Complexation of trypsin and alcohol dehydrogenase with poly(diallyldimethylammonium chloride)

Complexation of alcohol dehydrogenase (ADH) and trypsin with poly(diallyldimethyl-ammonium chloride) (PDADMAC) in dilute electrolyte solution was studied by turbidimetric titration, quasi-elastic light scattering (QELS), and electrophoretic light scattering (ELS). Both QELS and turbidimetric titration show that PDADMAC forms complexes with ADH and trypsin in 0.01M NaCl solution at pH ≥ 6.8 and pH ≥ 9.2, respectively. These complexes take the form of stable coacervates in 0.01M, pH 11.0, phosphate buffer solution. QELS shows sizes of 400 and 315 nm for the coacervates of ADH-PDMDAAC and trypsin-PDMDAAC, respectively, while ELS reveals that these coacervates carry a net positive charge. Activity measurements show that both ADH and trypsin are enzymatically active in their coacervated states. Complexation of trypsin and PDADMAC was also studied by fluorescence in 0.01M, pH 11.0, phosphate buffer, and the protein emission was found to be quenched by complexation. The fluorescence quenching data show that trypsin retains its three-dimensional structure in the complex. These and other results are consistent with the quenching of the two tryptophans on the protein surface, but not the interior ones.© 1997 John Wiley & Sons, Inc.     

Characterization of polyanion-protein complexes by frontal analysis continuous capillary electrophoresis and small angle neutron scattering: effect of polyanion flexibility

The binding constant (K(obs)) for the beta-lactoglobulin-poly(vinylsulfate) (BLG-PVS) complex was measured by frontal analysis continuous capillary electrophoresis at pH values above the isoelectric point of BLG, and the persistence length (L(p)) of PVS was measured by small angle neutron scattering, to examine the effect of polyelectrolyte chain stiffness on its binding efficiency to proteins. The values of K(obs) and L(p) were compared with those of BLG-PSS and BLG-PAMPS (poly(2-acrylamido-2-methylpropanesulfonate)) reported previously. The relationship between K(obs) and L(p) was reciprocal, indicating that protein binding is enhanced by the flexibility of the polyanion, at least in the case where the net protein charge is negative. In addition, at a fixed pH, the polymer systems displayed a similar ionic strength dependence of K(obs). This similarity was consistent with the proposal that the binding properties of PVS and PAMPS polyanions are governed purely by electrostatic interactions and are independent of their molecular structure.     

Quasielastic light scattering,electrophoresis, and fluorescence studies of lysozyme-poly(2-acrylamido-methylpropylsulfate) complexes

Complexation between lysozyme and sodium poly(2-acrylamido-2-methylpropanesulfonate) (PAMPS) was studied by quasielastic light scattering, electrophoretic light scattering, fluorescence, and turbidimetry in electrolyte solution. These techniques show that complexation occurs at pH 9.6 in an ionic strength buffer of 0.25M NaCl + 25 mM Na₂B₄O₇. At constant lysozyme concentration (C_pro). The structure of the complex depends on the polymer concentration. At low polymer concentration (relative to C_pro), an intrapolymer complex is formed. This intrapolymer complex aggregates to an interpolymer species upon increase in polymer concentration. Complex formation was also studied by fluorescence using pyrene-labeled PAMPS (Py-PAMPS). Energy transfer from singlet-excited tryptophan residues in lysozyme to the pyrene label occurs when the complex is formed. Fluorescence and turbidity data indicate that lysozyme interacts with Py-PAMPS preferentially at pyrene sites, which leads to static quenching of tryptophan fluorescence via energy transfer to the pyrene label. © 1995 John Wiley & Sons, Inc.     

Complexation of lysozyme with poly(sodium(sulfamate-carboxylate)isoprene)

The complexation between hen egg white lysozyme (HEWL) and a novel pH-sensitive and intrinsically hydrophobic polyelectrolyte poly(sodium(sulfamate-carboxylate)isoprene) (SCPI), was investigated by means of dynamic, static, and electrophoretic light scattering and isothermal titration calorimetry measurements. The complexation process was studied at both pH 7 and 3 (high and low charge density of the SCPI, respectively) and under low ionic strength conditions for two polyelectrolyte samples of different molecular weights. The solution behavior, structure, and effective charge of the formed complexes proved to be dependent on the pH, the [-]/[+] charge ratio, and the molecular weight of the polyelectrolyte. Increasing the ionic strength of the solution led to vast aggregation and eventually precipitation of the complexes. The interaction between HEWL and SCPI was found to be mainly electrostatic, associated with an exothermic enthalpy change. The structural investigation of the complexed protein by fluorescence, infrared, circular dichroism spectroscopic, and differential scanning calorimetric measurements revealed no signs of denaturation upon complexation.     

