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PubMedDate not supplied

Matching fusion protein systems for affinity analysis of two interacting families of proteins: the cohesin-dockerin interaction.

Cellulosomes are multi-enzyme complexes that orchestrate the efficient degradation of cellulose and related plant cell wall polysaccharides. The complex is maintained by the high-affinity protein-protein interaction between two complementary modules: the cohesin and the dockerin. In order to characterize the interaction between different cohesins and dockerins, we have developed matching fusion-protein systems, which harbor either the cohesin or the dockerin component. For this purpose, corresponding plasmid cassettes were designed, which encoded for the following carrier proteins: (i) a thermostable xylanase with an appended His-tag; and (ii) a highly stable cellulose-binding module (CBM). The resultant xylanase-dockerin and CBM-cohesin fusion products exhibited high expression levels of soluble protein. The expressed, affinity-purified proteins were extremely stable, and the functionality of the cohesin or dockerin component was retained. The fusion protein system was used to establish a sensitive and reliable, semi-quantitative enzyme-linked affinity assay for determining multiple samples of cohesin-dockerin interactions in microtiter plates. A variety of cohesin-dockerin systems, which had been examined previously using other methodologies, were revisited applying the affinity-based enzyme assay, the results of which served to verify the validity of the approach.

Bacterial Proteins↗
PubMed1975

Drug-biomolecule interactions: bioelectrometric study of the mechanism of carbachol interactions with the cornea and its relation to miotic activity.

The augmentation of carbachol miotic activity attributable to enhanced transcorneal absorption, which results from the action of cationic adjuvants included in ophthalmic vehicles, suggested a study of carbachol-corneal tissue interaction as a further step toward understanding the phenomenon. The present study was performed in vivo using an innocuous electrometric technique. A fixed charge density of the corneal epithelial surface versus carbachol concentration profile was obtained from the electrometric results; it revealed three distinct concentration regions defined by precipitous decreases of fixed charge over extremely small concentration ranges. This anomalous behavior is attributed to cooperative alterations in the binding affinities of fixed anionic sites on the tissue surface, which result in an all-or-none release of protons and/or other nicrocations. The unmasked anionic sites become reoccupied with carbachol except in the last region where the reoccupation by carbachol is competitive with other cations in the solution in contact with the surface. This behavior, postulated on the basis of the construction of a carbachol-tissue binding isotherm from which thermodynamic interaction affinities were computed, was corroborated by the observed dependency of the duration of miotic activity on carbachol concentration. Allosteric interactions between anionic binding sites, which are mediated through electron inductive and electrostatic field effects and likely involve a cooperative alteration in tissue water structure, are implicated as underlying the observed phenomena.

Animals↗
PubMed1977

Kinetics and mechanisms of monolayer interactions IV: Surface activity of alkanols and energies of their interaction with dipalmitoyllecithin and dipalmitoylphosphatidylethanolamine.

The free energies of adsorption of the C1 to C14 alkanols at the air--water interface, estimated from plots of the surface pressure (pi less than or equal to 5 dynes/cm) against the bulk concentration, were a linear function of the chain length for 1-alkanols. From C3 to C8, the 2- and 3-isomers showed lower values than the 1-isomers. The energies of interaction of the C1 to C14 alkanols with dipalmitoylphosphatidylethanolamine and dipalmitoyllecithin monolayers, previously spread at the air-water interface, were estimated from the increase of the surface pressure with increasing concentrations of the injected alkanol. The energies of interaction of the C1 to C5 1-alkanols were linear functions of the chain length. The energy of interaction per methylene group of the alkyl chain suggests that the phospholipid monolayers behaved as ultrathin "oil" phases. The 2- and 3-isomers presented marked departures from linearity. The literature data for reflection coefficients in biomembranes and for partition coefficients between olive oil and water, red cell membranes and water, and phospholipid liposomes and water for the C1 to C5 alkanols show similar linearities with the chain length for the 1-isomers and comparable departures for the 2- and 3-isomers.

Adsorption↗
PubMed1993

Interaction of heme with amphiphilic peptides: use of hemin-CN to probe the interaction of calmodulin with its target peptides.

