Association of protein-DNA recognition complexes: electrostatic and nonelectrostatic effects

In this study the electrostatic and nonelectrostatic contributions to the binding free energy of a number of different protein-DNA recognition complexes are investigated. To determine the electrostatic effects in the protein-DNA association the Poisson-Boltzmann approach was applied. Overall the salt-dependent electrostatic free energy opposed binding in all protein-DNA complexes except one, and the salt-independent electrostatic contribution favored binding in more than half of the complexes. Further the salt-dependent electrostatic free energy increased with higher ionic concentrations and therefore complex association is stronger opposed at higher ionic concentrations. The hydrophobic effect in the protein-DNA complexes was determined from the buried accessible surface area and the surface tension. A majority of the complexes showed more polar than nonpolar buried accessible surface area. Interestingly the buried DNA-accessible surface area was preferentially hydrophilic, only in one complex a slightly more hydrophobic buried accessible surface area was observed. A quite sophisticated balance between several different free energy components seems to be responsible for determining the free energy of binding in protein-DNA systems.     

Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions.

Recent single-macromolecule observations revealed that the force/extension characteristics of single-stranded DNA (ssDNA) are closely related to solution ionic concentration and DNA sequence composition. To understand this, we studied the elastic property of ssDNA through the Monte Carlo implementation of a modified freely jointed chain (FJC), with electrostatic, base-pairing, and base-pair stacking interactions all incorporated. The simulated force-extension profiles for both random and designed sequences have attained quantitative agreements with the experimental data. In low-salt solution, electrostatic interaction dominates, and at low forces, the molecule can be more easily aligned than an unmodified FJC. In high-salt solution, secondary hairpin structure appears in ssDNA by the formation of base pairs between complementary bases, and external stretching causes a hairpin-coil structural transition, which is continuous for ssDNA made of random sequences. In designed sequences such as poly(dA-dT) and poly(dG-dC), the stacking potential between base pairs encourages the aggregation of base pairs into bulk hairpins and makes the hairpin-coil transition a discontinuous (first-order) process. The sensitivity of elongation to the base-pairing rule is also investigated. The comparison of modeling calculations and the experimental data suggests that the base pairing of single-stranded polynucleotide molecules tends to form a nested and independent planar hairpin structure rather than a random intersecting pattern.     

Immobilization of fungal spores by adhesion

Immobilization of conidiospores of Phanerochaete chrysosporium by adhesion was investigated in static and flow conditions on flat and on porous supports. Reducing the electrostatic repulsion between the spores and the support by adsorption of polycations on the support allows a better adhesion efficiency and a higher density of adhering spores and does not affect germination and growth. Formation of spore aggregates either in the suspension (high ionic strength) or on the support tends to decrease the surface coverage and to give an inhomogeneous distribution of adhering spores due to detachment of aggregates. The density of spores adhering from a flowing suspension is lower as compared with static conditions and does not exceed about 2% of surface coverage; this is due to the influence of tangential forces, to the short contact time with the surface, and to perturbation of the hydrodynamics along the surface by the previously immobilized spores. Obtaining a high coverage of the support by immobilized spores requires the absence of a tangential motion. (c) 1995 John Wiley & Sons, Inc.     

Immobilization of microorganisms with PVA hardened by iterative freezing and thawing

In order to utilize polyvinyl alcohol (PVA) as a gel matrix for the immobilization of microorganisms, PVA was subjected to iterative freezing-thawing. The effects of the procedure on the mechanical characteristics of the PVA hydrogel and the stability of the immobilized microorganisms were investigated. PVA showed rubber-like elasticity after iterative freezing-thawing. Gel strength increased with the iteration number of freezing-thawing until seven iterations. Although the activities of both the free and immobilized cells decreased during the iteration of freezing-thawing, addition of cryoprotectants such as glycerol and skim milk was effective for preventing the decrease in activity.     

Growth of microorganisms in electrostatic fields

A significent and reproducible effect of alternating positive-negative and positive electric fields on the growth of E.COLI has been observed.Mean areas of E.COLI colonies, incubated in a specially designed electrostatic incubator, were up to 2.6 times larger than the mean areas of their controls. Negative electric fields were found to have no growth enhancing effect on the test organisms.

