Thesis Title: Subtitle - NMR Spectroscopy Research Group

More documents

Recommendations

Info

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
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:
Page 62 and 63:
Page 64 and 65:
Page 66 and 67:
Page 68 and 69:
Page 70 and 71:
Page 72 and 73:
Page 74 and 75:
Page 76 and 77:
Page 78 and 79:
Page 80 and 81:
Page 82 and 83: 66 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 and 110: 3.9 Acknowledgment. 93 variables, t
Page 111 and 112: 3.10 References. 95 Galassi M, Davi
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?