UNLABELLED: The interaction of heme with several amphiphilic peptides has been studied by absorption and fluorescence spectroscopy. The binding can be followed by the changes in the absorption spectrum of the heme group or by the decrease in the peptide tryptophan fluorescence due to energy transfer to the heme. Despite their small size, ranging from 26 residues for melittin to 14 for mastoporan, a high affinity for heme-CO and hemin-CN (Kd < 100 nM) may be observed. Spectral shifts in the absorption peaks and appreciable geminate recombination after photodissociation of CO from the complex peptide-heme-CO suggest the formation of a heme pocket, as for the natural heme proteins. APPLICATION: hemin-CN can be used as a probe for the interaction of calmodulin with these target peptides. Amphiphilic peptides such as melittin bind to calmodulin with a high (nM) affinity. While both the peptide and calcium-bound calmodulin bind heme-CO, only the peptide binds hemin-CN. These interactions permit studies of the competition between hemin-CN and calmodulin for binding to the peptide: while hemin-CN quenches the melittin tryptophan fluorescence, addition of calmodulin to the [melittin*hemin-CN] complex displaces the hemin-CN and the melittin tryptophan fluorescence is recovered.

Amino Acid Sequence↗
PubMed2001

Analysis of molecular interactions of the p53-family p51(p63) gene products in a yeast two-hybrid system: homotypic and heterotypic interactions and association with p53-regulatory factors.

p51 in the p53 tumor suppressor family, also referred to as p63, encodes multiple isoforms including p51A (TAp63gamma) and p51B (TAp63alpha). The p53 protein forms a tetramer, and its stability and activity are regulated by molecular association with viral and cellular proteins and by biochemical modifications. Using a yeast two-hybrid system, the p51A and p51B isoforms were examined for homotypic and heterotypic interactions in the p53 family proteins and for their affinity to the p53-regulatory factors. Results indicate a homotypic interaction dependent on the presumed oligomerization domain of the p51 proteins. The possibility of a weak heterotypic interaction between p51 and p73 proteins was suggested, while association between p51 and p53 appeared improbable. Furthermore, unlike p53, the p51 proteins failed to display an affinity to SV40 large T antigen or MDM2-family proteins. Having several features in common with p53, the p51 proteins may function in biological processes apart from p53.

Amino Acid Sequence↗
PubMed2000

pH-dependent interactions and the stability and folding kinetics of the N-terminal domain of L9. Electrostatic interactions are only weakly formed in the transition state for folding.

The role of electrostatic interactions in the stability and the folding of the N-terminal domain of the ribosomal protein L9 (NTL9) was investigated by determining the effects of varying the pH conditions. Urea denaturations and thermal unfolding experiments were used to measure the free energy of folding, DeltaG degrees, at 18 different pH values, ranging from pH 1.1 to pH 10.5. Folding rates were measured at 19 pH values between pH 2.1 and pH 9.5, and unfolding rates were determined at 15 pH values in this range using stopped-flow fluorescence experiments. The protein is maximally stable between pH 5.5 and 7.5 with a value of DeltaG degrees =4.45 kcal mol(-1). The folding rate reaches a maximum at pH 5.5, however the change in folding rates with pH is relatively modest. Over the pH range of 2.1 to 5.5 there is a small increase in folding rates, ln (k(f)) changes from 5.1 to 6.8. However, the change in stability is more dramatic, with a difference of 2.6 kcal mol(-1) between pH 2.0 and pH 5.4. The change in stability is largely due to the smaller barrier for unfolding at low pH values. The natural log of the unfolding rates varies by approximately four units between pH 2.1 and pH 5.5. The stability of the protein decreases above pH 7.5 and again the change is largely due to changes in the unfolding rate. ln (k(f)) varies by less than one unit between pH 5.5 and pH 9.5 while DeltaG degrees decreases by 2.4 kcal mol(-1) over the range of pH 5. 4 to pH 10.0, which corresponds to a change in ln K(eq) of 4.0. These studies show that pH-dependent interactions contribute significantly to the overall stability of the protein but have only a small effect upon the folding kinetics, indicating that electrostatic interactions are weakly formed in the transition state for folding.

Circular Dichroism↗
PubMed1998

Mapping neural interactivity onto regional activity: an analysis of semantic processing and response mode interactions.

Neuroimaging studies of cognition have typically been designed to identify brain regions that are active during a cognitive process. However, identifying how brain regions interact may be equally important. In a recent study we found that the pattern of activation associated with a semantic task differed depending on how subjects made a response, suggesting that there was an interaction between the neural systems underlying response mode and semantic processing (J. M. Jennings et al., 1997, NeuroImage 5, 229-239). This result raises two important questions, which we examined here: (1) How did the regions underlying semantic performance influence one another, or interact, to produce a different pattern of activation in each case? (2) What can be learned about the neurobiology of semantic processing when different regions are identified as a function of response? We addressed these questions using structural equation modeling. This technique produced functional network models representing the effect of different regions on each other during the semantic task for each response. A common network of regions associated with semantic processing was observed and included the left inferior frontal and left superior temporal cortices, with other regions brought into that network depending on response (e.g., right middle frontal). Moreover, changes in the influences among these regions across response condition predicted the pattern of activation found previously. These results show how an arbitrary response can affect the neural pathways associated with a cognitive process, likely due to the parallel and reentrant organization of the brain, and emphasize the importance of examining functional connections when studying cognition.

