

distance restraints; essential dynamics; molecular dyoamics; nuclear magnetic resonance; nuclear Overhauser effect; protein structure

Indexed keywords

CARRIER PROTEIN;

ARTICLE; ESCHERICHIA COLI; MOLECULAR DYNAMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN STRUCTURE;

BACTERIAL PROTEINS; COMPUTER SIMULATION; ESCHERICHIA COLI; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PHOSPHOENOLPYRUVATE SUGAR PHOSPHOTRANSFERASE SYSTEM; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; REPRODUCIBILITY OF RESULTS;

ESCHERICHIA COLI;

EID: 0029811307     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199611)26:3<314::AID-PROT7>3.0.CO;2-D     Document Type: Article

References (22)

1. Postma, P.W., Lengeler, J.W., Jacobson, G.R. Phosphoenolpyruvate: Carbohydrate phosphotransferase systems of bacteria. Microbiol. Rev. 57:543-594, 1993.
2. van Nuland, N.A.J., Hangyi, I.W., van Schaik, R.C., Berendsen, H.J.C., van Gunsteren, W.F., Scheek, R.M., Robillard, G.T. The high-resolution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from NMR-NOE data. J. Mol. Biol. 237:544-559, 1994.
3. Jia, Z., Quail, J.W., Waygood, E.B., Delbaere, L.T.J. The 2.0 Å-resolution structure of Escherichia coli histidine-containing phosphocarrier protein HPr: A redetermination. J. Biol. Chem. 268:22490-22501, 1993.
4. Amadei, A., Linssen, A.B.M., Berendsen, H.J.C. Essential dynamics of proteins. Proteins 17:412-425, 1993.
5. Garcia, A.E. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68:2696-2699, 1992.
6. van Aalten, D.M.F., Findlay, J.B.C., Amadei, A., Berendsen, H.J.C. Essential dynamics of the cellular retinol binding protein- evidence for ligand induced conformational changes. Prot. Eng. 8:1129-1136, 1995.
7. van Aalten, D.M.F., Amadei, A., Bywater, R., Findlay, J.B.C., Berendsen, H.J.C., Sander, C., Stouten, P.F.W. A comparison of structural and dynamic properties of different simulation methods applied to SH3. Biophys. J. 70: 684-692, 1996.
8. Clarage, J.B., Romo, T., Andrews, B.K., Pettitt, B.M. Jr., G.N.P. A sampling problem in molecular dynamics simulations of macromolecules. Proc. Natl. Acad. Sci. USA 92: 3288-3292, 1995.
9. Baisera, M.A., Wriggers, W., Oono, Y., Schulten, K. Principal component analysis and long time protein dynamics. J. Phys. Chem. 100:2567-2572, 1996.
10. Janezic, D., Venable, M., Brooks, B.R. Harmonic analysis of large systems. Comparison with molecular dynamics. J. Comp. Chem. 16:1554-1566, 1995.
11. Amadei, A., Linssen, A.B.M., de Groot, B.L., van Aalten, D.M.F., Berendsen, H.J.C. An efficient method for sampling the essential subspace of proteins. J. Biomol. Str. Dyn. 13:615-626, 1996.
12. de Groot, B.L., Amadei, A., van Aalten, D.M.F., Berendsen, H.J.C. Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. J. Biomol. Str. Dyn. 13:741-751, 1996.
13. van Nuland, N.A.J., Boelens, R., Scheek, R.M., Robillard, G.T. High resolution structure of the phosphorylated form of he histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from NMR-NOE data. J. Mol. Biol. 246:180-193, 1995.
14. Jia, Z., Vandonselaar, M., Quail, J.W., Delbaere, L.T.J. Active-center torsion angle strain revealed in 1.6 Å-resolution structure of histidine-containing phosphocarrier protein. Nature 361:94-97, 1993.
15. van Nuland, N.A.J., Wiersma, J.A., van der Spoel, D., de Groot, B.L., Scheek, R.M., Robillard, G.T. Phosphorylation-induced torsion-angle strain in the active center of HPr, detected by NMR and restrained molecular dynamics refinement. Prot. Sci. 5:442-446, 1996.
16. van Gunsteren, W.F., Berendsen, H.J.C. "Gromos Manual. BIOMOS, Biomolecular Software." The Netherlands: Laboratory of Physical Chemistry, University of Groningen, 1987.
17. Vriend, G. WHAT IF: A molecular modeling and drug design program. J. Mol. Graph. 8:52-56, 1990.
18. Kabsch, W., Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
19. Laskowski, R.A., MacArthur, M., Moss, D.S., Thornton, J.M. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl Crystalloqr 26:283-291, 1993.
20. van der Spoel, D., Berendsen, H.J.C., van Buuren, A.R., Apol, E., Meulenhoff, P.J., Sijbers, A.L.T.M., van Drunen, R. Gromacs User Manual. Nijenborgh 4, 9747 AG Groningen, The Netherlands. Internet: http: rugmdO.chem.rug.nl/~gmx 1995.
21. Scheek, R.M., van Nuland, N.A.J., de Groot, B.L., Amadei, A. Structure from NMR and molecular dynamics: distance restraining inhibits motion in the essential subspace. J. Biomol. NMR. 6:106-111, 1995.
22. Ramachandran, G.N., Ramakrishnan, C., Sasisekharan, V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7:95-99, 1963.