---

Zusammenfassung Es wurde eine signifikante und reproduzierbare Wirkung von wechselnd positiv-negativ und positiv elektrischen Feldern auf das Wachstum von E.COLI beobachtet.Die mittlere Grösse von in einem elektrostatischen WÄrmeschrank inkubierten E.COLI Kolonien war bis zu 2.6 mal grosser als die von Kontrollen.Negative elektrische leider hatten keine wachstumsverstÄrkende Wirkung auf die Bakterien.

---

Resume On a constaté un effet significatif et reproduisible des champs électriques alternatifs et constants positifs sur la croissance des bactéries E.COLI. La grandeur moyenne des colonies de E.COLI croissant dans un incubateur électrostatique était jusqu'à 2,6 fois plus grande que celle des contrÔles.Des champs électriques négatifs n'avaient pas d'effet stimulant sur la croissance des bactéries.

     

Binding of cationic pentapeptides with modified side chain lengths to negatively charged lipid membranes: Complex interplay of electrostatic and hydrophobic interactions

Basic amino acids play a key role in the binding of membrane associated proteins to negatively charged membranes. However, side chains of basic amino acids like lysine do not only provide a positive charge, but also a flexible hydrocarbon spacer that enables hydrophobic interactions. We studied the influence of hydrophobic contributions to the binding by varying the side chain length of pentapeptides with ammonium groups starting with lysine to lysine analogs with shorter side chains, namely ornithine (Orn), α,γ-diaminobutyric acid (Dab) and α, β-diaminopropionic acid (Dap). The binding to negatively charged phosphatidylglycerol (PG) membranes was investigated by calorimetry, FT-infrared spectroscopy (FT-IR) and monolayer techniques. The binding was influenced by counteracting and sometimes compensating contributions. The influence of the bound peptides on the lipid phase behavior depends on the length of the peptide side chains. Isothermal titration calorimetry (ITC) experiments showed exothermic and endothermic effects compensating to a different extent as a function of side chain length. The increase in lipid phase transition temperature was more significant for peptides with shorter side chains. FTIR-spectroscopy revealed changes in hydration of the lipid bilayer interface after peptide binding. Using monolayer techniques, the contributions of electrostatic and hydrophobic effects could clearly be observed. Peptides with short side chains induced a pronounced decrease in surface pressure of PG monolayers whereas peptides with additional hydrophobic interactions decreased the surface pressure much less or even lead to an increase, indicating insertion of the hydrophobic part of the side chain into the lipid monolayer.     

Immobilization of yeast cells by adhesion on tuff granules

Summary A method for immobilizing yeast cells (Saccharomyces cerevisiae) possessing invertase activity by direct adhesion on tuff granules coated with insolubilized gelatin is described. The immobilized cells, firmly fixed as a monolayer onto the surface of the support granules display catalytic properties (in terms of apparent K _m) close to free cells and are particularly suitable for continuous sucrose hydrolysis in a fixed-bed reactor. From an industrial point of view, the immobilization method described here has two advantages over other immobilization methods, i.e. the immobilized yeast cells have a fairly good operational stability and their proliferation on tuff granules can be controlled.     

Immobilization of Saccharomyces cerevisiae by adhesion: treatment of the cells by Al ions

The adsorption of aluminum ions by Saccharomyces cerevisiae has been investigated by determining adsorption isotherms and electrophoretic mobility. The adsorption of aluminum ensures a neutralization of the cell surface charge and allows adhesion of the cells to glass and polycarbonate. Glass slides have been taken as a negatively charged model support, allowing the authors to study in detail the process of adhesion. The cells are simply pretreated by an aluminum solution near pH 4. Bringing the Al-pretreated cells in contact with the support by sedimentation and washing the support and sediment makes it possible to obtain a single, dense, regular layer of cells adhering strongly to the support. Adhesion can also be obtained from a suspension flowing parallel to a vertical support, provided the flow velocity is sufficiently small; the amount of cells immobilized per unit support area is about one-half that obtained by sedimentation. The immobilized cells show a specific activity for ethanol production from glucose which is similar to cells in suspension.     

