Thesis Title: Subtitle - NMR Spectroscopy Research Group

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94 Chapter 3. Numbat: new user-friendly method built for automatic Δχ-tensor determination. Banci L, Dugad LB, La Mar GN, Keating KA, Luchinat C and Pierattelli R (1992) 1 H nuclear magnetic resonance investigation of cobalt(II) substituted carbonic anhydrase. Biophys J 63:530-543 Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN and Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235-242 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 U S A 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, Luchinat C and Parigi G (2002) Magnmagnetic suceptibility in paramgnetic nmr. Prog NMR Spectrosc 40:249-273 Bugayevskiy LM and Snyder JP (1995). Map projections: A reference manual. Taylor & Francis, London. Capozzi F, Cremonini MA, Luchinat C and Sola M (1993) Assignment of pseudo-contact-shifted 1 H NMR resonances in the EF site of Yb 3+ -substituted rabbit parvalbumin through a combination of 2D techniques and magnetic susceptibility tensor determination. Magn Reson Chem 31:S118-S127 Clore GM, Gronenborn AM and Bax A (1998) A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. J Magn Reson 133:216-221 Cornilescu G and Bax A (2000) Measurement of proton, nitrogen, and carbonyl chemical shielding anisotropies in a protein dissolved in a dilute liquid crystalline phase. J Am Chem Soc 122:10143-10154 DeLano WL (2002) The PyMOL molecular graphics system. Palo Alto, CA, USA. Dosset P, Hus JC, Blackledge M and Marion D (2000) Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J Biomol NMR 16:23-28 Eichmüller C and Skrynnikov NR (2007) Observation of μs time-scale protein dynamics in the presence of Ln 3+ ions: Application to the N-terminal domain of cardiac troponin C. J Biomol NMR 37:79-95 Emerson SD and La Mar GN (1990) NMR determination of the orientation of the magnetic- susceptibility tensor in cyanometmyoglobin: A new probe of steric tilt of bound ligand. Biochemistry 29:1556-1566
3.10 References. 95 Galassi M, Davies J, Theiler B, Gough G, Jungman M, Booth M and Rossi F (2006). GNU scientific library reference manual. Network Theory Ltd, Bristol. 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 Güntert P, Mumenthaler C and Wüthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283-298 Hess B and Scheek RM (2003) Orientation restraints in molecular dynamics simulations using time and ensemble averaging. J Magn Reson 164:19-27 Jensen MR, Hansen DF, Ayna U, Dagil R, Hass MAS, Christensen HEM and Led JJ (2006) On the use of pseudocontact shifts in the structure determination of metalloproteins. Magn Reson Chem 44:294-301 John M, Park AY, Pintacuda G, Dixon NE and Otting G (2005) Weak alignment of paramagnetic proteins warrants correction for residual CSA effects in measurements of pseudocontact shifts. J Am Chem Soc 127:17190-17191 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 Keniry MA, Park AY, Owen EA, Hamdan SM, Pintacuda G, Otting G and Dixon NE (2006) Structure of the θ subunit of Escherichia coli DNA polymerase III in complex with the ε subunit. J Bacteriol 188:4464-4473 Kirby TW, Harvey S, DeRose EF, Chalov S, Chikova AK, Perrino FW, Schaaper RM, London RE and Pedersen LC (2006) Structure of the Escherichia coli DNA polymerase III ε-HOT proofreading complex. J Biol Chem 281:38466-38471 Koradi R, Billeter M and Wüthrich K (1996) MOLMOL: A program for display and analysis of macromolecular structures. J Mol Graphics 14:51-55 Krause A (2007). Foundations of GTK+ development. Apress, Berkeley, CA, USA. Lee L and Sykes BD (1983) Use of lanthanide-induced nuclear magnetic-resonance shifts for determination of protein structure in solution: EF calcium binding site of carp parvalbumin. Biochemistry 22:4366-4373 Marquardt DW (1963) An algorithm for least-squares estimation of nonlinear parameters. J Soc Ind Appl Math 11:431-441 Nelder JA and Mead R (1965) A simplex method for function minimization. Comput J 7:308-313 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
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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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22 Chapter 1. Introduction. (ii) It
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Page 95 and 96: 3.5 Algorithm. 79 rhombic component
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Page 99 and 100: 3.6 Program Features. 83 A new PCS
Page 101 and 102: 3.6 Program Features. 85 Carlo prot
Page 103 and 104: 3.7 Study case. 87 The coordinates
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Page 109: 3.9 Acknowledgment. 93 variables, t
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