Thesis Title: Subtitle - NMR Spectroscopy Research Group

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118 Chapter 4. Protein Structure Determination from Pseudocontact Shifts using ROSETTA. Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu GH, Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D and Bax A (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc. Natl. Acad. Sci. USA. 105:4685-4690 Simons KT, Kooperberg C, Huang E and Baker D (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions. J. Mol. Biol. 268:209-225 Su XC, Liang H, Loscha KV and Otting G (2009a) [Ln(DPA)3] 3- Is a convenient paramagnetic shift reagent for protein NMR studies. J. Am. Chem. Soc. 131:10352-10353 Su XC, Man B, Beeren S, Liang H, Simonsen S, Schmitz C, Huber T, Messerle BA and Otting G (2008) A dipicolinic acid tag for rigid lanthanide tagging of proteins and paramagnetic NMR spectroscopy. J. Am. Chem. Soc. 130:10486-10487 Su XC and Otting G (2009b) Paramagnetic labelling of proteins and oligonucleotides. J. Biomol. NMR in press: Ubbink M, Ejdebäck M, Karlsson BG and Bendall DS (1998) The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid- body molecular dynamics. Structure 6:323-335 Wilton DJ, Tunnicliffe RB, Kamatari YO, Akasaka K and Williamson MP (2008) Pressure-induced changes in the solution structure of the GB1 domain of protein G. Proteins 71:1432-1440 Wüthrich K (1986). NMR of proteins and nucleic acids. Wiley, New York. Zhuang T, Lee HS, Imperiali B and Prestegard JH (2008) Structure determination of a Galectin-3- carbohydrate complex using paramagnetism-based NMR constraints. Protein Sci. 17:1220- 1231 4.8 Supporting information
4.8 Supporting information. 119 Figure S4.1 Fold identification by pseudocontact shift score and ROSETTA energy. 3000 decoys were generated using CS-ROSETTA. In order to ensure that some decoys with small rmsd to the target structure were obtained, the starting set of peptide fragments was reduced and included the fragments from the known target structures. A to J: ROSETTA energies plotted versus the C rmsd to the target structure. A’ to J’: PCS scores plotted versus the C rmsd to the target structure. The targets are labeled A-J as in Table 4.1.
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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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