Synthesis of conducting polyelectrolyte complexes of polyaniline and poly(2-acrylamido-3-methyl-1-propanesulfonic acid) catalyzed by pH-stable palm tree peroxidase

Comparison of the stability of five plant peroxidases (horseradish, royal palm tree leaf, soybean, and cationic and anionic peanut peroxidases) was carried out under acidic conditions favorable for synthesis of polyelectrolyte complexes of polyaniline (PANI). It demonstrates that palm tree peroxidase has the highest stability. Using this peroxidase as a catalyst, the enzymatic synthesis of polyelectrolyte complexes of PANI and poly(2-acrylamido-3-methyl-1-propanesulfonic acid) (PAMPS) was developed. The template polymerization of aniline was carried out in aqueous buffer at pH 2.8. Varying the concentrations of aniline, PAMPS, and hydrogen peroxide as reagents, favorable conditions for production of PANI were determined. UV-vis-NIR absorption and EPR demonstrated that PAMPS and PANI formed the electroactive complex similar to PANI doped traditionally using low molecular weight sulfonic acids. The effect of pH on conformational variability of the complex was evaluated by UV-vis spectroscopy. Atomic force microscopy showed that a size of the particles of the PANI-PAMPS complexes varied between 10 and 25 nm, depending on a concentration of PAMPS in the complex. The dc conductivity of the complexes depends also on the content of PAMPS, the higher conductivity being for the complexes containing the lower content of the polymeric template.     

Protein purification by polyelectrolyte coacervation: influence of protein charge anisotropy on selectivity

The effect of polyelectrolyte binding affinity on selective coacervation of proteins with the cationic polyelectrolyte, poly(diallyldimethylammonium chloride) (PDADMAC), was investigated for bovine serum albumin/β-lactoglobulin (BSA/BLG) and for the isoforms BLG-A/BLG-B. High-sensitivity turbidimetric titrations were used to define conditions of complex formation and coacervation (pH(c) and pH(?), respectively) as a function of ionic strength. The resultant phase boundaries, essential for the choice of conditions for selective coacervation for the chosen protein pairs, are nonmonotonic with respect to ionic strength, for both pH(c) and pH(?). These results are explained in the context of short-range attraction/long-range repulsion governing initial protein binding "on the wrong side of pI" and also subsequent phase separation due to charge neutralization. The stronger binding of BLG despite its higher isoelectric point, inferred from lower pH(c), is shown to result from the negative "charge patch" on BLG, absent for BSA, as visualized via computer modeling (DelPhi). The higher affinity of BLG versus BSA was also confirmed by isothermal titration calorimetry (ITC). The relative values of pH(?) for the two proteins show complex salt dependence so that the choice of ionic strength determines the order of coacervation, whereas the choice of pH controls the yield of the target protein. Coacervation at I = 100 mM, pH 7, of BLG from a 1:1 (w/w) mixture with BSA was shown by SEC to provide 90% purity of BLG with a 20-fold increase in concentration. Ultrafiltration was shown to remove effectively the polymer from the target protein. The relationship between protein charge anisotropy and binding affinity and between binding affinity and selective coacervation, inferred from the results for BLG/BSA, was tested using the isoforms of BLG. Substitution of glycine in BLG-B by aspartate in BLG-A lowers pH(c) by 0.2, as anticipated on the basis of DelPhi modeling. The stronger binding of BLG-A, confirmed by ITC, led to a difference in pH(?) that was sufficient to provide enrichment by a factor of 2 for BLG-A in the coacervate formed from "native BLG".     

On the protein–protein diffusional encounter complex

When two proteins diffuse together to form a bound complex, an intermediate is formed at the end‐point of diffusional association which is called the encounter complex. Its characteristics are important in determining association rates, yet its structure cannot be directly observed experimentally. Here, we address the problem of how to construct the ensemble of three‐dimensional structures which constitute the protein–protein diffusional encounter complex using available experimental data describing the dependence of protein association rates on mutation and on solvent ionic strength and viscosity. The magnitude of the association rates is fitted well using a variety of definitions of encounter complexes in which the two proteins are located at up to about 17 Å root‐mean‐squared distance from their relative arrangement in the bound complex. Analysis of the ionic strength dependence of bimolecular association rates shows that this is determined to a greater extent by the (protein charge) – (salt ion) separation distance than by the protein–protein charge separation distance. Consequently, ionic strength dependence of association rates provides little information about the geometry of the encounter complex. On the other hand, experimental data on electrostatic rate enhancement, mutation and viscosity dependence suggest a model of the encounter complex in which the two proteins form a subset of the contacts present in the bound complex and are significantly desolvated. Copyright © 1999 John Wiley & Sons, Ltd.     

