Thesis Title: Subtitle - NMR Spectroscopy Research Group

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xiv List of Tables Table 2.1 Automatic assignment of methyl groups by the program Possum a ................................. 45 Table S2.1 13 C and 1 H chemical shifts (ppm) of methyl groups of cz- 186 in the cz- 186/ /Ln 3+ complexes used in this study a ............................................................................................. 64 Table S2.2 Number of correctly assigned methyl groups of Met, Thr, and Ala residues of cz- 186 using the program Possum a ................................................................................................ 69 Table S2.3 Number of correctly assigned methyl groups of Val, Leu, and Ile residues of cz- 186 using the program Possum with methyl connectivity information in the Yb 3+ complex a .. 71 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 ............................................................................................................................. 73 Table 3.1 Δχ-tensors determined by Numbat in the frames of the ε186 and θ molecule .................. 87 Table 3.2 Error analysis for the Dy 3+ Δχ-tensors fitted to PCS of ε186 and θ a ............................... 89 Table S3.1 Experimentally determined 1 H N PCS for θ in complex with ε186 at pH 7.0 and 25°C a 97 Table S3.2 Comparison of θ Δχ-tensor parameters when using only conformer 10 a or all conformers b of the <strong>NMR</strong> structure of . ............................................................................. 99 Table 4.1 Protein structures used to evaluate the performance of PCS-ROSETTA ....................... 104 Table S4.1 PCS data information and grid search parameters used. .............................................. 125 Table S4.2 Protein structures used to evaluate the performance of PCS-ROSETTA. .................... 126
xv List of Abbreviations α Subunit α of the E. coli polymerase III ε186 N-terminal 185 residues of the E. coli polymerase III subunit ε θ Subunit θ of the E. coli polymerase III CCR Cross Correlated Relaxation CSA Chemical Shielding Anisotropy GUI Graphical User Interface HOT The bacteriophage P1-encoded homolog of θ MAP Multi-dimensional Assignment Problem <strong>NMR</strong> Nuclear Magnetic Resonances NOE Nuclear Overhauser Effect PCS Pseudocontact Shift ppm parts per million PRE Paramagnetic Relaxation Enhancement RACS Residual Anisotropic Chemical Shift RDC Residual Dipolar Coupling RMSD Root Mean Square Deviation UTR Unique Δχ-Tensor Representation
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
Page 11 and 12: xi List of Figures Figure 1.1 NMR e
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Page 18 and 19: 2 Chapter 1. Introduction. The scal
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Page 22 and 23: 6 Chapter 1. Introduction. as the c
Page 24 and 25: 8 Chapter 1. Introduction. Figure 1
Page 26 and 27: 10 Chapter 1. Introduction. Protein
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Page 36 and 37: 20 Chapter 1. Introduction. The det
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Page 40 and 41: 24 Chapter 1. Introduction. Chapter
Page 42 and 43: 26 Chapter 1. Introduction. Su XC,
Page 44 and 45: 28 Chapter 2. Possum: paramagnetica
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48 Chapter 2. Possum: paramagnetica
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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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3.11 Supporting information. 99 Tab
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102 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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