Protein Folding as an Autowave Process of Self-Organization in Active Media

Sidorova, A. E.; Malyshko, E. V.; Kotov, A. R.; Левашова, Н. Т.; Ustinin, M.N.; Твердислов, В. А.

doi:10.3103/s1062873819010246

Cited by 3 publications

(2 citation statements)

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“…Therefore, the transition from rings structure to helix structure is the topological transition. Recently such types of topological transitions have been in the focus of attention [110][111][112][113]. To explore this topological transition more thoroughly it is necessary to calculate full PES and transition path between ring and helix, going through some energy barrier.…”

Section: Influence Of Topology and Topological Transitionmentioning

confidence: 99%

“…It is also important to take into account the configurational contribution and to estimate the change in the enthalpy and entropy during such transitions [31,50,[110][111][112]. The approaches developed in [112,114,115] on quantitative assessment of chirality in the hierarchies of protein structures and protein folding as an autowave process of self-organization in active media, on the development and study of patterns, concerning the spontaneous formation of LD-alternating hierarchies of chiral structures in biomacromolecules, initially non-equilibrium due to homochirality of primary structures, are also very important, interesting and promising for further investigations opening new insight of our knowledge of these living self-assembling processes. These areas are both fundamental and interdisciplinary, placed on the intersection of many sciences, and have numerous possibilities for a variety of practical applications.…”

Section: Influence Of Topology and Topological Transitionmentioning

confidence: 99%

See 1 more Smart Citation

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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Section: Influence Of Topology and Topological Transitionmentioning

confidence: 99%