Synthesis and application of a targeting diagnosis system via quantum dots coated by amphiphilic polymer for the detection of liver cancer cells

Water‐soluble quantum dots (QDs) for liver cancer diagnosis were prepared using QDs with oleylamine ligand coated with poly(aspartate)–graft–poly(ethylene glycol)–dodecylamine (PASP–Na–g–PEG–DDA). Dynamic light scattering and transmission electron microscopy imaging showed that the novel QDs have an ellipsoidal morphology with a size of ~ 45 nm which could be used for biomedical application. Furthermore, the PASP–Na–g–PEG–DDA was then modified with anti‐(vascular endothelial growth factor) (VEGF antibody), and a 1‐(4,5‐dimethylthiazol‐2‐yl)‐3,5‐diphenylformazan (MTT) assay showed that the novel anti‐VEGF‐targeting QDs in vitro had low toxicity. Confocal laser scanning microscopy observations revealed an intracellular (HepG2) distribution of the novel anti‐VEGF‐targeting QDs and the targeting efficiency of anti‐VEGF. These novel QDs could be used as a probe for liver cancer cell imaging because of anti‐VEGF targeting. Copyright © 2014 John Wiley & Sons, Ltd.     

Use of the mitochondria toxicity assay for quantifying the viable cell density of microencapsulated jurkat cells

The mitochondria toxicity assay (MTT assay) is an established method for monitoring cell viability based on mitochondrial activity. Here the MTT assay is proposed for the in situ quantification of the living cell density of microencapsulated Jurkat cells. Three systems were used to encapsulate the cells, namely a membrane consisting of an interpenetrating polyelectrolyte network of sodium cellulose sulphate/poly(diallyldimethylammonium chloride) (NaCS/PDADMAC), a calcium alginate hydrogel covered with poly(L ‐lysine) (Ca‐alg‐PLL), and a novel calcium alginate‐poly(ethylene glycol) hybrid material (Ca‐alg‐PEG). MTT results were correlated to data obtained by the trypan blue exclusion assay after release of the cells from the NaCS/PDADMAC and Ca‐alg‐PLL capsules, while a resazurin‐based assay was used for comparison in case of the Ca‐alg‐PEG material. Analysis by MTT assay allows quick and reliable determination of viable cell densities of encapsulated cells independent of the capsule material. The assay is highly reproducible with inter‐assay relative standard deviations below 10%. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:986–993, 2013     

Chymotrypsin–poly vinyl sulfonate interaction studied by dynamic light scattering and turbidimetric approaches

The formation of non-soluble complexes between a positively charged protein and a strong anionic polyelectrolyte, chymotrypsin, and poly vinyl sulfonate, respectively, was studied under different experimental conditions such as pH (1–3.5), protein concentration, temperature, ionic strength, and the presence of anions that modifies the water structure. Turbidimetric titration and dynamic light scattering approaches were used as study methods. When low protein–polyelectrolyte ratio was used, the formation of a soluble complex was observed. The increase in poly vinyl sulfonate concentration produced the interaction between the soluble complex particules, thus inducing macro-aggregate formation and precipitation. Stoichiometry ratios of 500 to 780 protein molecules were found in the precipitate per polyelectrolyte molecule when the medium pH varied from 1.0 to 3.5. The kinetic of the aggregation process showed to be of first order with a low activation energy value of 4.2 ± 0.2 kcal/mol. Electrostatic forces were found in the primary formation of the soluble complex, while the formation of the insoluble macro aggregate was a process driven by the disorder of the ordered water around the hydrophobic chain of the polymer.     

