K. V. Shaitan

Mechanical properties of fibroblasts depend on level of cancer transformation.

Recently, it was revealed that tumor cells are significantly softer than normal cells. Although this phenomenon is well known, it is connected with many questions which are still unanswered. Among these questions are the molecular mechanisms which cause the change in stiffness and the correlation between cell mechanical properties and their metastatic potential. We studied mechanical properties of cells with different levels of cancer transformation. Transformed cells in three systems with different transformation types (monooncogenic N-RAS, viral and cells of tumor origin) were characterized according to their morphology, actin cytoskeleton and focal adhesion organization. Transformation led to reduction of cell spreading and thus decreasing the cell area, disorganization of actin cytoskeleton, lack of actin stress fibers and decline in the number and size of focal adhesions. These alterations manifested in a varying degree depending on type of transformation. Force spectroscopy by atomic force microscopy with spherical probes was carried out to measure the Youngs modulus of cells. In all cases the Youngs moduli were fitted well by log-normal distribution. All the transformed cell lines were found to be 40-80% softer than the corresponding normal ones. For the cell system with a low level of transformation the difference in stiffness was less pronounced than for the two other systems. This suggests that cell mechanical properties change upon transformation, and acquisition of invasive capabilities is accompanied by significant softening.

Cell attachment on poly(3-hydroxybutyrate)-poly (ethylene glycol) copolymer produced by Azotobacter chroococcum 7B

BackgroundThe improvement of biomedical properties, e.g. biocompatibility, of poly(3-hydroxyalkanoates) (PHAs) by copolymerization is a promising trend in bioengineering. We used strain Azotobacter chroococcum 7B, an effective producer of PHAs, for biosynthesis of not only poly(3-hydroxybutyrate) (PHB) and its main copolymer, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB-HV), but also alternative copolymer, poly(3-hydroxybutyrate)-poly(ethylene glycol) (PHB-PEG).ResultsIn biosynthesis we used sucrose as the primary carbon source and valeric acid or poly(ethylene glycol) 300 (PEG 300) as additional carbon sources. The chemical structure of PHB-PEG and PHB-HV was confirmed by 1H nuclear-magnetic resonance (1H NMR) analysis. The physico-chemical properties (molecular weight, crystallinity, hydrophilicity, surface energy) and surface morphology of films from PHB copolymers were studied. To study copolymers biocompatibility in vitro the protein adsorption and COS-1 fibroblasts growth on biopolymer films by XTT assay were analyzed. Both copolymers had changed physico-chemical properties compared to PHB homopolymer: PHB-HV and PHB-PEG had less crystallinity than PHB; PHB-HV was more hydrophobic than PHB in contrast to PHB-PEG appeared to have greater hydrophilicity than PHB; whereas the morphology of polymer films did not differ significantly. The protein adsorption to PHB-PEG was greater and more uniform than to PHB and PHB-PEG copolymer promoted better growth of COS-1 fibroblasts compared with PHB homopolymer.ConclusionsThus, despite low EG-monomers content in bacterial origin PHB-PEG copolymer, this polymer demonstrated significant improvement in biocompatibility in contrast to PHB and PHB-HV copolymers, which may be coupled with increased protein adsorption and hydrophilicity of PEG-containing copolymer.

Dynamic proteomics in modeling of the living cell. Protein-protein interactions

This review is devoted to describing, summarizing, and analyzing of dynamic proteomics data obtained over the last few years and concerning the role of protein-protein interactions in modeling of the living cell. Principles of modern high-throughput experimental methods for investigation of protein-protein interactions are described. Systems biology approaches based on integrative view on cellular processes are used to analyze organization of protein interaction networks. It is proposed that finding of some proteins in different protein complexes can be explained by their multi-modular and polyfunctional properties; the different protein modules can be located in the nodes of protein interaction networks. Mathematical and computational approaches to modeling of the living cell with emphasis on molecular dynamics simulation are provided. The role of the network analysis in fundamental medicine is also briefly reviewed.

