Spatial sign-alternating charge clusters in globular proteins

Large sign-alternating charge clusters formed by the charged side groups of amino acid residues and N- and C-terminal groups were found in the majority of considered globular proteins, namely 235 in a total of 274 protein structures, i.e. 85.8%. The clusters were determined by the criteria proposed earlier: charged groups were included in the cluster if their charged N and O atoms were located at distances between 2.4 and 7.0 A. The set of selected proteins consisted of known non-homologous protein structures from the Protein Data Bank with a resolution less than or equal to 2.5 A and pair sequence similarity less than 25%. Molecular masses of the proteins were from 5.5 to 91.5 kDa and protein chain length from 50 to 830 residues. The distribution of charged groups on the protein surface between isolated charged groups, small clusters with two and three groups, and large clusters with four or more groups were found to be approximately similar making 33, 35 and 32% of the total amount of protein charged groups, respectively. The large sign-alternating charge clusters with four or more charged groups were studied in greater detail. The amount of such clusters depends on the protein chain length. The small proteins contain 1-3 clusters while the large proteins display 4-6 or more clusters. On average, 1.5 clusters per each 100 residues were observed. In contrast with this, the size of a cluster, i.e. the number of charged groups inside a cluster, does not depend on the protein molecular mass, and large clusters are observed for proteins from a range of molecular masses. Clusters consisting of four to six charged groups occur most frequently, although extra large clusters are also often revealed. We can conclude that sign-alternating charge clusters are a common feature of the protein surface of globular protein. They are suggested to play a general functional role as a local polar factor of protein surface.     

Relevance of charged groups for the integrity of the S-layer from Bacillus coagulans E38-66 and for molecular interactions.

In this paper, the importance of charged amino and carboxyl groups for the integrity of the cell surface layer (S-layer) lattice from Bacillus coagulans E38-66 and for the self-assembly of the isolated subunits was investigated. Amidination of the free amino groups which preserved their positive net charge had no influence on both. On the other hand, acetylation and succinylation, which converted the amino groups into either neutral or negatively charged groups, and amidation of carboxyl groups were accompanied by the disintegration or at least by the loss of the regular structure of the S-layer lattice. Treatment of S-layer monolayers with the zero-length cross-linker carbodiimide led to the introduction of peptide bonds between activated carboxyl groups and amino groups from adjacent subunits. This clearly indicated that in the native S-layer lattice the charged groups are located closely enough for direct electrostatic interactions. Under disrupting conditions in which the S-layer polypeptide chains were unfolded, 58% of the Asx and Glx residues could be amidated, indicating that they occur in the free carboxylic acid form. As derived from chemical modification of monolayer self-assembly products, about 90% of the lysine and 70% of the aspartic and glutamic acid residues are aligned on the surface of the S-layer protein domains. This corresponded to 45 amino groups and to 63 carboxyl groups per S-layer subunit. Labelling experiments with macromolecules with different sizes and charges and adsorption studies with ion-exchange particles revealed a surplus of free carboxyl groups on the inner and on the outer faces of the S-layer lattice. Since the carboxyl groups on the outer S-layer face were accessible only for protein molecules significantly smaller then the S-layer protomers or for positively charged, thin polymer chains extending from the surface of ion-exchange beads, the negatively charged sites must be located within indentations of the corrugated S-layer protein network. This was in contrast to the carboxyl groups on the inner S-layer face, which were found to be exposed on elevations of the S-layer protein domains (D. Pum, M. Sára, and U.B. Sleytr, J. Bacteriol. 171:5296-5303, 1989).     

Influence of surface charge on the incorporation and orientation of cytochrome c oxidase in liposomes

Cytochrome c-oxidase is usually oriented 80-90% right-side-out when reconstituted with asolectin by the cholate dialysis method. Transformation of positively charged lysine groups at the matrix domain into negatively charged groups with succinic anhydride results in random orientation. A random orientation is also found after reconstitution in phosphatidylcholine, which can be changed into predominant right-side-out orientation by addition of cardiolipin. It is concluded that electrostatic interaction between positively charged groups of cytochrome c-oxidase with negative groups of phospholipids determines the asymmetric orientation of the enzyme in liposomes.     

A review of adsorption of amino acids on minerals: Was it important for origin of life?

