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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| 024 | 7 | 0 | |a 10.1007/s00894-015-2609-1 |2 doi |
| 035 | |a (NATIONALLICENCE)springer-10.1007/s00894-015-2609-1 | ||
| 245 | 0 | 0 | |a 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 |h [Elektronische Daten] |c [Agnieszka Lipska, Adam Sieradzan, Paweł Krupa, Magdalena Mozolewska, Sabato D'Auria, Adam Liwo] |
| 520 | 3 | |a 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. | |
| 540 | |a Springer-Verlag Berlin Heidelberg, 2015 | ||
| 690 | 7 | |a Arginine-binding protein |2 nationallicence | |
| 690 | 7 | |a Domain motion |2 nationallicence | |
| 690 | 7 | |a Molecular dynamics |2 nationallicence | |
| 690 | 7 | |a UNRES force field |2 nationallicence | |
| 700 | 1 | |a Lipska |D Agnieszka |u Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland |4 aut | |
| 700 | 1 | |a Sieradzan |D Adam |u Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland |4 aut | |
| 700 | 1 | |a Krupa |D Paweł |u Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland |4 aut | |
| 700 | 1 | |a Mozolewska |D Magdalena |u Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland |4 aut | |
| 700 | 1 | |a D'Auria |D Sabato |u Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131, Naples, Italy |4 aut | |
| 700 | 1 | |a Liwo |D Adam |u Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland |4 aut | |
| 773 | 0 | |t Journal of Molecular Modeling |d Springer Berlin Heidelberg |g 21/3(2015-03-01), 1-11 |x 1610-2940 |q 21:3<1 |1 2015 |2 21 |o 894 | |
| 856 | 4 | 0 | |u https://doi.org/10.1007/s00894-015-2609-1 |q text/html |z Onlinezugriff via DOI |
| 898 | |a BK010053 |b XK010053 |c XK010000 | ||
| 900 | 7 | |a Metadata rights reserved |b Springer special CC-BY-NC licence |2 nationallicence | |
| 908 | |D 1 |a research-article |2 jats | ||
| 949 | |B NATIONALLICENCE |F NATIONALLICENCE |b NL-springer | ||
| 950 | |B NATIONALLICENCE |P 856 |E 40 |u https://doi.org/10.1007/s00894-015-2609-1 |q text/html |z Onlinezugriff via DOI | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a Lipska |D Agnieszka |u Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland |4 aut | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a Sieradzan |D Adam |u Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland |4 aut | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a Krupa |D Paweł |u Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland |4 aut | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a Mozolewska |D Magdalena |u Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland |4 aut | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a D'Auria |D Sabato |u Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131, Naples, Italy |4 aut | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a Liwo |D Adam |u Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland |4 aut | ||
| 950 | |B NATIONALLICENCE |P 773 |E 0- |t Journal of Molecular Modeling |d Springer Berlin Heidelberg |g 21/3(2015-03-01), 1-11 |x 1610-2940 |q 21:3<1 |1 2015 |2 21 |o 894 | ||