The Terpolymer Produced by Azotobacter Chroococcum 7B: Effect of Surface Properties on Cell Attachment

The copolymerization of poly(3-hydroxybutyrate) (PHB) is a promising trend in bioengineering to improve biomedical properties, e.g. biocompatibility, of this biodegradable polymer. We used strain Azotobacter chroococcum 7B, an effective producer of PHB, for biosynthesis of not only homopolymer and its main copolymer, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB-HV), but also novel terpolymer, poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-poly(ethylene glycol) (PHB-HV-PEG), using sucrose as the primary carbon source and valeric acid and poly(ethylene glycol) 300 (PEG 300) as additional carbon sources. The chemical structure of PHB-HV-PEG was confirmed by 1H nuclear-magnetic resonance analysis. The physico-chemical properties (molecular weight, crystallinity, hydrophilicity, surface energy) of produced biopolymer, the protein adsorption to the terpolymer, and cell growth on biopolymer films were studied. Despite of low EG-monomers content in bacterial-origin PHB-HV-PEG polymer, the terpolymer demonstrated significant improvement in biocompatibility in vitro in contrast to PHB and PHB-HV polymers, which may be coupled with increased protein adsorption, hydrophilicity and surface roughness of PEG-containing copolymer.

The effects of confluency on cell mechanical properties

Mechanical properties of cells depend on various external and internal factors, like substrate stiffness and surface modifications, cell ageing and disease state. Some other currently unknown factors may exist. In this study we used force spectroscopy by AFM, confocal microscopy and flow cytometry to investigate the difference between single non-confluent and confluent (in monolayer) Vero cells. In all cases the stiffness values were fitted by log-normal rather than normal distribution. Log-normal distribution was also found for an amount of cortical actin in cells by flow cytometry. Cells in the monolayer were characterized by a significantly lower (1.4-1.7 times) Youngs modulus and amount of cortical actin than in either of the single non-confluent cells or cells migrating in the experimental wound. Youngs modulus as a function of indentation speed followed a weak power law for all the studied cell states, while the value of the exponent was higher for cells growing in monolayer. These results show that intercellular contacts and cell motile state significantly influence the cell mechanical properties.

Distinct impact of targeted actin cytoskeleton reorganization on mechanical properties of normal and malignant cells

The actin cytoskeleton is substantially modified in cancer cells because of changes in actin-binding protein abundance and functional activity. As a consequence, cancer cells have distinctive motility and mechanical properties, which are important for many processes, including invasion and metastasis. Here, we studied the effects of actin cytoskeleton alterations induced by specific nucleation inhibitors (SMIFH2, CK-666), cytochalasin D, Y-27632 and detachment from the surface by trypsinization on the mechanical properties of normal Vero and prostate cancer cell line DU145. The Youngs modulus of Vero cells was 1300±900 Pa, while the prostate cancer cell line DU145 exhibited significantly lower Youngs moduli (600±400 Pa). The Youngs moduli exhibited a log-normal distribution for both cell lines. Unlike normal cells, cancer cells demonstrated diverse viscoelastic behavior and different responses to actin cytoskeleton reorganization. They were more resistant to specific formin-dependent nucleation inhibition, and reinforced their cortical actin after detachment from the substrate. This article is part of a Special Issue entitled: Mechanobiology.

Voltage-gated ion channel modulation by lipids: Insights from molecular dynamics simulations

Cells commonly use lipids to modulate the function of ion channels. The lipid content influences the amplitude of the ionic current and changes the probability of voltage-gated ion channels being in the active or in the resting states. Experimental findings inferred from a variety of techniques and molecular dynamics studies have revealed a direct interaction between the lipid headgroups and the ion channel residues, suggesting an influence on the ion channel function. On the other hand the alteration of the lipids may in principle modify the overall electrostatic environment of the channel, and hence the transmembrane potential, leading to an indirect modulation, i.e. a global effect. Here we have investigated the structural and dynamical properties of the voltage-gated potassium channel Kv1.2 embedded in bilayers with modified upper or lower leaflet compositions corresponding to realistic biological scenarios: the first relates to the effects of sphingomyelinase, an enzyme that modifies the composition of lipids of the outer membrane leaflets, and the second to the effect of the presence of a small fraction of PIP2, a highly negatively charged lipid known to modulate voltage-gated channel function. Our molecular dynamics simulations do not enable to exclude the global effect mechanism in the former case. For the latter, however, it is shown that local interactions between the ion channel and the lipid headgroups are key-elements of the modulation.

