Abstract
This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA. Given a sufficiently complete list of assigned chemical shifts and one or several lists of cross-peak positions and columes from two-, three-, or four-dimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, the assignment of the NOESY cross-peaks and the three-dimensional structure of the protein in solution can be calculated automatically with CYANA.
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References
Moseley, H. N. B. and Montelione, G. T. (1999) Automated analysis of NMR assignments and structures for proteins. Curr. Opin. Struct. Biol. 9, 635–642.
Solomon, I. (1955) Relaxation processes in a system of two spins. Phys. Rev. 99, 559–565.
Macura, S. and Ernst, R. R. (1980) Elucidation of cross relaxation in liquids by 2D NMR spectroscopy. Mol. Phys. 41, 95–117.
Neuhaus, D. and Williamson, M. P. (1989) The Nuclear Overhauser Effect in Structural and Conformational Analysis. VCH, Weinheim, Germany.
Herrmann, T., Güntert, P., and Wüthrich, K. (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319, 209–227.
Gropp, W., Lusk, E., Doss, N., and Skjellum, A. (1996) A high-performance, portable implementation of the MPI message passing interface standard. Parallel Computing 22, 789–828.
Koradi, R., Billeter, M., and Wüthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51–55.
Bartels, C., Xia, T. H., Billeter, M., Güntert, P., and Wüthrich, K. (1995) The program XEASY for computer-supported NMR-spectral analysis of biological macromolecules. J. Biomol. NMR 6, 1–10.
Johnson, B. A. and Blevins, R. A. (1994) NMR View—a computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603–614.
Kraulis, P. J. (1989) ANSIG—a program for the assignment of protein H-1 2D NMR spectra by interactive computer graphics. J. Magn. Reson. 24, 627–633.
Helgstrand, M., Kraulis, P., Allard, P., and Härd, T. (2000) ANSIG for Windows: an interactive computer program for semiautomatic assignment of protein NMR spectra J. Biomol. NMR 18, 329–336.
Koradi, R., Billeter, M., Engeli, M., Güntert, P., and Wüthrich, K. (1998) Toward fully automatic peak picking and integration of biomolecular NMR spectra. J. Magn. Reson. 135, 288–297.
Herrmann, T., Güntert, P., and Wüthrich, K. (2002) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J. Biomol. NMR 24, 171–189.
Doreleijers, J. F., Mading, S., Maziuk, D., Sojourner, K., Yin, L., Zhu, J., Markley, J. L., et al. (2003) BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank. J. Biomol. NMR 26, 139–146.
Mumenthaler, C. and Braun, W. (1995) Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry. J. Mol. Biol. 254, 465–480.
Mumenthaler, C., Güntert, P., Braun, W., and Wüthrich, K. (1997) Automated procedure for combined assignment of NOESY spectra and three-dimensional protein structure determination. J. Biomol. NMR 10, 351–362.
Nilges, M., Macias, M., O’Donoghue, S. I., and Oschkinat, H. (1997) Automated NOESY interpretation with ambiguous distance constraints: the refined NMR solution structure of the pleckstrin homology domain from β-spectrin. J. Mol. Biol. 269, 408–4228
Nilges, M. and O’Donoghue, S. I. (1998) Ambiguous NOEs and automated NOE assignment. Prog. NMR Spectrosc. 32, 107–139.
Linge, J. P., O’Donoghue, S. I., and Nilges, M. (2001) Automated assignment of ambiguous nuclear Overhauser effects with ARIA. Methods Enzymol. 339, 71–90.
Linge, J. P., Habeck, M., Rieping, W., and Nilges, M. (2003) ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 19, 315–316.
Nilges, M. (1993) A calculation strategy for the structure determination of symmetric dimers by 1H NMR. Proteins 17, 297–309.
Nilges, M. (1995) Calculation of protein structures with ambiguous distance restraints: automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. J. Mol. Biol. 245, 645–660.
Güntert, P., Braun, W., and Wüthrich, K. (1991) Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217, 517–530.
Güntert, P., Mumenthaler, C., and Wüthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283–298.
Kirkpatrick, S., Gelatt, C. D., Jr., and Vecchi, M. P. (1983) Optimization by simulated annealing. Science 220, 671–680.
Katz, H., Walter, R., and Somorjay, R. L. (1979) Rotational dynamics of large molecules. Computers Chemistry 3, 25–32.
Bae, D. S. and Haug, E. J. (1987) A recursive formulation for constrained mechanical system dynamics, part I: open loop systems. Mech. Struct. Mech. 15, 359–382.
Mazur, A. K. and Abagyan, R. A. (1989) New methodology for computer-aided modelling of biomolecular structure and dynamics (I): non-cyclic structures. J. Biomol. Struct. Dyn. 4, 815–832.