Minerals more readily adsorb amino acids with charged R groups than uncharged R groups, so that the incorporation of amino acids with charged R groups into peptides would be more frequent than for amino acids with uncharged R groups. However, 74% of the amino acids in the proteins of modern organisms contain uncharged R groups. Thus, what could have been the mechanisms that produced peptides/proteins with more amino acids with uncharged R groups than precursors with charged R groups? Should we expect the composition of amino acids adsorbed on minerals to be similar to those of present proteins? Was the adsorption of amino acids on minerals important for the origin of life? The lipid world offers an alternative view of origin of life. Liposomes contributed to elongation of peptides as well as select hydrophobic amino acids and peptides. These experiments could be showing the mechanism, which hydrophobic amino acids have been selected. However, liposomes have no influence on the stereoselectivity in the oligomerization of amino acids. In the present paper, several other mechanisms are also discussed that could produce peptides with a greater proportion of amino acids with uncharged R groups.     

Synthesis and preliminary characterisation of charged derivatives and hydrogels from scleroglucan

The synthesis of negatively and positively charged polyelectrolytes from scleroglucan is described. Polycarboxylates were synthesised through nucleophilic substitution with chloroacetic acid or through a selective 2,2,6,6-tetramethyl-l-piperidinyloxy (TEMPO)-mediated oxidation of the primary alcohol groups. Amine groups were introduced through nucleophilic substitution with 2-chloroethylamine or 3-chloropropylamine. Reaction conditions were varied to obtain insight into the influence of variables on the degree of substitution. The conformational behaviour of the obtained polyelectrolytes was studied as a function of pH, temperature and solvent. For the products with a low degree of modification, evidence of an ordered conformation was found, whereas the polymers with a higher degree of modification behaved as random coils in solution. The negatively charged polymers were reticulated using the Ugi four-component condensation, obtaining negatively charged hydrogels. The positively charged polymers were reticulated using diethyl squarate (3,4-diethoxy-3-cyclobutene-1,2-dion, DES) to obtain positively charged hydrogels.     

Anion binding to nucleic acids

Nucleic acids are generally considered as efficient cation binders. Therefore, the likelihood that negatively charged ions might intrude their first hydration shell is rarely considered. Here, we show on the basis of (i) a survey of the Nucleic Acid Database, (ii) several structures extracted from the Cambridge Structural Database, and (iii) molecular dynamics simulations, that the nucleotide electropositive edges involving mainly amino, imino, and hydroxyl groups can cast specific anion binding sites. These binding sites constitute also good locations for the binding of the negatively charged groups of the Asp and Glu residues or the nucleic acid phosphate groups. Furthermore, it is observed in several instances that anions, like water molecules and cations, do mediate protein/nucleic acid interactions. Thus, anions as well as negatively charged groups are directly involved in specific recognition and folding phenomena involving polyanionic nucleic acids.     

Concentration of plant proteases by precipitation with polyacrylic acids

Sulphydryl plant proteases can be precipitated from dilute solutions by the addition of polyacrylic acid at low pH, provided an appropriate ratio of protein to polyacrylic acid is used. An interaction between negatively charged groups on polyacrylic acid and positively charged groups on protein molecules to form a large insoluble aggregate is proposed. Protease activity can be substantially recovered by resuspending the precipitate at pH 7.0 and polyacrylic acid removed by the addition of calcium chloride. This method is suitable for convenient large-scale preparation of these enzymes.     

Permeability properties of chemically modified porin trimers from Escherichia coli B

The pore-forming protein of the outer membrane of Escherichia coli, porin, was chemically modified with acetic anhydride, succinic anhydride, and glycinamide. Extensive modification of amino groups of the functional porin trimers caused reduced diffusion rates of the negatively charged solutes such as p-nitrophenyl phosphate and AMP, but did not reduce significantly the diffusion of positively charged molecules carbobenzoxy-glycyl-prolyl-arginine-p-nitranilide and tosyl-glycyl-prolyl-arginine-p-nitranilide. Modification of carboxyl groups of trimers caused decreased diffusion rates of the positively charged solutes more significantly than the diffusion rates of negatively charged solutes. The results suggest that the ionic interactions play an important role for the diffusion of charged solutes through the porin pore. The diffusion of p-nitrophenyl alpha-D-glucoside, an uncharged solute, ws not influenced significantly by modification of either amino or carboxyl groups. This observation suggests that modifications only occurred in areas outside of the narrowest portion of the pore or, alternatively, that amino and carboxyl groups are exclusively located at noncylindrical area of the pore. The structural integrity of the acetylated and the succinylated trimers seemed well preserved. On the other hand, modification of carboxyl groups decreased the thermal stability of trimers and extensive modifications caused the dissociation of trimers into monomers at 37 degrees C.     

