Thesis Title: Subtitle - NMR Spectroscopy Research Group

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72 Chapter 2. Possum: paramagnetically orchestrated spectral solver of unassigned methyls. a Calculations were performed using the experimental data of Table S2.1 and simulated data as described in the footnote of Table S2.2. As each Val, Leu and Ile residue contains two methyl groups, methyl specificity and methyl connectivity information can be used as additional information to support the resonance assignment. (Methyl specificity information refers to stereospecific assignments of the methyl groups of Val and Leu and the a priori distinction of 2 and 1 methyl groups of Ile. Methyl connectivity information refers to the knowledge of which peaks arise from the same residue.) The results of four different combinations are shown, with and without methyl specificity information in the paramagnetic complexes, and with and without methyl specificity information in the diamagnetic complex. It was assumed that no methyl connectivity information can be established for the Dy 3+ complex because of strong PRE. The data are presented in the same format as in Table S2.2. Assignments were counted as correct whenever a methyl cross-peak was assigned to the correct residue, disregarding the stereospecific correctness of the assignment. Note that the maximum number of assignable methyl groups reported in the column marked “La max” can vary when both Dy 3+ and Yb 3+ data are used, because Possum has the freedom not to assign every HSQC cross-peak observed for the Dy 3+ complex to a peak observed for the Yb 3+ complex. This results in a small variation of the number of residues for which the program has paramagnetic information available and can attempt an assignment of the diamagnetic data.
2.9 Supporting information. 73 Table S2.4 Number of correctly assigned methyl groups of valine, leucine, and isoleucine residues of cz- 186 using the program Possum without methyl connectivity information in the Yb 3+ complex a a The data are presented as in Table S2.3.
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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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18 Chapter 1. Introduction. (Bugaye
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20 Chapter 1. Introduction. The det
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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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122 Chapter 4. Protein Structure De
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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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