Protein Helical Structures: Defining Handedness and Localization Features

Abstract

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.

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

“…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.…”

“…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.…”

Structural Elucidation of Rift Valley Fever Virus L Protein towards the Discovery of Its Potential Inhibitors

“…Structural components of L protein were analyzed by PDBsum [56]; results showed the presence of multiple structural components such as 18 Beta-hairpins, 84 helices, 1Psi-loops, 40 strands, 155 Beta-turns, 44 Gamma-turns, 1 Beta-alpha-beta-unit, and 111 helix-helix interactions. Since we detected the 84 helices and 111 helix-helix interactions, such a high number of helices content determines the high chirality of proteins and thus provides structural compactness [57]. The distribution of structural components suggested the potential stability of the newly designed model, which was cross-validated by MD-simulations in subsequent steps.…”

Methods for calculating the chirality of secondary and supersecondary protein structures

“…5). Более подробно этапы метода определения знака хиральности суперспиральных структур рассмотрены в работах [4,5]. Знак хиральности суперспиралей рассчитывается с помощью усреднения значения косинуса соответствующего угла для всех спиралей, образующих суперспираль:…”