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

Abstract

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 techniques, such as the contrast variation, the neutron spin-echo, and the solution of direct and inverse problems of three-dimensional reconstruction of the structures of macromolecules from SAS spectra by means of molecular modeling. A special section is devoted to specific objects of research, such as supramolecular complexes, influenza virus nucleoprotein, and chromatin.

Cold and distant: structural features of the nucleoprotein complex of a cold-adapted influenza A virus strain

Two influenza A nucleoprotein variants (wild-type: G102R; and mutant: G102R and E292G) were studied with regard to macro-molecular interactions in oligomeric form (24-mers). The E292G mutation has been previously shown to provide cold adaptation. Molecular dynamics simulations of these complexes and trajectory analysis showed that the most significant difference between the obtained models was distance between nucleoprotein complex strands. The isolated complexes of two ribonucleoprotein variants were characterized by transmission electron microscopy and differential scanning fluorimetry (DSF). Presence of the E292G substitution was shown by DSF to affect nucleoprotein complex melting temperature. In the filament interface peptide model, it was shown that the peptide corresponding in primary structure to the wild-type NP (SGYDFEREGYS) is prone to temperature-dependent self-association, unlike the peptide corresponding to E292G substitution (SGYDFGREGYS). It was also shown that the SGYDFEREGYS peptide is capable of interacting with a monomeric nucleoprotein (wild type); this interaction's equilibrium dissociation constant is five orders of magnitude lower than for the SGYDFGREGYS peptide. Using small-angle neutron scattering (SANS), the supramolecular structures of isolated complexes of these proteins were studied at temperatures of 15, 32, and 37 °C. SANS data show that the structures of the studied complexes at elevated temperature differ from the rod-like particle model and react differently to temperature changes. The data suggest that the mechanism behind cold adaptation with E292G is associated with a weakening of the interaction between strands of the ribonucleoprotein complex and, as a result, the appearance of inter-chain interface flexibility necessary for complex function at low temperature.Communicated by Ramaswamy H. Sarma.

Induced-Charge Enhancement of the Diffusion Potential in Membranes with Polarizable Nanopores

When a charged membrane separates two salt solutions of different concentrations, a potential difference appears due to interfacial Donnan equilibrium and the diffusion junction. Here, we report a new mechanism for the generation of a membrane potential in polarizable conductive membranes via an induced surface charge. It results from an electric field generated by the diffusion of ions with different mobilities. For uncharged membranes, this effect strongly enhances the diffusion potential and makes it highly sensitive to the ion mobilities ratio, electrolyte concentration, and pore size. Theoretical predictions on the basis of the space-charge model extended to polarizable nanopores fully agree with experimental measurements in KCl and NaCl aqueous solutions.

[Current insights into chromatin structure organization]

This review summarizes current insights into organization of chromatin structure at different levels of DNA compaction. Analysis of available experimental data allowed concluding that only nucleosomal level of structural organization was sufficiently investigated, whereas structure of a 30-nm chromatin fiber remains an open issue. The data on the chromatin structure obtained at the level of the nucleus speak in favor of a biphasic fractal organization of chromatin.

[Genetic identification and study of the ability of lactobacilli isolated from the oral cavity of healthy individuals to form biofilms]

The highly antagonistic lactobacillus strains isolated from the oral cavity of human individuals were genetically passported as L. fermentum 39, L. rhamnosus 50, and L. rhamnosus 24, by applying the RAPD-PCR technique with two types of primers (M13, MSP). These lactobacillus strains showed high degrees of autoaggregation, surface hydrophobicity, coaggregation, and adhesion. These characteristics determine the obvious capacity of lactobacilli to form biofilms, which may be used to design new probiotic agents.

[Genetic identification of antagonistically active lactobacillus strains isolated from the oral cavity of healthy individuals]

Examination of dental deposits from 45 healthy individuals detected 3 lactobacillus strains showing a high antagonism toward test cultures. The api 50 CH "bio Merieux" test systems were employed to identify strains as Lactobacillus fermentum 39, Lactobacillus rhamnosus 24 and Lactobacillus paracasei 50. The results of analyzing the sequences of the 16S rRNA genes of the test strains confirmed this identification, except for the latter strain. The taxonomic status of the third strain L. rhamnosus 50 was determined by the bioinformative analysis of the nucleotide sequence of the 16S rRNA genes.

