Self-association reaction of denatured staphylococcal nuclease fragments characterized by heteronuclear NMR

The self-association reaction of denatured staphylococcal nuclease fragments, urea-denatured G88W110, containing residues 1-110 and mutation G88W, and physiologically denatured 131-residue Delta 131 Delta, have been characterized by NMR at close to neutral pH. The two fragments differ in the extent and degree of association due to the different sequence and experimental conditions. Residues 13-39, which show significant exchange line broadening, constitute the main association interface in both fragments. A second weak association region was identified involving residues 79-105 only in the case of urea-denatured G88W110. For residues involved in the association reaction, significant suppression of the line broadening and small but systematic chemical shift variation of the amide protons were observed as the protein concentration decreased. The direction of chemical shift change suggests that the associated state adopts mainly beta-sheet-like conformation, and the beta-hairpin formed by strands beta 2 and beta 3 is native-like. The apparent molecular size obtained by diffusion coefficient measurements shows a weak degree of association for Delta 131 Delta below 0.4 mM protein concentration and for G88W110 in 4 M urea. In both cases the fragments are predominantly in the monomeric state. However, the weak association reaction can significantly influence the transverse relaxation of residues involved in the association reaction. The degree of association abruptly increases for Delta 131 Delta above 0.4 mM concentration, and it is estimated to form a 4 to 8 mer at 2 mM. It is proposed that the main region involved in association forms the core structure, with the remainder of residues largely disordered in the associated state. Despite the obvious influence of the association reaction on the slow motion of the backbone, the restricted mobility on the nanosecond timescale around the region of strand beta 5 is essentially unaffected by the association reaction and degree of denaturation.     

The accessibility of protein-bound dinitrophenyl groups to univalent fragments of anti-dinitrophenyl antibody.

A series of N-(N-dinitrophenylaminoalkyl)maleimides were sythesized with alkyl-chain lengths of two, four and six carbon atoms. When these compounds reacted with the thiol group of mercaptalbumin, the tryptophan fluorescence of the protein was quenched. This change in fluorescence was used to determine the rate of reaction of the Dnp (dinitrophenyl)-maleimides with mercaptalbumin. The second-order rate constants were similar to those observed in reactions between low-molecular-weight thiol compounds and maleimides. When N-(N-Dnp-aminoalkyl)succinimidomercaptalbumins were added to univalent fragments of anti-Dnp antibody the antibody fluorescence was quenched. Florescence-quenching titrations showed that the protein-bound Dnp groups were fully available to the antibody even when the alkyl chain was short. The apparent dissociation constants were significantly greater than that of the interaction between anti-Dnp antibody and the free hapten, 6-(N-Dnp)-aminohexanoate. The antibody fluorescence was quenched efficienty by [dnp-Lys41]ribonuclease A, also with an increased dissociation constant. It could be concluded from the increase in dissociation constant that the Dnp group spent no more than 0.1% of its time in the dissociated state, available to antibody. The second-order rate constants for the association between the Dnp-mercaptablumins and the antibody were determined and were similar in magnitude to those observed in other interactions between protein and anti-protein antibody.     

Long-lasting in vitro immune response to a distinct antigenic determinant of a bacterial protein. Cyclic changes of antibody titer and affinity.

Long-lasting (60 days or more) antibody responses in vitro by rabbit lymph node fragments to a distinct determinant of Escherichia coli beta-D-galactosidase were obtained by supplementing culture medium with fetal calf and horse serum. Antibodies released in the supernatant were removed every 3rd to 5th day together with the spent medium, without pooling to minimize intermixing of molecules synthesized far apart in time. Antibody titer, association constant, and heterogeneity index were measured in medium samples collected throughout the response in order to draw profiles of their changes under conditions whereby a limited number of clones synthesize antibodies in a closed system without connection to antigen depots, central lymphoid organs, and circulating cell and antibody pools. It was found that antibody affinity changes cyclically and that such cycles may be repeated. Cycles are composed of an ascendant limb with a gradual increase in affinity and a parallel diminution of heterogeneity. A descendant limb follows with the opposite modifications. High affinity antibodies predominate at the peak of the cycles, whereas low affinity molecules take over at the end of the cycles until the next ascendant limb begins; these persist after the last cycle has waned.     

