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Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field

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Abstract

Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.

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Acknowledgments

The numerical calculations reported in this paper were performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA Resources). We thank them for providing us superb computational resources and technical help for this research. Scientific Research Projects Office (BAP) of Yuzuncu Yil University has supported this research under the project number 2015-FBE-YL008.

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Authors and Affiliations

  1. Department of Physics, Faculty of Science, Yuzuncu Yil University, Van, Turkey

    Hulya Unan & Mustafa Tekpinar

  2. Department of Physics, Faculty of Science and Arts, Siirt University, Siirt, Turkey

    Ahmet Yildirim

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  1. Hulya Unan
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  2. Ahmet Yildirim
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  3. Mustafa Tekpinar
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Correspondence to Mustafa Tekpinar.

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Unan, H., Yildirim, A. & Tekpinar, M. Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field. J Comput Aided Mol Des 29, 655–665 (2015). https://doi.org/10.1007/s10822-015-9849-0

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  • DOI: https://doi.org/10.1007/s10822-015-9849-0

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