Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap

Proteins: Structure, Function and Genetics

Volumn 31, Issue 4, 1998, Pages 370-382

  Abseher, Roger ^a   Horstink, Lennard ^b   Hilbers, Cornelis W ^b   Nilges, Michael ^a,c  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^c NONE   (Germany)

Author keywords

Correlated collective motion; Essential dynamics analysis; Gene V protein; NMR structure refinement; PH domain; Single stranded DNA binding protein

Indexed keywords

DNA BINDING PROTEIN;

ARTICLE; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; STRUCTURE ANALYSIS;

COMPUTER SIMULATION; DNA-BINDING PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PROTEIN CONFORMATION; SPECTRIN; STRUCTURE-ACTIVITY RELATIONSHIP; VIRAL PROTEINS;

PSEUDOMONAS PHAGE PF3;

EID: 0032101346     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980601)31:4<370::AID-PROT4>3.0.CO;2-M     Document Type: Article

References (42)

1. 1, a case study. J. Mol. Biol. 266:400-423, 1997.
2. Koning, T.M.G., Boelens, R., van der Marel, G.A., van Boom, J.H., Kaptein, R. Structure determination of a DNA octamer in solution by NMR spectroscopy. Effect of fast local motions. Biochemistry 30:3787-3797, 1991.
3. Berndt, K.D., Güntert, P., Wüthrich, K. Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water. Proteins 24:304-313, 1996.
4. Berendsen, H.J.C. Bio-molecular dynamics comes of age. Science 271:954-955, 1996.
5. Amadei, A., Linssen, A.B.M., Berendsen, H.J.C. Essential dynamics of proteins. Proteins 17:412-425, 1993.
6. Ichiye, T., Karplus, M. Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins 11:205-217, 1991.
7. van der Spoel, D., de Groot, B., Hayward, S., Berendsen, H.J.C., Vogel, H.J. Bending of the calmodulin central helix: A theoretical study. Protein Sci. 5:2044-2053, 1996.
8. 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.
9. van Aalten, D.M.F., Jones, P.C., de Sousa, M., Findlay, J.B.C. Enginneering protein mechanics: Inhibition of concerted motions of the cellular retinol binding protein by site-directed mutagenesis. Protein Eng. 10:31-37, 1997.
10. Macias, M.J., Musacchio, A., Ponstingl, H., Nilges, M., Saraste, M., Oschkinat, H. Structure of the pleckstrin homology domain from β-spectrin. Nature 369:675-677, 1994.
11. Nilges, M., Macias, M., O'Donoghue, S.I., Oschkinat, H. Automated NOESY interpretation with ambiguous distance restraints: The refined NMR solution structure of the pleckstrin homology domain from β-spectrin. J. Mol. Biol. 269:408-422, 1997.
12. Folmer, R.H.A., Nilges, M., Konings, R.N.H., Hilbers, C.W. Solution structure of the single-stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: Similarity to other proteins binding to single-stranded nucleic acids. EMBO J. 14:4132-4142, 1995.
13. 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 5:106-111, 1995.
14. Feher, V.A., Baldwin, E.P., Dahlquist, F.W. Access of ligands to cavities within the core of a protein is rapid. Nat. Struct. Biol. 3:516-521, 1996.
15. Hyvönen, M., Macias, M.J., Nilges, M., Oschkinat, H., Saraste, M., Wilmanns, M. Structure of the binding site for inositol phosphates in a PH domain. EMBO J. 14:4676-4685, 1995.
16. Folmer, R.H.A., Nilges, M., Folkers, P.J.M., Konings, R.N.H., Hilbers, C.W. A model of the complex between single-stranded DNA and the single-stranded DNA binding protein encoded by gene V of filamentous bacteriophage M13. J. Mol. Biol. 240:341-357, 1994.
17. Folmer, R.H.A., Nilges, M., Papavoine, C.H.M., Harmsen, B.J.M., Konings, R.N.H., Hilbers, C.W. Refined structure, DNA binding studies, and dynamics of the bacteriophage Pf3 encoded single-stranded DNAbinding protein. Biochemistry 36:9120-9135, 1997.
