Thesis Title: Subtitle - NMR Spectroscopy Research Group

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54 Chapter 2. Possum: paramagnetically orchestrated spectral solver of unassigned methyls. domain of the 434 repressor by biosynthetically directed fractional 13 C labeling. Biochemistry 28:7510-7516 Nicholson LK, Kay LE, Baldisseri DM, Arango J, Young PE, Bax A and Torchia DA (1992) Dynamics of methyl groups in proteins as studied by proton-detected 13 C NMR spectroscopy. Application to the leucine residues of staphylococcal nuclease. Biochemistry 31:5253-5263 Ostler G, Soteriou A, Moody CM, Khan JA, Birdsall B, Carr MD, Young DW and Feeney J (1993) Stereospecific assignments of the leucine methyl resonances in the 1 H NMR spectrum of Lactobacillus casei dihydrofolate reductase. FEBS Lett 318:177-180 Park AY (2006) Ph.D. Thesis. Australian National University, Australia. Pintacuda G, John M, Su XC and Otting G (2007) NMR structure determination of protein-ligand complexes by lanthanide labeling. Acc Chem Res 40:206-212 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 Prudêncio M, Rohovec J, Peters JA, Tocheva E, Boulanger MJ, Murphy MEP, Hupkes HJ, Kosters W, Impagliazzo A and Ubbink M (2004) A caged lanthanide complex as a paramagnetic shift agent for protein NMR. Chem Eur J 10:3252-3260 Rodriguez-Castañeda F, Haberz P, Leonov A and Griesinger C (2006) Paramagnetic tagging of diamagnetic proteins for solution NMR. Magn Reson Chem 44:S10-S16 Rosen MK, Gardner KH, Willis RC, Parris WE, Pawson T and Kay LE (1996) Selective methyl group protonation of perdeuterated proteins. J Mol Biol 263:627-636 Sattler M, Schwalbe H and Griesinger C (1992) Stereospecific assignment of leucine methyl groups with 13 C in natural abundance or with random 13 C labeling. J Am Chem Soc 114:1126-1127 Schell E (1955) Distribution of a product over several properties. E 2nd Sym. Linear Program 615– 642 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 Senn H, Werner B, Messerle BA, Weber C, Traber R and Wüthrich K (1989) Stereospecific assignment of the methyl 1 H NMR lines of valine and leucine in polypeptides by nonrandom 13 C labelling. FEBS Lett 249:113-118
2.8 References. 55 Senn H and Wüthrich K (1985) Amino-acid-sequence, hem-hiron coordination geometry and functional-properties of mitochondrial and bacterial c-type cytochromes. Quart Rev Biophys 18:111-134 Sibille N, Bersch B, Covès J, Blackledge M and Brutscher B (2002) Side chain orientation from methyl 1 H- 1 H residual dipolar couplings measured in highly deuterated proteins. J Am Chem Soc 124:14616-14625 Siivari K, Zhang M, Palmer AG and Vogel HJ (1995) NMR studies of the methionine methyl groups in calmodulin. FEBS Lett 366:104-108 Sprangers R and Kay LE (2007) Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature 445:618-622 Su XC, Huber T, Dixon NE and Otting G (2006) Site-specific labelling of proteins with a rigid lanthanide-binding tag. Chembiochem 7:1599-1604 Tang C, Iwahara J and Clore GM (2005) Accurate determination of leucine and valine side-chain conformations using U-[ 15 N/ 13 C/ 2 H]/[ 1 H-(methine/methyl)-Leu/Val] isotope labeling, NOE pattern recognition, and methine Cγ-Hγ /Cβ-Hβ residual dipolar couplings: application to the 34-kDa enzyme IIA Chitobiose . J Biomol NMR 33:105-121 Tugarinov V and Kay LE (2003a) Ile, Leu, and Val methyl assignments of the 723-residue malate synthase G using a new labeling strategy and novel NMR methods. J Am Chem Soc 125:13868-13878 Tugarinov V and Kay LE (2003b) Side chain assignments of Ile δ1 methyl groups in high molecular weight proteins: An application to a 46 ns tumbling molecule. J Am Chem Soc 125:5701-5706 Tugarinov V and Kay LE (2004) Stereospecific NMR assignments of prochiral methyls, rotameric states and dynamics of valine residues in malate synthase G. J Am Chem Soc 126:9827- 9836 Tugarinov V and Kay LE (2005a) Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins. Chembiochem 6:1567-+ Tugarinov V, Ollerenshaw JE and Kay LE (2005b) Probing side-chain dynamics in high molecular weight proteins by deuterium NMR spin relaxation: An application to an 82-kDa enzyme. J Am Chem Soc 127:8214-8225 Wand AJ, Urbauer JL, McEvoy RP and Bieber RJ (1996) Internal dynamics of human ubiquitin revealed by 13 C-relaxation studies of randomly fractionally labeled protein. Biochemistry 35:6116-6125
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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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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
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104 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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