Relating the Surface Properties of Superparamagnetic Iron Oxide Nanoparticles (SPIONs) to Their Bactericidal Effect towards a Biofilm of Streptococcus mutans

This study was designed to determine the effects of superparamagnetic iron oxide nanoparticles (SPIONs) on the biological activity of a bacterial biofilm (Streptococcus mutans). Our hypothesis was that the diffusion of the SPIONs into biofilms would depend on their surface properties, which in turn would largely be determined by their surface functionality. Bare, positively charged and negatively charged SPIONs, with hydrodynamic diameters of 14.6 ± 1.4 nm, 20.4 ± 1.3 nm and 21.2 ± 1.6 nm were evaluated. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) and electrophoretic mobility (EPM) measurements were used to confirm that carboxylic functional groups predominated on the negatively charged SPIONS, whereas amine functional groups predominated on the positively charged particles. Transmission electron microscopy (TEM) showed the morphology and sizes of SPIONs. Scanning electron microscopy (SEM) and EPM measurements indicated that the surfaces of the SPIONs were covered with biomolecules following their incubation with the biofilm. Bare SPIONs killed bacteria less than the positively charged SPIONs at the highest exposure concentrations, but the toxicity of the bare and positively charged SPIONs was the same for lower SPION concentrations. The positively charged SPIONs were more effective in killing bacteria than the negatively charged ones. Nonetheless, electrophoretic mobilities of all three SPIONs (negative, bare and positively charged) became more negative following incubation with the (negatively-charged) biofilm. Therefore, while the surface charge of SPIONS was important in determining their biological activity, the initial surface charge was not constant in the presence of the biofilm, leading eventually to SPIONS with fairly similar surface charges in situ. The study nonetheless suggests that the surface characteristics of the SPIONS is an important parameter controlling the efficiency of antimicrobial agents. The analysis of the CFU/mL values shows that the SPIONs have the same toxicity on bacteria in solution in comparison with that on the biofilm.     

Anti-HIV activity of a series of cosalane amino acid conjugates

The binding of the anti-HIV agent cosalane to CD4 is thought to involve ionic interactions of negatively charged carboxylates of the ligand with positively charged residues on the surface of the protein. The purpose of the present study was to examine the hypothesis that the two carboxyl groups of cosalane could be sacrificed through conjugation to amino acids, and the anti-HIV activity still be retained, provided that at least two new carboxyl groups are contributed by the amino acid residues.     

Studies on cell adhesion in tissue culture : XV. Some effects of cycloheximide on cell detachment

Attempts were made to identify positively charged groups at the surfaces of Ehrlich ascites tumour (EAT) cells, and particles of polystyrene polymer which had adsorbed proteins after incubation in serum-containing culture medium. The cells and particles were treated with 2,4,6-trinitrobenzene sulphonic acid (TNBS) or 2,3-dimethylmaleic anhydride (DMA), which react with amino and other cationic groups. The increases in cell and particle anodic electrophoretic mobility were consistent with approx. 5% of the total surface charge of each, being due to positively charged groups. The effects of DMA or TNBS treatment of the cells and/or polystyrene surfaces, on the rates of cell adhesion to these surfaces were then determined. The significantly slower rates of adhesion after some modes of treatment suggest that positively charged groups at the surfaces of EAT cells play a part in their initial contact with and adhesion to, protein-coated plastic surfaces. However, quantitatively the role of cationic groups is a minor one in this part of the adhesion process.     

Phenothiazine derivatives as enhancers of peroxidase-dependent chemiluminescence

Some N-alkyl phenothiazines with different ionic groups were studied as enhancers of chemiluminescence catalyzed by soybean peroxidase. It was shown that under experimental conditions, the compounds with positively charged groups do not exhibit enhancing ability, while the addition of phenothiazines with negatively charged groups to a substrate mixture significantly increased the chemiluminescence intensity. The relationship between the enhancing activity of phenothiazines and their capacity for enzymatic oxidation by hydrogen peroxide was found. The enhancers discovered new opportunities for increasing the sensitivity of determination of analytes by chemiluminescent enzyme immunoassay.     