Cooperative, excluded-site binding and its dynamics for the interaction of gene 5 protein with polynucleotides

The binding of gene 5 protein to various single-stranded polynucleotides is investigated by fluorescence titrations and stopped-flow measurements. The association state of gene 5 protein itself is analyzed by equilibrium sedimentation: the monomer-dimer equilibrium found in the micromolar concentration range is described by a stability constant of 8 X 10(5) M-1. The fluorescence quenching upon binding to polynucleotides, studied over a broad concentration range and analyzed in terms of a cooperative excluded-site binding model, provides binding constants for "isolated" and for "cooperative" sites. The cooperativity for various ribo- and deoxyribopolymers is between 400 and 800 and is virtually independent of the ionic strength. The binding to isolated sites is strongly dependent upon the ionic strength; analysis in terms of polyelectrolyte theory indicates the compensation of 4 +/- 0.5 charges upon complex formation. The number of nucleotide residues covered by one protein molecule is also found to be 4 +/- 0.5 units. The affinity of gene 5 protein for polynucleotides increases in the series poly(C) less than poly(dA) less than poly(A) less than poly(U) much less than poly(dT); the binding constant for poly(dT) is roughly a factor of 1000 higher than that for the other polymers. Model studies with Lys-Tyr-Lys and Lys-Trp-Lys suggest that the preferential interaction with poly(dT) is not simply due to enhanced stacking interactions between the aromatic amino acids and the thymine residues. Stopped-flow reaction curves obtained by mixing of gene 5 protein with poly(dT) in the micromolar concentration range show three relaxation processes with time constants between 1 ms and 1 s.(ABSTRACT TRUNCATED AT 250 WORDS)     

Landscape of protein–small ligand binding modes

Elucidating the mechanisms of specific small‐molecule (ligand) recognition by proteins is a long‐standing conundrum. While the structures of these molecules, proteins and ligands, have been extensively studied, protein–ligand interactions, or binding modes, have not been comprehensively analyzed. Although methods for assessing similarities of binding site structures have been extensively developed, the methods for the computational treatment of binding modes have not been well established. Here, we developed a computational method for encoding the information about binding modes as graphs, and assessing their similarities. An all‐against‐all comparison of 20,040 protein–ligand complexes provided the landscape of the protein–ligand binding modes and its relationships with protein‐ and chemical spaces. While similar proteins in the same SCOP Family tend to bind relatively similar ligands with similar binding modes, the correlation between ligand and binding similarities was not very high (R² = 0.443). We found many pairs with novel relationships, in which two evolutionally distant proteins recognize dissimilar ligands by similar binding modes (757,474 pairs out of 200,790,780 pairs were categorized into this relationship, in our dataset). In addition, there were an abundance of pairs of homologous proteins binding to similar ligands with different binding modes (68,217 pairs). Our results showed that many interesting relationships between protein–ligand complexes are still hidden in the structure database, and our new method for assessing binding mode similarities is effective to find them.     

Chymotrypsin-poly vinyl sulfonate interaction studied by dynamic light scattering and turbidimetric approaches

The formation of non-soluble complexes between a positively charged protein and a strong anionic polyelectrolyte, chymotrypsin, and poly vinyl sulfonate, respectively, was studied under different experimental conditions such as pH (1-3.5), protein concentration, temperature, ionic strength, and the presence of anions that modifies the water structure. Turbidimetric titration and dynamic light scattering approaches were used as study methods. When low protein-polyelectrolyte ratio was used, the formation of a soluble complex was observed. The increase in poly vinyl sulfonate concentration produced the interaction between the soluble complex particules, thus inducing macro-aggregate formation and precipitation. Stoichiometry ratios of 500 to 780 protein molecules were found in the precipitate per polyelectrolyte molecule when the medium pH varied from 1.0 to 3.5. The kinetic of the aggregation process showed to be of first order with a low activation energy value of 4.2+/-0.2 kcal/mol. Electrostatic forces were found in the primary formation of the soluble complex, while the formation of the insoluble macro aggregate was a process driven by the disorder of the ordered water around the hydrophobic chain of the polymer.     

Non‐interacting surface solvation and dynamics in protein–protein interactions

Protein–protein interactions control a plethora of cellular processes, including cell proliferation, differentiation, apoptosis, and signal transduction. Understanding how and why proteins interact will inevitably lead to novel structure‐based drug design methods, as well as design of de novo binders with preferred interaction properties. At a structural and molecular level, interface and rim regions are not enough to fully account for the energetics of protein–protein binding, even for simple lock‐and‐key rigid binders. As we have recently shown, properties of the global surface might also play a role in protein–protein interactions. Here, we report on molecular dynamics simulations performed to understand solvent effects on protein–protein surfaces. We compare properties of the interface, rim, and non‐interacting surface regions for five different complexes and their free components. Interface and rim residues become, as expected, less mobile upon complexation. However, non‐interacting surface appears more flexible in the complex. Fluctuations of polar residues are always lower compared with charged ones, independent of the protein state. Further, stable water molecules are often observed around polar residues, in contrast to charged ones. Our analysis reveals that (a) upon complexation, the non‐interacting surface can have a direct entropic compensation for the lower interface and rim entropy and (b) the mobility of the first hydration layer, which is linked to the stability of the protein–protein complex, is influenced by the local chemical properties of the surface. These findings corroborate previous hypotheses on the role of the hydration layer in shielding protein–protein complexes from unintended protein–protein interactions. Proteins 2015; 83:445–458. © 2014 Wiley Periodicals, Inc.     

