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Probing the ATP-induced conformational flexibility of the PcrA helicase protein using molecular dynamics simulation

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Abstract

Helicases are enzymes that unwind double-stranded DNA (dsDNA) into its single-stranded components. It is important to understand the binding and unbinding of ATP from the active sites of helicases, as this knowledge can be used to elucidate the functionality of helicases during the unwinding of dsDNA. In this work, we investigated the unbinding of ATP and its effect on the active-site residues of the helicase PcrA using molecular dynamic simulations. To mimic the unbinding process of ATP from the active site of the helicase, we simulated the application of an external force that pulls ATP from the active site and computed the free-energy change during this process. We estimated an energy cost of ~85 kJ/mol for the transformation of the helicase from the ATP-bound state (1QHH) to the ATP-free state (1PJR). Unbinding led to conformational changes in the residues of the protein at the active site. Some of the residues at the ATP-binding site were significantly reoriented when the ATP was pulled. We observed a clear competition between reorientation of the residues and energy stabilization by hydrogen bonds between the ATP and active-site residues. We also checked the flexibility of the PcrA protein using a principal component analysis of domain motion. We found that the ATP-free state of the helicase is more flexible than the ATP-bound state.

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Acknowledgments

We would like to thank Prof. Dr. Olav Schiemann University of Bonn, Germany for useful discussions. Authors ARM, CKC, and SR would like to thank Ms. Swagata Pahari for helping with the quantum-chemical calculations. The authors would also like to acknowledge the financial support from the Board of Research in Nuclear Sciences (project code GAP295526), India, for this work. Author Anil R. Mhashal would like to thank CSIR-UGC, India for providing the fellowship. Author Sudip Roy gratefully acknowledges CSIR-4PI for computational time and NCL (project code CSC0129) for funding.

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  1. Physical Chemistry Division, National Chemical Laboratory, Pune, 411008, India

    Anil R. Mhashal, Chandan Kumar Choudhury & Sudip Roy

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  1. Anil R. Mhashal
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  3. Sudip Roy
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Correspondence to Sudip Roy.

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Mhashal, A.R., Choudhury, C.K. & Roy, S. Probing the ATP-induced conformational flexibility of the PcrA helicase protein using molecular dynamics simulation. J Mol Model 22, 54 (2016). https://doi.org/10.1007/s00894-016-2922-3

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