Positively charged amino acids are essential for electron transfer and protein-protein interactions in the soluble methane monooxygenase complex from Methylococcus capsulatus (Bath)

The soluble methane monooxygenase (sMMO) complex from Methylococcus capsulatus (Bath) catalyses oxygen- and NAD(P)H-dependent oxygenation of methane, propene, and other substrates. Whole-complex sMMO oxygenase activity requires all three sMMO components: the hydroxylase, the reductase, and protein B. Also, in the presence of hydrogen peroxide, the hydroxylase alone catalyzes substrate oxygenation via the peroxide shunt reaction. We investigated the effect of amine cross-linking on hydroxylase activity to probe the role of a gross conformational change that occurs in the hydroxylase upon binding of the other protein components. The cross-linker inhibited hydroxylase activity in the whole complex, but this effect was due to covalent modification of primary amine groups rather than cross-linking. Covalent modification of arginine side-chains on the hydroxylase had a similar effect, but, most remarkably, neither form of modification affected the activity of the hydroxylase via the peroxide shunt reaction. It was shown that covalent modification of positively charged groups on the hydroxylase, which occurred at multiple sites, interfered with its physical and functional interactions with protein B and with the passage of electrons from the reductase. These results indicate that protein B and the reductase of the sMMO complex interact via positively charged groups on the surface of the hydroxylase to induce a conformational change that is necessary for delivery of electrons into the active site of the hydroxylase. Modification of positively charged groups on protein B had no effect on its function, consistent with the hypothesis that positively charged groups on the hydroxylase interact with negative charges on protein B. Thus, we have discovered a means of specifically inactivating the interactions between the sMMO complex while preserving the catalytic activity of the hydroxylase active site which provides a new method of studying intercomponent interactions within sMMO.     

Surface charge distribution on the endothelial cell of liver sinusoids

The topography of the charged residues on the endothelial cell surface of liver sinusoid capillaries was investigated by using electron microscopic tracers of different size and charge. The tracers used were native ferritin (pl 4.2-4.7) and its cationized (pl 8.4) and anionized (pl 3.7) derivatives, BSA coupled to colloidal gold (pl of the complex 5.1), hemeundecapeptide (pl 4.85), and alcian blue (pl greater than 10). The tracers were either injected in vivo or perfused in situ through the portal vein of the mouse liver. In some experiments, two tracers of opposite charge were sequentially perfused with extensive washing in between. The liver was processed for electron microscopy and the binding pattern of the injected markers was recorded. The electrostatic nature of the tracer binding was assessed by perfusion with high ionic strength solutions, by aldehyde quenching of the plasma membrane basic residues, and by substituting the cell surface acidic moieties with positively charged groups. Results indicate that the endothelial cells of the liver sinusoids expose on their surface both cationic and anionic residues. The density distribution of these charged groups on the cell surface is different. While the negative charge is randomly and patchily scattered all over the membrane, the cationic residues seem to be accumulated in coated pits. The charged groups co-exist in the same coated pit and bind the opposite charged macromolecule. It appears that the fixed positive and negative charges of the coated pit glycocalyx are mainly segregated in space. The layer of basic residues is located at 20-30-nm distance of the membrane, while most of the negative charges lie close to the external leaflet of the plasmalemma.     

Theoretical study of the distal-side steric and electrostatic effects on the vibrational characteristics of the FeCO unit of the carbonylheme proteins and their models.