Genetic control of immune response to staphylococcal nuclease. XII: Analysis of nuclease antigenic determinants using anti-nuclease monoclonal antibodies

Summary SJL mice, which are high responders to Staphylococcal nuclease (nuclease), were immunized and used to produce hybridoma cell lines secreting anti-nuclease monoclonal antibodies (mAb). Ten stable clones were derived from a single fusion. Seven of these produced antibodies of the IgG_1, isotype and were more precisely characterized for antigenic specificity. Only one hybridoma cell line (54-10-4) produced anti-nuclease antibodies capable of inhibiting enzymatic activity of nuclease. Binding inhibition analyses strongly suggest that the other monoclonal antibodies, which failed to inhibit nuclease activity detect two different antigenic regions, or epitopes, of the molecule: epitope cluster 1 domain is defined by hybridomas 54-2-7, 54-5-2, 54-9-8, and 54-10-8; epitope cluster 2 by 54-5-1 and 54-1-9. Because of its capacity to inhibit nuclease enzymatic activity mAb 54-10-4 was considered specific for a third epitope of the nuclease molecule called epitope 3. Binding studies of these monoclonal antibodies were extended to peptide fragments of the nuclease molecule in order to examine possible cross-reactions with such fragments, as has previously been reported for antibodies purified from polyclonal antisera. Monoclonal antibodies specific for epitope cluster 1 on the native molecule also bound to the fragments 1–126 and 49–149 but failed to bind to fragment 99–149, suggesting that the corresponding epitope(s) is determined by amino acids localized between residues 49 and 99. The epitope clusters 2 and 3 appeared to be expressed only on the native molecule. Monoclonal antibodies of different clusters exhibited very different migration patterns on isoelectric focusing while monoclonal antibodies of the same cluster were indistinguishable, which suggests that they may have originated from the same B cell precursor. Taken together these data suggest that this panel of monoclonal antibodies detects at least three distinct epitopes of the nuclease molecule, one of which could be involved in the determination of the enzymatic site.     

Searching for folding initiation sites of staphylococcal nuclease: a study of N-terminal short fragments

The N-terminal short fragments of staphylococcal nuclease (SNase), SNase20, SNase28, and SNase36, corresponding to the sequence regions, Ala1-Gly20, Ala1-Lys28, and Ala1-Leu36, respectively, as well as an 8-residue peptide (Ala17-Ile18-Asp19-Gly20-Asp21-Thr22-Val23-Lys24) have been synthesized. The conformational states of these fragments were investigated using CD and NMR spectroscopy in aqueous solution and in trifluoroethanol (TFE)-H(2)O mixture. SNase20 containing a sequence corresponding to a bent peptide in native SNase shows a transient population of bend-like conformation around Ala12-Thr13-Leu14 in TFE-H(2)O mixture. The sequence region of Ala17-Thr22 of SNase28 displays a localized propensity for turn-like conformation in both aqueous solution and TFE-H(2)O mixture. The conformational ensemble of SNase36 in aqueous solution includes populated turn-like conformations localized in sequence regions Ala17-Thr22 and Tyr27-Gln30. The analysis suggests that these sequence regions, which form the regular secondary structures in native protein, may serve as the folding nucleation sites of SNase fragments of different chain lengths starting from the N-terminal end. Thus, the formation of bend- and turn-like conformations of these sequence regions may be involved in the early folding events of the SNase polypeptide chain in vitro.     

金黄色葡萄球菌核酸酶A与不同外源DNA片段融合表达的作用比较

金黄色葡萄球菌核酸酶A(Staphylococcal nuclease A,SNA)可用于菌蜕制备中宿主菌的进一步灭活及残存遗传物质的去除。关于SNA在去除了信号肽后是否仍能分泌至胞外以及是否需要融合其他氨基酸片段才能在宿主菌胞质中发挥作用尚存争议。为厘清这一争议,分别构建一系列含SNA、SNA与λ噬菌体cro基因或结核杆菌脲酶基因部分序列的融合片段c SNA或u SNA的温控质粒并对其在大肠杆菌内的作用进行评价。结果显示,SNA、c SNA和u SNA的表达产物对大肠杆菌的4 h灭活率分别为99.9%、99.8%和74.2%。升温诱导30 min后,SNA和c SNA即可在宿主菌胞内被检出,而u SNA需1 h;相较之下,SNA和c SNA在培养液上清中的被检出时间要晚1 h,u SNA则晚2 h。对三者的核酸酶活性检测均为:SNA﹥c SNA﹥u SNA,且胞外活性都显著低于胞内。此外,SNA和c SNA在诱导2 h后即将宿主基因组成功降解,而u SNA则在整个实验期间均未能使宿主基因组完全降解。这表明SNA、c SNA和u SNA的表达产物均具有核酸酶活性,可被动释放至胞外,外源DNA片段的融入反而会降低SNA的核酸酶活性。     

