Thesis Title: Subtitle - NMR Spectroscopy Research Group

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96 Chapter 3. Numbat: new user-friendly method built for automatic Δχ-tensor determination. Pintacuda G, Keniry MA, Huber T, Park AY, Dixon NE and Otting G (2004) Fast structure-based assignment of 15 N HSQC spectra of selectively 15 N-labeled paramagnetic proteins. J Am Chem Soc 126:2963-2970 Pintacuda G, Park AY, Keniry MA, Dixon NE and Otting G (2006) Lanthanide labeling offers fast NMR approach to 3D structure determinations of protein-protein complexes. J Am Chem Soc 128:3696-3702 Schmitz C, John M, Park AY, Dixon NE, Otting G, Pintacuda G and Huber T (2006) Efficient χ- tensor determination and NH assignment of paramagnetic proteins. J Biomol NMR 35:79- 87 Schwieters CD, Kuszewski JJ and Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. Prog NMR Spectrosc 48:47-62 Schwieters CD, Kuszewski JJ, Tjandra N and Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:65-73 Sherry AD and Pascual E (1977) Proton and carbon lanthanide-induced shifts in aqueous alanine. Evidence for structural changes along lanthanide series. J Am Chem Soc 99:5871-5876 Su XC, McAndrew K, Huber T and Otting G (2008) Lanthanide-binding peptides for NMR measurements of residual dipolar couplings and paramagnetic effects from multiple angles. J Am Chem Soc 130:1681-1687 Tolman JR, Flanagan JM, Kennedy MA and Prestegard JH (1995) Nuclear magnetic dipole interactions in field-oriented proteins: Information for structure determination in solution. Proc Natl Acad Sci U S A 92:9279-9283 Valafar H and Prestegard JH (2004) REDCAT: A residual dipolar coupling analysis tool. J Magn Reson 167:228-241 Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE and Berendsen HJC (2005) GROMACS: Fast, flexible, and free. J Comput Chem 26:1701-1718 Veitch NC, Whitford D and Williams RJP (1990) An analysis of pseudocontact shifts and their relationship to structural features of the redox states of cytochrome b5. FEBS Lett 269:297- 304 Wang X, Srisailam S, Yee AA, Lemak A, Arrowsmith C, Prestegard JH and Tian F (2007) Domain-domain motions in proteins from time-modulated pseudocontact shifts. J Biomol NMR 39:53-61 Wei Y and Werner MH (2006) iDC: A comprehensive toolkit for the analysis of residual dipolar couplings for macromolecular structure determination. J Biomol NMR 35:17-25
3.11 Supporting information. 97 Zweckstetter M and Bax A (2000) Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR. J Am Chem Soc 122:3791-3792 3.11 Supporting information Table S3.1 Experimentally determined 1 H N PCS for θ in complex with ε186 at pH 7.0 and 25°C a Residue PCS Dy 3+ (ppm) PCS Er 3+ (ppm) ASP 9 -1.28 0.31 GLN 10 -1.19 0.3 THR 11 -1.11 0.25 GLU 12 -1.24 0.27 MET 13 -1.84 0.38 ASP 14 -2 0.32 LYS 15 -1.5 VAL 16 -1.97 0.13 VAL 18 -1.91 0.14 ASP 19 -1.32 -0.03 LEU 20 -1.29 -0.03 ALA 21 -1.37 -0.14 ALA 22 -0.57 -0.18 ALA 23 0.15 -0.38 GLY 24 0.37 -0.46 VAL 25 0.29 -0.26 ALA 26 0.54 -0.3 PHE 27 1.21 LYS 28 0.85 -0.31 GLU 29 0.68 -0.19 ARG 30 0.81 -0.23 ASN 32 0.72
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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: 3.10 References. 95 Galassi M, Davi
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