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The phage lambda terminase enzyme: 2. Refolding of the gpNu1 subunit from the detergent-denatured and guanidinium hydrochloride-denatured state yields different oligomerization states and altered protein stabilities.

The terminase enzyme from bacteriophage lambda is responsible for packaging a single genome within the viral capsid. Gold and co-workers have developed a scheme for the solubilization of the small terminase subunit (gpNu1) from inclusion bodies using the strong detergent sarkosyl and purification of the protein to homogeneity (gpNu1SRK) (Parris et al., J Biol Chem 1994;269:13564-13574). We have developed a similar purification scheme except that guanidinium hydrochloride was used to denature the insoluble protein (gpNu1GDN). The circular dichroism (CD) spectra of both protein preparations suggest that they are predominantly alpha-helical when purified and stored in Tris buffers. Moreover, thermal denaturation of the proteins thus purified yielded similar thermodynamic parameters for unfolding (T(m), delta Hm and delta Sm of unfolding of approximately 306 K, approximately 22 kcal/mol and approximately 70 cal/mol.K, respectively). Interestingly, however, when the proteins were purified and stored in imidazole buffers, the gpNu1SRK preparation lost a significant amount of secondary structure and was more stable to both thermally-induced and guanidinium HCl-induced denaturation than was gpNu1GDN. The purified gpNu1 monomers oligomerize into apparent tetramers and hexamers in solution and the distribution between these two oligomeric states and into higher order aggregates depends upon buffer composition, salt concentration and protein concentration. Moreover, differences in the oligomerization state of gpNu1SRK and gpNu1GDN under identical buffer conditions were observed. The significance of these results with respect to the biological role of the phage lambda gpNu1 protein are discussed.

Bacteriophage lambda↗

Eosin interaction of alpha-synuclein leading to protein self-oligomerization.

Among various dyes including congo red, thioflavin S, thioflavin T, eosin, rhodamine 6G, and phenol red, the eosin was the only dye that induced self-oligomerization of alpha-synuclein in the presence of a chemical coupling reagent of N-(ethoxycarbonyl)-2-ethoxy-1, 2-dihydroquinoline. To analyze chemical nature of the eosin interaction with alpha-synuclein, the phenomenon of self-oligomerization was further examined with eosin congeners such as ethyl eosin, eosin B, phloxine B, erythrosin B, and rose bengal. The followings are the conclusions we have reached. First of all, intactness of the benzoate moiety of eosin and the negative charge on the carboxylic group of the dye are important factors leading to the specific interaction with alpha-synuclein. Secondly, the localized negative charge on the xanthene moiety of eosin is another critical factor for the interaction. As far as substituting halides are concerned, bromides and iodides on the xanthene moiety of the dyes do not make any difference on the alpha-synuclein interaction because both eosin and erythrosin B have induced the common phenomenon of self-oligomerization. The binding curve between eosin and alpha-synuclein was sigmoidal as the dye concentrations were increased. A double reciprocal plot of the saturation curve showed that the maximum number of eosin binding sites on alpha-synuclein was 1.85 with a dissociation constant of 390 microM. The dye binding to the protein appeared to occur via a positive cooperativity. The eosin binding site(s) was suggested to be located predominantly on the NAC region and partly related to the acidic C-terminus of alpha-synuclein. It has been, therefore, expected that this information might be useful to develop alpha-synuclein interactive molecules, which could provide eventual preventive or possible therapeutic means against various alpha-synuclein related disorders including Parkinson's disease.

Dose-Response Relationship, Drug↗

Involvement of the HIV-1 external envelope glycoprotein 120 (gp120) C2 region in gp120 oligomerization.

A synthetic peptide resembling the C2 region of human immunodeficiency virus type 1 (HIV-1) gp120 (C2-Lai: amino acids (aa) 273-288), inhibited (C50 = 200 microM) gp120 calcium-dependent binding of N-acetyl-beta-D-glucosaminyl and mannosyl residues exposed on natural glycoprotein bovine fetuin whereas a peptide derived from an aa sequence downstream of C2-Lai (C2-SC19) had no such effect (C50 > 1000 microM). No calcium-carbohydrate-specific binding of C2-Lai to fetuin was detected. In addition, C2-Lai was also found to inhibit the calcium-dependent oligomerization of gp120: while recombinant gp120 (rgp120) was recovered mainly as oligomers (78%) in 10 mM CaCl2, in contrast to 100% monomers in 1mM CaCl2, mostly monomers (67%) were found in 10 mM CaCl2 in the presence of C2-Lai. Peptide C2-SC19 and carbohydrate structures such as fetuin, fucoidin, dextran or mannan did not significantly affect gp120 oligomerization. Electrophoresis and gel filtration analysis also showed that C2-Lai aggregated in the form of 20 kDa compounds, which is compatible with association of 10 molecules. Taken together, these results demonstrate that the C2 domain is involved in gp120 oligomerization and suggest that gp120 oligomers but not monomers have specific carbohydrate binding properties.

