Thesis Title: Subtitle - NMR Spectroscopy Research Group

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6 Chapter 1. Introduction. as the chemical shift difference. RDC is measured as the difference in line splitting. PRE and CCR can be determined from the differential line broadening. The paramagnetic relaxation enhancement (PRE): The PRE yields distance information between the paramagnetic lanthanide and the spin of interest (Figure 1.2.c). It depends on the distance r between the paramagnetic center and the nuclear spin with 1/r 6 (equation (1.4)) and accounts for the difference of line broadening between the paramagnetic and diamagnetic chemical shift (Figure 1.3). with: (1.4) (1.5) where ηr is the rotational correlation time, ωH the Larmor frequency of the proton, μ0 the vacuum permeability, gJ the g-factor, μB the Bohr magneton, and J the total spin moment. The cross correlated relaxation (CCR): This effect is also measured by the observed line broadening; more precisely by comparing the width between the two components of the antiphase doublet (Figure 1.3). This effect combines distance and angle dependence (equation (1.6) and Figure 1.2.d). with: (1.6) (1.7) All four paramagnetic effects can be used to study protein structure. Residual dipolar coupling has been widely used to help determining protein structures (Rohl et al., 2002), but when carefully comparing RDCs measured by NMR with RDCs predicted from a crystal structure, it was observed that small discrepancies between the N-H bond orientation in crystal and liquid state can
1.2 Paramagnetic NMR. 7 lead to large deviations between measurement and prediction. PCSs are less sensitive to the difference between the crystal model and the solution structure. The focus in my PhD has been on using PCS to study proteins and their interactions. Figure 1.4 The PCS is less sensitive than RDC to small discrepancies between X-ray and solution structure. A large change in the orientation of the N-H vector will considerably affect the calculation of the RDC (equation (1.2) and Figure 1.2.b). On the other hand, the PCS will be less affected as the relative position of the hydrogen with respect to the tensor frame is almost unchanged when PCS are measurable (d > 10 Å). 1.2.2 The pseudocontact shift as a restraint PCSs can be calculated using equation (1.1) if the magnitude (two parameters: Δχax and Δχrh, Figure 1.5.a), location (three Cartesian coordinates x, y and z, Figure 1.5.b) and orientation (three Euler angles α, β and γ, Figure 1.5.c) of the Δχ-tensor are known, and if a structure is available. The paramagnetic chemical shift of a spin located close to the paramagnetic center is broadened beyond detection due to PRE, and consequently, its PCS cannot be observed. The cutoff radius is typically about 10 Å. The NMR resonances have first to be assigned in order to measure PCSs. Three kinds of assignment have to be distinguished (Figure 1.6): (i) The assignment of the diamagnetic NMR spectrum: it is routinely performed with conventional sequential assignment methods using one or a combination of COSY, TOCSY, NOESY NMR and triple resonance experiments.
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
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Chapter 3 Numbat: new user-friendly
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3.4 Introduction 3.4 Introduction.
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3.5 Algorithm. 79 rhombic component
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3.6 Program Features. 81 each fitti
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3.6 Program Features. 83 A new PCS
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3.6 Program Features. 85 Carlo prot
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3.7 Study case. 87 The coordinates
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3.7 Study case. 89 illustrates how
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3.7 Study case. 91 can be used to a
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3.9 Acknowledgment. 93 variables, t
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3.10 References. 95 Galassi M, Davi
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3.11 Supporting information. 97 Zwe
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Chapter 5 Conclusion and perspectiv
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5.3 The use of PCS for protein dock
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Thesis Title: Subtitle - NMR Spectroscopy Research Group

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