Precipitation of soluble affinity complexes by a second affinity interaction: a model study

Lactate dehydrogenase was purified by affinity precipitation. The enzyme bound to Blue Dextran (the Cibacron blue residues) and was precipitated by addition of concanavalin A. The lectin functions as a crosslinking agent, building up large flocs of dextran that subsequently precipitate, thus co-precipitating the affinity-bound lactate dehydrogenase.     

Neocarzinostatin: interaction between the antitumor-active chromophore and the carrier protein.

Conformational analysis of neocarzinostatin, an antibiotic protein with antitumor activity, in its holo-state in solution was carried out by NMR-spectroscopy. The results showed a beta-barrel structure for the carrier protein, in which the chromophore is tightly enwrapped and thus shielded from exposure to the solvent. The three-dimensional structure of this complex led to the proposal of a possible mechanism for the exposure or release of the active principle due to subtle environmental changes, e.g., in pH.     

Detergent extraction of the human alpha-beta interferon receptor: a soluble form capable of binding interferon.

After examining a variety of detergents we find that receptors for human alpha interferon can be solubilized, in active form, from plasma membranes of lymphoid cells using the detergent CHAPS. The complexes formed, in solution, with interferon are stable enough to be separated chromatographically.     

Relationships between membrane binding, affinity and cell internalization efficacy of a cell-penetrating peptide: penetratin as a case study

Background

Penetratin is a positively charged cell-penetrating peptide (CPP) that has the ability to bind negatively charged membrane components, such as glycosaminoglycans and anionic lipids. Whether this primary interaction of penetratin with these cell surface components implies that the peptide will be further internalized is not clear.

Methodology

Using mass spectrometry, the amount of internalized and membrane bound penetratin remaining after washings, were quantified in three different cell lines: wild type (WT), glycosaminoglycans- (GAG^neg) and sialic acid-deficient (SA^neg) cells. Additionally, the affinity and kinetics of the interaction of penetratin to membrane models composed of pure lipids and membrane fragments from the referred cell lines was investigated, as well as the thermodynamics of such interactions using plasmon resonance and calorimetry.

Principal Findings

Penetratin internalized with the same efficacy in the three cell lines at 1 µM, but was better internalized at 10 µM in SA^neg>WT>GAG^neg. The heat released by the interaction of penetratin with these cells followed the ranking order of internalization efficiency. Penetratin had an affinity of 10 nM for WT cells and µM for SA^neg and GAG^neg cells and model membrane of phospholipids. The remaining membrane-bound penetratin after cells washings was similar in WT and GAG^neg cells, which suggested that these binding sites relied on membrane phospholipids. The interaction of penetratin with carbohydrates was more superficial and reversible while it was stronger with phospholipids, likely because the peptide can intercalate between the fatty acid chains.

Conclusion/Significance

These results show that accumulation and high-affinity binding of penetratin at the cell-surface do not reflect the internalization efficacy of the peptide. Altogether, these data further support translocation (membrane phospholipids interaction) as being the internalization pathway used by penetratin at low micromolecular concentration, while endocytosis is activated at higher concentration and requires accumulation of the peptide on GAG and GAG clustering.     

Spectroscopic studies on the interaction of a water soluble porphyrin and two drug carrier proteins

The interaction of meso-tetrakis(p-sulfonatophenyl)porphyrin (TSPP) sodium salt to human serum albumin and beta-lactoglobulin was studied by steady-state and dynamic fluorescence at different pH of aqueous solutions. The formation of TSPP J-aggregates and a noncovalent TSPP-protein complex was monitored by fluorescence titrations, which depend on pH and on the protein nature and concentration. The complex between TSPP and protein displays a heterogeneous equilibrium with large changes in the binding strength versus pH. The large reduction of the effective binding constant from pH 2 to 7 suggests that electrostatic interactions are a major contribution to the binding of TSPP to the aforementioned proteins. TSPP aggregates and TSPP-protein complex exhibit circular dichroism induced by the presence of the protein. Circular dichroism spectra in the ultraviolet region show that the secondary structure of both proteins is not extensively affected by the TSPP presence. Protein-TSPP interaction was also examined by following the intrinsic fluorescence of the tryptophan residues of the proteins. Fluorescence quenching by acrylamide and TSPP itself also point to small changes on the protein tertiary structure and a critical distance R(0) approximately 56 A, between tryptophan and bound porphyrin, was estimated using the long distance F?rster-type energy transfer formalism.     

The silent carrier of beta thalassemia: interaction with the typical beta thalassemic trait.

