Thesis Title: Subtitle - NMR Spectroscopy Research Group

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2 Chapter 1. Introduction. The scalar J-coupling results from an indirect magnetic interaction of two nuclear spins via their surrounding electrons. The effect is exclusively intramolecular because it is propagated through the bonds between two nuclei. Typically, it can be measured for nuclei separated by up to three bonds. In this case, it is referred as 3 J coupling. The 3 J-coupling constant yields angle information, as shown in Figure 1.1.b. NMR experiments measure the effects described above. One can classify NMR experiments in two groups: Those that yield structural information, and those that yield information to facilitate resonance assignment. The structural information comes mainly from direct dipole-dipole couplings providing short-range distance restraints between two spins, and from 3 J-couplings which offer dihedral angle restraints between the three bonds concerned. Some examples of NMR experiments that offer structural information are: 1D proton experiment: It provides the chemical shifts of the protons. Each 1 H has a different chemical shift, and each corresponding signal may be split into multiplets due to scalar couplings. The spectrum gets more complex as the number of spins increases. To reduce spectral overlap, two- or multi-dimensional NMR spectra can be recorded. 1D carbon experiment is equivalent to the 1D proton experiment, but measured on carbon. Only 1% of natural carbon is 13 C and often the protein has to be 13 C labeled in order to observe carbon chemical shifts because the natural isotope of carbon ( 12 C) has no nuclear spin. NOESY: This experiment correlates spins that are separated in space by a distance of up to 6 Å. The NOE observed in the NOESY experiment is based on the direct dipole-dipole coupling and provides valuable inter-spin distance information for the structure determination of proteins. NOE restraints are measured from the peak intensity in the NOESY experiment and provide distance information (Figure 1.1.a). As the effect is through-space and independent of chemical bonds, it is also useful for investigations of protein-ligand and protein-protein interactions. A major task and challenge of structure determination is to assign resonances to their corresponding atoms in order to apply experimental restraints to the correct set of atoms. Additional correlation NMR experiments are routinely recorded to assist in the chemical shift assignment task. These include: 2D 15 N-HSQC experiments correlate protons with nitrogens of a 15 N labeled protein. These correlations simplify the analysis of a 1D spectrum since the additional dimension allows the
1.1 Liquid State Nuclear Magnetic Resonance. 3 separation of the resonances into cross-peaks observed in a 2D plane. The recording time of the experiment is however longer. 3D 13 C- 15 N-correlation experiments are 3-dimensional heteronuclear experiments that correlate C, N and H atoms. The resulting spectrum is in particular beneficial for large proteins, because resonance overlap is reduced in 3D. The disadvantage of these experiments is, however, that they are less sensitive than the 15 N-HSQC experiment and usually require that the protein is 13 C and 15 N double labeled. COSY experiments correlate 1 H spins via scalar couplings. They are used to identify groups of spins connected by less than four bonds (spin systems). TOCSY experiments correlate 1 H resonances that belong to the same spin-system, where pairs of spins are separated by no more than three bonds. TOCSY spectra include the COSY information, and are used to identify connected spin systems. TOCSY spectra are useful for sequential resonance assignment. NOESY experiments can also be used in the assignment procedure. COSY and TOCSY experiment should provide the amino acid type information of the resonances, whereas the NOESY experiment allows the sequential piecing together of the assignment by exploiting the distance dependency of the NOE effect. Figure 1.1 NMR effects used for structure determination. (a) The NOE effect provides distance information (up to 0.6 nm) between two protons. The intensity of the NOE signal is proportional to 1/d 6 , where d is the interproton distance. (b) The 3 J-coupling gives dihedral angle restraints. The relationship between the angle Φ and the 3 J-coupling is given by the Karplus equation (Karplus, 1959) and the allowed values for Φ is illustrated by the plot 3 J = f(Φ). Figures adapted from web resources.
Page 1 and 2: Computational study of proteins wit
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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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3.9 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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Thesis Title: Subtitle - NMR Spectroscopy Research Group

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