Thesis Title: Subtitle - NMR Spectroscopy Research Group

More documents

Recommendations

Info

80 Chapter 3. Numbat: new user-friendly method built for automatic Δχ-tensor determination. 3.6 Program Features 3.6.1 GUI The graphical user interface (GUI) of Numbat was built with the GTK+ library (Krause, 2007) that is part of standard installations of recent Linux systems. Figure 3.1 shows two screenshots of the main interface of Numbat illustrating the intuitive and flexible user interface. Figure 3.1 Screenshots of Numbat main windows. (a) Graphical User Interface for the selection Structure and Data. Four PCS data sets can be loaded simultaneously under the tabs PCS1 to PCS4. The list of all atoms is displayed in the main frame and can be filtered with the Display tab to show only the atom or residue types of interest. The experimental PCS and the tolerance can be directly modified, and only atoms that are selected (see the column labelled “use?”) are taken into account in the calculations. The distance between the respective atom to the metal ion, the calculated PCS and the deviation between experimental and predicted PCS are calculated and displayed after
3.6 Program Features. 81 each fitting procedure. (b) Graphical User Interface for Tensor Calculation. A Δχ- tensor can be fitted for each of the data sets PCS1 to PCS4. An additional tab (Multiple PCS) is for fitting different data sets that share the same metal-ion centre. The frame PDB selector allows the choice of the model(s) to be used from a family of conformers loaded. The Tensor search restraints frame allows the individual selection of each of the eight variables to be free, fixed or constrained between two values. The computed Δχ-tensor values are displayed with error estimates from the GSL implementation of the Levenberg-Marquardt algorithm and the corresponding unique tensor representation (“UTR”) is reported. 3.6.2 Input files Numbat reads atomic coordinates from protein data bank (PDB; (Berman et al., 2000)) files. In the case of <strong>NMR</strong> structures, the entire ensemble of conformers is loaded and any subset can be selected for subsequent calculations. When optimizing the Δχ-tensor, PCS are back-calculated for each selected structure and averaged for the computation of the cost function c (equation (3.2)). PCS data can be read either in the Xplor-NIH format or in a format specific to Numbat. For test purposes, Numbat also allows the generation of PCS data (optionally with addition of Gaussian noise) for a user-specified Δχ-tensor. 3.6.3 Methyl group definition The 1 H chemical shift of a rotating methyl group can be described as the average of the chemical shifts of the three 1 H spins. The selection ―methyl association‖ in the GUI allows definition of pseudoatom names for any methyl group for which the experimental PCS value is to be treated as the average of the PCS of the three 1 H nuclei. The pseudoatom names can be used to identify the experimental PCS values of methyl groups in the input file. Alternatively, the PCS values of methyl groups can be interactively entered via the user-interface. 3.6.4 Optimization of the tensor parameters In order to give the user a maximum of flexibility, any subset of the eight Δχ-tensor variables can be optimized with the remaining ones fixed to user-specified values. Such a situation occurs, for example, when a protein-ligand complex is studied where the protein is tagged with a lanthanide. First, the Δχ-tensor can be determined using the PCS measured for the protein. Fitting of the position and orientation of the Δχ-tensor with respect to the ligand can subsequently be
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: 30 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: 3.5 Algorithm. 79 rhombic component
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 and 108: 3.7 Study case. 91 can be used to a
Page 109 and 110: 3.9 Acknowledgment. 93 variables, t
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?