IIIT Hyderabad Publications |
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Detailed Investigation of the Thermal Stabilization of DNA by Sac7dAuthors: G Harika,U Deva Priyakumar Conference: Of Molecules and Materials Date: 2009-12-28 Report no: IIIT/TR/2009/236 AbstractSac7d is a protein present in Sulfolobus acidocaldarius, a hyperthermophilic archaeon, which is stable at extreme conditions. It is a chromosomal protein, which is capable of binding DNA thereby increasing its melting temperature. It was suggested to stabilize central 3 to 5 base pair steps in DNA. It binds to the minor groove of the DNA causing a kink in the helix without any sequential preference. We have used molecular dynamics (MD) simulations to study the binary complexes of Sac7d bound to DNA at 300 and 360 K. The objective is to understand the atomic detailed mechanism of the capability of Sac7d in facilitating DNA stability at higher temperature. As has been shown before, the structure of the protein is highly stable both at 300 and 360 K. The DNA duplex was found to be stable at 300 K and is similar to the X-ray crystal structure. Consistent with experiments, at least the central four base pairs of the DNA were found to be base paired during most of the simulation at 360 K. The dynamic properties of the protein in the protein-DNA complexes remained unchanged compared to when the protein is unbound. Interestingly, B- to A-form transitions occur in both the DNA molecules when bound to Sac7d, which was confirmed by sugar puckering angles, and backbone dihedral angles. Detailed examination of the protein-DNA interactions reveals that the stabilization of the DNA molecules is mostly due to the favorable interaction of the protein with the backbone of the DNA. Full paper: pdf Centre for Computational Natural Sciences and Bioinformatics |
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