Chirality As a Symmetric Basis of Self-Organization of Biomacromolecules

Твердислов, В. А.; Sidorova, A. E.; Bagrova, Olga E.; Belova, Ekaterina; Bystrov, Vladimir; Левашова, Н. Т.; Lutsenko, Aleksey; Semenova, E. V.; Shpigun, Denis

doi:10.1134/s0006350922050190

Cited by 6 publications

(6 citation statements)

References 75 publications

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“…For example, with horizontal preincubation of test tubes and their horizontal rotation on the "vortex", the activity remains at the usual level, but it decreases with a combination of horizontal preincubation and vertical mechanical shaking. The role of the symmetry factor was also noted by other authors [113,124].…”

Section: Characteristics Of Tumor Growth In the Lewis Lung Carcinoma ...supporting

confidence: 75%

The Supramolecular Matrix Concept

Epstein

2023

Symmetry

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It has been established that dilutions of a variety of substances, when exposed to vibration in the process of their preparation, acquire not only new structural characteristics in the form of nano-associates but also new physical properties, regardless of the presence of the initial substance. One of the most important properties of these dilutions is the ability to modify the physico–chemical and biological activity of the initial substance as well as exert non-contact, “distant”, effects. Here, we propose a novel hypothesis that the basis of modifying activity is the transformation of target molecules to a more harmonious (symmetrical) state supported by a supramolecular matrix, a structural unit of a structured space.

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Section: Characteristics Of Tumor Growth In the Lewis Lung Carcinoma ...supporting

confidence: 75%

The Supramolecular Matrix Concept

Epstein

2023

Symmetry

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“…To determine the chirality of the structure, an algorithm based on the mixed product of vectors proposed in [ 18 , 44 , 45 ] was used here. The vectors connecting the Cα-atoms of the system acted as support vectors ( Figure 3 ).…”

Section: Main Methodsmentioning

confidence: 99%

“…For the convenience of estimating the chirality value of helical structures, a normalized value of the chirality value was also introduced [ 44 , 45 ]:

where the normalization factor is calculated as

, where k = 5.…”

Section: Main Methodsmentioning

confidence: 99%

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Molecular Dynamics Simulation of Self-Assembly Processes of Diphenylalanine Peptide Nanotubes and Determination of Their Chirality

et al. 2023

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In this work, we further developed a new approach for modeling the processes of the self-assembly of complex molecular nanostructures using molecular dynamics methods; in particular, using a molecular dynamics manipulator. Previously, this approach was considered using the example of the self-assembly of a phenylalanine helical nanotube. Now, a new application of the algorithm has been developed for implementing a similar molecular dynamic self-assembly into helical structures of peptide nanotubes (PNTs) based on other peptide molecules—namely diphenylalanine (FF) molecules of different chirality L-FF and D-FF. In this work, helical nanotubes were assembled from linear sequences of FF molecules with these initially different chiralities. The chirality of the obtained nanotubes was calculated by various methods, including calculation by dipole moments. In addition, a statistical analysis of the results obtained was performed. A comparative analysis of the structures of nanotubes was also performed using the method of visual differential analysis. It was found that FF PNTs obtained by the MD self-assembly method form helical nanotubes of different chirality. The regimes that form nanotubes of right chirality D from initial L-FF dipeptides and nanotubes of left chirality L from D-FF dipeptides are revealed. This corresponds to the law of changing the sign of the chirality of molecular helical structures as the level of their hierarchical organization becomes more complicated.

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“…Для определения хиральности структуры был использован алгоритм, основанный на смешанном произведении векторов, предложенный в работах [18,45].…”

Section: расчет и определение хиральностиunclassified

Assembly of a Diphenylalanine Peptide Nanotube by Molecular Dynamics Methods

Likhachev¹,

Bystrov²,

Filippov³

2023

Math.Biol.Bioinf.

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The paper develops an approach to modeling the processes of self-assembly of complex molecular nanostructures by molecular dynamics methods using a molecular dynamics manipulator. Previously, this approach was considered using the example of assembling a phenylalanine helical nanotube from a linear set of chains of phenylalanine (F) molecules of different chirality: left-handed L-F and right-handed D-F chirality L-FF and D-FF. The process of self-assembly of dipeptide chains into helical structures of nanotubes is an imitation of applying certain forces to the existing initial linear structure in order to obtain the final structure of the same chemical composition, but with a different helical geometry. The PUMA-CUDA molecular dynamics simulation software package was used as the main software. Using this tool, one can investigate the formation of helical structures from a linear sequence of any amino acids. A comparative analysis of the structures of nanotubes obtained by assembling by molecular dynamics methods and by their experimental self-assembly was performed using the method of visual differential analysis. It has been established that the obtained data correspond to the law of the sign change of chirality of molecular helical structures with the complication of their hierarchical level of organization.

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Chirality As a Symmetric Basis of Self-Organization of Biomacromolecules

Cited by 6 publications

References 75 publications

The Supramolecular Matrix Concept

The Supramolecular Matrix Concept

Molecular Dynamics Simulation of Self-Assembly Processes of Diphenylalanine Peptide Nanotubes and Determination of Their Chirality

Assembly of a Diphenylalanine Peptide Nanotube by Molecular Dynamics Methods

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