The case of a girl affected by a Colley's disease of moderate severity is reported. A brother and a sister had levels of Hb F respectively of 18% and 45%. The father showed all the hematological signs of heterozygous thalassemia. The mother, however, was normal so far as osmotic fragility, red cell morphology, and Hb A2 level are concerned. In vitro hemoglobin chains biosynthesis was performed in all the subjects. Both the parents showed an alfa/non alfa ratio typical of beta thalassemia. Therefore, the mother has to be considered a "silent" carrier of the trait. The daughters and the son have a less severe Colley disease originating by such a double heterozygosity.     

O-GlcNAc inhibits interaction between Sp1 and sterol regulatory element binding protein 2

O-linked N-acetylglucosamine (O-GlcNAc), a monosaccharide N-acetylglucosamine on the serine and threonine residues of nucleocytoplasmic proteins, is a novel protein modification that is ubiquitous among eukaryotes and implicated in cell regulation. Recent evidence indicates that O-GlcNAc regulates protein-protein interactions. Here we provide evidence that O-GlcNAc interrupts a known interaction between Sp1 and sterol regulatory element binding protein 2 (SREBP2), thereby inhibiting expression of the gene encoding acetyl-CoA synthetase 1, which is involved in lipid synthesis. This study suggests a novel mechanism in which lipid biosynthesis may be regulated by O-GlcNAc.     

Exploring the interaction energies for the binding of hydroxydiphenyl ethers to enoyl-acyl carrier protein reductases

It is now well established that the potent anti-microbial compound, triclosan, interrupts the type II fatty acid synthesis by inhibiting the enzyme enoyl-ACP reductase in a number of organisms. Existence of a high degree of similarity between the recently discovered enoyl-ACP reductase from P. falciparum and B. napus enzyme permitted building of a satisfactory model for the former enzyme that explained some of the key aspects of the enzyme such as its specificity for binding to the cofactor and the inhibitor. We now report the interaction energies between triclosan and other hydroxydiphenyl ethers with the enzymes from B. napus, E. coli and P. falciparum. Examination of the triclosan-enzyme interactions revealed that subtle differences exist in the ligand binding sites of the enzymes from different sources i.e., B. napus, E. coli and P. falciparum. A comparison of their binding propensities thus determined should aid in the design of effective inhibitors for the respective enzymes.     

Specific binding of human alpha interferon to a high affinity cell surface binding site on bovine kidney cells

Virus-induced human alpha interferon (HuIFN-alpha) derived from Namalwa cells and purified to a specific activity of 2 X 10(8) units/mg of protein was radiolabeled with 125I-labeled Bolton and Hunter reagent to a specific activity of 4-12 microCi/micrograms of protein. The binding of this 125I-IFN to bovine kidney cells was examined at 4 degrees C. Scatchard analysis of the binding data indicate the presence of 650 binding sites/cell and binding of the ligand with an apparent Kd of 6 X 10(-11) M. Trypsin or acid treatment of cells to which 125I-IFN was bound resulted in the release of greater than or equal to 77% of the radioactivity, indicating a majority of radiolabeled material was bound to the cell surface. Antibodies against human leukocyte IFN but not antibodies against human fibroblast IFN inhibited the binding of radiolabeled IFN to the cells. The binding of 125I-IFN was not inhibited by a 75-fold molar excess of mouse IFN but was inhibited 30% by a 200-fold molar excess of human beta (fibroblast) IFN. These data are compatible with the Lower biological activities of these IFNs on bovine kidney cells. Several Escherichia coli derived HuIFN-alpha s inhibited the binding of the radiolabeled IFN to the same extent as native HuIFN-alpha s, but four fragments of HuIFN-alpha 1, an E. coli-derived 86 amino acid NH2-terminal fragment as well as 3 different synthetic carboxy-terminal fragments of 140, 56, or 46 amino acids did not inhibit binding.     

Unravelling the binding affinity between model transport protein and a prospective tuberculosis therapeutic agent: a spectroscopic and theoretical simulation exploration

