Thesis Title: Subtitle - NMR Spectroscopy Research Group

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124 Chapter 4. Protein Structure Determination from Pseudocontact Shifts using ROSETTA. Figure S4.6 Expected C α rmsd of the lowest energy structure calculated with PCS-ROSETTA. A given number n of structures (x axis) was randomly chosen 5000 times from the total of 10 000 generated structures and the averaged C α rmsd of the lowest energy (over the 5000 trials) is graphed. The curves show a posteriori that 1000 structures calculated for all the targets would have been ample to ensure convergence of PCS-ROSETTA calculations. The targets are labeled A- J as in Table 4.1. The curve for the target parvalbumin (H) and ε (J) are not shown.
Table S4.1 PCS data information and grid search parameters used. 4.8 Supporting information. 125 Protein name Residues a Metal ions used Atom types cs corr b w(c) cg c sg d co d ci d protein G (A) 1-56 Tb 3+ Tm 3+ Er 3+ H N Ce 0.53 15.5 E19 CA 6 17 7 calbindin (B) 2-75 3+ Dy 3+ Er 3+ Eu 3+ Ho 3+ Nd 3+ Pr 3+ Sm 3+ Tb 3+ Tm 3+ Yb 3+ H N , N, C’ 2.72 48.9 D54 CA 6 8 4 θ subunit (C) 10-64 Dy 3+ Er 3+ H N -0.16 7.1 D14 CA 6 25 15 ArgN (D) 8-70 Tb 3+ Tm 3+ Yb 3+ H N , N 2.09 13.5 C68 CB 6 10 4 ArgN (E) 8-70 Tb 3+ Tm 3+ H N 2.09 48.9 K12 CB 6 15 0 N-calmodulin (F) 3-79 Tb 3+ Tm 3+ H N , CA, CB 0.00 4.7 D60 CA 6 8 4 thioredoxin (G) 2-108 Ni 2+ H N 1.23 106.3 S1 N 3.8 4 0 parvalbumin (H) 2-109 Dy 3+ H N , N 2.65 2.86 D93 CA 6 8 4 calmodulin (I) 3-146 Tb 3+ Tm 3+ Yb 3+ Dy 3+ H N 0.59 5.1 D60 CA 6 8 4 ε186 (J) 7-180 Tb 3+ Dy 3+ Er 3+ H N , N, C’ 0.53 8.2 D12 CA 6 8 4 a Ordered residues b Uniform offset used for 13 C chemical shifts (in ppm) compared to published values. In the case of thioredoxin, the offset was applied to 15 N chemical shifts c Residue and atom name defining the center of the grid search to position the paramagnetic center. d In Ångstrom
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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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28 Chapter 2. Possum: paramagnetica
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Page 95 and 96: 3.5 Algorithm. 79 rhombic component
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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
Page 113 and 114: 3.11 Supporting information. 97 Zwe
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Thesis Title: Subtitle - NMR Spectroscopy Research Group

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