Streptococcal protein G: a sensitive tool for detection of antibodies to human immunodeficiency virus proteins in Western blot analysis

A Dynamic Model of pH-Induced Protein G'e Higher Order Structure Changes derived from Mass Spectrometric Analyses

To obtain insight into pH change-driven molecular dynamics, we studied the higher order structure changes of protein G'e at the molecular and amino acid residue levels in solution by using nanoESI- and IM-mass spectrometry, CD spectroscopy, and protein chemical modification reactions (protein footprinting). We found a dramatic change of the overall tertiary structure of protein G'e when the pH was changed from neutral to acidic, whereas its secondary structure features remained nearly invariable. Limited proteolysis and surface-topology mapping of protein G'e by fast photochemical oxidation of proteins (FPOP) under neutral and acidic conditions reveal areas where higher order conformational changes occur on the amino-acid residue level. Under neutral solution conditions, lower oxidation occurs for residues of the first linker region, whereas greater oxidative modifications occur for amino-acid residues of the IgG-binding domains I and II. We propose a dynamic model of pH-induced structural changes in which protein G'e at neutral pH adopts an overall tight conformation with all four domains packed in a firm assembly, whereas at acidic pH, the three IgG-binding domains form an elongated alignment, and the N-terminal, His-tag-carrying domain unfolds. At the same time the individual IgG-binding domains themselves seem to adopt a more compacted fold. As the secondary structure features are nearly unchanged at either pH, interchange between both conformations is highly reversible, explaining the high reconditioning power of protein G'e-based affinity chromatography columns.

"De-novo" amino acid sequence elucidation of protein G'e by combined "top-down" and "bottom-up" mass spectrometry

Mass spectrometric de-novo sequencing was applied to review the amino acid sequence of a commercially available recombinant protein G´ with great scientific and economic importance. Substantial deviations to the published amino acid sequence (Uniprot Q54181) were found by the presence of 46 additional amino acids at the N-terminus, including a so-called "His-tag" as well as an N-terminal partial α-N-gluconoylation and α-N-phosphogluconoylation, respectively. The unexpected amino acid sequence of the commercial protein G' comprised 241 amino acids and resulted in a molecular mass of 25,998.9 ± 0.2 Da for the unmodified protein. Due to the higher mass that is caused by its extended amino acid sequence compared with the original protein G' (185 amino acids), we named this protein "protein G'e." By means of mass spectrometric peptide mapping, the suggested amino acid sequence, as well as the N-terminal partial α-N-gluconoylations, was confirmed with 100% sequence coverage. After the protein G'e sequence was determined, we were able to determine the expression vector pET-28b from Novagen with the Xho I restriction enzyme cleavage site as the best option that was used for cloning and expressing the recombinant protein G'e in E. coli. A dissociation constant (K(d)) value of 9.4 nM for protein G'e was determined thermophoretically, showing that the N-terminal flanking sequence extension did not cause significant changes in the binding affinity to immunoglobulins.

Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy

MOTIVATION

Hot spots are residues comprising only a small fraction of interfaces yet accounting for the majority of the binding energy. These residues are critical in understanding the principles of protein interactions. Experimental studies like alanine scanning mutagenesis require significant effort; therefore, there is a need for computational methods to predict hot spots in protein interfaces.

RESULTS

We present a new intuitive efficient method to determine computational hot spots based on conservation (C), solvent accessibility [accessible surface area (ASA)] and statistical pairwise residue potentials (PP) of the interface residues. Combination of these features is examined in a comprehensive way to study their effect in hot spot detection. The predicted hot spots are observed to match with the experimental hot spots with an accuracy of 70% and a precision of 64% in Alanine Scanning Energetics Database (ASEdb), and accuracy of 70% and a precision of 73% in Binding Interface Database (BID). Several machine learning methods are also applied to predict hot spots. Performance of our empirical approach exceeds learning-based methods and other existing hot spot prediction methods. Residue occlusion from solvent in the complexes and pairwise potentials are found to be the main discriminative features in hot spot prediction.

