Methods to Determine the Chirality Sign for Helical and Superhelical Protein Structures

Sidorova, A. E.; Lutsenko, Aleksey; Shpigun, Denis; Malyshko, E. V.; Твердислов, В. А.

doi:10.1134/s0006350921030180

Cited by 6 publications

(2 citation statements)

References 22 publications

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“…These data also fully comply with the regularity of the change in the chirality sign of molecular structures with the complication of their hierarchical level of organization [ 15 , 16 , 17 ]. Therefore, this method for calculating the magnitude and sign of chirality based on the mixed product of vectors method earlier proposed by Sidorova et al [ 74 , 75 ], using the values of the dipole moment vectors in the sequence of individual peptides and dipeptides (or amino acids) as vectors, is also quite adequate and can be successfully applied for assessment of the magnitude and sign of chirality of complex self-organizing helix-like nanostructures based on amino acids and various peptides/dipeptides.…”

Section: Discussionmentioning

confidence: 99%

“…Using these vectors of dipole moments, located in series along the line of the nanotube helix, we construct and calculate the value of their mixed (vector–scalar) product. Recently, in the works [ 74 , 75 ] such a method was proposed and developed for determining the chirality of protein structures by the mixed (vector–scalar) product of vectors. As noted in these works, to estimate the sign of chirality of protein structures, a sufficient condition is the mutual arrangement of α-carbon atoms—reference points in helices, turns and loops of protein molecules.…”

Section: Calculation Of the Chirality Of Phenylalanine Helical Nanotu...mentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: Calculation Of the Chirality Of Phenylalanine Helical Nanotu...mentioning

confidence: 99%

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

et al. 2022

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Chirality As a Symmetric Basis of Self-Organization of Biomacromolecules

et al. 2022

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Methods for calculating the chirality of secondary and supersecondary protein structures

Sidorova¹,

Lutsenko²,

Shpigun³

2022

Proceedings of the International Conference "Mathematical Biology and Bioinformatics"

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Рассмотрены авторские методы определения хиральности регулярных и нерегулярных вторичных структур белков, а также суперспиралейнадвторичных структур. Рассчитаны знак и величина хиральности регулярных вторичных структур -α-, 3 10 -и π-спиралей, нерегулярных вторичных структур -β-и α-поворотов, Ω-петель, а также надвторичных структур белковсуперспиралей. В качестве входных данных используется информация о взаимном расположении α-углеродов аминокислотных остатков цепи. Для расчетов использовались координаты атомов из файлов PDB. Методы реализованы посредством компьютерной программы на языке Python и опробованы на большом количестве белковых структур. Эти методы можно рассматривать как части общего подхода к универсальному определению хиральности на различных иерархических уровнях белков. Такой подход мог бы поспособствовать выявлению важных физических закономерностей в белках.

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Methods to Determine the Chirality Sign for Helical and Superhelical Protein Structures

Cited by 6 publications

References 22 publications

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

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

Chirality As a Symmetric Basis of Self-Organization of Biomacromolecules

Methods for calculating the chirality of secondary and supersecondary protein structures

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