A periodic system of chiral structures in molecular biology

Твердислов, В. А.; Malyshko, E. V.; Ilchenko, Serguei; Zhulyabina, O. A.; Yakovenko, L. V.

doi:10.1134/s0006350917030228

Cited by 32 publications

(27 citation statements)

References 37 publications

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“…Eventually the same principles can be applied even to artificial systems. A unifying biophysical basis of these phenomena was discussed earlier by the authors [19][20][21][22]. Here we propose that homochirality may serve as an essential factor that invokes the physical and chemical mechanisms required to control the formation of discrete structural hierarchies in macromolecules and macromolecular assemblies, even determining to a large extent their function, like in the case of macromolecular machines.…”

Section: Introductionmentioning

confidence: 58%

“…In other words, the hierarchies of structural levels of organization of proteins and nucleic acids in cells, normally described qualitatively, may instead be represented as a regular interconnected chiral system. Starting from the level of an asymmetric carbon atom in the amino acids of the primary structure of a protein and in DNA deoxyribose, we earlier noted that there is a tendency to switch the chirality sign at subsequent structural levels, resulting in sequences of the types L-D-L-D in proteins and D-L-D-L in DNA [19][20][21][22]. An interesting manifestation of this principle is found in helical structures.…”

Section: The Hierarchies Of Chiral Structures In Proteins and Nucleicmentioning

confidence: 99%

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Chiral Dualism as an Instrument of Hierarchical Structure Formation in Molecular Biology

Твердислов

Malyshko

2020

Symmetry

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The origin of chiral asymmetry in biology has attracted the attention of the research community throughout the years. In this paper we discuss the role of chirality and chirality sign alternation (L-D-L-D in proteins and D-L-D-L in DNA) in promoting self-organization in biology, starting at the level of single molecules and continuing to the level of supramolecular assemblies. In addition, we also discuss chiral assemblies in solutions of homochiral organic molecules. Sign-alternating chiral hierarchies created by proteins and nucleic acids are suggested to create the structural basis for the existence of selected mechanical degrees of freedom required for conformational dynamics in enzymes and macromolecular machines. Author Contributions: Conceptualization, V.A.T.; investigation, E.V.M.; writing-original draft preparation, V.A.T. and E.V.M. All authors have read and agreed to the published version of the manuscript.

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Section: Introductionmentioning

confidence: 58%

Section: The Hierarchies Of Chiral Structures In Proteins and Nucleicmentioning

confidence: 99%

Chiral Dualism as an Instrument of Hierarchical Structure Formation in Molecular Biology

Твердислов

Malyshko

2020

Symmetry

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“…It should be noted that the role of symmetry and asymmetry [21][22][23], which are manifested here, in particular in such an important property as chirality [2,24,25] of the original molecules, plays here a key role in the physical laws and processes at various levels of the organization of these structures [26][27][28][29][30][31]. Moreover, this is generally characteristic of the whole self-organization of matter and complex molecular systems [1,2,[21][22][23][24].…”

Section: Introductionmentioning

confidence: 99%

“…Modern advances in molecular biology and biophysics have already allowed a sufficiently detailed description of the structures and functions of almost all the major biomacromolecules at different levels of their hierarchy and structural organization [24][25][26][27][28][29][30][31]. A huge number of chiral molecules, such as amino acids, sugars, etc., exist in nature and play a crucial role in the living organisms [2].…”

Section: Introductionmentioning

confidence: 99%

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Chiral Peculiar Properties of Self-Organization of Diphenylalanine Peptide Nanotubes: Modeling Of Structure and Properties

Bystrov¹,

Zelenovskiy²,

Nuraeva³

et al. 2019

Math.Biol.Bioinf.

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The structure and properties of diphenylalanine peptide nanotubes based on phenylalanine were investigated by various molecular modeling methods. The main approaches were semi-empirical quantum-chemical methods (PM3 and AM1), and molecular mechanical ones. Both the model structures and the structures extracted from their experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by naturally-occurring self-assembly showed their important differences depending on D- and L-chirality. In both the cases, the effect of chirality on the results of self-assembly of diphenylalanine peptide nanotubes was established: peptide nanotubes based on the D-diphenylalanine (D-FF) has high condensation energy E0 in transverse direction and forms thicker and shorter peptide nanotubes bundles, than that based on L-diphenylalanine (L-FF). A topological difference was established: model peptide nanotubes were optimized into structures consisting of rings, while naturally self-assembled peptide nanotubes consisted of helical coils. The latter were different for the original L-FF and D-FF. They formed helix structures in which the chirality sign changes as the level of the macromolecule hierarchy raises. Total energy of the optimal distances between two units are deeper for L-FF (–1.014 eV) then for D-FF (–0.607 eV) for ring models, while for helix coil are approximately the same and have for L-FF (–6.18 eV) and for D-FF (–6.22 eV) by PM3 method; for molecular mechanical methods energy changes are of the order of 2–3 eV for both the cases. A topological transition between a ring and a helix coil of peptide nanotube structures is discussed: self-assembled natural helix structures are more stable and favourable, they have lower energy in optimal configuration as compared with ring models by a value of the order of 1 eV for molecular mechanical methods and 5 eV for PM3 method.

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Chirality and the Origins of Life

LESEIGNEUR,

MEIERHENRICH

2023

The First Steps of Life

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A periodic system of chiral structures in molecular biology

Cited by 32 publications

References 37 publications

Chiral Dualism as an Instrument of Hierarchical Structure Formation in Molecular Biology

Chiral Dualism as an Instrument of Hierarchical Structure Formation in Molecular Biology

Chiral Peculiar Properties of Self-Organization of Diphenylalanine Peptide Nanotubes: Modeling Of Structure and Properties

Chirality and the Origins of Life

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