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Grininger, Martin (2006): The Function of the Halophilic Dodecin. Dissertation, LMU München: Faculty of Chemistry and Pharmacy
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Abstract

Flavins are physiologically relevant cofactors that catalyze various redox and light-induced reactions. Due to a high intrinsic reactivity, these compounds are found tightly bound to proteins with the chemistry of the flavin either narrowed to a defined reaction channel (flavoenzymes) or reduced to (almost) non-reactivity (flavin binding and carrier proteins). Lumichrome is a product of flavin photodegradation. In spite of the structural similarity to flavins, lumichrome has electronic properties which differ from flavins, preventing this compound from any physiological relevance as a cofactor. The interest in lumichrome is basically focussed on its role as a photosensitizing compound. Lumichrome is excited by the absorption of visible light and relaxes by transferring electrons or electronic energy to surrounding substrates and oxygen, exerting an unspecific toxic effect on the cellular environment. Dodecin is a dodecameric flavin binding protein comprising a novel ligand binding fold. It incorporates dimers of ligands arranged in antiparallel manner within each of the six identical binding pockets. In this thesis, structure and function of dodecin from the archaeal organism Halobacterium salinarum are reported. X-ray structural investigations supplemented with functional data revealed that this protein is an unspecific binder of flavins and binder of the flavin-like compound lumichrome. Dissociation constants were obtained in the nanomolar to micromolar range and found to correlate positively with the ligand size. The preference of dodecin for the small ligands lumichrome and lumiflavin is described as a gated ligand binding mode, based on the low plasticity of the dodecin binding pocket which sterically restricts the bulkier ligands from arranging the flavin aromatic subunit in a high affinity position. Site directed mutagenesis of the halophilic dodecin allowed to spread the idea of dodecin as a small ligand binding particle among homologous proteins. These mutational studies could moreover show that the halophilic type of dodecins is outstanding in additionally exhibiting a high affinity for riboflavin. The stabilization of the ribityl chain by an H-bond network to a single residue was found to suspend restrictions of the gated ligand binding mode and to enable H. salinarum dodecin to exhibit multiple (high) affinity. In Western-Blot and RT-PCR analysis of the dodecin expression level, it could be demonstrated that after a short lag period dodecin is constitutively expressed in light and in dark. In the late stationary phase, a clear influence of dodecin on the riboflavin cellular concentrations could be observed. While high levels of riboflavin were found in H. salinarum wild type cells, in cells of the dodecin deficient strain riboflavin cellular concentrations were depressed. Lumichrome concentrations on the other hand were unaffected from dodecin; however; increased concentrations of lumichrome were found in light, according to a photolytic degradation of riboflavin. In vivo data fully agreed with the deductions from the dodecin structural and functional investigations. Dodecin is a riboflavin binding and carrier protein (RfBP). Its function is to store riboflavin under non-favorable environmental conditions while preventing this flavin from photodegradation. The lumichrome-collecting property represents an extra-feature which allows binding of lumichrome if degradation of riboflavin occurs in order to protect the cellular environment from high amounts of this photo-toxic compound.