[Ability of human oral cavity indigenous lactobacilli to form biofilms]

AIM

To determine ability of lactobacilli strains indigenous for oral cavity of healthy persons to adhesion, autoaggregation, surface hydrophobicity, coaggregation and formation of biofilms.

MATERIALS AND METHODS

Twenty-three anatagonistically active isolates of lactobacilli, including 5 strains of Lactobacillus plantarum, 6--L. rhamnosus, 4--L. paracasei, and 8--L. fermentum, were studied. Characteristics of lactobacilli associated with adhesion, autoaggregation, surface hydrophobicity, coaggregation, and formation of biofilms were determined.

RESULTS

Bacteria were characterized by high and intermediate level of adhesion, autoaggregation, surface hydrophobicity, expressed ability to form biofilms and different coaggregation activity relative to test-strains Staphylococcus aureus, Escherichia coli, Candida albicans, Pseudomonas aeruginosa, and Bacillus subtilis.

CONCLUSION

Studied characteristics of lactobacilli could be used for development of new probiotics aimed at stabilization of oral cavity normoflora.

[Lateral mechanics of muscle fibres and its role in signaling]

Different aspects of the lateral mechanics of muscle fibres have been considered. The current data on the transverse stiffness of intact muscle cells, demenbranized muscle fibres, and isolated myofibrils under various conditions and at different stages of the differentiation of myofibers. The signaling role of cytoskeleton proteins and possible mechanisms of their involvement in the structural basis of transverse stiffness are dissussed.

[Oral cavity microbiocenose in healthy teenagers and patients with chronic gastritis and gastroduodenitis]

Microbial association distinctive features and colonization degree of different oral cavity biotope were established in healthy teenagers and patients with chronic gastritis and gastroduodenitis. There were studied mucous membrane surfaces of cheek, tongue, content of gingival crevice, oral fluid and dental plaque of 24 healthy persons of the age 12-17 years and 29 patients of the same age with gastritis and gastroduodenitis. On the mucous membranes of the ill teenagers there were found Porphiromonas type bacteria, 20% more Staphylococcus, 90% less Peptostreptococcus, 30% less Lactobacillus, 20% less Veillonella and Stomatococcus. In saliva anaerobic Peptostreptococcus and facultative anaerobic Streptococcus (7 lg COE/ml); Porphiromonas, Veillonella, Peptococcus and Staphylococcus (6 lg COE/ml); Neisseria (5 lg COE/ml); Stomatococcus, Enterobacteriaceae and Bacillus (4.6 lg COE/ml); Lactobacillus and Candida (4 lg COE/ml) predominated. In patients with chronic pathology in all tested biotopes there was found the increase of the whole microbiota spectra (representatives of opportunistic pathogenic microfiora were detected more often) as well as the bacteria number if compared with healthy teenagers.

[Spatial distribution of transverse stiffness of relaxed and activated rat soleus myofibers]

The transverse stiffness of isolated glycerinated and demembranized muscle fibers from soleus muscle of Wistar rat were measured in different functional states by atomic force microscopy. It was shown that transverse stiffness of relaxed fibers near the Z-disk projection is approximately twice as high as near the M-line. The transverse stiffness of demembranized fibers is much higher than that of glycerinated fibers for both the Z-disk and M-line. The activation of the fiber resulted in a significant increase in transverse stiffness. However, while the stiffness of activated glycerinated fibers near the Z-disk increased about twofold, demembranized fibers showed a more than fourfold increase in transverse stiffness compared to relaxed fibers. The stiffness of both glycerinated and demembranized fibers near the M-line increased approximately threefold.

[Oral cavity microbiocenosis in healthy adolescents and patients with chronic gastroduodenitis]

AIM

To determine characteristics of microbial associations and degree of oral cavity colonization by different biotopes in healthy adolescents and patients with chronic gastroduodenitis.

MATERIALS AND METHODS

Saliva, dental deposit, content of tooth-gingival cavity and material from buccal and lingual mucous surfaces of 24 healthy adolescents and 29 patients of the same age with gastroduodenitis were used for bacteriological analysis. Inoculation were made on the following growth media: yolk-salt agar, Endo, Saburo, MRS as well as on Columbia and Saedler blood agars.

