Quantitative Criteria of Chirality in Hierarchical Protein Structures

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

doi:10.1134/s0006350919020167

Cited by 10 publications

(6 citation statements)

References 35 publications

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“…In contrast to α-helix proteins, supramolecular PNTs are comprised of individual FF molecules held by relatively weak hydrogen bonds [ 31 , 32 , 33 ]. Therefore, the chirality quantification method developed earlier for protein structures [ 21 , 22 , 23 , 24 ] cannot be directly applied for PNTs and requires some adaptations.…”

Section: Resultsmentioning

confidence: 99%

“…Despite the concept of chirality, in its qualitative sense, being widespread in natural sciences, its quantitative aspects (the magnitude and sign of chirality) are still poorly studied [ 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 ]. In structural biology, it is of great importance to obtain the quantitative estimates of the magnitude of chirality and the chirality sign to compare both molecular constructs with the same symmetry type and those with different types of the symmetry.…”

Section: Introductionmentioning

confidence: 99%

“…Recently, a new method for the chirality quantification based on the scalar triple product of three consecutive vectors connecting Cα carbon atoms of neighboring amino acid residues in the polypeptide helical or superhelical structures was proposed [ 21 , 22 , 23 , 24 ]. Despite this approach being successfully applied to a variety of proteins [ 24 ] taken from the Protein Data Bank [ 25 ], until now it has not been used for helix-like supramolecular structures such as peptide nanotubes.…”

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: 99%

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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“…Previously, we proposed a method for quantitative analysis of the chirality of protein helical structures, based on the construction of consecutive vectors between neighboring carbons in the chain and determination of their vector product [47]. The method is based on the mutual arrangement of α-carbons (C α ) atoms in the amino acid chain-the reference points in the model.…”

Section: Methods For Quantitative Analysis Of the Chirality Of Protein Helical Structuresmentioning

confidence: 99%

Protein Helical Structures: Defining Handedness and Localization Features

et al. 2021

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The quantitative evaluation of the chirality of macromolecule structures remains one of the exciting issues in biophysics. In this paper, we propose methods for quantitative analysis of the chirality of protein helical and superhelical structures. The analysis of the chirality sign of the protein helical structures (α-helices and -helices) is based on determining the mixed product of every three consecutive vectors between neighboring reference points—α-carbons atoms. The method for evaluating the chirality sign of coiled-coil structures is based on determining the direction and value of the angle between the coiled-coil axis and the α-helices axes. The chirality sign of the coiled coil is calculated by averaging the value of the cosine of the corresponding angle for all helices forming the superhelix. Chirality maps of helical and superhelical protein structures are presented. Furthermore, we propose an analysis of the distributions of helical and superhelical structures in polypeptide chains of several protein classes. The features common to all studied classes and typical for each protein class are revealed. The data obtained, in all likelihood, can reflect considerations about molecular machines as chiral formations.

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“…Together with colleagues, we develop a method for evaluating the chirality of structures based on cross products [83]. In contrast to the mentioned methods, the developed approach for estimating chiral structures is more general and allows us to more fully determine the secondary structure (its type and sign of chirality with information about the spatial structure).…”

Section: Cytoskeletonmentioning

confidence: 99%

Chiral Dualism as a Unifying Principle in Molecular Biophysics

et al. 2021

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The origin and potential role of chiral asymmetry remain one of the most exciting issues in biology. In this paper we review the chirality of biological macromolecules, starting at the level of single molecules and continuing to the level of supramolecular assemblies. We discuss the physical and chemical consequences of the presence of chirality and their role in the self-organization and formation of structural hierarchies in cells. Homochirality may serve as an essential factor that invokes mechanisms required to control the formation of discrete structural hierarchies in macromolecules and macromolecular assemblies. Symmetry is of fundamental importance not only for all molecular biology as a systemic factor of its organization but also for pharmacology, as well as a systemic factor of drug stereospecificity.

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Quantitative Criteria of Chirality in Hierarchical Protein Structures

Cited by 10 publications

References 35 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

Protein Helical Structures: Defining Handedness and Localization Features

Chiral Dualism as a Unifying Principle in Molecular Biophysics

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