Torsion angle dynamics for NMR structure calculation with the new program DYANA

Journal of Molecular Biology

Volumn 273, Issue 1, 1997, Pages 283-298

  Guntert P ^a   Mumenthaler, C ^a,b   Wuthrich K ^a  

^a ETH ZURICH   (Switzerland)

^b BOSTON CONSULTING GROUP   (United States)

Author keywords

Molecular dynamics in torsion angle space; NMR structure determination; Nucleic acid structure; Protein structure; Simulated annealing

Indexed keywords

NUCLEIC ACID;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CHEMICAL BOND; COMPUTER PROGRAM; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; TORSION; X RAY CRYSTALLOGRAPHY;

EID: 0031576336     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1284     Document Type: Article

References (53)

1. Abe H., Braun W., Noguti T., Go N. Rapid calculation of first and second derivatives of conformational energy with respect to dihedral angles in proteins. General recurrent equations. Comput. Chem. 8:1983;239-247.
2. Allen M. P., Tildesley D. J. Computer Simulation of Liquids. 1987;Clarendon Press, Oxford.
3. Antuch W., Güntert P., Wüthrich K. Ancestral βγ-crystallin precursor structure in a yeast killer toxin. Nature Struct. Biol. 3:1996;662-665.
4. Arnold V. I. Mathematical Methods of Classical Mechanics. 1978;Springer, New York.
5. Bae D. S., Haug E. J. A recursive formulation for constrained mechanical system dynamics: Part I. Open loop systems. Mech. Struct. Mech. 15:1987;359-382.
6. Bartels C., Xia T. H., Billeter M., Güntert P., Wüthrich K. The program XEASY. J. Biomol. NMR. 5:1995;1-10.
7. Bartels C., Güntert P., Billeter M., Wüthrich K. GARANT. J. Comput. Chem. 18:1997;139-149.
8. Beeman D. Some multistep methods for use in molecular dynamics calculations. J. Comput. Phys. 20:1976;130-139.
9. Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F. Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
10. Berendsen H. J. C., Postma J. P. M., van Gunsteren W. F., DiNola A., Haak J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:1984;3684-3690.
11. Berndt K. D., Güntert P., Orbons L. P. M., Wüthrich K. Determination of a high-quality NMR solution structure of the bovine pancreatic trypsin inhibitor (BPTI) and comparison with three crystal structures. J. Mol. Biol. 227:1992;757-775.
12. Braun W., Go N. Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. J. Mol. Biol. 186:1985;611-626.
13. Brooks B. R., Bruccoleri R. E., Olafson B. D., States D. J., Swaminathan S., Karplus M. CHARMM. J. Comput. Chem. 4:1983;187-217.
14. Brünger, A. T. 1992, X-PLOR, Version 3.1. A System for X-ray Crystallography and NMR, Yale University Press, New Haven, USA.
15. Brünger A. T., Nilges M. Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy. Quart. Rev. Biophys. 26:1993;49-125.
16. 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. 117:1995;5179-5197.
17. Davies G. J., Gamblin S. J., Littlechild J. A., Dauter Z., Wilson K. S., Watson H. C. Structure of the ADP complex of the 3-phosphoglycerate kinase fromBacillus sterothermophilus. Acta Crystallog. sect. D. 50:1994;202-209.
18. Fernández C., Szyperski T., Bruyère T., Ramage P., Mössinger E., Wüthrich K. NMR solution structure of the pathogenesis-related protein P14a. J. Mol. Biol. 266:1997;576-593.
19. Güntert, P. 1993, Neue Rechenverfahren für die Proteinstrukturbestimmung mit Hilfe der magnetischen Kernspinresonanz, PhD thesis, 10135 ETH, Zurich.
20. Güntert P., Wüthrich K. Improved efficiency of protein structure calculations from NMR data using the program DIANA. J. Biomol. NMR. 1:1991;446-456.
21. 1. J. Am. Chem. Soc. 111:1989;3997-4004.
22. Güntert P., Braun W., Wüthrich K. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANAALIBAABASLOMSA. J. Mol. Biol. 217:1991a;517-530.
23. Güntert P., Qian Y. Q., Otting G., Müller M., Gehring W. J., Wüthrich K. Structure determination of theAntpC39SIANAALIBAABASLOMSA. J. Mol. Biol. 217:1991b;531-540.
24. Güntert P., Dötsch V., Wider G., Wüthrich K. Processing of multi-dimensional NMR data with the new software Prosa. J. Biomol. NMR. 2:1992;619-629.