RESULTS

It was shown that rate of isolation of peptostreptococci from oral cavity of patients was 90% lower compared with controls; rate of isolation of lactobacilli, Veillonella, and stomatococci was 30% lower, whereas hemolytic Porphyromonas, staphylococci and streptococci were isolated 20% more frequently. Concentration of peptostreptococci and streptococci was 7.0 lg CFU/ml, whereas concentration of Porphyromonas, Veillonella, peptococci and staphylococci was 6.0 lg CFU/ml, Neisseria--5.0 lg CFU/ml, stomatococci, bacilli and Candida fungi --4.5 lg CFU/ml. Decrease of concentration of lactobacilli to 4.0 lg CFU/ml was noted.

CONCLUSION

Compared with healthy group of children, widened spectrum of microorganisms in all studied biotopes of oral cavity was observed in patients with chronic gastroduodenitis; species belonging to pathogenic microflora were detected in patients more frequently and in more quantities.

[Transverse stiffness of muscular fibers. Methods of measuring and physiological foundations]

The article contains the data about transverse stiffness of both native and demembraned fibers of different muscles. Under consideration is atomic force microscopy as the most promising method of investigating the cell and molecular mechanic properties of living objects.

[Dynamic properties of recA protein filaments from E. coli and P. aeruginosa investigated by neutron spin-echo]

Bacterial RecA protein is the key enzyme in the processes of homologous recombination, post-replication repair and induction of SOS-repair functions. While a significant amount of data on the structure of RecA protein and its functional analogs has been obtained, there is little information about the molecular dynamics of this protein. In this work we present the results of neutron spin-echo measurements of the relaxation kinetics of filaments formed by RecA proteins from E. coli and P. aeruginosa. The results suggest that the protein filaments exhibit both diffusion and internal relaxation modes, which change during the formation of complexes of these proteins with ATP and single-stranded DNA.

Atomic Force Microscopy Study of Peptides Homologous to Beta-Domain of Alpha-Lactalbumins

Symmetrical peptide GYDTQAIVENNESTEYG (WT, Wild Type) identical to 35-51 aminoacid residues of human alpha-lactalbumin (HLA) and peptide GYDTQTVVNNNGHTDYG (ID, IDeal symmetry) homologous to beta-domain of mammalian alpha-lactalbumins can form amyloid-like fibrils in conditions required for fibrillogenesis of HLA. The latter peptide can also form fibrils in deionized water. Fibrils formed by these peptides can cause forming of HLA amyloid-like aggregates in physiological conditions. These results provide an evidence for presence of amyloidogenic determinant in beta-domain of alpha-lactalbumin. Thus, symmetry in the primary structure may play the role in fibrillogenesis of proteins.

[Comparative value of molecular forms of prostate-specific antigen in diagnosis of prostatic cancer]

The aim of the study was to compare diagnostic significance of free PSA (fPSA)/total PSA (tPSA) versus PSA complex with alpha1-antichymotrypsin (cPSA) in tPSA level within 4-10 ng/ml in differential diagnosis of prostatic cancer (PC). A complete urological examination (digital rectal test, transrectal ultrasound investigation, serum assay for fPSA and tPSA, multifocal transperineal prostatic biopsy) was made in 108 patients with tPSA blood level 4-10 ng/ ml. Prostatic adenoma (PA) was histologically verified in 61 of 108 patients, fPSA/tPSA was normal. In the other 39 of 108 patients fPSA/tPSA was under 15% while cPSA was in the range 3.8-9.6 ng/ml. A course of etiotropic therapy of chronic prostatic inflammation produced no significant changes in fPSA/tPSA and cPSA in 28 out of 39 patients. Histologically, these 28 patients had PC. In the rest 11 of 39 patients chronic prostatitis treatment fPSA/tPSA significantly rose to 18.2%, on the average. CPSA decreased to 2.4 ng/ml. These 11 patients were found histologically to have PA and signs of chronic inflammation. In 8 of 108 patients fPSA/tPSA was not indicative of PC being 18,2% on the average while cPSA indicated the presence of PC and was 4.2 ng.ml, on the average. PC was verified histologically in these 8 patients. Thus, cPSA in PC suspects is more informative than fPSA/tPSA in PC diagnosis. CPSA in the serum depends on prostatic inflammation making difficult differential diagnosis of PC in interpretation of tPSA, fPSA/tPSA and cPSA. Therefore, estimation of PSA variants and molecular forms in PC suspects and prostatic inflammation should be made after etiotropic therapy.