Binding Sites↗

Oligomerization properties of the acidic ribosomal P-proteins from Saccharomyces cerevisiae: effect of P1A protein phosphorylation on the formation of the P1A-P2B hetero-complex.

Acidic ribosomal P-proteins form, in all eukaryotic cells, a lateral protuberance, the so-called 'stalk', which is directly involved in translational activity of the ribosomes. In Saccharomyces cerevisiae cells, there are four distinct P-proteins: P1A, P1B, P2A and P2B. In spite of the high level of their structural homology, they are not completely equivalent and may perform different functions. As yet, the protein-protein interactions between yeast P-proteins have not been fully defined. In this paper, the interplay between yeast P-proteins has been investigated by means of a two-hybrid system, chemical cross-linking and gel filtration. The data presented herein show that all P-proteins are able to form homo-oligomeric complexes. By analyzing hetero-interactions, we were able to detect strong interactions between P1A and P2B proteins. Additionally, the pair of P1B and P2A proteins is also able to form a hetero-complex, though at a very low efficiency. All P-proteins are phosphorylated by numerous protein kinases. Using the multifunctional protein kinase CK II, we have shown that incorporation of phosphate into P1A protein can exert its effect on the hetero-oligomerization process, namely by preventing the formation of the hetero-oligomer P1A-P/P2B. These findings are the first to show differences in the oligomerization behavior of the yeast P-proteins; moreover, they emphasize a significant impact of the phosphorylation on the formations of P-protein complex.

Chromatography, Gel↗

Vaccine-induced antibodies to the native, oligomeric envelope glycoproteins of primary HIV-1 isolates.

A simple and sensitive method for measuring antibodies to primary human immunodeficiency virus type 1 (HIV-1) isolates has been developed. The flow cytometric immuno-fluorescence assay detects antibodies that bind to the native, oligomeric form of the envelope glycoprotein (gp120) expressed on the surface of PM-1 cells infected with primary isolates of HIV-1. Sera from people infected with HIV-1 or those immunized with recombinant gp120 vaccines were tested. Significant correlation was observed between neutralizing activity and oligomeric gp120 binding activity. Thirteen to 100% of individuals immunized with the subtype B bivalent vaccine AIDSVAX B/B developed oligomeric gp120 binding antibodies against a variety of subtype B primary isolates. For several isolates, AIDSVAX B/B sera reacted better than monovalent AIDSVAX B sera, suggesting that addition of the second immunogen improved the breadth of the antibody response. Cross-subtype binding activities, induced by AIDSVAX B/B, were lower than activities to subtype B isolates, suggesting that additional immunogen(s) may be desirable in vaccine(s) formulated for geographic regions where non-B subtypes are dominant.

AIDS Vaccines↗

Oligomerization of Escherichia coli enterotoxin b through its C-terminal hydrophobic alpha-helix.

Using a chemical cross-linker and gel electrophoresis or a dot blot overlay assay, we studied protein-protein interaction of STb toxin, a 48-residue amphiphilic polypeptide causing intestinal disorders. For the first time, we report on the oligomerization property of STb. This enterotoxin forms hexamers and heptamers in a temperature-independent fashion in presence or absence of its receptor (sulfatide) anchored in a 50-nm liposome or as a free molecule. Full STb structure integrity is necessary for its oligomerization as this process is not observed under reducing conditions in the presence of beta-mercaptoethanol. STb treatment with tetramethylurea (TMU) and different detergents prevented oligomerization. Site-directed mutagenesis decreasing overall STb hydrophobicity in the hydrophobic alpha-helix resulted in the incapacity to form oligomers. Taken together, these data suggest that the C-terminal hydrophobic alpha-helix corresponds to the domain of STb-STb inter-binding where hydrophobic interaction is involved.

Amino Acid Sequence↗

What are oligomerization domains good for?

Collagen triple helices, coiled coils and other oligomerization domains mediate the subunit assembly of a large number of proteins. Oligomerization leads to functional advantages of multivalency and high binding strength, increased structure stabilization and combined functions of different domains. These features seen in naturally occurring proteins can be engineered by protein design by combining oligomerization domains with functional domains.

Animals↗

Oligomeric ring structure of the Bloom's syndrome helicase.

Bloom's syndrome is a recessive human genetic disorder associated with an elevated incidence of many types of cancer. The Bloom's syndrome gene product, BLM, belongs to the RecQ subfamily of DNA helicases and is required for the maintenance of genomic stability in human cells - in particular, the suppression of reciprocal exchanges between sister chromatids. We have investigated the quaternary structure of BLM using a combination of size-exclusion chromatography and electron microscopy with reference-free image processing. We found that BLM forms hexameric ring structures with an overall diameter of approximately 13 nm surrounding a central hole of approximately 3.5 nm diameter. A fourfold symmetric square form with approximately 11 nm sides and a hole of approximately 4 nm diameter was also detected, which might represent a distinct oligomeric species or a side view of the hexameric form. Chromatography studies indicated that the majority of enzymatically active BLM has an apparent molecular mass of > 700 kDa, which is consistent with an oligomeric structure for BLM. This provides the first structural analysis of an oligomeric ring helicase of eukaryotic cellular origin. These results have implications for the mechanism of action of BLM and suggest that other RecQ family helicases, including the WRN protein associated with Werner's syndrome, might also adopt ring structures.

