Thesis Title: Subtitle - NMR Spectroscopy Research Group

More documents

Recommendations

Info

22 Chapter 1. Introduction. (ii) It could displace the position of the paramagnetic center with respect to the protein frame. The amplitude of those movements depends on the size and rigidity of the tag used. Small displacements have mostly small impact on the value of the PCS because PCSs are usually observable only more than ten Angstroms from the lanthanide. To assess this principle further, the comparison between a static metal ion and a mobile one following a realistic trajectory is illustrated in Figure 1.16. Figure 1.16 Effect of the mobility of the tag on the PCS. (a) Twelve tensors are being used to represent a realistic trajectory of the tag. They have random orientation, random axial and rhombic values, and are located three Angstroms away from the anchor point (black dot). The range of angles covers 110 degrees, in steps of 10 degrees. (b) The isosurfaces resulting from the ensemble of tensors in (a). The red surface represents the isolevel of 5.0 ppm, the blue one corresponds to -5.0 ppm. The shapes are distorted compared to the typical shape of an isosurface shown in Figure 1.12. (c) PCSs cannot be measured closer than 10 Angstroms from the paramagnetic center. The cutoff area is shown in grey. (d) Surfaces of isolevel 1.0 ppm and -1.0 ppm are shown superimposed to (b). They exhibit a classical profile as seen in Figure 1.12. (e) The cutoff of 10 Angstroms is superimposed on figure (d).
1.4 Scope of the thesis. 23 Once the PCSs have been measured, the next step is to use them appropriately in order to extract structural information. Using the PCSs to filter the correct structure(s) (by comparing calculated and experimental values) among a large ensemble of generated structures would not be enough. The PCS-based restraint needs to be directly incorporated into the process of structure generation to bias the outputted conformations towards the native one. Several options are to be considered: incorporating a PCS-restraint into a molecular dynamics software, a molecular refinement package that employs simulated annealing routines, or into a molecular fragment replacement software. The main question is which one of those approaches is the most suited to capture the global nature of the PCS effect. The merit of the PCS for de novo structure determination in the context of a molecular fragment replacement is described in Chapter 4. A PCS score function has been added to the package CS-ROSETTA (Shen et al., 2008). The ability of the PCS to drive CS-ROSETTA calculations towards the native conformation and to identify native like structures is discussed. 1.4 Scope of the thesis This thesis covers different aspects of paramagnetic NMR from a computational point of view. This includes the use of PCSs for NMR resonance assignment, for Δχ-tensor determination in preparation of rigid body complex calculations, and de novo structure determinations of proteins. The rest of the thesis is organized as follow: In Chapter 2 is described an experimental and a computational approach to assign chemical shifts of methyl groups from the paramagnetic and diamagnetic NMR spectra. The computational route is supported by the development of the software Possum which was tested on artificial data first before being applied to experimental data. In Chapter 3 is presented a newly developed software that works specifically with pseudocontact shifts. The possibilities offered by the software are discussed and illustrated by the rapid reconstruction of the complex between the subunit ε and θ of the DNA polymerase III. In Chapter 4 is reported the incorporation of the PCS into the molecular fragment replacement software CS-ROSETTA, and the development of a new protocol to perform, for the first time, de novo protein structure determination using only PCSs and chemical shifts as experimental restraints.
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 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 88 and 89:
72 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 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 120 and 121:
Page 122 and 123:
Page 124 and 125:
Page 126 and 127:
Page 128 and 129:
Page 130 and 131:
Page 132 and 133:
Page 134 and 135:
Page 136 and 137:
Page 138 and 139:
Page 140 and 141:
Page 142 and 143:
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

Create successful ePaper yourself

Delete template?

Save as template?