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Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field

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Abstract

The arginine-binding protein (ArgBP) from the hyperthermophilic eubacterium Thermotoga maritima (TmArgBP) is responsible for arginine transport through the bacterial cell membrane. The protein binds a single molecule of l-arginine, which results in conformational changes due to hinge bending. Thereby, TmArgBP acquires one of two possible conformations: open (without the presence of the arginine ligand) and closed (in the presence of the arginine ligand). Here we report a molecular dynamics study of the influence of the presence or absence of the ligand on the dynamics of TmArgBP, using the coarse-grained UNRES force field. The results of our studies indicate that binding of the arginine ligand promotes a closed conformation, which agrees with experimental data. However, the sensitivity of the TmArgBP conformation to the presence of arginine decreases and the protein becomes more flexible with increasing temperature, which might be related to the functionality of this protein in the thermophilic organism T. maritima.

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Acknowledgments

A.G.L. is grateful for the support from the University of Gdansk within the Young Scientist Grant program (grant BMN 538-8370-B351-14). This work was also supported by the National Science Center of Poland (NCN), grant DEC-2012/06/A/ST4/00376. A.K.S. was supported by FNP START (100.2014) and Iuventus Plus (0558/IP3/2013/72). Calculations were carried out using our 488-processor Beowulf cluster at the Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdansk; the supercomputer resources at the Informatics Center of the Academic Computer Centre in Gdansk (CI TASK); and the Interdisciplinary Center of Mathematical and Computer Modeling (ICM) at the University of Warsaw.

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Authors and Affiliations

  1. Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland

    Agnieszka G. Lipska, Adam K. Sieradzan, Paweł Krupa, Magdalena A. Mozolewska & Adam Liwo

  2. Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131, Naples, Italy

    Sabato D’Auria

  3. Institute of Food Science, CNR, Avellino, Italy

    Sabato D’Auria

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  1. Agnieszka G. Lipska
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  2. Adam K. Sieradzan
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  3. Paweł Krupa
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  4. Magdalena A. Mozolewska
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  5. Sabato D’Auria
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  6. Adam Liwo
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Correspondence to Adam Liwo.

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This paper belongs to Topical Collection 6th conference on Modeling & Design of Molecular Materials in Kudowa Zdrój (MDMM 2014)

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Lipska, A.G., Sieradzan, A.K., Krupa, P. et al. Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field. J Mol Model 21, 64 (2015). https://doi.org/10.1007/s00894-015-2609-1

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