Application of the Johnson-Kendall-Roberts model in AFM-based mechanical measurements on cells and gel.

The force-distance curves (FCs) obtained by the atomic force microscope (AFM) with colloid probes contain information about both the viscoelastic properties and adhesion of a sample. Here, we processed both the approach and retraction parts of FCs obtained on polyacrylamide gels (in water or PBS) and Vero cells (in a culture medium). The Johnson-Kendall-Roberts model was applied to the retraction curves to account for the adhesion. The effects of loading rate, holding time and indentation depth on adhesion force and Youngs modulus, calculated from approach and retraction curves, were studied. It was shown that both bulk and local interfacial viscoelasticity can affect the observed approach-retraction hysteresis and measured parameters. The addition of 1% bovine serum albumin (BSA) decreased adhesion of the probe to the PAA gel surface, so interfacial viscoelasticity effects were diminished. On the contrary, the adhesiveness of Vero cells increased after BSA addition, indicating the complex nature of the cell-probe interaction.

Computer-aided molecular design of nanocontainers for inclusion and targeted delivery of bioactive compounds

Nanotubes may serve as non-immunogenic containers of biocompounds and vehicles for selective delivery to the cell membrane. These two properties – selective inclusion and transportation – are interconnected and establish the main challenge in nanovehicle design. Molecular dynamics (MD) simulation of systems containing a carbon nanotube, water, a lipid bilayer, and a molecule to be delivered is a way to explore the problem. Absorptive properties of the nanotube were studied using the example of a pentadecapeptide and cholesterol. The uptake of these molecules turned out to be susceptible to details of the nanotube’s interfacial structure and functional groups of the molecules contacting the nanotube. Incorporation of the peptide was found to be a spontaneous process and considered as a model self-assembly of a nanodevice, further referred to as a nanosyringe. For the design of the nanosyringe the steered molecular dynamics (SMD) approach was used. Release of the peptide was performed by expulsing it through the lipid membrane. The conformational state of the peptide was studied in view of chemical stability of the substance under shock action. In principle, styling the nanotube (by adding functional groups or ligands) may achieve the selectivity of the nanotube’s landing area on the cellular membrane and implement it in drug delivery system construction.

Solvent Accessible Surface Area of Amino Acid Residues in Globular Proteins: Correlation of Apparent Transfer Free Energies with Experimental Hydrophobicity Scales

It is known that the distribution of amino acid residues in globular proteins between surface and interior is in certain correlation with various experimental scales based on partitioning of amino acids or their analogs between water and organic solvents. These scales are often used in various quantitative structure-activity relationship (QSAR) studies as well as for evaluation of stability of proteins. In this work we have analyzed the distribution of residues based on their solvent accessible surface area in more than 8000 protein structures. Using extensive statistical sampling, we have computed residue apparent free energies of transfer between protein interior and surface applying various criteria for classifying residues as exposed or buried. The correlation of these statistical energies with several experimental hydrophobicity scales is discussed. We propose three types of statistical apparent transfer free energy scales and show that each of these scales is in better correlation with one of the experimental hydrophobicity scales (water/vapor, water/cyclohexane, and water/octanol transfer scales). The data are interpreted through the application of theoretical considerations by Finkelstein et al. (Protein Struct. Funct. Genet. 1995, 23, 142) based on random energy model of heteropolymer globules. The deviation of apparent transfer free energies from experimental scales is discussed and analyzed. The variations of amino acid distribution in proteins with the size of protein structure is discussed and the final protein set is chosen to minimize these variations.