Interaction of dinitrophenyl groups bound to bovine serum albumin with univalent fragments of anti-dinitrophenyl antibody

Two lysine residues of bovine serum albumin reacted with 1-fluoro-2,4-dinitrobenzene with apparent second-order rate constants approx. 500-times greater than those observed in similar reactions with low-molecular-weight lysine derivatives. A series of dinitrophenyl (Dnp)-bovine serum albumins were prepared and their ability to bind univalent fragments of anti-Dnp antibody was measured by fluorescence-quenching titrations. Compared with the Dnp group of the free hapten, 6-N-Dnp-aminohexanoate, the majority of the protein-bound Dnp groups were unavailable to the antibody at pH8.0. When the same Dnp-albumins were titrated at pH3.0 the availability of the Dnp groups increased approx. 3-fold. Dnp-albumins were treated with pepsin at pH3.0 and Dnp-containing fragments isolated by chromatography on DE-52 DEAE-cellulose. Fluorescence-quenching titrations showed that the Dnp groups on the fragments behaved like the free hapten with respect to quenching efficiency, although with an increased dissociation constant. The association between the Dnp-albumins and the antibody was measured also by difference-spectral titrations at high protein concentrations. Antibody binding was increased under these conditions, but the Dnp group of mono-Dnp-albumin remained unavailable to antibody. We propose that the reactive lysine residues are located in clefts between the globular sub-domains of the single polypeptide chain. Dnp groups attached to these lysine residues are fully exposed to the solvent, but binding of the macromolecular probe, anti-Dnp antibody, is sterically hindered by the adjacent surface of the albumin molecule.     

Residual structure in large fragments of staphylococcal nuclease: effects of amino acid substitutions

In an attempt to develop a model of the denatured state of staphylococcal nuclease that can be analyzed experimentally under physiological conditions, a series of four large fragments of this small protein which extend from residues 1 to 103, 1 to 112, 1 to 128, and 1 to 136 have been generated through the overexpression of nuclease genes containing stop codons at defined positions. Large amounts of protein fragments were accumulated in induced cells and were purified by carrying out all fractionation steps in the presence of 6 M urea. The far-ultraviolet circular dichroism spectra of all four fragments suggested the presence of small to moderate amounts of residual structure. When the CD spectra were monitored as a function of concentrations of the tight-binding ligands Ca2+ and thymidine 3',5'-bisphosphate and the known affinity constants for wild-type nuclease (1-149) were used, apparent equilibrium constants of 160 and 2000 for the reversible denaturation reaction for fragments 1-136 and 1-128, respectively, were estimated. Four single and two double mutations, all of which exhibit unusual behavior in the full-length protein on solvent denaturation [Shortle, D., & Meeker, A. K. (1986) Proteins: Struct., Funct., Genet. 1, 81-89] and thermal denaturation [Shortle, D., Meeker, A. K., & Freire, E. (1988) Biochemistry 27, 4761-4768], were recombined into the 1-136 and 1-128 fragment expression vectors, and purified mutant fragments were characterized.(ABSTRACT TRUNCATED AT 250 WORDS)     

The antigenic surface of staphylococcal nuclease. I. Mapping epitopes by site-directed mutagenesis.

The analysis of the antigenic surface of staphylococcal nuclease was begun by generating and characterizing a panel of mAb. Twelve mAb were selected from a large number of anti-nuclease mAb and characterized for affinity and isotype, by their ability to block enzyme activity, and by complementation and competitive inhibition assays for the relative location of epitopes. The mAb were placed in complementation groups based on their distinct binding patterns. These groups define a series of eight overlapping epitopes that are estimated to cover a large portion of the nuclease surface. Four mAb blocked the enzyme activity of nuclease. The epitopes defined by two of these four mAb were localized on the surface of nuclease using single amino acid variant Ag generated by site-directed mutagenesis of the cloned nuclease coding sequence. mAb-25 maps to residue 46 which is located at the edge of the enzyme active site consistent with its ability to inhibit enzyme activity. mAb-19, which also blocks enzyme activity and belongs to the same complementation group as mAb-25, was unaffected by the substitution at position 46. This suggests that mAb-19 and mAb-25, if they do react with the same epitope, have differences in fine specificity. mAb-22 blocks enzyme activity and belongs to an overlapping complementation group. The fourth mAb, mAb-1, which belongs to a distinct, nonoverlapping, complementation group, does not blocks enzyme activity, and is directed to a region of nuclease that includes the amino acid at position 133. This residue is located a short distance from the active site in a region that has been suggested to participate in binding of DNA, a substrate for nuclease. Therefore, the four epitopes defined by these mAb are localized at or near the enzyme active site.     

