caa a22 4500 605511934 CHVBK 20210128100653.0 cr unu---uuuuu 210128e20150301xx s 000 0 eng 10.1007/s00894-015-2609-1 doi (NATIONALLICENCE)springer-10.1007/s00894-015-2609-1 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 [Elektronische Daten] [Agnieszka Lipska, Adam Sieradzan, Paweł Krupa, Magdalena Mozolewska, Sabato D'Auria, Adam Liwo] 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. Springer-Verlag Berlin Heidelberg, 2015 Arginine-binding protein nationallicence Domain motion nationallicence Molecular dynamics nationallicence UNRES force field nationallicence Lipska Agnieszka Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland aut Sieradzan Adam Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland aut Krupa Paweł Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland aut Mozolewska Magdalena Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland aut D'Auria Sabato Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131, Naples, Italy aut Liwo Adam Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland aut Journal of Molecular Modeling Springer Berlin Heidelberg 21/3(2015-03-01), 1-11 1610-2940 21:3<1 2015 21 894 https://doi.org/10.1007/s00894-015-2609-1 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-015-2609-1 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Lipska Agnieszka Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland aut NATIONALLICENCE 700 1- Sieradzan Adam Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland aut NATIONALLICENCE 700 1- Krupa Paweł Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland aut NATIONALLICENCE 700 1- Mozolewska Magdalena Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland aut NATIONALLICENCE 700 1- D'Auria Sabato Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131, Naples, Italy aut NATIONALLICENCE 700 1- Liwo Adam Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/3(2015-03-01), 1-11 1610-2940 21:3<1 2015 21 894