25. Güntert, P. Mumenthaler, C. Wüthrich, K. 1996, DYANA, Keystone/Colorado, USA, August 18-23, 1996, Abstracts XVIIth International Conference on Magnetic Resonance in Biological Systems.
26. 11. Bull. Math. Biol. 46:1984;673-698.
27. Jain A., Vaidehi N., Rodriguez G. A fast recursive algorithm for molecular dynamics simulation. J. Comput. Phys. 106:1993;258-268.
28. Kang H., Hines J. V., Tinoco I. Jr. Conformation of a non-frameshifting RNA pseudoknot from mouse mammary tumor virus. J. Mol. Biol. 259:1996;135-147.
29. Katz H., Walter R., Somorjay R. L. Rotational dynamics of large molecules. Comput. Chem. 3:1979;25-32.
30. Kneller G. R., Hinsen K. Generalized Euler equations for linked rigid bodies. Phys. Rev. ser. E. 50:1994;1559-1564.
31. Koradi R., Billeter M., Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14:1996;51-55.
32. Luginbühl P., Güntert P., Billeter M., Wüthrich K. The new program OPAL. J. Biomol. NMR. 8:1996;136-146.
33. Mathiowetz A. M., Jain A., Karasawa N., Goddard W. A. III. Protein simulations using techniques suitable for large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. Proteins: Struct. Funct. Genet. 20:1994;227-247.
34. Mazur A. K., Abagyan R. A. New methodology for computer-aided modelling of biomolecular structure and dynamics. (I) Non-cyclic structures. J. Biomol. Struct. Dynam. 4:1989;815-832.
35. Mazur A. K., Dorofeev V. E., Abagyan R. A. Derivation and testing of explicit equations of motion for polymers described by internal coordinates. J. Comput. Phys. 92:1991;261-272.
36. Momany F. A., McGuire R. F., Burgess A. W., Scheraga H. A. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79:1975;2361-2381.
37. Mumenthaler C., Braun W. Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry. J. Mol. Biol. 254:1995;465-480.
38. Mumenthaler C., Güntert P., Braun W., Wüthrich K. Automated procedure for combined assignment of NOESY spectra and three-dimensional protein structure determination. J. Biomol. NMR. 1997;in the press.
39. Némethy G., Pottle M. S., Scheraga H. A. Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 87:1983;1883-1887.
40. Nilges M., Clore G. M., Gronenborn A. M. Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Letters. 229:1988;317-324.
41. Nilges M., Kuszewski J., Brünger A. T. Sampling properties of simulated annealing and distance geometry. Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy. 1991;Plenum Press, New York.
42. Ottiger M., Szyperski T., Luginbühl P., Ortenzi C., Luporini P., Bradshaw R. A., Wüthrich K. The NMR solution structure of the pheromone ErEuplotes raikovi. Protein Sci. 3:1994;1515-1526.
43. Ottiger M., Zerbe O., Güntert P., Wüthrich K. The NMR solution conformation of unligated human Cyclophilin A. J. Mol. Biol. 272:1997;64-81.
44. Riek R., Hornemann S., Wider G., Billeter M., Glockshuber R., Wüthrich K. NMR structure of the mouse prion protein domain PrP(121-231). Nature. 382:1996;180-182.
45. Rice L. M., Brünger A. T. Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins: Struct. Funct. Genet. 19:1994;277-290.
46. Schultze P., Feigon J. Chirality errors in nucleic acid structures. Nature. 387:1997;668.
47. Stein E. G., Rice L. M., Brünger A. T. Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J. Magn. Reson. 124:1997;154-164.
48. van Gunsteren W. F., Berendsen H. J. C. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34:1977;1311-1327.
49. van Gunsteren W. F., Billeter S. R., Eising A. A., Hünenberger P. H., Krüger P., Mark A. E., Scott W. R. P., Tironi I. G. Biomolecular Simulation: The GROMOS. 1996;vdf Hochschulverlag, Zürich.
50. Vendrell J., Billeter M., Wider G., Avilés F. X., Wüthrich K. The NMR structure of the activation domain isolated from porcine procarboxypeptidase B. EMBO J. 10:1991;11-15.
51. Wolynes P., Onuchic J. N., Thirumalai D. Navigating the folding routes. Science. 267:1995;1619-1620.
52. Wüthrich K. NMR of Proteins and Nucleic Acids. 1986;Wiley, New York.
53. Wüthrich K., Billeter M., Braun W. 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. 169:1983;949-961.