Epithelia migration: A spatiotemporal interplay between contraction and adhesion

Epithelial tissues represent 60% of the cells that form the human body and where more than 90% of all cancers derived. Epithelia transformation and migration involve altered cell contractile mechanics powered by an actomyosin-based cytoskeleton and influenced by cell-cell and cell-extracellular matrix interactions. A balance between contractile and adhesive forces regulates a large number of cellular and tissue properties crucial for epithelia migration and tumorigenesis. In this review, the forces driving normal epithelia transformation into highly motile and invasive cells and tissues will be discussed.     

Immobilization of yeast cells by entrapment and adhesion using siliceous materials

Yeast cells (Saccharomyces cerevisiae) have been immobilized by entrapment in silica hydrogel, without significantly changing their biological activity; a simple model describes the rate of oxygen uptake by a film of immobilized cells. The cells have also been immobilized by direct adhesion to a glass surface; this is achieved by a well-controlled drying procedure, sufficient to bring the cells into close contact with the support, but without cell dehydration. The immobilized cells consume glucose at a rate which is about half of the rate obtained in suspension and they are resistant to strong mechanical strains.     

Immobilization of cells by electrostatic droplet generation: a model system for potential application in medicine

The process of electrostatic extrusion as a method for cell immobilization was investigated that could be used for potential applications in medicine. An attempt was made to assess the effects of cell addition and polymer concentration on the overall entrapment procedure, ie, on each stage of immobilization: polymer-cell suspension rheological characteristics, electrostatic extrusion process, and the process ofgelation. The findings should contribute to a better understanding of polymer-cell interactions, which could be crucial in possible medical treatments. Alginate-yeast was used as a model system for carrier-cells. The electrostatic extrusion was considered as a complex two-phase flow system and the effects of cell and alginate concentrations on the resulting microbead size and uniformity were assessed. Under investigated conditions, microbeads 50-600 microm in diameter were produced and the increase in both alginate and cell concentrations resulted in larger microbeads with higher standard deviations in size. We attempted to rationalize the findings by rheological characterization of the cell-alginate suspensions. Rheological characterization revealed non-Newtonian, pseudoplastic behavior of cell-alginate suspensions with higher viscosities at higher alginate concentrations. However, the presence of cells even at high concentrations (5x10(8) and 1x10(9) cells/mL) did not significantly affect the rheological properties of Na-alginate solution. Lastly, we investigated the kinetics of alginate gelation with respect to the quantity of Ca2+ ions and cell presence. The gelation kinetics were examined under conditions of limited supply with Ca2+ ions, which can be essential for immobilization of highly sensitive mammalian cells that require minimal exposure to CaCl2 solution. The molar ratio of G units to Ca2+ ions of 3.8:1 provided complete crosslinking, while the increase in alginate concentration resulted in prolonged gelation times but higher strength of the resulting gel. The cell presence decreased the rate of network formation as well as the strength of the obtained Ca-alginate hydrogel.     

Mutual interplay between phytopathogenic powdery mildew fungi and other microorganisms

Powdery mildew is a common and widespread plant disease of considerable agronomic relevance. It is caused by obligate biotrophic fungal pathogens which, in most cases, epiphytically colonize aboveground plant tissues. The disease has been typically studied as a binary interaction of the fungal pathogen with its plant hosts, neglecting, for the most part, the mutual interplay with the wealth of other microorganisms residing in the phyllo- and/or rhizosphere and roots. However, the establishment of powdery mildew disease can be impacted by the presence/absence of host-associated microbiota (epi- and endophytes) and, conversely, plant colonization by powdery mildew fungi might disturb indigenous microbial community structures. In addition, other (foliar) phytopathogens could interact with powdery mildews, and mycoparasites may affect the outcome of plant–powdery mildew interactions. In this review, we discuss the current knowledge regarding the intricate and multifaceted interplay of powdery mildew fungi, host plants and other microorganisms, and outline current gaps in our knowledge, thereby setting the basis for potential future research directions.     

Immobilization of yeast cells by adhesion to glass surface using polyethylenimine

Summary A method has been described for immobilization of yeast cells by adsorption to glass surface using polyethylenimine for coating cells or glass or both. The immobilized yeast cells were found to be viable and adhered strongly as a monolayer, which could not be desorbed by washing with running tap water or under extreme conditions of pH and ionic strength or during repeated uses in sucrose solutions.     

