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| Volume 20 Issue 2 Year 2025 | ||
Molecular dynamics of the α-helical hairpin and its surrounding inside the protein S16 from Thermus thermophilus
Chirgadze Y.N.1, Likhachev I.V.2, Balabaev N.K.2, Brazhnikov E.V.1 1Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia Abstract. Dynamics of the α-helical hairpin inside the ribosomal protein S16 from Thermus thermophilus has been considered. The analysis of polypeptide chain dynamics was carried out on five independent trajectories with a total time of 370 ns. It was shown that relaxed fluctuations of Cα-atoms of the polypeptide backbone at the final part of the trajectory of 60–80 ns become constant: in the β-sheet – 0.4 Å, in helix1 – 0.8 Å, in helix2 – 0.6 Å, and in loops – 1.1 Å. The predicted dynamic profile of the Cα-atom shifts clearly indicates a decreasing in mobility of the α-hairpin in the regions where hydrophobic clusters are located. The restriction factor of such movements is directly related to the interaction of their residues with the other protein residues.
Key words: molecular dynamics; α-helix; hairpin; globular protein; molecular dynamics simulation program PUMA-CUDA, Trajectory Analyzer of Molecular Dynamics (TAMD) |
Table of Contents
Original Article
Chirgadze Y.N., Likhachev I.V., Balabaev N.K., Brazhnikov E.V. Molecular dynamics of the α-helical hairpin and its surrounding inside the protein S16 from Thermus thermophilus. Ìàthematical biology and bioinformatics. 2025;20(2):369-378. doi: 10.17537/2025.20.369 (published in English) Abstract (eng.) Abstract (rus.) Full text (eng., pdf) References
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