Changes in thermodynamic properties of DNA base pairs in protein-DNA recognition

Journal of Biomolecular Structure & Dynamics
Sudipta SamantaDhananjay Bhattacharyya

Abstract

The mechanism of protein-DNA recognition, particularly the induced fit mechanism, is poorly understood due to ineffective analysis of the protein-DNA complex crystal structures. It is expected that upon protein binding the DNA becomes structurally more rigid. However, a previous analysis (W.K. Olson, A. A. Gorin, X. Lu, L. M. Hock and V. Zhurkin,Proc. Natl. Acad. Sci. USA, 95, 11163 (1998)) indicates increase in the flexibility of the DNA segment complexed with protein. We have considered an ensemble of configurations from crystallographic data of the TBP-TATA box complex structures under a given thermodynamic condition. Analysis of the ensemble of structures of this complex indicates that the DNA deforms significantly to form specific hydrogen bonds and as a consequence, its structure attains more rigidity. We calculate the free energy profiles in term of the DNA base pair (bp) step parameters via the binding patterns in the ensemble of the given complex, and for free DNA bp steps as well. The rigidities estimated from these free energies for small deformations around the minimum indicate enhanced structural rigidities of DNA upon complexation with protein. Further, the changes in the thermodynamic properties of the bp steps u...Continue Reading

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Citations

Jan 13, 2015·Journal of Computer-aided Molecular Design·Manas MondalDhananjay Bhattacharyya
Jan 21, 2010·Journal of Biomolecular Structure & Dynamics·Aditi BorkarDhananjay Bhattacharyya
Jul 26, 2018·Journal of Experimental Zoology. Part A, Ecological and Integrative Physiology·Jayant KumarSangeeta Rani
Jan 3, 2012·Journal of Biomolecular Structure & Dynamics·Vigneshwar RamakrishnanRaj Rajagopalan
May 1, 2017·The Journal of Chemical Physics·Sudipta Samanta, Sanchita Mukherjee
Jan 3, 2012·Journal of Biomolecular Structure & Dynamics·Yu N ChirgadzeV V Ivanov

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