Abstract

Haloxyfop was reported to exhibit inhibition effect targeting Mycobacterium tuberculosis and pathogenic parasites. To pave its way for drug development, more research is required to determine the affinities interacting with biological receptors in vivo. In this work, the interactions of Haloxyfop with two model transport proteins were investigated by spectroscopic techniques and theoretical simulation. The interaction mechanism, thermodynamic properties and the impact of Haloxyfop-induced conformational change in serum albumins were revealed by series of fluorescence, UV-Vis absorption and circular dichroic spectroscopy. The specific binding sites were determined by site-competitive replacement experiment. Molecular docking and dynamic simulation provided a visual screening in the microscopic binding mode. The structure of Haloxyfop was roughly divided into three parts that exhibit different covalent interaction affinities. The two isomers of Haloxyfop showed a certain degree of affinity difference. Hydrophobic, polar interaction and π-effect were analyzed in detail, and the surface electrostatic potential energy maps were simulated to provide references. The free energy, calculated by the molecular mechanics-generalized born surface area (MM-GBSA) and molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) methods, was decomposed to per-residues, which intuitively revealed relevant contributions in binding process. The role of water existence was explored through molecular dynamic refinement, and the frontier molecular orbital analysis explored the ionic interaction mechanism in electronic level. In general, multiple chemistry method was adopted to fully unravel the properties of Haloxyfop-binding for the sake of rationalizing the applicability as a therapeutic agent.

Communicated by Ramaswamy H. Sarma     

The plasma membrane calcium pump: regulation by a soluble Ca2+ binding protein

The Ca2+ pump of the plasma membrane of human red blood cells is associated with the activity of a (Ca2+ + Mg2+)-ATPase. Both the ATPase and the pump are stimulated above basal activities by calmodulin, an ubiquitous Ca2+-binding protein. Calmodulin isolated from human red blood cells was shown to be equipotent and equieffective with that isolated from beef brain. Half-maximal activation of ATPase (isolated red blood cell membranes, 37 C) and transport (inside-out red blood cell membrane vesicles, 25 C) were obtained with 2.5 and 4.4 nM calmodulin, respectively. Ca2+ dependence of Ca2+ transport was measured in the absence and in the presence of 50 nM calmodulin. At all Ca2+ concentrations above 2 X 10(-7) M Ca2+, the rate of transport was greater in the presence of calmodulin. The results implicate calmodulin in the regulation of the plasma membrane Ca2+ pump, but the mechanism(s) remain to be elucidated.     

Selective DNA binding and association with the CREB binding protein coactivator contribute to differential activation of alpha/beta interferon genes by interferon regulatory factors 3 and 7

Recent studies implicate the interferon (IFN) regulatory factors (IRF) IRF-3 and IRF-7 as key activators of the alpha/beta IFN (IFN-alpha/beta) genes as well as the RANTES chemokine gene. Using coexpression analysis, the human IFNB, IFNA1, and RANTES promoters were stimulated by IRF-3 coexpression, whereas the IFNA4, IFNA7, and IFNA14 promoters were preferentially induced by IRF-7 only. Chimeric proteins containing combinations of different IRF-7 and IRF-3 domains were also tested, and the results provided evidence of distinct DNA binding properties of IRF-3 and IRF-7, as well as a preferential association of IRF-3 with the CREB binding protein (CBP) coactivator. Interestingly, some of these fusion proteins led to supraphysiological levels of IFN promoter activation. DNA binding site selection studies demonstrated that IRF-3 and IRF-7 bound to the 5'-GAAANNGAAANN-3' consensus motif found in many virus-inducible genes; however, a single nucleotide substitution in either of the GAAA half-site motifs eliminated IRF-3 binding and transactivation activity but did not affect IRF-7 interaction or transactivation activity. These studies demonstrate that IRF-3 possesses a restricted DNA binding site specificity and interacts with CBP, whereas IRF-7 has a broader DNA binding specificity that contributes to its capacity to stimulate delayed-type IFN gene expression. These results provide an explanation for the differential regulation of IFN-alpha/beta gene expression by IRF-3 and IRF-7 and suggest that these factors have complementary rather than redundant roles in the activation of the IFN-alpha/beta genes.     

Molecular characterization of bovine brain P75, a high affinity binding protein for the regulatory subunit of cAMP-dependent protein kinase II beta

In mammalian brain, physiological signals carried by cAMP seem to be targeted to intraneuronal sites by the association of cAMP-dependent protein kinase II beta with anchoring proteins that bind the regulatory subunit (RII beta) of the enzyme. Previously, an RII beta-binding domain was characterized in a large (Mr approximately 150,000) candidate anchor protein, rat brain P150 (Bregman, D. B., Bhattacharyya, N., and Rubin, C. S. (1989) J. Biol. Chem. 264, 4648-4656). RII beta-binding proteins with Mr values of 65,000-80,000 were detected in the brains of other species. Since little was known about the structural features of these lower Mr proteins, we undertook the characterization of bovine brain P75 as a prototype. A cDNA encoding 258 amino acid residues at the C terminus of P75 was cloned by probing a lambda gt11 expression library with 32P-RII beta. The cDNA insert was ligated into the pET-3b expression plasmid, and large amounts of the partial P75 polypeptide (designated P47) were produced in Escherichia coli. A purification scheme that yielded 9 mg of soluble P47 from a 1-liter bacterial culture was devised. Antibodies directed against the P47 polypeptide revealed that P75 is expressed almost exclusively in brain. The sequence of 117 amino acid residues at the C terminus of P75 contains the RII beta-binding site and is 80% identical to the corresponding region of P150. In contrast, a lower level of identity (36%) between P75 and P150 at a more N-terminal region indicates that the two RII beta-binding proteins are related, but distinct proteins. P75 is not homologous to microtubule-associated protein 2, an RII alpha-selective binding protein, or any other previously studied proteins. C-terminal truncation analysis disclosed that the final 26 residues in P75 are essential for binding RII beta.     

Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect

Solvation effect is an important factor for protein–ligand binding in aqueous water. Previous scoring function of protein–ligand interactions rarely incorporates the solvation model into the quantification of protein–ligand interactions, mainly due to the immense computational cost, especially in the structure‐based virtual screening, and nontransferable application of independently optimized atomic solvation parameters. In order to overcome these barriers, we effectively combine knowledge‐based atom–pair potentials and the atomic solvation energy of charge‐independent implicit solvent model in the optimization of binding affinity and specificity. The resulting scoring functions with optimized atomic solvation parameters is named as specificity and affinity with solvation effect (SPA‐SE). The performance of SPA‐SE is evaluated and compared to 20 other scoring functions, as well as SPA. The comparative results show that SPA‐SE outperforms all other scoring functions in binding affinity prediction and “native” pose identification. Our optimization validates that solvation effect is an important regulator to the stability and specificity of protein–ligand binding. The development strategy of SPA‐SE sets an example for other scoring function to account for the solvation effect in biomolecular recognitions. Proteins 2015; 83:1632–1642. © 2015 Wiley Periodicals, Inc.     

A possible calcium binding site in D1 protein: A fluorescence and FTIR study of the interaction between lanthanides and a synthetic peptide

A peptide ranging from residue 229 to 240 of the D₁ protein of Photosystem (PS) II was synthesized and lanthanides were used as candidates of calcium. Fluorescence and FTIR spectroscopy were used to test the conformational adaptation after lanthanide additions. Fluorescence spectroscopy showed that the synthetic peptide provides lanthanide binding site, and that glutamic acids are involved in lanthanide binding. Resolution enhancement techniques were combined with band curve-fitting procedures to quantitate the FTIR spectral information from the amide 1 bands. The relative areas of these component bands indicate that lanthanide induced a substantial decrease in the amount of unordered structure and turns, while a corresponding increase in the amount of -helix and open loop was also observed. This indicates that a relatively compact structure of the synthetic peptide is formed if lanthanides are applied. The results may reflect on the physiological and biochemical function of calcium in PS II, including preventing D₁ from trypsin digestion.Abbreviations DCMU 3-(3,4-Dichlorophenyl)-1,1-dimethylurea - FTIR Fourier transform infrared - FSD Fourier self-deconvolution - PS Photosystem - Q_B Secondary plastoquinone electron acceptor of PS II     

Characterization of the interaction of a recombinant soluble neuroligin-1 with neurexin-1beta

Neuroligins, proteins of the alpha/beta-hydrolase fold family, are found as postsynaptic transmembrane proteins whose extracellular domain associates with presynaptic partners, proteins of the neurexin family. To characterize the molecular basis of neuroligin interaction with neurexin-beta, we expressed five soluble and exportable forms of neuroligin-1 from recombinant DNA sources, by truncating the protein before the transmembrane span near its carboxyl terminus. The extracellular domain of functional neuroligin-1 associates as a dimer when analyzed by sedimentation equilibrium. By surface plasmon resonance, we established that soluble neuroligins-1 bind neurexin-1beta, but the homologous alpha/beta-hydrolase fold protein, acetylcholinesterase, failed to associate with the neurexins. Neuroligin-1 has a unique N-linked glycosylation pattern in the neuroligin family, and glycosylation and its processing modify neuroligin activity. Incomplete processing of the protein and enzymatic removal of the oligosaccharides chain or the terminal sialic acids from neuroligin-1 enhance its activity, whereas deglycosylation of neurexin-1beta did not alter its association capacity. In particular, the N-linked glycosylation at position 303 appears to be a major determinant in modifying the association with neurexin-1beta. We show here that glycosylation processing of neuroligin, in addition to mRNA splicing and gene selection, contributes to the specificity of the neurexin-beta/neuroligin-1 association.