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

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. There...

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Bibliographic Details
Published in:Journal of molecular modeling 2015-03, Vol.21 (3), p.64-64, Article 64
Main Authors: Lipska, Agnieszka G., Sieradzan, Adam K., Krupa, Paweł, Mozolewska, Magdalena A., D’Auria, Sabato, Liwo, Adam
Format: Article
Language:English
Subjects:
6th conference on Modeling & Design of Molecular Materials in Kudowa Zdrój (MDMM 2014)
Amino Acid Sequence
Arginine - chemistry
Arginine - metabolism
Bacterial Proteins - chemistry
Carrier Proteins - chemistry
Characterization and Evaluation of Materials
Chemistry
Chemistry and Materials Science
Computer Appl. in Life Sciences
Computer Applications in Chemistry
Ligands
Molecular Conformation
Molecular Dynamics Simulation
Molecular Medicine
Original Paper
Protein Conformation
Theoretical and Computational Chemistry
Thermotoga maritima - chemistry
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Summary: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 .
ISSN:1610-2940
0948-5023
DOI:10.1007/s00894-015-2609-1