On regularities in the spontaneous formation of structural hierarchies in chiral systems of nonliving and living matter

Твердислов, В. А.; Malyshko, E. V.

doi:10.3367/ufnr.2018.08.038401

Cited by 18 publications

(14 citation statements)

References 41 publications

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“…This result is confirmed by the previous crystallographic studies [ 31 , 38 ] and the individual dipole moments completely follow this arrangement ( Figure 5 ). It is worth noting that the chirality alternating observed earlier for natural proteins and DNA [ 9 , 10 , 11 , 12 ] preserves in the supramolecular PNTs as well. The type of chirality of the helix-like PNT is opposite to that of the individual dipeptide.…”

Section: Resultsmentioning

confidence: 71%

“…Among them, α-helices, a common type of regular secondary structure of many proteins, are the simplest and most energetically favorable structures [ 1 , 6 ]. For natural proteins consisting of L-amino acids, a chirality sign alternation from the “left-handed” type to the “right-handed” is observed at different levels of hierarchical organization [ 9 , 10 , 11 , 12 ]. In the case of DNA, the sequence of the chirality sign is “right-handed deoxyribose carbohydrate”–“left-handed nucleotides”–“right-handed DNA double helix”–“left-handed superhelix” with the increasing complexity of their level of organization.…”

Section: Introductionmentioning

confidence: 99%

“…In the case of DNA, the sequence of the chirality sign is “right-handed deoxyribose carbohydrate”–“left-handed nucleotides”–“right-handed DNA double helix”–“left-handed superhelix” with the increasing complexity of their level of organization. This feature of chirality is one of the key points in the hierarchy and self-organization of any biological system [ 9 , 10 , 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

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Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations

et al. 2021

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The chirality quantification is of great importance in structural biology, where the differences in proteins twisting can provide essentially different physiological effects. However, this aspect of the chirality is still poorly studied for helix-like supramolecular structures. In this work, a method for chirality quantification based on the calculation of scalar triple products of dipole moments is suggested. As a model structure, self-assembled nanotubes of diphenylalanine (FF) made of L- and D-enantiomers were considered. The dipole moments of FF molecules were calculated using semi-empirical quantum-chemical method PM3 and the Amber force field method. The obtained results do not depend on the used simulation and calculation method, and show that the D-FF nanotubes are twisted tighter than L-FF. Moreover, the type of chirality of the helix-like nanotube is opposite to that of the initial individual molecule that is in line with the chirality alternation rule general for different levels of hierarchical organization of molecular systems. The proposed method can be applied to study other helix-like supramolecular structures.

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Section: Resultsmentioning

confidence: 71%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations

et al. 2021

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“…As a result of such self-assembly, they usually form helix-like or more complex self-organizing structures of different levels of their hierarchical organization [ 11 , 12 , 13 ]. At the same time, chirality plays an important role in the processes of self-assembly of biomacromolecules, both in their initial structures and in various complicated structures at subsequent levels of their hierarchical organization [ 14 , 15 , 16 , 17 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

“…It creates the L-D-L-D sequence for proteins. While for the DNA-based replication system, the sequence is different—D-L-D-L, “conjugated” to peptide and protein molecules [ 15 , 16 , 17 ]. The alternation of the sign of chirality upon transition to a higher hierarchical level turns out to be a necessary factor [ 15 , 16 , 17 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulation Study of the Self-Assembly of Phenylalanine Peptide Nanotubes

et al. 2022

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In this paper, we propose and use a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure using external force actions. A molecular dynamics manipulator (MD manipulator) is a controlled MDS type. As an example, the applicability of the developed algorithm for assembling peptide nanotubes (PNT) from linear phenylalanine (F or Phe) chains of different chirality is presented. The most adequate regimes for the formation of nanotubes of right chirality D from the initial L-F and nanotubes of left chirality L of their initial dipeptides D-F modes were determined. We use the method of a mixed (vector–scalar) product of the vectors of the sequence of dipole moments of phenylalanine molecules located along the nanotube helix to calculate the magnitude and sign of chirality of self-assembled helical phenylalanine nanotubes, which shows the validity of the proposed approach. As result, all data obtained correspond to the regularity of the chirality sign change of the molecular structures with a hierarchical complication of their organization.

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Introduction to the special issue on physics of mind

Schoeller

2019

Physics of Life Reviews

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On regularities in the spontaneous formation of structural hierarchies in chiral systems of nonliving and living matter

Cited by 18 publications

References 41 publications

Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations

Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations

Molecular Dynamics Simulation Study of the Self-Assembly of Phenylalanine Peptide Nanotubes

Introduction to the special issue on physics of mind

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