Cold denaturation of staphylococcal nuclease

It has been shown that the structure of staphylococcal nuclease breaks down reversibly both at a temperature increase above 20 degrees C and at its decrease. Both the heat and cold denaturations of protein are well approximated by a transition between two states differing in heat capacity, which means that the whole protein molecule represents a unique cooperative system with a well developed hydrophobic core. The transfer to a denatured state at a temperature decrease is accompanied by heat release and leads to a complete loss of the unique tertiary structure, decrease of the helicity and increase of the hydrodynamic volume of the molecule.     

Thermal denaturation of staphylococcal nuclease

The fully reversible thermal denaturation of staphylococcal nuclease in the absence and presence of Ca2+ and/or thymidine 3',5'-diphosphate (pdTp) from pH 4 to 8 has been studied by high-sensitivity differential scanning calorimetry. In the absence of ligands, the denaturation is accompanied by an enthalpy change of 4.25 cal g-1 and an increase in specific heat of 0.134 cal K-1 g-1, both of which are usual values for small globular proteins. The temperature (tm) of maximal excess specific heat is 53.4 degrees C. Each of the ligands, Ca2+ and pdTp, by itself has important effects on the unfolding of the protein which are enhanced when both ligands are present. Addition of saturating concentrations of these ligands raises the denaturational enthalpy to 5.74 cal g-1 in the case of Ca2+ and to 6.72 cal g-1 in the case of pdTp. The ligands raise the tm by as much as 11 degrees C depending on ligand concentration. From the variation of the denaturational enthalpies with ligand concentrations, binding constants at 53 degrees C equal to 950 M-1 and 1.4 X 10(4) M-1 are estimated for Ca2+ and pdTp, respectively, and from the enthalpies at ligand saturation, binding enthalpies at 53 degrees C of -15.0 and -19.3 kcal mol-1.     

Characterization of the antigenic determinant on Fusarium oxysporum recognized by a genus-specific monoclonal antibody

The antigenic determinant of a monoclonal antibody (MAb) (API9-2) having specific reactivity with the fungi grouped into the genus Fusarium was analyzed. The culture supernatant of the fungi showed antigenicity against MAb API9-2, proving that the antigen exists as an exoantigen. The heat-resistant, proteinase K-resistant and periodate oxidation-labile features of the antigenic determinant indicated its carbohydrate nature. Also, lectin affinity tests and thin-layer chromatography analysis suggested that the monosaccharide making up the antigenic determinant was mainly mannose. Considering previous reports that the antigen exists on the surface of mycelia (by immunofluorescence assay) and is a - 55 kDa molecule (by Western blotting analysis), it was concluded that the antigenic determinant of MAb API9-2 on F. oxysporum is a mannan component existing on the surface of mycelia.     

Genetic control of the immune response to staphylococcal nuclease

Summary Antibody responses of inbred strains of mice to staphylococcal nuclease were studied by isoelectric focusing in polyacrylamide gels followed by in situ labeling of focused antibodies with radioactive antigen. All A/J mice examined produced antinuclease antibodies of limited heterogeneity, and although there was individual variation in the focusing patterns observed, a characteristic spectrotype produced by all of the animals could be discerned. In order to determine the possible relationship between this characteristic spectrotype and the cross-reactive idiotypes of A/J antinuclease antibodies previously described (7), focused antibodies were also examined with a radioactively labeled pig anti-(A/J antinuclease) anti-idiotypic antibody preparation. Using this reagent, similar spectrotypes to those observed for antigen binding were seen in all of the individual A/J sera, suggesting that cross-reactive idiotype expression is a reflection of the characteristic spectrotypes observed. The same labeled anti-idiotypic reagent revealed characteristic but different spectrotypes when used to develop focused antinuclease antibodies from individual mice of other strains, suggesting that the use of similar variable region structures may be a common feature of the antinuclease response in mice of different allotypes. These studies thus provide a structural basis for the genetics of idiotype expression defined previously by serologic analysis.