Next Article in Journal
Temperature Distribution Design Based on Variable Lattice Density Optimization and Metal Additive Manufacturing
Next Article in Special Issue
Microwave-Assisted Synthesis of 2-Methyl-1H-indole-3-carboxylate Derivatives via Pd-Catalyzed Heterocyclization
Previous Article in Journal
Antimatter Free-Fall Experiments and Charge Asymmetry
 
 
Article

Use of the Molecular Dynamics Method to Investigate the Stability of α-α-Corner Structural Motifs in Proteins

1
Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
2
V.N. Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia
3
Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia
4
Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
*
Author to whom correspondence should be addressed.
Academic Editor: Francesco Merlino
Symmetry 2021, 13(7), 1193; https://doi.org/10.3390/sym13071193
Received: 12 June 2021 / Revised: 24 June 2021 / Accepted: 28 June 2021 / Published: 2 July 2021
(This article belongs to the Special Issue Medicinal Chemistry: Topics and Advances)
This study investigated the stability of structural motifs via molecular dynamics, using α-α-corners as an example. A molecular dynamics experiment was performed on a sample of α-α-corners selected by the authors from the PDB database. For the first time during a molecular dynamics experiment, we investigated the characteristics of structural motifs by describing their geometry, including the interplanar distance, area of polygon of the helices projections intersection, and torsion angles between axes of helices in helical pairs. The torsion angles for the constriction amino acids in the equilibrium portion of the molecular dynamics trajectory were analyzed. Using the molecular dynamics method, α-α-corners were found to be autonomous structures that are stable in aquatic environments. View Full-Text
Keywords: structural motifs of proteins; helical pairs; stability; molecular dynamics structural motifs of proteins; helical pairs; stability; molecular dynamics
Show Figures

Figure 1

MDPI and ACS Style

Rudnev, V.R.; Kulikova, L.I.; Kaysheva, A.L.; Efimov, A.V.; Tikhonov, D.A. Use of the Molecular Dynamics Method to Investigate the Stability of α-α-Corner Structural Motifs in Proteins. Symmetry 2021, 13, 1193. https://doi.org/10.3390/sym13071193

AMA Style

Rudnev VR, Kulikova LI, Kaysheva AL, Efimov AV, Tikhonov DA. Use of the Molecular Dynamics Method to Investigate the Stability of α-α-Corner Structural Motifs in Proteins. Symmetry. 2021; 13(7):1193. https://doi.org/10.3390/sym13071193

Chicago/Turabian Style

Rudnev, Vladimir R., Liudmila I. Kulikova, Anna L. Kaysheva, Alexander V. Efimov, and Dmitry A. Tikhonov. 2021. "Use of the Molecular Dynamics Method to Investigate the Stability of α-α-Corner Structural Motifs in Proteins" Symmetry 13, no. 7: 1193. https://doi.org/10.3390/sym13071193

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop