Generation and characterization of a specific polyclonal antibody against the mouse serotonin receptor 1A: a state-of-the-art recommendation on how to characterize antibody specificity

A series of different antibodies against serotonin receptor 1A (5HT1A_R) have been reported although only limited information on the specificity of these antibodies and the antigens recognized is available. Herein, we characterized reactivity of an antibody by a gel-based proteomics method that should represent a model how antibodies may be defined in the future. An antibody against the 5HT1A_R was generated, used for immunoprecipitation and immunoblotting on blue-native gels containing a 5HT1A_R complex. The 5HT1A_R was isolated from tissue and was defined by nano-LC-ESI-MS/MS. A single band on the native gel and a single spot representing the denatured receptor in the 3rd dimensional step of gel electrophoresis was detected. Immunoprecipitation revealed a single band for the denatured 5HT1A_R. Herein, a procedure is proposed to characterize an antibody by the use of a robust method unambiguously identifying and characterizing the antigen, 5HT1A_R, from mouse whole brain.     

Cross-reactivity of antibodies to actin- depolymerizing factor/cofilin family proteins and identification of the major epitope recognized by a mammalian actin-depolymerizing factor/cofilin antibody

Members of the actin-depolymerizing factor (ADF)/cofilin family of proteins are expressed in all eukaryotic cells. In higher vertebrates, cells often express as many as three different ADF/cofilin genes and each of these proteins may be phosphorylated on serine 3, giving rise to up to six different species. Also, many avian, amphibian, and invertebrate systems have been useful in studying different aspects of ADF/cofilin function. Antibodies have been prepared against different members of the ADF/cofilin family, but no systematic examination of their cross-reactivity has been reported. Although ADF and cofilins within a single vertebrate species have about a 70% sequence homology, antibodies often differentiate between these proteins. Here, Western blotting was used with chemiluminescence substrates of different sensitivities to determine the relative immunoreactivities of different polyclonal rabbit antibodies and a mouse monoclonal antibody to purified ADF/cofilins from plants, protists, nematodes, insects, echinoderms, birds, and mammals. From immunocross-reactivities and sequence alignments, the principal epitope in mammalian ADF and cofilin-1 recognized by an antibody raised against avian ADF was identified. The specificity of an antibody to the phosphopeptide epitope of metazoan ADF/cofilins was confirmed by two-dimensional (2-D) immunoblot analysis. Futhermore, this bank of antibodies was used to identify by Western blotting a putative member of the ADF/cofilin family in the sea slug, Aplysia californica.     

Tamm-Horsfall glycoprotein enhances PMN phagocytosis by binding to cell surface-expressed lactoferrin and cathepsin G that activates MAP kinase pathway

The molecular basis of polymorphonuclear neutrophil (PMN) phagocytosis-enhancing activity (PEA) by human purified urinary Tamm-Horsfall glyco- protein (THP) has not been elucidated. In this study, we found human THP bound to lactoferrin (LF) and cathepsin G (CG) expressed on the surface of PMN, identified by a proteomic study with MALDI-TOF- LC/LC/mass spectrometric analysis. Pre-incubation of 10% SDS-PAGE electrophoresed PMN lysates with monoclonal anti-LF or anti-CG antibody reduced the binding with THP. To elucidate the signaling pathway of THP on PMN activation, we found THP enhanced ERK1/2 phosphorylation, reduced p38 MAP kinase phosphorylation, but had no effect on DNA binding of the five NF-kB family members in PMN. To further clarify whether the carbohydrate-side chains or protein-core structure in THP molecule is responsible for THP-PEA, THP was cleaved by different degrading enzymes with carbohydrate specificity (neuraminidase and β-galactosidase), protein specificity (V8 protease and proteinase K) or glycoconjugate specificity (carboxylpeptidase Y and O-sialoglycoprotein endopeptidase). We clearly demonstrated that the intact protein-core structure in THP molecule was more important for THP-PEA than carbohydrate-side chains. Putting these results together, we conclude that THP adheres to surface-expressed LF and CG on PMN and transduces signaling via the MAP kinase pathway to enhance PMN phagocytosis.     

Identification of immunoreactive proteins of Chlamydia trachomatis by Western blot analysis of a two-dimensional electrophoresis map with patient sera.

Western blots of two-dimensional electrophoretic maps of proteins from Chlamydia trachomatis were probed with sera from 17 seropositive patients with genital inflammatory disease. Immunoblot patterns (comprising 28 to 2 spots, average 14.8) were different for each patient; however, antibodies against a spot-cluster due to the chlamydia-specific antigen outer membrane protein-2 (OMP2) were observed in all sera. The next most frequent group of antibodies (15/17; 88%) recognized the hsp60 GroEL-like protein, described as immunopathogenic in chlamydial infections. Reactivity to the major surface-exposed and variable antigen major outer membrane protein (MOMP) was observed at a relatively lower frequency (13/17; 76%). The hsp70 DnaK-like protein was also frequently recognized (11/17; 64.7%) in this patient group. Besides the above confirmatory findings, the study detected several new immunoreactive proteins, with frequencies ranging from 11/17 to 1/17. Some were characterized also by N-terminal amino acid sequencing and homology searches. Amongst these were a novel outer membrane protein (OmpB) and, interestingly, five conserved bacterial proteins: four (23%) sera reacted with the RNA polymerase alpha-subunit, five (29%) recognized the ribosomal protein S1, eight (47%) the protein elongation factor EF-Tu, seven (41%) a putative stress-induced protease of the HtrA family, and seven sera (41%) the ribosomal protein L7/L12. Homologs of the last two proteins were shown to confer protective immunity in other bacterial infections. The data show that immunological sensitization processes commonly thought to play a role in chlamydial pathogenicity may be sustained not only by the hsp60 GroEl-like protein, but also by other conserved bacterial antigens, some of which may be also considered as potential vaccine candidates.     

Effect of small molecule surfactants on molecular parameters and thermodynamic properties of legumin in a bulk and at the air–water interface depending on a protein structure in an aqueous medium

This paper presents the effect of fatty acid salts, namely, Na-caprate and Na-palmitate on the legumin (11S globulin of Vicia Faba broad beans) molecular and thermodynamic properties in the bulk aqueous medium and at the air–water interface under different molecular states of the protein. That are the native state of the protein globule (pH 7.2, ionic strength of 0.05 mol dm⁻³), as well as the acidic denatured (pH 3.0, ionic strength of 0.01 mol dm⁻³) and the heat denatured ones (after heating at 90°C for 30 min, pH 7.2, ionic strength of 0.05 mol dm⁻³). In turn, an importance of the state of the small molecule surfactants in a solution in reference to the critical concentrations of micelle formation (CMC), for their effect on the protein properties, was also under our studying. The peculiarities of the legumin structure in the aqueous medium appeared in the different nature of the interactions between the protein and the fatty acid salts, as was indicated by the mixing calorimetry data. So, the hydrophobic contacts provided a basis for interactions between both the native and heat denatured legumin with the fatty acid salts. At the same time, the electrostatic interactions between the oppositely charged functional groups of the fatty acid salts and the acidic denatured protein formed principally a basis of their interactions in an aqueous medium. In response to interactions of the fatty acid salts with legumin the essential changes in the protein conformational stability, depending on both the protein molecular state and concentration of the fatty acid salts, were found using differential scanning calorimetry (DSC). The rather high level of the protein association was observed by light scattering in the bulk aqueous medium in the presence of the fatty acid salts. As this takes place, the surface hydrophilicity of the protein increased under the formation of the associates. The combined data of mixing calorimetry, differential scanning calorimetry and light scattering suggested the complex formation between legumin and the fatty acid salts. The interactions of the fatty acid salts with the protein produced a change in the surface activity for the mixture of the protein with the fatty acid salts. That is a decrease in the protein surface tension at the air–water interface for the mixed solutions in comparison with ones for both the protein and small molecule surfactant alone in the case of Na-caprate, and those are the intermediate values of the surface tension in the case of Na-palmitate. These results were observed independently of the protein state (native or acidic/heat denatured) in an aqueous medium. As this took place, the most dramatic increase in the surface activity was found for the mixtures of the acidic denatured protein with Na-caprate as if the most hydrophobic species were formed in this case. The combined data of mixing calorimetry, DSC, light scattering and tensiometry showed that the effect of the fatty acid salts on the legumin thermodynamic properties in a bulk and at interfaces is governed by a number of the key factors such as: a structure of both the protein and fatty acid salt (a length of the hydrocarbon chain); a degree of the protein association in the bulk aqueous phase (as a result of the interactions with the small molecule surfactants); a change in the protein conformational stability (flexibility) under the influence of the small molecule surfactants; as well as by the nature (hydrophobic, electrostatic) of the protein–small molecule surfactant interactions, determining ultimately the hydrophilic–lipophilic balance of the protein surface.     

The role of tonicity responsive enhancer sites in the transcriptional regulation of human hsp70-2 in response to hypertonic stress

The inducible 70 kDa heat shock proteins (Hsp70) in mice are encoded by two almost identical genes, hsp70.1 and hsp70.3. Studies have found that only hsp70.1 is induced by hypertonic stress while both hsp70.1 and hsp70.3 genes are expressed in response to heat shock stress. It is unclear if the human counterparts, hsp70-2 and hsp70-1, are differentially regulated by heat shock and osmotic stress. This study found that only hsp70-2 was induced by hypertonic stress in human embryonic kidney epithelial cells and fibroblasts, while heat shock stress induced both hsp70-1 and hsp70-2. The human hsp70-2 promoter region contains three TonE (tonicity-responsive enhancer) sites, which were reported to play an important role in the response to hypertonicity. When the reporter plasmids containing different parts of the 5' flanking region of hsp70-2 were transfected into human embryonic kidney epithelial cells or fibroblasts, one TonE site at -135 was found to play a key role in the response to hypertonicity. The inactivation of the TonE site using site-directed mutagenesis led to the complete loss of induction by hypertonicity, which demonstrates the essential role of the TonE site. This suggests that the TonE site and the TonEBP (TonE binding protein) are the major regulators for the cellular response against high osmolarity in human kidney tissue.     

Purification of the 90 kDa heat shock protein (hsp90) and simultaneous purification of hsp70/hsc70, hsp90 and hsp96 from mammalian tissues and cells using thiophilic interaction chromatography

Heat shock proteins (HSPs) hsp70/hsc70, hsp90 and hsp96 were separated from mammalian cells and tissues on a gel obtained by the reaction of β‐mercaptoethanol with divinyl sulfone‐activated Sepharose CL‐6B (thiophilic gel or T‐gel). Hsp90 revealed a much higher affinity towards the T‐gel than the other HSPs. One‐step thiophilic interaction chromatography of proteins resulted in a more than 80% purity and 85% yield of hsp90. Based on this observation, a simple and efficient method for the purification of hsp90 and a procedure for the simultaneous purification of several HSPs (hsp70/hsc70, hsp90 and hsp96) using thiophilic interaction chromatography was developed. All the HSPs were recovered with a high yield and purity (90–99%). The results indicated that the thiophilic gel is a highly efficient affinity matrix for the purification of hsp90 and can be used in the protocols of purification of different HSPs from cells and tissues of various animal species. Copyright © 2009 John Wiley & Sons, Ltd.     

Fast-scan cyclic voltammetry with thiol-modified mercury electrodes distinguishes native from denatured BSA

We studied native and denatured bovine serum albumin (BSA) at bare and dithiothreithol (DTT)-modified hanging mercury drop electrode (HMDE) by fast-scan cyclic voltammetry (fsCV) and chronopotentiometric stripping (CPS) to compare these methods for their ability to recognize changes in BSA structure. Using fsCV and bare HMDE, denatured BSA could be distinguished from its native form only between 10 and 20 V/s but at lower resolution than with CPS. At DTT-HMDE denatured BSA was recognized from native BSA in a wider range of scan rates suggesting new possibilities in development of voltammetric protein structure-sensitive sensing.     

Hydration of thermally denatured lysozyme studied by sorption calorimetry and differential scanning calorimetry

We have studied hydration (and dehydration) of thermally denatured hen egg lysozyme using sorption calorimetry. Two different procedures of thermal denaturation of lysozyme were used. In the first procedure the protein was denatured in an aqueous solution at 90 degrees C, in the other procedure a sample that contained 20% of water was denatured at 150 degrees C. The protein denatured at 90 degrees C showed very similar sorption behavior to that of the native protein. The lysozyme samples denatured at 150 degrees C were studied at several temperatures in the range of 25-60 degrees C. In the beginning of sorption, the sorption isotherms of native and denatured lysozyme are almost identical. At higher water contents, however, the denatured lysozyme can absorb a greater amount of water than the native protein due to the larger number of available sorption sites. Desorption experiments did not reveal a pronounced hysteresis in the sorption isotherm of denatured lysozyme (such hysteresis is typical for native lysozyme). Despite the unfolded structure, the denatured lysozyme binds less water than does the native lysozyme in the desorption experiments at water contents up to 34 wt %. Glass transitions in the denatured lysozyme were observed using both differential scanning calorimetry and sorption calorimetry. Partial molar enthalpy of mixing of water in the glassy state is strongly exothermic, which gives rise to a positive temperature dependence of the water activity. The changes of the free energy of the protein induced by the hydration stabilize the denatured form of lysozyme with respect to the native form.     

