Дизайн структуры химерного белка ДНК-экзотрансферазы быка и SSB-белка E. coli

С целью изучения влияния дополнительного ДНК-связывающего домена SSB-белка E. coli, присоединенного к транкированной и нативной ДНК-экзотрансферазе быка, на ДНК-аффинность и стабильность фермента, проведен анализ траекторий молекулярной динамики и пространственных структур гомологичных моделей химерного белка с различными линкерами. Установлено, что более предпочтительным для присоединения SSB-белка является C-концевая последовательность фермента, при этом прогнозируемая стабильность транкированного химерного фермента выше, чем у нативного. Согласно данным молекулярной динамики, введение линкеров между двумя белками для нативной (GGGGSGGGSGGGGS, GGGSGGGS и TCT) и транкированной (GGSGGGSGG, GGGGGG, GTGSGT и 5xGGGGS) формы фермента не только способствует повышению его стабильности, но и увеличивает взаимную подвижность ДНК-аффинных доменов.The analysis of the trajectories of molecular dynamics simulation and spatial structures of homologous models of fusion protein with various linkers was performed to understand the effect of the additional DNA-binding domain of the E. coli SSB protein attached to the truncated and native bovine DNA exotransferase on its stability and activity. It is found that the C-terminus of the enzyme is the preferred end for attachment of the E. coli protein, while the stability of the truncated fusion enzyme is higher than the native one. According to molecular dynamics data, introducing linkers between two proteins for the native (GGGGSGGGSGGGGS, GGGSGGGS, and TCT) and truncated (GGSGGGSGG, GGGGGG, GTGSGT, and 5xGGGGS) forms of the enzyme not only improves its stability, but also increases the mutual mobility of DNA-affinity domains.

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