CONCLUSION

Our empirical method is a simple approach in hot spot prediction yet with its high accuracy and computational effectiveness. We believe that this method provides insights for the researchers working on characterization of protein binding sites and design of specific therapeutic agents for protein interactions.

AVAILABILITY

The list of training and test sets are available as Supplementary Data at http://prism.ccbb.ku.edu.tr/hotpoint/supplement.doc.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Cloning and expression of Rift Valley fever virus nucleocapsid (N) protein and evaluation of a N-protein based indirect ELISA for the detection of specific IgG and IgM antibodies in domestic ruminants

Serodiagnosis of Rift Valley fever (RVF) currently relies on the use of live or inactivated whole virus as antigens. The recombinant nucleocapsid (N) protein of RVF virus was tested for diagnostic applicability in an indirect enzyme-linked immunosorbent assay (I-ELISA), using sera from experimentally infected sheep (n=128), vaccinated sheep (n=240), and field-collected sera from sheep (n=251), goats (n=362) and cattle (n=100). The N-protein based I-ELISA performed at least as good as VN and HI tests. In goat the diagnostic sensitivity (D-Sn) and specificity (D-Sp) of the I-ELISA was 100% when using the anti-species IgG conjugate. Using protein G as a detection system, the D-Sn and D-Sp in goats were 99.4% and 99.5%, in sheep field sera both 100%, in cattle 100% and 98.3%, respectively. The I-ELISA based on recombinant N-protein has the potential to complement the traditional assays for serodiagnosis of RVF. Advantages of the N-protein are its safety, stability and cost-effectiveness in use and production.

Binding properties of Streptococcus suis for immunoglobulin G and other plasma proteins

Immunoglobulin G (IgG) binding proteins on the surface of Streptococcus suis could be readily detected by direct cultivation of the bacteria on nitrocellulose membranes and subsequent treatment of the membranes with human IgG. Among the 75 S. suis isolates tested two cultures (S. suis P43, S. suis P143) caused a blue colouration of the membranes indicating IgG binding activities. The IgG binding proteins could be solubilized by heat treatment of the bacteria at an acid pH and also by mutanolysin treatment. Western blot analysis revealed numerous protein bands with IgG binding activities. The IgG binding proteins were also released into the culture supernatant of the bacteria. This could be detected for 51 of the 75 S. suis using a microfiltration assay. In binding studies with 125I-IgG S. suis P43 and S. suis P143 but none of the other S. suis isolates showed a significant binding of the protein. These two cultures additionally bound 125I-albumin, 125I-alpha 2-macroglobulin and 125I-fibrinogen all from humans but not 125I-chicken IgG or 125I-human haptoglobin 2-1. The binding profiles of the two S. suis cultures tested indicate a close relation of these binding proteins with streptococcal protein G.

Further studies on immunoglobulin G- and albumin-binding properties of streptococci of serological group L

In this study, all 88 streptococci of serological group L isolated from cows, pigs, poultry and humans bound 125I-immunoglobulin G, and, in addition, 22 cultures interacted with 125I-albumin. IgG- and albumin-binding sites were solubilized from the streptococcal surface by heat extraction at an acid pH and also by mutanolysin treatment of the bacteria. Western blot analysis of these binding proteins revealed that almost identical protein bands were responsible for 125I-IgG and -albumin binding. Certain protein fractions of the cultures interacted exclusively with 125I-IgG, indicating that there are two groups of IgG receptors among streptococci of this serogroup.

