I want to express my gratitude to all those who have given me valuable scientific and personal support during this work. Most of all, I want to thank Prof. Holzhütter for introducing me to the field of antigen processing, which keeps on fascinating me. During my entire work, he always assisted me when I his needed expert advice and many ideas presented here were the results of our fruitful discussions.
I was privileged to be the first exchange student between the Bioinformatics program at Boston University and the graduate program "Dynamics and Evolution of Cellular and Macromolecular Processes" in Berlin, and I would like to thank Prof. Heinrich as the head of the Berlin graduate program and Prof. DeLisi from Boston University for making this possible and financing my stay.
During this stay from January to April of 2002, most of the work presented in the chapter on MHC-I binding was made. This was a joint project with my supervisor in Boston, Prof. Weng, W. Tong and the experimentalists that supplied us with the affinity data J. Sidney and A. Sette.
The chapter on TAP transport owes a great deal to Sascha Bulik, who is writing his diploma thesis on this subject, and to Prof. van Endert and Prof. Tampe who supplied us with TAP affinity data, and helped us with the resulting manuscript. I also want to thank K. Udaka for supplying us with affinity matrix data for several mouse MHC-I alleles.
The experimental analysis of proteasomal digests was carried out by several members of the Institute of Biochemistry at the Charite. This cooperation would not have been possible without the steady interest and support of Prof. Kloetzel and U. Kuckelkorn. The analysis of the dependencies between MS-signals and peptide amounts is based on discussions and much more experimental data than presented here from K. Jannek and T. Ruppert. Discussions with Prof. Kloetzel, U. Kuckelkorn and Prof. Dahlmann helped form my understanding of proteasomal digests. The isolation of proteasomes and the accomplishment of the peptide digests was carried out by I. Drung, peptides were synthesized by P. Henklein, and B. Brecht, K. Textoris-Taube and B. Strehl helped with the analysis of MS data.
I also want to thank everyone in the group of Professor Frömmel for providing a good working atmosphere, in which I found many people willing to help me as a trained physicist learn basic biochemistry. Special thanks go to K. Rother for supplying me with the figures in the introduction.
For their personal support, I want to thank my parents, my girlfriend and good friends for keeping me in contact with the outside world.
Without them and the many people that I have not mentioned here by name, this work would not have been possible.
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