Thesis Title: Subtitle - NMR Spectroscopy Research Group

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92 Chapter 3. Numbat: new user-friendly method built for automatic Δχ-tensor determination. 3.8 Conclusion Figure 3.4 The four degenerate solutions arising from the symmetry of the Δχ-tensor around the x, y and z axes. All four possibilities result in the same calculi of PCS, hence in the same isosurfaces. Figure 3.5 The complex between ε186 and θ determined by superimposition of Δχ-tensors. The ε186/HOT complex (PDB accession code 2IDO) is shown for reference, with ε186 coloured in silver and HOT (residues 9-66) in orange. The isosurfaces correspond to the PCS induced by the Dy 3+ ion (from individual optimisation) contoured at +/-1.5 ppm and +/-0.5 ppm. Blue and red isosurfaces represent regions with positive and negative PCS, respectively. Residues 9-66 of θ are shown as a thin ribbon in the position defined by the fixed Dy 3+ and Er 3+ data (brown). The program Numbat is the first software package for fitting Δχ-tensors from PCS data with a user-friendly graphical user interface (GUI). Numbat calculations are fast, as it was written with open-source Linux routines in C. While the main task of Numbat is the fit of the eight Δχ-tensor
3.9 Acknowledgment. 93 variables, the intuitive GUI combined with convenient data handling, including Monte-Carlo error analysis and links to the molecular viewers MOLMOL and PyMOL, offer high flexibility of use. The study case of the complex formed between the subunits ε186 and θ of E. coli DNA polymerase III illustrates the simplicity of use of Numbat. The program is freely available under the GNU General Public License (GPL) upon request (see also http://compbio.chemistry.uq.edu.au/bmmg/christophe/numbat.html). 3.9 Acknowledgment Financial support from the Australian Research Council for project grants to G.O and T.H. is gratefully acknowledged. 3.10 References Allegrozzi M, Bertini I, Janik MBL, Lee YM, Lin GH and Luchinat C (2000) Lanthanide-induced pseudocontact shifts for solution structure refinements of macromolecules in shells up to 40 Å from the metal ion. J Am Chem Soc 122:4154-4161 Banci L, Bertini I, Bren KL, Cremonini MA, Gray HB, Luchinat C and Turano P (1996) The use of pseudocontact shifts to refine solution structures of paramagnetic metalloproteins: Met80Ala cyano-cytochrome c as an example. J Biol Inorg Chem 1:117-126 Banci L, Bertini I, Cavallaro G, Giachetti A, Luchinat C and Parigi G (2004) Paramagnetism-based restraints for Xplor-NIH. J Biomol NMR 28:249-261 Banci L, Bertini I, Cremonini MA, Savellini GG, Luchinat C, Wüthrich K and Güntert P (1998) PSEUDYANA for NMR structure calculation of paramagnetic metalloproteins using torsion angle molecular dynamics. J Biomol NMR 12:553-557 Banci L, Bertini I, Savellini GG, Romagnoli A, Turano P, Cremonini MA, Luchinat C and Gray HB (1997) Pseudocontact shifts as constraints for energy minimization and molecular dynamics calculations on solution structures of paramagnetic metalloproteins. Proteins 29:68-76
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Computational study of proteins wit
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v Acknowledgements I would like to
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vii Keywords paramagnetic nmr, pseu
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