Computational investigation of proton transfer,pKa shifts and pH‐optimum of protein–DNA and protein–RNA complexes

Protein–nucleic acid interactions play a crucial role in many biological processes. This work investigates the changes of pKa values and protonation states of ionizable groups (including nucleic acid bases) that may occur at protein–nucleic acid binding. Taking advantage of the recently developed pKa calculation tool DelphiPka, we utilize the large protein–nucleic acid interaction database (NPIDB database) to model pKa shifts caused by binding. It has been found that the protein's interfacial basic residues experience favorable electrostatic interactions while the protein acidic residues undergo proton uptake to reduce the energy cost upon the binding. This is in contrast with observations made for protein–protein complexes. In terms of DNA/RNA, both base groups and phosphate groups of nucleotides are found to participate in binding. Some DNA/RNA bases undergo pKa shifts at complex formation, with the binding process tending to suppress charged states of nucleic acid bases. In addition, a weak correlation is found between the pH‐optimum of protein–DNA/RNA binding free energy and the pH‐optimum of protein folding free energy. Overall, the pH‐dependence of protein–nucleic acid binding is not predicted to be as significant as that of protein–protein association. Proteins 2017; 85:282–295. © 2016 Wiley Periodicals, Inc.     

Binding of azide ion to methemoglobin at elevated temperatures and the reality of the "compensation" temperature

We have studied the binding of azide ion to ferrihemoglobin at elevated temperatures. Up to a temperature of 45°C there is no difference in the ligand binding behavior of hemoglobin when compared with the results obtained at lower temperatures. The compensation temperature Tc of 290.6 ± 5.3°K, obtained in this study within the temperature range 303–318°K, confirms that the compensation pattern obtained by Lumry and Rajender is not dependent on the temperature range of the experiment but an intrinsic property of the protein conformation.     

Effect of polyelectrolyte adsorption on lateral distribution and dynamics of anionic lipids: a Monte Carlo study of a coarse-grain model

We employ Monte Carlo simulations to investigate the interaction between an adsorbing linear flexible cationic polyelectrolyte and a ternary mixed fluid membrane containing neutral (phosphatidylcholine, PC), monovalent (phosphatidylserine, PS), and multivalent (phosphatidylinositol, PIP₂) anionic lipids. We systematically explore the influences of polyelectrolyte chain length, polyelectrolyte charge density, polyelectrolyte total charge amount, and salt solution ionic strength on the static and dynamic properties of different anionic lipid species. Our results show that the multivalent PIP₂ lipids dominate the polyelectrolyte–membrane interaction and competitively inhibit polyelectrolyte–PS binding. When the total charge amount of the polyelectrolyte is less than that of the local oppositely charged PIP₂ lipids, the polyelectrolyte can drag the bound multivalent lipids to diffuse on the membrane, but cannot interact with the PS lipids. Under this condition, the diffusion behaviors of the polyelectrolyte closely follow the prediction of the Rouse model, and the polyelectrolyte chain properties determine the adsorption amount, concentration gradients, and hierarchical mobility of the bound PIP₂ lipids. However, when the total charge amount of the polyelectrolyte is larger than that of the local PIP₂ lipids, the polyelectrolyte further binds the PS lipids around the polyelectrolyte–PIP₂ complex to achieve local electrical neutrality. In this condition, parts of the polyelectrolyte desorb from the membrane and show faster mobility, and the bound PS presents much faster mobility than the segregated PIP₂. This work provides an explanation for heterogeneity formation in different anionic lipids induced by polyelectrolyte adsorption.     

Binding of azide and thiocyanate ligands to copper(II) model complexes

Summary Binding of azide to a series of copper(II) complexes has been investigated by absorption, CD and EPR spectroscopy. Axial binding of azide to Cu(II) can be differentiated from equatorial binding through the lower intensity and lack of optical activity of the LMCT band. The affinity of azide for Cu(II) increases with the overall positive charge of the complex. The preliminary data on thiocyanate binding to Cu(II) seem to agree with the trends observed for the corresponding azide adducts.