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Local conformational changes of proteins in DNA interfaces

Sunami, Tomoko; Kono, Hidetoshi

DNA-protein interaction plays a key role in many cellular functions such as transcription, replication, recombination and DNA packaging. Understanding the mechanisms by which the protein recognizes DNA is one of the main topics in biology. With increased amount of crystal structures, conformational changes of proteins in DNA interfaces are suggested to be one of important factors in DNA recognition. To better understand a role of the flexibility of proteins in DNA recognition, quantitative analyses of local conformational changes in DNA interfaces of proteins are required. In order to analyze such conformational changes in DNA interfaces, we extracted crystal structures of DNA-unbound and DNA-bound states from PDB. The backbone structures were described by 7 letters that were pre-defined according to conformations of consecutive overlapping fragments of 4-residues. Using the letter codes, any conformational change from DNA-unbound state to DNA-bound state was described as one of 49 patterns of changes. We statistically analyzed the frequency of these conformational changes in DNA interfaces and protein surfaces. As a result, we found 4 structural changes preferred in DNA interfaces compared with that of protein interfaces.

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