The vibronic theory of activation and quantum chemical intermediate neglect of differential overlap (INDO) calculations are used to study the activation of carbon monoxide (change of the C-O bond index and force field constant) by the imidazole complex with heme in dependence on the distortion of the porphyrin ring, geometry of the CO coordination, iron-carbon and iron-imidazole distances, iron displacement out of the porphyrin plane, and presence of the charged groups in the heme environment. It is shown that the main contribution to the CO activation stems from the change in the sigma donation from the 5 sigma CO orbital to iron, and back-bonding from the iron to the 2 pi orbital of CO. It follows from the results that none of the studied distortions can explain, by itself, the wide variation of the C-O vibrational frequency in the experimentally studied model compounds and heme proteins. To study the dependence of the properties of the FeCO unit on the presence of charged groups in the heme environment, the latter are simulated by the homogeneous electric field and point charges of different magnitude and location. The results show that charged groups can strongly affect the strength of the C-O bond and its vibrational frequency. It is found that the charges located on the distal side of the heme plane can affect the Fe-C and C-O bond indexes (and, consequently, the Fe-C and C-O vibrational frequencies), both in the same and in opposite directions, depending on their position. The theoretical results allow us to understand the peculiarities of the effect of charged groups on the properties of the FeCO unit both in heme proteins and in their model compounds.     

Electrostatic deformation of DNA by a DNA-binding protein

Complementary electrostatic interactions between negatively charged B-DNA and a positively charged array on the lambda Cro repressor protein are shown to substantially contribute to the formation energy of sequence-specific and nonspecific Cro-DNA complexes. The electrostatic interactions favor Cro binding to a bent form of DNA, a geometry which optimizes hydrogen-bonding contacts between Cro and exposed base pair groups in the DNA major groove.     

Interaction of basic polypeptides with phospholipid monolayers

Adsorption of the polylysine and of the copolypeptides: L-lysine/L-serine and L-lysine/L-phenylalanine on phospholipid monolayers has been investigated. The charge density of the monolayers was varied by using the negatively charged phosphatidyl serine and the neutral phosphatidyl choline at different ratios. The surface concentrations of the adsorbed polypeptides was determined by measuring the surface radiation of their radioactive label.The adsorbing capacity of the monolayer surfaces increases with their negative charge, however with respect to polypeptides the surface activity sequence is pL < pLS < pLφ. From the dependence of adsorption on the ionic strength it was concluded that it is controlled by three types of interaction: (1) electrostatic attraction to the negatively charged surface; (2) electrostatic repulsion between adsorbed polybases; (3) hydrophobic interactions involving specific structural arrangements. This is true even of the apparently neutral PC monolayer where the fixed phosphate groups form an electrical double layer with the more mobile choline groups which can be interpenetrated by the charged groups of the basic polypeptides.     

Preparation of electroendosmosis-free agarose gel and exemplification of its use in crossed immunoelectrophoresis

Preparation of electroendosmosis-free agarose is described. The method is based upon the covalent bonding to agarose of a small number of positively charged groups which counterbalance the electroendosmosis-producing effect of the negatively charged groups present in commercial agarose. It is shown how such electroendosmosis-free agarose gel can be combined with advantage with polyacrylamide gels in crossed immunoelectrophoresis.     

Hydration of polyacids

The hydration of several polyacids has been investigated with special attention to the effects of neighboring charged groups and hydrophobic groups on the hydration regions. The molar volume change due to the structural change of water by the hydration was obtained by the method of refractivity measurement. The polyacids employed were poly(acrylic acid), poly(methacrylic acid), poly(L -glutamic acid), and a copolymer of maleic acid and vinyl acetate. The measurement of the refractive index was performed for the solutions of these polymers neutralized to varying degrees by tetrabutyl-ammonium hydroxide and sodium hydroxide. The results confirm the characteristics of the previous model of the hydration of polyelectrolytes, that is, the cooperative action of neighboring charged groups induce the second hydration region in addition to the intrinsic hydration region. The stiff structure of water in these regions restricts the mobility of counterions forced to enter into these regions by the strong electrostatic potential of polyions. The results indicate also that hydrophobic groups induce an additional hydration region around their neighboring charged groups. Small but negative volume changes were observed for conformational changes of poly(L -glutamic acid) and poly(methacrylic acid) induced by the neutralization of carboxyl groups.     

Elastin coacervate as a matrix for calcification

A calcifying system has been developed which, for the first time, demonstrates the capacity of α-elastin, as the coacervate, to initiate calcification in an $\text{in}\text{vitro}$ system. This is achieved with blocking the amino and carboxyl charged groups by N-formylation and O-methylation. The calcification system is of particular interest as it demonstrates the initiation of calcification after blockage of the charged amino and carboxyl groups. This leaves either neutral sites or the charged pyridinium moieties as the sites of initiation.