Europium-labelled recombinant protein G. A fast and sensitive universal immunoreagent for time-resolved immunofluorometry

Recombinant protein G was labelled with europium by conjugating the protein with Eu3+ chelate of a p-isothiocyanatobenzyl derivative of diethylenetriaminetetraacetic acid, a bifunctional chelating agent specifically optimized for labelling of immunoreagents with lanthanide ions. The labelling produced a universal reagent for time-resolved fluorometric immunoassays based on the principle of dissociative fluorescence enhancement (DELFIA). The optimum labelling level of about eight chelates per protein yielded a highly sensitive and stable reagent which retained its affinity for IgG and exhibited low non-specific binding to coated solid surfaces. The reagent was evaluated in an immunoassay of anti-tetanus antibodies in human serum samples and the results were compared to those obtained with Eu-labelled polyclonal and Eu-labelled monoclonal anti-human IgG antibodies. The detection limit of the assay was 0.003 mU/ml (0.3 microU per assay well). After a 100-fold dilution of the samples, the assay range extended from 0.3 mU/ml to 100,000 mU/ml with a linear range of five log orders. The incubation with Eu-labelled protein G reached equilibrium after a 15 min incubation. The rapid kinetics, the low non-specific background and the high specific binding suggest that Eu-protein G can serve as a universal label for immunoassays based on IgG binding to solid surfaces.

Isolations of protein A and protein G from the bacterial surface

Ten tested cultures each of Staphylococcus aureus (S. aureus) and of Streptococcus belonging to serological group G bound human IgG to a high extent. Protein A could be solubilized from strain Cowan I of S. aureus by lysozyme, mutanolysine, hydroxylammoniumchloride, hot acid extraction or lysostaphin and subsequently purified by affinity chromatography on human IgG-sepharose. The purified protein A preparation had molecular weights between 29,000 and 63,000 D and inhibited binding of 125I-labeled human IgG to S. aureus Cowan I. Protein G could be solubilized from strain 26540 of the G-streptococci with lysozyme or hot acid extraction and purified by affinity chromatography on human IgG-sepharose. The purified protein G revealed a molecular weight of 67,000 D and inhibited binding of human IgG to the G-streptococci.

Protein G genes: structure and distribution of IgG-binding and albumin-binding domains

Protein G (also designated Fc receptor type III) is the IgG-binding protein of group C and G streptococci. Protein G has also been shown to bind human serum albumin but at a site that is structurally separated from the IgG-binding region. From the known gene sequence of protein G, two synthetic oligonucleotides were constructed for use as probes in DNA-hybridization experiments to study the structure and distribution of the albumin- and IgG-binding regions in bacterial strains belonging to different species. Thus, one of the probes corresponded to repeats within the IgG-binding region (I) and the other corresponded to repeats in the albumin-binding encoding region (II). Probe I showed strong hybridization to DNA isolated from 31 human group C and G strains, whereas hybridization to probe II was variable. With the three restriction endonucleases used, three restriction patterns were found in Southern blot experiments. No fundamental difference could be detected in hybridization experiments, either between strains of group C and G streptococci, or between isolates of different clinical origin. No hybridization to DNA from other bacterial species was found.

Enzyme linked immunosorbent assay using alkaline phosphatase conjugated with streptococcal protein G

Protein G, an IgG-binding protein, purified from the surface of group G streptococci, was coupled to alkaline phosphatase. The conjugate was used for detection of polyclonal goat and rabbit antibodies and monoclonal mouse IgG1, IgG2a and IgG2b in an enzyme-linked immunosorbent assay. A two-step coupling procedure was used, in which glutaraldehyde was allowed to react with the enzyme, excess glutaraldehyde was then removed by dialysis, and finally protein G added to the glutaraldehyde-activated and polymerized alkaline phosphatase. The activity and yield of the conjugates were then tested in an enzyme-linked immunosorbent assay. Coupling of 25 micrograms protein G to 5 mg alkaline phosphatase gave a conjugate which could be used for more than 10,000 determinations with maximal antibody binding giving an absorbance of 2.0. Under these conditions, there was no need for separation of the reactants before using the protein G-alkaline phosphatase complex.