Dynamic interplay between adhesion surfaces in carcinomas:Cell-cell and cell-matrix crosstalk

Cell-cell and cell-matrix signaling and communication between adhesion sites involve mechanisms which are required for cellular functions during normal development and homeostasis; however these cellular functions and mechanisms are often deregulated in cancer. Aberrant signaling at cell-cell and cell-matrix adhesion sites often involves downstream mediators including Rho GTPases and tyrosine kinases. This review discusses these molecules as putative mediators of cellular crosstalk between cell-cell and cell-matrix adhesion sites, in addition to their attractiveness as therapeutic targets in cancer. Interestingly, inter-junctional crosstalk mechanisms are frequently typified by the way in which bacterial and viral pathogens opportunistically infect or intoxicate mammalian cells. This review therefore also discusses the concept of learning from pathogen-host interaction studies to better understand coordinated communication between cell-cell and cell-matrix adhesion sites, in addition to highlighting the potential therapeutic usefulness of exploiting pathogens or their products to tap into inter-junctional crosstalk. Taken together, we feel that increased knowledge around mechanisms of cell-cell and cell-matrix adhesion site crosstalk and consequently a greater understanding of their therapeutic targeting offers a unique opportunity to contribute to the emerging molecular revolution in cancer biology.     

Immobilization of microorganisms on latex for producing artificial flocs

Microorganisms belonging to the genera Pseudomonas, Micrococcus, Bacillus and Rhodotorula are flocculated with divinyl styrene latex. The process of flocculation depends on a number of physico-chemical factors but, all in all, is universal for microorganisms with different taxonomy, morphology and physiology. The structure of artificial bioflocs has been studied using optical and scanning electron microscopy.     

Thermal aggregation of alpha-chymotrypsin: role of hydrophobic and electrostatic interactions

We have recently reported that electrostatic interactions may play a critical role in alcohol-induced aggregation of alpha-chymotrypsin (CT). In the present study, we have investigated the heat-induced aggregation of this protein. Thermal aggregation of CT obeyed a characteristic pattern, with a clear lag phase followed by a sharp rise in turbidity. Intrinsic and ANS fluorescence studies, together with fluorescence quenching by acrylamide, suggested that the hydrophobic patches are more exposed in the denatured conformation. Typical chaperone-like proteins, including alpha- and beta-caseins and alpha-crystalline could inhibit thermal aggregation of CT, and their inhibitory effect was nearly pH-independent (within the pH range of 7-9). This was partially counteracted by alpha-, beta- and especially gamma-cyclodextrins, suggesting that hydrophobic interactions may play a major role. Loss of thermal aggregation at extreme acidic and basic conditions, combined with changes in net charge/pH profile of aggregation upon chemical modification of lysine residues are taken to support concomitant involvement of electrostatic interactions.     

The optimization of protein-solvent interactions: thermostability and the role of hydrophobic and electrostatic interactions.

Protein-solvent interactions were analyzed using an optimization parameter based on the ratio of the solvent-accessible area in the native and the unfolded protein structure. The calculations were performed for a set of 183 nonhomologous proteins with known three-dimensional structure available in the Protein Data Bank. The dependence of the total solvent-accessible surface area on the protein molecular mass was analyzed. It was shown that there is no difference between the monomeric and oligomeric proteins with respect to the solvent-accessible area. The results also suggested that for proteins with molecular mass above some critical mass, which is about 28 kDa, a formation of domain structure or subunit aggregation into oligomers is preferred rather than a further enlargement of a single domain structure. An analysis of the optimization of both protein-solvent and charge-charge interactions was performed for 14 proteins from thermophilic organisms. The comparison of the optimization parameters calculated for proteins from thermophiles and mesophiles showed that the former are generally characterized by a high degree of optimization of the hydrophobic interactions or, in cases where the optimization of the hydrophobic interactions is not sufficiently high, by highly optimized charge-charge interactions.     

Control of redox properties of cytochrome c by special electrostatic interactions

An assessment is made of the proposal: electrostatic interactions between the ferric ion of oxidised cytochrome c and its haem propionate sidechains assists in determining the value of the redox potential and plays an important role in the redox state conformation change. Differences between the properties of homologous cytochromes are proposed to be due to differences associated with the charge on their haem propionates.