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| Volume 20 Issue 1 Year 2025 | ||
Molecular Dynamics of Twisted β-Sheet inside a Protein Dimer of TTHA1013 Thermus thermophilus
Chirgadze Y.N.1, Likhachev I.V.2, Balabaev N.K.2, Brazhnikov E.V.1 1Institute of Protein Research of Russian Academy of Sciences, Pushchino, Moscow Region, Russia Abstract. α-Helix and β-sheet are two basic secondary structure motifs of protein molecules. A true native protein state is realized in a water solution. Under these conditions the proteins carry out the dynamic properties and, what is important, fulfill their various functions. We recently studied molecular dynamics of α-helical fragment of the T. thermophilus TTHA1013 protein in a water solution. Here we consider dynamics of β-sheet in the dimer of this protein. Dynamics of only main chain Cα-atoms were studied. One of the most distinctive type of fluctuations was detected along four independent dynamic trajectories with a total time of 200 nanoseconds. This fluctuation, called a “butterfly wing”, corresponds to the movements of Cα-atoms of the peripheral residues of the β-sheet fragment. While Cα-atoms of the central part of the sheet remain immobile because of hydrophobic interaction of the side chains within the molecular core.
Key words: β-sheet; globular protein; molecular dynamics; 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 Twisted β-Sheet inside a Protein Dimer of TTHA1013 Thermus thermophilus. Ìàthematical biology and bioinformatics. 2025;20(1):47-53. doi: 10.17537/2025.20.47 (published in English) Abstract (eng.) Abstract (rus.) Full text (eng., pdf) References
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