Thesis Title: Subtitle - NMR Spectroscopy Research Group

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24 Chapter 1. Introduction. Chapters 5 concludes this thesis by presenting some perspective of further development to better exploit PCS information in structural biology. 1.5 References Allegrozzi M, Bertini I, Janik MBL, Lee YM, Lin GH and Luchinat C (2000) Lanthanide-induced pseudocontact shifts for solution structure refinements of macromolecules in shells up to 40 angstrom from the metal ion. J Am Chem Soc 122:4154-4161 Banci L, Bertini I, Savellini GG, Romagnoli A, Turano P, Cremonini MA, Luchinat C and Gray HB (1997) Pseudocontact shifts as constraints for energy minimization and molecular dynamics calculations on solution structures of paramagnetic metalloproteins. Proteins 29:68-76 Bertini I, Felli IC and Luchinat C (1998) High magnetic field consequences on the NMR hyperfine shifts in solution. J Magn Reson 134:360-364 Bugayevskiy LM and Snyder JP (1995). Map projections: A reference manual. Taylor & Francis, London. 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 Donaldson LW, Skrynnikov NR, Choy WY, Muhandiram DR, Sarkar B, Forman-Kay JD and Kay LE (2001) Structural characterization of proteins with an attached ATCUN motif by paramagnetic relaxation enhancement NMR spectroscopy. J Am Chem Soc 123:9843-9847 John M, Headlam MJ, Dixon NE and Otting G (2007) Assignment of paramagnetic 15 N-HSQC spectra by heteronuclear exchange spectroscopy. J Biomol NMR 37:43-51 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 Karp RM (1972) Reducibility Among Combinatorial Problems. Complexity of Computer Computations. New York: Plenum, R. E. Miller and J. W. Thatcher. Karplus M (1959) Contact electron-spin coupling of nuclear magnetic moments. J Chem Phys 30:11-15 Kobe B, Guss M and Huber T (2008). Structural Proteomics: High Throughput Methods. Humana Press, Totowa, NJ, USA.
1.5 References. 25 Kuhn HW (1955) The Hungarian Method for the assignment problem. Naval Res Logistics Quart 2:83-97 McCoy MA and Wyss DF (2002) Structures of protein-protein complexes are docked using only NMR restraints from residual dipolar coupling and chemical shift perturbations. J Am Chem Soc 124:2104-2105 Nguyen BD, Xia ZC, Yeh DC, Vyas K, Deaguero H and La Mar GN (1999) Solution NMR determination of the anisotropy and orientation of the paramagnetic susceptibility tensor as a function of temperature for metmyoglobin cyanide: Implications for the population of excited electronic states. J Am Chem Soc 121:208-217 Pintacuda G, Keniry MA, Huber T, Park AY, Dixon NE and Otting G (2004) Fast structure-based assignment of 15 N HSQC spectra of selectively 15 N-labeled paramagnetic proteins. J Am Chem Soc 126:2963-2970 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 Rohl CA and Baker D (2002) De novo determination of protein backbone structure from residual dipolar couplings using rosetta. J Am Chem Soc 124:2723-2729 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 Schwieters CD, Kuszewski JJ and Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. Prog NMR Spectrosc 48:47-62 Schwieters CD, Kuszewski JJ, Tjandra N and Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:65-73 Shen Y and Bax A (2007) Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J Biomol NMR 38:289-302 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 U S A 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 Smith DJ, Maggio ET and Kenyon GL (1975) Simple alkanethiol groups for temporary blocking of sulfhydryl groups of enzymes. Biochemistry 14:766-71
Page 1 and 2: Computational study of proteins wit
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3.4 Introduction 3.4 Introduction.
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3.5 Algorithm. 79 rhombic component
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3.6 Program Features. 81 each fitti
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3.6 Program Features. 83 A new PCS
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3.6 Program Features. 85 Carlo prot
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3.7 Study case. 87 The coordinates
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3.7 Study case. 89 illustrates how
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3.9 Acknowledgment. 93 variables, t
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3.10 References. 95 Galassi M, Davi
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3.11 Supporting information. 97 Zwe
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102 Chapter 4. Protein Structure De
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Chapter 5 Conclusion and perspectiv
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5.3 The use of PCS for protein dock
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Thesis Title: Subtitle - NMR Spectroscopy Research Group

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