Thesis Title: Subtitle - NMR Spectroscopy Research Group

More documents

Recommendations

Info

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
Page 1 and 2:
Computational study of proteins wit
Page 3 and 4:
iii Schmitz C, Stanton-Cook MJ, Su
Page 5 and 6:
v Acknowledgements I would like to
Page 7 and 8:
vii Keywords paramagnetic nmr, pseu
Page 9 and 10:
ix 2.3.3 Manual resonance assignmen
Page 11 and 12:
xi List of Figures Figure 1.1 NMR e
Page 13 and 14:
xiii
Page 15:
xv List of Abbreviations α Subunit
Page 18 and 19:
2 Chapter 1. Introduction. The scal
Page 20 and 21:
4 Chapter 1. Introduction. In contr
Page 22 and 23:
6 Chapter 1. Introduction. as the c
Page 24 and 25:
8 Chapter 1. Introduction. Figure 1
Page 26 and 27:
10 Chapter 1. Introduction. Protein
Page 28 and 29:
12 Chapter 1. Introduction. 1.3 Com
Page 30 and 31:
14 Chapter 1. Introduction. Figure
Page 32 and 33:
16 Chapter 1. Introduction. Figure
Page 34 and 35:
18 Chapter 1. Introduction. (Bugaye
Page 36 and 37:
20 Chapter 1. Introduction. The det
Page 38 and 39:
22 Chapter 1. Introduction. (ii) It
Page 40 and 41:
24 Chapter 1. Introduction. Chapter
Page 42 and 43:
26 Chapter 1. Introduction. Su XC,
Page 44 and 45:
28 Chapter 2. Possum: paramagnetica
Page 46 and 47:
Page 48 and 49:
Page 50 and 51:
Page 52 and 53:
Page 54 and 55:
Page 56 and 57:
Page 58 and 59:
Page 60 and 61: 44 Chapter 2. Possum: paramagnetica
Page 91 and 92: Chapter 3 Numbat: new user-friendly
Page 93 and 94: 3.4 Introduction 3.4 Introduction.
Page 95 and 96: 3.5 Algorithm. 79 rhombic component
Page 97 and 98: 3.6 Program Features. 81 each fitti
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
Page 105 and 106: 3.7 Study case. 89 illustrates how
Page 107 and 108: 3.7 Study case. 91 can be used to a
Page 109: 3.9 Acknowledgment. 93 variables, t
Page 113 and 114: 3.11 Supporting information. 97 Zwe
Page 115: 3.11 Supporting information. 99 Tab
Page 118 and 119: 102 Chapter 4. Protein Structure De
Page 145 and 146: Chapter 5 Conclusion and perspectiv
Page 147 and 148: 5.1 The use of PCS for structure de
Page 149 and 150: 5.1 The use of PCS for structure de
Page 151 and 152: 5.3 The use of PCS for protein dock
show all

Thesis Title: Subtitle - NMR Spectroscopy Research Group

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?