Using Zernike moments for analysis of images

A method for analyzing AFM images of the cell nuclei of higher organisms by expanding these images by Zernike moments is proposed. This method allows for expanding the pilot image by Zernike moments whose spatial harmonics are Zernike polynomials. It is shown that the reverse procedure of image reconstruction using Zernike polynomials converges to the experimental image and the expansion amplitude is a quantitative spectral characteristic in comparing the morphological features of different images. It is shown that expansion amplitudes can be used as input vectors for cluster analysis of images by PCA.     

Erratum to:Neutron Scattering Techniques and Complementary Methods for Structural and Functional Studies of Biological Macromolecules and Large Macromolecular Complexes

Crystallography Reports - An Erratum to this paper has been published: https://doi.org/10.1134/S1063774521340034     

Modeling of conformational transitions of fibrillogenic peptide,homologous to beta-domain of human alpha-lactalbumin

The behavior of the peptide corresponding to beta domain of human alpha-lactalbumin (GYDTQAIVENNESTEYG, WT) has been simulated by the molecular dynamics method. It is shown that, within the model considered, the monomer of this peptide does not tend to form a stable secondary structure; however, simulation of the behavior of several peptide molecules revealed the occurrence of beta structures due to the formation of intermolecular hydrogen bonds. Since the aforementioned interactions involve the terminal portions of peptides, the influence of the tetrapeptide corresponding to the N-terminal portion of WT, TDYG (R), on the secondary structure has been analyzed. The model calculations show that the interaction of this peptide with WT monomer facilitates formation of beta-structures. It is suggested that peptide R may affect the quaternary structure of WT.     

Neutron Scattering Techniques and Complementary Methods for Structural and Functional Studies of Biological Macromolecules and Large Macromolecular Complexes

Crystallography Reports - The review describes the application of small-angle scattering (SAS) of neutrons and complementary methods to study the structures of biomacromolecules. Here we cover SAS...     

Comparative analysis of the nucleosome structure of cell nuclei by small-angle neutron scattering

The nucleosome structure in native nuclei of normal (chicken erythrocyte and rat leukocyte nuclei) and anomalously proliferating (the human cervical adenocarcinoma cell line HeLa and the Chinese hamster fibroblast cell line A238) cells has been investigated using small-angle neutron scattering. The experimental results obtained allow one to make the inference that the parameters of the nucleosome structure for the chicken erythrocyte and rat leukocyte nuclei (on average over the nucleus) are close to the universally accepted values and that the distance distribution function is bimodal. The bimodality of the distance distribution function reflects a narrow distribution of distances between nucleosomes (on average over the nucleus) at the fibril level of the chromatin organization. The histone core of the nucleosome structure in the nuclei of the HeLa and A238 cells (on average over the nucleus) is considerably less compact than that in the chicken erythrocyte and rat leukocyte nuclei, and the distance distribution function does not exhibit indications of the bimodality.     

Distance distribution functions of replication origins in HeLa and glioma human cells according to the data of confocal microscopy

The distribution of replication origins in the nuclei of different cells is studied by confocal microscopy. Based on the obtained images, three-dimensional maps of the positions of the origin centers is constructed and the distribution functions of the pair distances between them are calculated. It is established that the distance distribution function for HeLa and glioma human cells is linear at sizes up to 2 μm, which indicates that the size of the origin system is close to 2. The amplitude of the distance distribution function at small sizes has a power dependence on the nucleus size and is inversely proportional to the nucleus volume to the power of 0.9. Thus, the replication-origin distribution in a nucleus cannot be described by a model with a single Hausdorff dimension in the whole range of sizes.     

Method for calculating small-angle neutron scattering spectra using all-atom molecular dynamics trajectories

A method for calculating small-angle neutron scattering (SANS) spectra based on data obtained using the method of the all-atom molecular dynamics of biomacromolecular structures is considered. When interpreting the SANS data, this approach makes it possible to take into account the fact that the structure of biomacromolecules in a solution is not a static object. This method is implemented in the form of a module for the GROMACS software package and will be available in version 4.6 of this popular program package for simulating biomacromolecular-structure dynamics.     

Small-angle scattering study of <Emphasis Type="Italic">Aspergillus awamori</Emphasis> glycoprotein glucoamylase

Glucoamylase from fungus Aspergillus awamori is glycoside hydrolase that catalyzes the hydrolysis of α-1,4- and α-1,6-glucosidic bonds in glucose polymers and oligomers. This glycoprotein consists of a catalytic domain and a starch-binding domain connected by an O-glycosylated polypeptide chain. The conformation of the linker, the relative arrangement of the domains, and the structure of the full-length enzyme are unknown. The structure of the recombinant glucoamylase GA1 was studied by molecular modelling and small-angle neutron scattering (SANS) methods. The experimental SANS data provide evidence that glucoamylase exists as a monomer in solution and contains a glycoside component, which makes a substantial contribution to the scattering. The model of full-length glucoamylase, which was calculated without taking into account the effect of glycosylation, is consistent with the experimental data and has a radius of gyration of 33.4 ± 0.6 Å.     

Characterization of oligomerization of a peptide from the ebola virus glycoprotein by small-angle neutron scattering

Transmission electron microscopy (TEM) and small-angle neutron scattering (SANS) studies showed that model peptides QNALVCGLRQ (G33) and QNALVCGLRG (G31) corresponding to region 551–560 of the GP protein of the Sudan Ebola virus are prone to oligomerization in solution. Both peptides can form amyloid-like fibrills. The G33 peptide forms fibrils within one day of incubation, whereas the fibrillogenesis of the G31 peptide is observed only after incubation for several months. The possible role of the observed processes in the pathogenesis and the possibility of applying a combination of the TEM and SANS techniques to search for new compounds that are able to influence the protein oligomerization are discussed.     

On the structural features of influenza A nucleoprotein particles from small-angle X-ray scattering data

The structure of ribonucleic particles of influenza A virus of the A/California/07/09pdm strain is investigated by transmission electron microscopy and small-angle X-ray scattering. The small-angle X-ray scattering data obtained at room temperature correspond to previously reported data of ribonucleic particles of this virus. At higher temperatures, noticeable changes in the morphology of ribonucleic complexes are observed.