Thesis Title: Subtitle - NMR Spectroscopy Research Group

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viii Table of Contents Declaration by author ......................................................................................................................... ii Statement of Contributions to Jointly Authored Works Contained in the Thesis .............................. ii Statement of Contributions by Others to the Thesis as a Whole ....................................................... iii Statement of Parts of the Thesis Submitted to Qualify for the Award of Another Degree ............... iii Published Works by the Author Incorporated into the Thesis ........................................................... iii Additional Published Works by the Author Relevant to the Thesis but not Forming Part of it ........ iv Acknowledgements .............................................................................................................................. v Abstract .............................................................................................................................................. vi Keywords .......................................................................................................................................... vii Australian and New Zealand Standard Research Classifications (ANZSRC) .................................. vii Table of Contents ............................................................................................................................. viii List of Figures .................................................................................................................................... xi List of Tables ................................................................................................................................... xiv List of Abbreviations ......................................................................................................................... xv 1. Introduction ................................................................................................................................ 1 1.1 Liquid State Nuclear Magnetic Resonance .......................................................................... 1 1.2 Paramagnetic NMR .............................................................................................................. 4 1.2.1 The four paramagnetic effects in NMR ........................................................................ 4 1.2.2 The pseudocontact shift as a restraint ........................................................................... 7 1.3 Computational study of paramagnetic proteins .................................................................. 12 1.3.1 The assignment problem ............................................................................................. 12 1.3.2 The Δχ-tensor determination problem ........................................................................ 16 1.3.3 De novo structure determination of proteins .............................................................. 19 1.4 Scope of the thesis .............................................................................................................. 23 1.5 References .......................................................................................................................... 24 2. Possum: paramagnetically orchestrated spectral solver of unassigned methyls ...................... 27 2.1 Abstract .............................................................................................................................. 28 2.2 Introduction ........................................................................................................................ 28 2.3 Experimental section .......................................................................................................... 30 2.3.1 Sample preparation ..................................................................................................... 30 2.3.2 NMR spectroscopy ..................................................................................................... 30
ix 2.3.3 Manual resonance assignments from PCS ................................................................. 32 2.3.4 The program Possum .................................................................................................. 32 2.4 Results ................................................................................................................................ 36 2.4.1 13 C-HSQC spectra of the cz- 186/ /Ln 3+ complexes ................................................. 36 2.4.2 Methyl CZ-EXSY experiments ................................................................................... 38 2.4.3 Resonance assignment of Met, Ala and Thr methyl groups ....................................... 39 2.4.4 Assignments of Val, Leu, and Ile methyl groups ....................................................... 41 2.4.5 Automatic assignments without EXSY data .............................................................. 44 2.4.6 PCS and flexibility ..................................................................................................... 46 2.5 Discussion .......................................................................................................................... 48 2.6 Acknowledgement .............................................................................................................. 50 2.7 Supporting Information Available ..................................................................................... 50 2.8 References .......................................................................................................................... 51 2.9 Supporting information ...................................................................................................... 56 3. Numbat: new user-friendly method built for automatic Δχ-tensor determination ................... 75 3.1 Abstract .............................................................................................................................. 76 3.2 Keywords ........................................................................................................................... 76 3.3 Abbreviations ..................................................................................................................... 76 3.4 Introduction ........................................................................................................................ 77 3.5 Algorithm ........................................................................................................................... 78 3.6 Program Features ................................................................................................................ 80 3.6.1 GUI ............................................................................................................................. 80 3.6.2 Input files .................................................................................................................... 81 3.6.3 Methyl group definition .............................................................................................. 81 3.6.4 Optimization of the tensor parameters ....................................................................... 81 3.6.5 Residual Anisotropic Chemical Shifts (RACS) ......................................................... 82 3.6.6 Multiple PCS data sets ................................................................................................ 82 3.6.7 PCS modification ........................................................................................................ 83 3.6.8 PCS selection .............................................................................................................. 83 3.6.9 Conventions ................................................................................................................ 83 3.6.10 Error analysis ............................................................................................................ 84 3.6.11 Visualization ............................................................................................................. 85 3.6.12 Output ....................................................................................................................... 86 3.7 Study case ........................................................................................................................... 86
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: vii Keywords paramagnetic nmr, pseu
Page 11 and 12: xi List of Figures Figure 1.1 NMR e
Page 13 and 14: xiii
Page 15: xv List of Abbreviations α Subunit
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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42 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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