Thesis Title: Subtitle - NMR Spectroscopy Research Group

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68 Chapter 2. Possum: paramagnetically orchestrated spectral solver of unassigned methyls. I97 2 9.1 18.43 1.01 8.34 19.69 2.37 I97 1 11.4 14.99 0.88 9.50 15.78 1.68 I104 2 16.0 17.84 0.90 15.86 -2.05 18.13 1.19 I104 1 14.4 10.34 0.71 7.50 10.70 1.14 I118 2 22.6 15.96 0.66 15.47 0.17 16.02 0.75 I118 1 23.0 13.16 0.86 12.89 0.58 13.23 0.91 I154 2 13.7 16.96 0.76 23.43 15.97 -0.23 I154 1 16.3 11.78 0.73 17.48 6.40 10.94 -0.16 I170 2 9.5 18.41 0.71 40.65 15.06 -2.55 I170 1 8.6 12.88 0.68 32.52 10.26 -1.98 I193 2 17.46 0.81 17.55 0.91 17.42 0.78 I193 1 13.04 0.83 13.15 0.94 13.00 0.80 a Conditions: 25 ºC, pH 7.2. The chemical shifts in the cz- 186/ /La 3+ complex were measured from 13 C-HSQC spectra of the sample containing 13 C/ 15 N labeled cz- 186 in the presence of 1 equivalent La 3+ . Whenever possible, chemical shifts of the cz- 186/ /Dy 3+ and cz- 186/ /Yb 3+ complexes were measured from 13 C-HSQC spectra of samples prepared with 1:1 mixtures of La 3+ and Dy 3+ , or La 3+ and Yb 3+ , respectively. 13 C chemical shifts of methyl groups for which no 1 H chemical shift is reported were measured from the pd exchange peaks in 2D or 3D methyl Cz-EXSY spectra, whichever gave better resolution. When neither 13 C nor 1 H chemical shifts are indicated, the expected cross-peak could not be identified either because of spectral overlap (e.g. in the case of vanishing PCS) or strong PRE.
2.9 Supporting information. 69 Table S2.2 Number of correctly assigned methyl groups of Met, Thr, and Ala residues of cz- 186 using the program Possum a a Calculations were performed using the experimental data of Table S2.1 and simulated data, where the paramagnetic chemical shifts of Table S2.1 were replaced by chemical shifts back- calculated from the crystal structure of 186 and the tensors used in the present study. Two additional sets of simulated data were generated by addition of structural noise to the PDB coordinates of 186. The structural noise followed a Gaussian distribution of 0.25 and 0.5 Å standard deviation, resulting in a Maxwell-Boltzmann distribution of atomic displacements with maxima at 0.35 and 0.7 Å, respectively. The columns marked “Dy max”, “Yb max”, and “La max” report the number of methyl groups for which data in the paramagnetic state were available to the program. (Additional peaks observed in the diamagnetic state remained unassigned.) The results are reported for calculations where the diamagnetic chemical shifts were supplemented only with data from Dy 3+ (light yellow), Yb 3+ (light blue) or both (grey). The rows marked with the % symbol
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Computational study of proteins wit
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iii Schmitz C, Stanton-Cook MJ, Su
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v Acknowledgements I would like to
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vii Keywords paramagnetic nmr, pseu
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ix 2.3.3 Manual resonance assignmen
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xi List of Figures Figure 1.1 NMR e
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xiii
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xv List of Abbreviations α Subunit
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2 Chapter 1. Introduction. The scal
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4 Chapter 1. Introduction. In contr
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6 Chapter 1. Introduction. as the c
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8 Chapter 1. Introduction. Figure 1
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10 Chapter 1. Introduction. Protein
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12 Chapter 1. Introduction. 1.3 Com
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14 Chapter 1. Introduction. Figure
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16 Chapter 1. Introduction. Figure
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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
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Page 109 and 110: 3.9 Acknowledgment. 93 variables, t
Page 111 and 112: 3.10 References. 95 Galassi M, Davi
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Chapter 5 Conclusion and perspectiv
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5.1 The use of PCS for structure de
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5.1 The use of PCS for structure de
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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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