Fractal nature of chromatin organization in interphase chicken erythrocyte nuclei: DNA structure exhibits biphasic fractal properties

Arrangement of chromatin in intact chicken erythrocyte nuclei was investigated by small angle neutron scattering. The scattering spectra have revealed that on the scales between 15 nm and 1.5 microm the interior of the nucleus exhibited properties of a mass fractal. The fractal dimension of the protein component of cell nucleus held constant at approximately 2.5, while the DNA organization was biphasic, with the fractal dimension slightly higher than 2 on the scales smaller than 300 nm and approaching 3 on the larger scales.

Analytical model for determination of parameters of helical structures in solution by small angle scattering: comparison of RecA structures by SANS

The filament structures of the self-polymers of RecA proteins from Escherichia coli and Pseudomonas aeruginosa, their complexes with ATPgammaS, phage M13 single-stranded DNA (ssDNA) and the tertiary complexes RecA::ATPgammaS::ssDNA were compared by small angle neutron scattering. A model was developed that allowed for an analytical solution for small angle scattering on a long helical filament, making it possible to obtain the helical pitch and the mean diameter of the protein filament from the scattering curves. The results suggest that the structure of the filaments formed by these two RecA proteins, and particularly their complexes with ATPgammaS, is conservative.

[Diagnostic and prognostic value of quantitative monitoring of prostate specific antigen in blood serum and urine from patients with prostate cancer after radical prostatectomy]

AIM

To study values of prostate-specific antigen (PSA) in the blood serum and urine before and after massage of the prostatic bed in patients with prostatic cancer (PC) after radical prostatectomy.

MATERIAL AND METHODS

Changes in serum and urine PSA concentrations were followed up in 17 patients with PC (T2-3N0M0) 14 months (4-24 mon) after radical prostatectomy. Control examinations were made once a month. MRT or CT and osteoscintigraphy were made in suspected recurrence and/or metastases of PC.

RESULTS

There were no changes in PSA consentrations in the serum and urine before and after the massage of prostatic bed in 10 of 17 patients. In 3 patients PSA concentrations in blood and serum increased after the massage, in one of them blood levels of PSA after the massage went up 5 months after PSA increase in the urine. In 4 of 17 patients urine PSA levels increased after the massage, the blood levels remaining the same.

CONCLUSION

Follow-up measurements of blood and urinary levels in PC patients after radical prostatectomy before and following massage of the prostatic bed allow detection of prostatic PSA-positive cells which were not removed at surgery. We suggest that these cells may be the basis of recurrent disease.

[Prostate-specific membrane antigen and its role in diagnosis of prostate cancer]

This paper reviews recent achievements of the employment of prostate specific membrane antigen in the diagnostics of prostate cancer.

Swelling-activated amino acid efflux in the human neuroblastoma cell line CHP-100

1. The effects of hypoosmotic stress on cell volume and amino acid efflux were evaluated in the human neuroblastoma cell line CHP-100 with the Coulter Counter Multisizer and radiolabeled amino acid efflux, respectively. 2. CHP-100 cells swelled by approximately 35 +/- 5% (means +/- SE) when the osmolarity of the solution was decreased from 290 to 190 mOsm/kg H2O. The rapid swelling was followed by a biphasic regulatory volume decrease (RVD). 3. In cells loaded with 14C-taurine, hypoosmotic stress induced a 300 +/- 22% (n = 23, P < 0.05) increase in taurine efflux compared with controls. This efflux was inhibited by the chloride channel blockers 5-nitro-2-(3-phenylpropylamino)-benzoic acid (NPPB), 4,4'-diisothio-cyanostilbene-2,2'-disulfonic acid (DIDS), niflumic acid and by the volume-activated anion channel blocker tamoxifen. In addition, the swelling-activated taurine efflux was dependent upon extracellular calcium. 4. Similarly, in cells loaded with 14C-glycine, hypoosmotic stress significantly increased glycine efflux, which was also sensitive to NPPB. In contrast, efflux of 3H-glutamate was not significantly altered after hypoosmotic stress. 5. With the use of patch clamp recording techniques, Cl- channels were activated in cell attached patches after exposure to hypoosmotic solutions. 6. In nystatin perforated patches, permeability of the hypoosmotically activated anion channel was observed to be SCN- > I- > Br- > Cl- >> Glutamate. 7. It is concluded that in CHP-100 cells, anion channels are activated during hypoosmotic stress and these channels represent a pathway for efflux of amino acids.