18. Nilges, M., Gronenborn, A.M., Brünger, A.T., Clore, G.M. Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: Application to crambin, potato carboxypeptidase inhibitor and barley serine protease inhibitor 2. Protein Eng. 2:27-38, 1988.
19. Nilges, M., Kuszewski, J., Brünger, A.T. Sampling properties of simulated annealing and distance geometry. In: Hoch, J.C., Poulsen, F.M., Redfield, C. (eds). "Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy." New York: Plenum Press, 1991:451-455.
20. Brünger, A. "X-PLOR. A System for X-ray Crystallography and NMR." New Haven: Yale University Press, 1992.
21. Nilges, M. Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. J. Mol. Biol. 245:645-660, 1995.
22. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217, 1983.
23. van Gunsteren, W.F., Berendsen, H.J.C. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34:1311-1327, 1977.
24. Loncharich, R.J., Brooks, B.R. The effects of truncating long-range forces on protein dynamics. Proteins 6:32-45, 1989.
25. Darden, T., York, D., Pedersen, L. Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092, 1993.
26. Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E. III, Ferguson, D.M., Seibel, G.L., Chandra Singh, U., Weiner, P.K., Kollman, P.A. AMBER 4.1. San Francisco: University of California, 1995.
27. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M. Jr., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., Kollman, P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197, 1995.
28. Madura, J.D., Briggs, J.M., Wade, R.C., Davis, M.E., Luty, B.A., Ilin, A., Antosiewicz, J., Gilson, M.K., Bagheri, B., Scott, L.R., McCammon, J.A. Electrostatics and diffusion in solution: Simulations with the University of Houston Brownian dynamics program. Comp. Phys. Comm. 91:57-85, 1995.
29. Berendsen, H.J.C., Postma, J.P.M., DiNola, A., Haak, J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690, 1984.
30. Vriend, G. WHATIF: A molecular modelling and drug design program. J. Mol. Graph. 8:52-56, 1990.
31. de Groot, B.L., van Aalten, D.M.F., Amadei, A., Berendsen, H.J.C. The consistency of large concerted motions in proteins in molecular dynamics simulations. Biophys. J. 71: 1707-1713, 1996.
32. van Aalten, D.M.F., de Groot, B.L., Findlay, J.B.C., Berendsen, H.J.C., Amadei, A. A comparison of techniques for calculating protein essential dynamics. J. Comp. Chem. 18:169-181, 1997.
33. Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950, 1991.
34. Widmer, H., Widmer, A., Braun, W. Extensive distance geometry calculations with different NOE calibrations: New criteria for structure selection applied to Sandostatin and BPTI. J. Biomol. NMR 3:307-324, 1993.
35. Kabsch, W., Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
36. Ramachandran, G.N., Ramakrishnan, C., Sasisekharan, V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7:95-99, 1963.
37. Nilges, M., Clore, G.M., Gronenborn, A.M. Determination of three-dimensional structures of proteins by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett. 229:317-324, 1988.
38. 1H NMR. Proteins 17:297-309, 1993.
39. Bonvin, A.M.J.J., Brünger, A.T. Conformational variability of solution nuclear magnetic resonance structures. J. Mol. Biol. 250:80-93, 1995.
40. Torda, A.E., Scheek, R.M., van Gunsteren, W.F. Time-dependent distance restraints in molecular dynamics simulation. Chem. Phys. Lett. 157:289-294, 1989.
41. Torda, A.E., Scheek, R.M., van Gunsteren, W.F. Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat. J. Mol. Biol. 214:223-235, 1990.
42. Chillemi, G., Falconi, M., Amadei, A., Zimatore, G., Desideri, A., Di Nola, A. The essential dynamics of Cu, Zn superoxide dismutase: Suggestion of intersubunit communication. Biophys. J. 73:1007-1018, 1997.