Thesis Title: Subtitle - NMR Spectroscopy Research Group

More documents

Recommendations

Info

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
Page 1 and 2:
Computational study of proteins wit
Page 3 and 4:
iii Schmitz C, Stanton-Cook MJ, Su
Page 5 and 6:
v Acknowledgements I would like to
Page 7 and 8:
vii Keywords paramagnetic nmr, pseu
Page 9 and 10:
ix 2.3.3 Manual resonance assignmen
Page 11 and 12:
xi List of Figures Figure 1.1 NMR e
Page 13 and 14:
xiii
Page 15:
xv List of Abbreviations α Subunit
Page 18 and 19:
2 Chapter 1. Introduction. The scal
Page 20 and 21:
4 Chapter 1. Introduction. In contr
Page 22 and 23:
6 Chapter 1. Introduction. as the c
Page 24 and 25:
8 Chapter 1. Introduction. Figure 1
Page 26 and 27:
10 Chapter 1. Introduction. Protein
Page 28 and 29:
12 Chapter 1. Introduction. 1.3 Com
Page 30 and 31:
14 Chapter 1. Introduction. Figure
Page 32 and 33:
16 Chapter 1. Introduction. Figure
Page 34 and 35:
18 Chapter 1. Introduction. (Bugaye
Page 36 and 37:
20 Chapter 1. Introduction. The det
Page 38 and 39:
22 Chapter 1. Introduction. (ii) It
Page 40 and 41:
24 Chapter 1. Introduction. Chapter
Page 42 and 43:
26 Chapter 1. Introduction. Su XC,
Page 44 and 45:
28 Chapter 2. Possum: paramagnetica
Page 46 and 47:
Page 48 and 49:
Page 50 and 51:
Page 52 and 53:
Page 54 and 55:
Page 56 and 57:
Page 58 and 59: 42 Chapter 2. Possum: paramagnetica
Page 91 and 92: Chapter 3 Numbat: new user-friendly
Page 93 and 94: 3.4 Introduction 3.4 Introduction.
Page 95 and 96: 3.5 Algorithm. 79 rhombic component
Page 97 and 98: 3.6 Program Features. 81 each fitti
Page 99 and 100: 3.6 Program Features. 83 A new PCS
Page 101 and 102: 3.6 Program Features. 85 Carlo prot
Page 103 and 104: 3.7 Study case. 87 The coordinates
Page 105 and 106: 3.7 Study case. 89 illustrates how
Page 107: 3.7 Study case. 91 can be used to a
Page 111 and 112: 3.10 References. 95 Galassi M, Davi
Page 113 and 114: 3.11 Supporting information. 97 Zwe
Page 115: 3.11 Supporting information. 99 Tab
Page 118 and 119: 102 Chapter 4. Protein Structure De
Page 145 and 146: Chapter 5 Conclusion and perspectiv
Page 147 and 148: 5.1 The use of PCS for structure de
Page 149 and 150: 5.1 The use of PCS for structure de
Page 151 and 152: 5.3 The use of PCS for protein dock
show all

Thesis Title: Subtitle - NMR Spectroscopy Research Group

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?