Adult↗
PubMed1991

Protein-water interactions from 2H NMR relaxation studies: influence of hydrophilic, hydrophobic, and electrostatic interactions.

The importance of water interactions with proteins in food systems is well documented. A controversy exists, however, as to the nature of these interactions and the effect of protein structural changes on them. To clarify these questions, a method has been developed for determining hydration from the protein concentration-dependence of deuteron resonance relaxation rates. Measurements were made in D2O on beta-lactoglobulin A to study effects of hydrophilic interactions, and on both casein micelles and submicelles to study hydrophobic and electrostatic effects. From the protein concentration-dependent relaxation rates, the second viral coefficients of the proteins were obtained by nonlinear regression analysis. Using either an isotropic tumbling or an intermediate asymmetry model, hydrations, upsilon, and correlation times, tau c, were calculated for the protein-associated water; from tau c, the Stokes radius, R, was obtained. Variations in upsilon and R were in accord with known structural changes in molecular states of the proteins. The NMR results are compared with hydrations and structural information derived independently from small-angle X-ray scattering.

Chemical Phenomena↗
PubMed2000

Identification of interacting mixed cultures of lactic acid bacteria by their exclusion from a model predicting the acidifying activity of non-interacting mixed cultures.

A model predicting the acidifying activity of mixed cultures of lactic acid bacteria and based on the lack of interaction between the strains has been investigated to identify interacting cultures. Three mixed cultures with Streptococcus thermophilus TH3 and ST7 and Lactobacillus delbrueckii ssp. bulgaricus LB10 were grown on milk. The acidifying activities of the two mixed cultures TH3/LB10 and TH3/ST7 were predicted accurately by the model, with mean prediction errors of 7.7% and 14.1%, respectively. However, the model underestimated the acidifying activity of the mixed culture ST7/LB10, with a mean prediction error of 43.5%, which provides evidence of positive interaction between the strains ST7 and LB10 during acidification.

Animals↗
PubMed1983

Protein-protein interactions: analysis of the interaction of concanavalin A with serum glycoproteins by sedimentation equilibrium using an air-driven ultracentrifuge.

An air-driven ultracentrifuge has been used for the quantitative analysis of the interaction of concanavalin A with a number of serum glycoproteins. Concanavalin A significantly affected the sedimentation equilibrium behavior of 125I-labeled human alpha 1-acid glycoprotein, rat alpha 1-acid glycoprotein, and rat transferrin containing two N-acetylneuraminic acid residues per molecule (Tf2). The weight-average molecular weight of the labeled component increased and there was a corresponding decrease in the concentration of the labeled component at the meniscus. In contrast, concanavalin A did not significantly alter the sedimentation equilibrium behavior of the 125I-labeled rat transferrin containing three N-acetyl neuraminic acid residues per molecule. Sedimentation equilibrium results for interacting mixtures of concanavalin A and labeled glycoprotein and at various concentrations of the competitive inhibitor alpha-methyl mannoside were analyzed in terms of a model. Values of 5 X 10(4), 2 X 10(5), and 6 X 10(5) M-1 were obtained for the equilibrium constants for the interaction of concanavalin A with Tf2, human alpha 1-acid glycoprotein, and rat alpha 1-acid glycoprotein, respectively.

Chemical Phenomena↗
PubMed1991

Interaction of human protein Z with thrombin: evaluation of the species difference in the interaction between bovine and human protein Z and thrombin.

Protein Z is a vitamin K-dependent protein of unknown function present in normal human and bovine plasma. Binding and kinetic studies showed that bovine protein Z interacts with bovine thrombin with a dissociation constant of 0.11 microM in a Ca(2+)-independent fashion and that thrombin becomes associated with phospholipid vesicles in the presence of protein Z but not in its absence (Hogg, P. J. and Stenflo, J. (1991) J. Biol. Chem., in press). In the present study the interaction of human protein Z with human thrombin and the influence of human protein Z on the association of thrombin with phospholipid vesicles was evaluated. In contrast to bovine protein Z, human protein Z bound human DIP-thrombin with a 20-fold weaker affinity at 1.5 mM Ca2+ and in a Ca(2+)-dependent fashion. Human protein Z was also less effective than bovine protein Z in promoting the association of thrombin with phospholipid vesicles. Also, bovine protein Z cleaved by thrombin at Arg-365 bound DIP-thrombin with a 10-fold weaker affinity than did native bovine protein Z. The data suggest that the species difference in the interaction between protein Z and thrombin can be explained by a difference in the COOH-terminal region of bovine protein Z versus human protein Z.

