Protein-protein arayüzeylerinin nitelendirilmesi ve analizi

The diverse range of cellular functions is performed by the limited number of protein folds existing in nature. One may similarly expect that the number of protein-protein interface architectures would also be restricted. In this study, the recently derived dataset of protein-protein interfaces is analyzed and compared with older datasets to address questions like (i) how many different protein-protein interaction types are expected to exist in nature for necessary biological diversity; (ii) what fraction of interactions is already known toward elucidation of the organization of the cell; and (iii) whether the increase in the number of interface architectures and consequently the functional coverage and interaction map of the PDB are reaching a plateau. The results show that number of protein interfaces increases at a much faster rate compared to the number of folds and is not yet to level off. Functional coverage is also found to steadily increase. As an estimation of this study, the total number of different interfaces will be around 8000 and it will take almost 30 years to discover at the current rate of experiment. Also, despite the diversity of interface architectures, some are more favorable and frequently used, and of particular interest, those are the ones which are also preferred in single chains. Another significant result is that some species, especially eukaryotes, prefer intra chain domain-domain interactions; others, less complex organisms, prefer inter chain interaction. This adaptation may be the result of the crowded traffic in the eukaryotic cells. This thesis presents the multidirectional analysis and applications of the protein ? protein interfaces. We believe in that the dataset of protein ? protein interfaces is a rich source for researchers dealing with protein ? protein interactions, protein recognition mechanisms, drug design etc.