This article is cited in 1 paper

Mathematical Modeling

Molecular dynamics of twisted $\beta$-sheet inside a protein dimer of TTHA1013 Thermus thermophilus

Yu. N. Chirgadze^a, I. V. Likhachev^b, N. K. Balabaev^b, E. V. Brazhnikov<sup>a

a</sup> Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moskovskaya obl.
^b Institute of Mathematical Problems of Biology RAS, Pushchino, Moskovskaya obl.

Abstract: $\alpha$-Helix and $\beta$-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 $\alpha$-helical fragment of the T. thermophilus TTHA1013 protein in a water solution. Here we consider dynamics of $\beta$-sheet in the dimer of this protein. Dynamics of only main chain C$\alpha$-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 C$\alpha$-atoms of the peripheral residues of the $\beta$-sheet fragment. While C$\alpha$-atoms of the central part of the sheet remain immobile because of hydrophobic interaction of the side chains within the molecular core.

Key words: $\beta$-sheet; globular protein; molecular dynamics; molecular dynamics simulation program PUMA-CUDA, Trajectory Analyzer of Molecular Dynamics (TAMD).

Received 21.01.2025, 11.02.2025, Published 14.02.2025

Language: English

DOI: 10.17537/2025.20.47

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