Animals↗
PubMed1996

The interaction of antitumor-active anthraquinones with biologically important redox couples: I. Spectrophotometric investigation of the interaction of carminic acid and mitoxantrone with the iron (II, III) and copper (I, II) redox couples.

Studying the interaction of antitumor-active anthraquinones with biologically important redox couples is important in understanding the possible reductive or oxidative mode of metabolism of these antineoplastic agents coupled with the formation of free radicals. The interactions of such anthraquinones, i.e., carminic acid (CA) and mitoxantrone (Mx) with iron(II, III) and copper(I, II) redox couples in oxygenated and deaerated solutions, were investigated by UV-Visible and IR-spectroscopy. The superoxide radical reagent, nitroblue tetrazolium (NBT), was added to the metal and anthraquinone solutions and their binary mixtures at varying pH. Formazan, the reduction product of NBT, was produced mainly as a result of Fe(II)-NBT and Fe(II)-Mx-NBT interactions. The ternary mixtures of the lower valencies of iron and copper with CA and NBT exhibited intensive charge-transfer bands in the visible region, while metal-Mx-NBT combinations did not produce such bands, possibly due to the blockage of the redox-active aminoethanolamine side-chains of Mx through coordination with the metals. Copper-Mx combinations showed an oxygen sensitivity as spectral evidence was obtained for the oxidative transformation of Mx to the cyclic primary metabolite. The results were evaluated in regard to the possible oxidative activation of the studied anthracenediones with iron and copper systems.

Anthraquinones↗
PubMed1989

A physico-chemical approach to the study of the binding interaction between S-adenosyl-L-methionine and polyanions: binding constants and nature of the interaction with sodium poly(styrene sulfonate).

The interaction between S-adenosyl-L-methionine (AdoMet) and sodium poly(styrene sulfonate) NaPSS) was studied by means of ultrafiltration and ultraviolet absorption spectroscopy at several pH values and sodium sulfate concentrations. The results obtained are interpreted mainly in terms of electrostatic interactions and permit the evaluation of the binding constants under different experimental conditions. Furthermore, ultraviolet absorption spectroscopy data show a specific short-range interaction between the aromatic electronic system of AdoMet and the NaPSS aromatic ring. The results indicate that the binding strength is greatly affected by the AdoMet positive charge on the adenine ring. The other positive charges on both the sulfonic pole and the amino acidic group of AdoMet contribute only weakly to the binding to the polyanionic matrix, thus assuring some stability of AdoMet even at physiological pH.

Anions↗
PubMed1981

Comparative analysis of specificity in protein-protein interactions. Part I.: A theoretical and mathematical approach to specificity in protein-protein interactions.

The definition of informational complementarity (IC) is introduced and a comparative computer method is described to analyse the possible sources of the specificity in some protein-protein (P-P) interactions. The essence of this method is the step-by-step comparison of the primary structures of the proteins regarding the frequency and sequence (distribution) of one or more selected amino acids. The calculation of the probability of finding two different amino acids in two different protein parts by the same frequency and distribution (Random Pair Building, RPB) and it's checking with the number of actually found pairs (Concrete Pair Building, CPB) and with the number of maximal available pair forming (Maximal Pair Building, MPB) may give the chance to find IC sequences and to understand the nature of specific P-P interactions. The usefulness of this method for analysing intramolecular structures and intermolecular interactions is discussed and an example is presented how it may be used.

Amino Acid Sequence↗
PubMed2004

The alpha-helical membrane spanning domain of cytochrome b5 interacts with cytochrome P450 via nonspecific interactions.

