Thesis Title: Subtitle - NMR Spectroscopy Research Group

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116 Chapter 4. Protein Structure Determination from Pseudocontact Shifts using ROSETTA. Banci L, Bertini I, Cavallaro G, Giachetti A, Luchinat C and Parigi G (2004) Paramagnetism-based restraints for Xplor-NIH. J. Biomol. NMR 28:249-261 Banci L, Bertini I, Cremonini MA, Savellini GG, Luchinat C, Wüthrich K and Güntert P (1998) PSEUDYANA for NMR structure calculation of paramagnetic metalloproteins using torsion angle molecular dynamics. J. Biomol. NMR 12:553-557 Barry CD, North ACT, Glasel JA, Williams RJP and Xavier AV (1971) Quantitative determination of mononucleotide conformations in solution using lanthanide ion shift and broadening NMR probes. Nature 232:236-245 Bertini I, Del Bianco C, Gelis I, Katsaros N, Luchinat C, Parigi G, Peana M, Provenzani A and Zoroddu MA (2004) Experimentally exploring the conformational space sampled by domain reorientation in calmodulin. Proc. Natl. Acad. Sci. USA. 101:6841-6846 Bertini I, Donaire A, Jiménez B, Luchinat C, Parigi G, Piccioli M and Poggi L (2001) Paramagnetism-based versus classical constraints: An analysis of the solution structure of Ca Ln calbindin D9k. J. Biomol. NMR 21:85-98 Bertini I, Kursula P, Luchinat C, Parigi G, Vahokoski J, Wilmanns M and Yuan J (2009) Accurate solution structures of proteins from X-ray data and a minimal set of NMR data: Calmodulin-peptide complexes as examples. J. Am. Chem. Soc. 131:5134-5144 Bertini I, Longinetti M, Luchinat C, Parigi G and Sgheri L (2002a) Efficiency of paramagnetism- based constraints to determine the spatial arrangement of α-helical secondary structure elements. J. Biomol. NMR 22:123-136 Bertini I, Luchinat C and Parigi G (2002b) Magnetic susceptibility in paramagnetic NMR. Prog. NMR Spectr. 40:249-273 Bradley P and Baker D (2006) Improved beta-protein structure prediction by multilevel optimization of NonLocal strand pairings and local backbone conformation. Proteins 65:922-929 Bradley P, Misura KMS and Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309:1868-1871 Chandrasekhar K, Krause G, Holmgren A and Dyson HJ (1991) Assignment of the 15 N NMR spectra of reduced and oxidized Escherichia Coli thioredoxin. FEBS Lett. 284:178-183 Cornilescu G, Delaglio F and Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13:289-302 Cornilescu G, Marquardt JL, Ottiger M and Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J. Am. Chem. Soc. 120:6836-6837
4.7 References. 117 DeRose EF, Li DW, Darden T, Harvey S, Perrino FW, Schaaper RM and London RE (2002) Model for the catalytic domain of the proofreading epsilon subunit of Escherichia coli DNA polymerase III based on NMR structural data. Biochemistry 41:94-110 Gaponenko V, Sarma SP, Altieri AS, Horita DA, Li J and Byrd RA (2004) Improving the accuracy of NMR structures of large proteins using pseudocontact shifts as long-range restraints. J. Biomol. NMR 28:205-212 Jensen MR and Led JJ (2006) Metal-protein interactions: Structure information from Ni 2+ -induced pseudocontact shifts in a native nonmetalloprotein. Biochemistry 45:8782-8787 John M, Pintacuda G, Park AY, Dixon NE and Otting G (2006) Structure determination of protein- ligand complexes by transferred paramagnetic shifts. J. Am. Chem. Soc. 128:12910-12916 Lemaster DM and Richards FM (1988) NMR sequential assignment of Escherichia Coli thioredoxin utilizing random fractional deuteriation. Biochemistry 27:142-150 Mueller GA, Kirby TW, DeRose EF, Li D, Schaaper RM and London RE (2005) Nuclear magnetic resonance solution structure of the Escherichia coli DNA polymerase III θ subunit. J. Bacteriol. 187:7081-7089 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, 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 Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ and Baker D (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450:259-264 Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV and Baker D (2009) Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins online: Saio T, Ogura K, Yokochi M, Kobashigawa Y and Inagaki F (2009) Two-point anchoring of a lanthanide-binding peptide to a target protein enhances the paramagnetic anisotropic effect. J. Biomol. NMR 44:157-166 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 Schmitz C, Stanton-Cook MJ, Su XC, Otting G and Huber T (2008) Numbat: an interactive software tool for fitting Δχ-tensors to molecular coordinates using pseudocontact shifts. J. Biomol. NMR 41:179-189
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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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