Interplay of secondary structures and side-chain contacts in the denatured state of BBA1

The denatured state of a miniprotein BBA1 is studied under the native condition with the AMBER/Poisson-Boltzmann energy model and with the self-guided enhanced sampling technique. Forty independent trajectories are collected to sample the highly diversified denatured structures. Our simulation data show that the denatured BBA1 contains high percentage of native helix and native turn, but low percentage of native hairpin. Conditional population analysis indicates that the native helix formation and the native hairpin formation are not cooperative in the denatured state. Side-chain analysis shows that the native hydrophobic contacts are more preferred than the non-native hydrophobic contacts in the denatured BBA1. In contrast, the salt-bridge contacts are more or less nonspecific even if their populations are higher than those of hydrophobic contacts. Analysis of the trajectories shows that the native helix mostly initiates near the N terminus and propagates to the C terminus, and mostly forms from 3(10)-helix/turn to alpha helix. The same analysis shows that the native turn is important but not necessary in its formation in the denatured BBA1. In addition, the formations of the two strands in the native hairpin are rather asymmetric, demonstrating the likely influence of the protein environment. Energetic analysis shows that the native helix formation is largely driven by electrostatic interactions in denatured BBA1. Further, the native helix formation is associated with the breakup of non-native salt-bridge contacts and the accumulation of native salt-bridge contacts. However, the native hydrophobic contacts only show a small increase upon the native helix formation while the non-native hydrophobic contacts stay essentially the same, different from the evolution of hydrophobic contacts observed in an isolated helix folding.     

酸性红73多克隆抗体的制备及其应用

在酸性红73分子的羟基上引入一个带有羧基的“间隔臂”,采用N-羟基琥珀亚胺活性酯法将酸性红73分别与牛血清白蛋白(BSA)、卵清蛋白(OA)偶联,合成免疫原和包被原,经免疫新西兰白兔获得多克隆抗体,所得抗体最大效价可达2.56×105,建立了酸性红73的间接竞争ELISA检测方法.本方法的半数抑制浓度(IC50)为181.2 μg/L,检出限(LOD)为7.9 μg/L.交叉反应实验表明,除苏丹红3号(1.13％)外,抗AR73抗体与其它竞争物均无交叉反应.在虾仁中的空白添加回收率为63.5％～90.7％,RSD＜6.8％.说明本方法可用于虾仁中酸性红73的残留检测.     

Understanding the folding rates and folding nuclei of globular proteins

The first part of this paper contains an overview of protein structures, their spontaneous formation ("folding"), and the thermodynamic and kinetic aspects of this phenomenon, as revealed by in vitro experiments. It is stressed that universal features of folding are observed near the point of thermodynamic equilibrium between the native and denatured states of the protein. Here the "two-state" ("denatured state" <--> "native state") transition proceeds without accumulation of metastable intermediates, but includes only the unstable "transition state". This state, which is the most unstable in the folding pathway, and its structured core (a "nucleus") are distinguished by their essential influence on the folding/unfolding kinetics. In the second part of the paper, a theory of protein folding rates and related phenomena is presented. First, it is shown that the protein size determines the range of a protein's folding rates in the vicinity of the point of thermodynamic equilibrium between the native and denatured states of the protein. Then, we present methods for calculating folding and unfolding rates of globular proteins from their sizes, stabilities and either 3D structures or amino acid sequences. Finally, we show that the same theory outlines the location of the protein folding nucleus (i.e., the structured part of the transition state) in reasonable agreement with experimental data.     

Mechanism of simultaneously refolding and purification of proteins by hydrophobic interaction chromatographic unit and applications

The hydrophobic amino acid residues of a denatured protein molecule tend to react with the particles of the stationary phase of hydrophobic interaction chromatography (STHIC). These hydrophobic interactions prevent the denatured protein molecules from aggregating with each other. The STHIC can provide high enough energy to a denatured protein molecule to make it dehydration and to refold it into its native or various intermediate states. The outcome not only depends on the specific interactions between amino acids, the structure of STHIC, but also depends on the association between the STHIC and mobile phase. The mechanism of protein refolding and the principle of its quality control by HPHIC were also presented. By appropriate selection of the chromatographic condition, several denatured proteins can be refolded and separated simultaneously in a single chromatographic run. A specially designed unit, with diameter much larger than its length, was designed and employed for both laboratory and preparative     

2D correlation analysis of the continuum in single molecule surface enhanced Raman spectroscopy

The role and the nature of the continuum in Surface Enhanced Raman Spectroscopy (SERS) are unclear. Here, two-dimensional (2D) covariance and correlation analysis is applied to single molecule SERS spectra on silver colloids with and without rhodamine 6G (native colloid). The resulting 2D covariance and correlation maps show that the sharp molecular Raman peaks from rhodamine 6G and the molecule responsible for the SERS peaks from the native colloid are correlated to different continua even though both continua are present in each data set. This suggests that two distinct active sites on the silver colloids produce the two different continua, and that each site has some molecular specificity.     

Heat shock protein (hsp 70)-related epitopes are common allergenic determinants for barley and corn antigens

IgE reactive components of barley and corn were compared using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotted with sera from workers exposed to complex bioaerosols. The antibody made against Arabdopsis heat shock protein (hsp 70) was used to identify those components equivalent to hsp 70 in molecular size. Components with a molecular mass of 69 kDa and 33 kDa were positively reacted, and immunoblots of two-dimensional polyacrylamide gel electrophoresis were compared.     

In situ electrochemical scanning tunnelling microscopy investigation of structure for horseradish peroxidase and its electricatalytic property

Immobilization of protein molecules is a fundamental problem for scanning tunnelling microscopy (STM) measurements with high resolution. In this paper, an electrochemical method has been proved to be an effective way to fix native horseradish peroxidase (HRP) as well as inactivated HRP from electrolyte onto a highly oriented pyrolytic graphite (HOPG) surface. This preparation is suitable for both ex situ and in situ electrochemical STM (ECSTM) measurements. In situ STM has been successfully employed to observe totally different structures of HRP in three typical cases: (1) in situ ECSTM reveals an oval-shaped pattern for a single molecule in neutral buffer solution, which is in good agreement with the dimension determined as 6.2×4.3×1.2. nm³ by ex situ STM for native HRP; (2) in situ ECSTM shows that the adsorbed HRP molecules on HOPG in a denatured environment exhibit swelling globes at the beginning and then change into a V-shaped pattern after 30 min; (3) in situ ECSTM reveals a black hole in every ellipsoidal sphere for inactivated HRP in strong alkali solution. The cyclic voltammetry results indicate that the absorbed native HRP can directly catalyse the reduction of hydrogen peroxide, demonstrating that a direct electron transfer reduction occurred between the enzyme and HOPG electrode, whereas the corresponding cyclic voltammograms for denatured HRP and inactivated HRP adsorbed on HOPG electrodes indicate a lack of ability to catalyse H₂O₂ reduction, which confirms that the HRP molecules lost their biological activity. Obviously, electrochemical results powerfully support in situ STM observations.     

Molecular dynamics for surfactant-assisted protein refolding

Surfactants are widely used to refold recombinant proteins that are produced as inclusion bodies in E. Coli. However, the microscopic details of the surfactant-assisted protein refolding processes are yet to be uncovered. In the present work, the authors aim to provide insights into the effect of hydrophobic interactions of a denatured protein with surfactant molecules on the refolding kinetics and equilibrium by using the Langevin dynamics for coarse-grained models. The authors have investigated the folding behavior of a beta-barrel protein in the presence of surfactants of different hydrophobicities and concentrations. It is shown that the protein folding process follows a "collapse-rearrangement" mechanism, i.e., the denatured protein first falls into a collapsed state before acquiring the native conformation. In comparison with the protein folding without surfactants, the protein-surfactant hydrophobic interactions promote the collapse of a denatured protein and, consequently, the formation of a hydrophobic core. However, the surfactants must be released from the hydrophobic core during the rearrangement step, in which the native conformation is formed. The simulation results can be qualitatively reproduced by experiments.     

Development and validation of a highly sensitive ELISA for the determination of pharmaceutical indomethacin in water samples

The development and validation of a highly sensitive and specific indirect competitive enzyme-linked immunosorbent assay (ELISA) for the detection of pharmaceutical indomethacin in water samples was presented. The immunogen and coating antigen were prepared by covalently linking indomethacin to bovine serum albumin and ovalbumin by anhydride ester method. Two rabbits were immunized by standard immunization processes and the superior antibody was characterized in terms of sensitivity, specificity, precision, accuracy and stability. Under optimal experimental conditions, the standard curve was constructed in the concentration range of 0.01-10 ng/mL. For 10 consecutive standard curves run in 2 weeks, IC₅₀ value (the concentration of analyte producing 50% of inhibition) were found within 0.10-0.25 ng/mL, and the detection limit (DL) at a signal-to-noise ratio of 3 (S/N = 3) was about 0.01 ng/mL. The antiserum recognized acemetacin, a precursor of indomethacin with 92.3% cross-reactivity, while the cross-reactivity values of antiserum with other tested compounds were very low. From the spiking experiments, the recoveries were found within 98-123%. The ELISA was applied for the determination of indomethacin in different water samples and the results were confirmed by conventional HPLC. The correlation coefficient of 0.988 was obtained, demonstrating a good correlation of ELISA with HPLC.