Cytochrome b5 (cyt b5) is an amphipathic membrane-bound heme protein found in the endoplasmic reticulum of eukaryotes. It consists of three domains, an N-terminal cytosolic, hydrophilic domain containing the heme, a short flexible linker and an alpha-helical membrane-spanning domain. This study investigated whether there are specific side chain helix-helix packing interactions between the COOH-terminal membrane anchor of cyt b5 and cytochrome P450 (cyt P450) 2B4 in a purified reconstituted system. Alanine was inserted at six positions in the membrane anchor of cyt b5. Insertion of alanine into an alpha-helix causes all amino acids at its carboxyl terminus to be rotated by 100 degrees . The ability of the alanine insertion mutants of cyt b5 to bind to cyt P450 2B4 was similar to that of the wild-type protein as was the ability of the mutant cyts b5 to stimulate the metabolism of the anesthetic, methoxyflurane. These results demonstrate that the C-terminal hydrophobic alpha-helix of cyt b5 does not interact with cyt P450 2B4 through a specific stereochemical fit of amino acid side chains, but rather through nonspecific interactions.

Aryl Hydrocarbon Hydroxylases↗
PubMed2005

Analysis of protein-surfactant interactions--a titration calorimetric and fluorescence spectroscopic investigation of interactions between Humicola insolens cutinase and an anionic surfactant.

We have studied interactions of cutinase (HiC) from Humicula insolens and sodium dodecyl sulphate (SDS) by parallel calorimetric and fluorescence investigations of systems in which the concentration of both components was changed systematically. Results from the two methods exhibit a number of synchronous characteristics, when plotted against the total SDS concentration, [SDS]tot. The molecular origin of several of these anomalies was assigned, and five intervals of [SDS]tot in which different modes of interactions dominated were identified. Going from low to high [SDS]tot, these modes were: binding of (a few) SDS to native HiC, formation of oligomeric protein aggregates, denaturation of HiC and adsorption of SDS on denatured protein. For [SDS]tot>3-6 mM (depending on the protein concentration), the adsorption saturated, and no further protein-detergent interaction could be detected. Two particularly conspicuous anomalies in the calorimetric data were ascribed to respectively denaturation and saturation. It was found that [SDS]tot at these points depended linearly on the (total) protein concentration, [HiC]. We suggest that this reflects the balance between bound and free SDS [SDS]tot=[SDS]aq+[HiC] Nb where [SDS]aq and Nb are, respectively, the aqueous ("free") concentration of SDS and the average number of SDS bound per protein. Interpretation of the results along these lines showed that at 22 degrees C and pH 7.0, HiC denatures with approximately 14 bound surfactant molecules at [SDS]aq=1.0 mM. Saturation is characterized by Nb approximately 39 and [SDS]aq=2.2 mM. The latter value is equal to CMC in the (protein free) buffer. These results are discussed with respect to the SDS-binding capacity of HiC and the origin and location of the saturation point.

Ascomycota↗
PubMed2004

Ski-interacting protein, a bifunctional nuclear receptor coregulator that interacts with N-CoR/SMRT and p300.

Ski-interacting protein (SKIP), a vitamin D receptor (VDR) coactivator, also functions as a repressor in Notch signalling in association with the corepressor SMRT. Here we show that SKIP bifunctionally modulates (activates or represses) Retinoid-X receptor (RXR)- and VDR-dependent gene transcription in a cell line-specific manner, with activation in CV-1 and repression in P19 cells. The coactivator function of SKIP in these cells appeared to correlate with the relative level and ratio of expression of N-CoR and p300, with greater SKIP activation in higher p300-expressing and lower N-CoR-expressing cell-lines. C-terminal deletion of SKIP (delta334-536 aa) was associated with strong activation in both CV-1 and P19 cells. The corepressors N-CoR and SMRT and the coregulator p300 interacted with SKIP through the same N-terminal region (1-200 aa). Overall these results suggest that transcriptional action of SKIP may depend on distinct functional domains and cell line-specific interactions with both corepressors and coactivators.

Acetyltransferases↗
PubMed2006

Role of ionic interactions and linker in the domain interaction and modulation of functional activity of hyaluronate lyases.

Hyaluronate lyases from Streptococcus pneumoniae (SpnHL) and Streptococcus agalactiae (SagHL) are composed of four domains; N-terminal domain, spacer domain, alpha-domain and C-terminal domain, which are connected through peptide linkers. We have earlier shown that the recombinant alpha- and C-terminal domains of SpnHL/SagHL interact with each other even in absence of the linker and form a functional complex with enhanced enzymatic activity. Here, we looked into the role of ionic interactions in the enzyme stability and also the role of C-terminal domain and linker in the functional regulation. Domain swapping studies showed that the C-terminal domain does not bind directly to the substrate; instead the domain contributes to the interaction with the polymeric hyaluronan for catalysis. Furthermore, the substrate specificity exchanges with the size of catalytic cleft. The role of linker connecting alpha-domain to C-terminal domain was found to hold the C-terminal domain in a conformation suitable for achieving maximum activity.

Binding Sites↗