Thesis Title: Subtitle - NMR Spectroscopy Research Group

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136 Chapter 5. Conclusion and perspectives. (Chapter 1). Pseudocontact shifts therefore present particularly powerful experimental data to construct a model of the complex between two molecules by rigid body docking, and to shortcut the computationally expensive task of sampling the conformational space. PCS cannot, however, provide the high resolution accuracy that crystallography achieves and more detailed models will still require structural refinement software that optimizes the intermolecular packing and any other structural adjustments. At least, however, the computational effort of protein docking can focus on the atomic details when starting from a valid rigid body model. Another challenge facing the modeling of a protein-protein complex arises when one of the proteins undergoes a large conformational change. Protein docking software can tackle the problem to some extent by adapting the conformations of the side chains and the backbone close to the complex interface. As this approach greatly increases the conformational space to search, it is computationally challenging. Paramagnetic NMR and PCS could assist the modeling of large conformational changes by directing the conformational alterations toward the correct conformation. A protein that undergoes a large conformational change due to motions about a hinge that separates two rigid domains would present an attractive example. In a situation, where such a hinge motion occurs as a result of association with a binding partner, a technique for rigid body docking with the help of PCS as presented in this thesis could be particularly fruitfully applied to assist the modeling of the complex. 5.4 References Bertini I, Longinetti M, Luchinat C, Parigi G and Sgheri L (2002) Efficiency of paramagnetism- based constraints to determine the spatial arrangement of α-helical secondary structure elements. J Biomol NMR 22:123-136 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 Su XC and Otting G (2009) Paramagnetic labelling of proteins and oligonucleotides. J Biomol NMR in press
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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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Chapter 3 Numbat: new user-friendly
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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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Thesis Title: Subtitle - NMR Spectroscopy Research Group

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