Mazur, A. K., Dorofeev, V. E., and Abagyan, R. A. (1991) Derivation and testing of explicit equations of motion for polymers described by internal coordinates. J. Comp. Phys. 92, 261–272.
Jain, A., Vaidehi, N., and Rodriguez, G. (1993) A fast recursive algorithm for molecular dynamics simulation. J. Comp. Phys. 106, 258–268.
Kneller, G. R. and Hinsen, K. (1994) Generalized Euler equations for linked rigid bodies. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 50, 1559–1564.
Mathiowetz, A. M., Jain, A., Karasawa, N., and Goddard, W. A., III. (1994) 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 20, 227–247.
Rice, L. M. and Brünger, A. T. (1994) Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 19, 277–290.
Stein, E. G., Rice, L. M., and Brünger, A. T. (1997) Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J. Magn. Reson. 124, 154–164.
Nilges, M., Clore, G. M., and Gronenborn, A. M. (1988) Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett. 229, 317–324.
Brünger, A. T. (1992) X-PLOR version 3.1: a system for X-ray crystallography and NMR. Yale University Press, New Haven, CT.
Enggist, E., Thöny-Meyer, L., Güntert, P., and Pervushin, K. (2002) NMR structure of the heme chaperone CcmE reveals a novel functional motif. Structure 10, 1551–1557.
Jee, J. G. and Güntert, P. (2003) Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment. J. Struct. Funct. Genomics 4, 179–189.
Güntert, P. (1998) Structure calculation of biological macromolecules from NMR data. Q. Rev. Biophys. 31, 145–237.
Antuch, W., Güntert, P., and Wüthrich, K. (1996) Ancestral βγ-crystallin precursor structure in a yeast killer toxin, Nat. Struct. Biol. 3, 662–665
Calzolai, L., Lysek, D. A., Güntert, P., von Schroetter, C., Riek, R., Zahn, R., et al. (2000) NMR structures of three single-residue variants of the human prion protein. Proc. Natl. Acad. Sci. USA 97, 8340–8345.
Zahn, R., Güntert, P., von Schroetter, C., and Wüthrich, K. (2003) NMR structure of a human prion protein with two disulfide bridges. J. Mol. Biol. 326, 225–234.
Ellgaard, L., Riek, R., Herrmann, T., Güntert, P., Braun, D., Helenius, A., et al. (2001) NMR structure of the calreticulin P-domain. Proc. Natl. Acad. Sci. USA 98, 3133–3138.
Horst, R., Damberger, F., Luginbühl, P., Güntert, P., Peng, G., Nikonova, L., et al. (2001) NMR structure reveals intramolecular regulation mechanism for pheromone binding and release. Proc. Natl. Acad. Sci. USA 98, 14,374–14,379.
Lee, D., Damberger, F. D., Peng, G., Horst, R., Güntert, P., Nikonova, L., et al. (2002) NMR structure of the unliganded Bombyx mori pheromone-binding protein at physiological pH. FEBS Lett. 531, 314–318.
Miura, T., Klaus, W., Ross, A., Güntert, P., and Senn, H. (2002) The NMR structure of the class I human ubiquitin-conjugating enzyme 2b. J. Biomol. NMR 22, 89–92.
Hilge, M., Siegal, G., Vuister, G. W., Güntert, P., Gloor, S. M., and Abrahams, J. P. (2003) ATP-induced conformational changes of the nucleotide binding domain of Na,K-ATPase. Nat. Struct. Biol. 10, 10–18.
Allen, M. P. and Tildesley, D. J. (1987) Computer Simulation of Liquids. Clarendon Press, Oxford, UK.
Abe, H., Braun, W., Noguti, T. and Go, N. (1984) Rapid calculation of first and second derivatives of conformational energy with respect to dihedral angles in proteins: general recurrent equations. Computers Chemistry 8, 239–247.
Hockney, R. W. (1970) The potential calculation and some applications. Meth. Comput. Phys. 9, 136–211.
Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., and Haak, J. R. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684–3690.
Hare, B. J. and Wagner, G. (1999) Application of automated NOE assignment to three-dimensional structure refinement of a 28 kDa single-chain T cell receptor. J. Biomol. NMR 15, 103–113.
Ösapay, K. and Case, D. A. (1991) A new analysis of proton chemical shifts in proteins. J. Am. Chem. Soc. 113, 9436–9444.
Sitkoff, D. and Case, D. A. (1997) Density functional calculations of proton chemical shifts in model peptides. J. Am. Chem. Soc. 119, 12,262–12,273.
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Güntert, P. (2004). Automated NMR Structure Calculation With CYANA. In: Downing, A.K. (eds) Protein NMR Techniques. Methods in Molecular Biology™, vol 278. Humana Press. https://doi.org/10.1385/1-59259-809-9:353
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DOI: https://doi.org/10.1385/1-59259-809-9:353
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