Adenosine Triphosphatases↗

The structure of an engineered domain-swapped ribonuclease dimer and its implications for the evolution of proteins toward oligomerization.

BACKGROUND: Domain swapping has been proposed as a mechanism that explains the evolution from monomeric to oligomeric proteins. Bovine and human pancreatic ribonucleases are monomers with no biological properties other than their RNA cleavage ability. In contrast, the closely related bovine seminal ribonuclease is a natural domain-swapped dimer that has special biological properties, such as cytotoxicity to tumour cells. Several recombinant ribonuclease variants are domain-swapped dimers, but a structure of this kind has not yet been reported for the human enzyme. RESULTS: The crystal structure at 2 A resolution of an engineered ribonuclease variant called PM8 reveals a new kind of domain-swapped dimer, based on the change of N-terminal domains between the two subunits. The swapping is fastened at both hinge peptides by the newly introduced Gln101, involved in two intermolecular hydrogen bonds and in a stacking interaction between residues of different chains. Two antiparallel salt bridges and water-mediated hydrogen bonds complete a new interface between subunits, while the hinge loop becomes organized in a 3(10) helix structure. CONCLUSIONS: Proteins capable of domain swapping may quickly evolve toward an oligomeric form. As shown in the present structure, a single residue substitution reinforces the quaternary structure by forming an open interface. An evolutionary advantage derived from the new oligomeric state will fix the mutation and favour others, leading to a more extended complementary dimerization surface, until domain swapping is no longer necessary for dimer formation. The newly engineered swapped dimer reported here follows this hypothetical pathway for the rapid evolution of proteins.

Amino Acid Sequence↗

Crystal structure of transcription factor MalT domain III: a novel helix repeat fold implicated in regulated oligomerization.

BACKGROUND: MalT from Escherichia coli, the best-studied member of the MalT family of ATP-dependent transcriptional activators, regulates the genes for malto-oligosaccharide utilization. The active form of this 4 domain protein is a homooligomer, and its multimerization is induced by the binding of maltotriose. Domains II and III of MalT were suggested to mediate the oligomerization process, but its molecular mechanism and the specific functions of these domains remain to be identified. RESULTS: We solved the crystal structure of MalT domain III at 1.45 A resolution by multiple isomorphous replacement phasing. The structure reveals eight copies of a two-helix bundle motif arranged in a novel, right-handed superhelix fold with closed walls, followed by a small C-terminal subdomain. The MalT superhelix contains a potential maltotriose binding site and forms a large hydrophobic protein-protein interaction interface that mediates the contact between two MalT domain III molecules. Structure-based analysis of the two-helix bundle motifs revealed a novel degenerated sequence pattern, and repeats of this pattern could be identified in other regulator proteins. CONCLUSIONS: MalT domain III contains a novel superhelix fold. Its protein-protein interaction interface, however, resembles protein binding sites of other superhelical proteins, suggesting a model with domain III mediating MalT oligomerization. Maltotriose seems to modulate the interaction interface and MalT oligomerization by occupying the ligand binding site inside the superhelix. Similar structural and mechanistic features in other MalT protein-family members and unrelated regulator proteins are indicated by the reappearance of a novel sequence motif derived from the MalT domain III structure.

Amino Acid Motifs↗

Comparative ESI-MS study of approximately 2.2 MDa native hemocyanins from deep-sea and shore crabs: from protein oligomeric state to biotope.

In the past years, the potential of electrospray ionization mass spectrometry (ESI-MS) for the observation of intact weak interactions, such as non-covalent protein-ligand, protein-protein, protein-DNA complexes, has spread out. The coupling of ESI with time-of-flight (TOF) and quadrupole-time-of-flight (Q-TOF) analyzers has even enabled the detection of larger complexes with molecular weights greatly higher than 200 kDa. In this paper, we report a comparative ESI-MS study on the protein quaternary structure of native hemocyanins (Hc) from crabs living in different biotopes: a shore crab (Carcinus maenas) and two deep-sea crabs (Segonzacia mesatlantica and Bythograea thermydron). Hc is an extracellular blood protein, composed of several protein chains which can associate in large multimers. The goal of this study is to point out that the oligomerization state of native Hcs is biotope-dependent. Depending on the crab, ESI-MS analyses under non-denaturing conditions reveal different oligomeric forms present in equilibrium in solution. Molecular weights up to 2,235 kDa were measured for the associations of 30 subunits of the Bythograea thermydron Hc. Thanks to ESI-MS analyses, it could be concluded for the first time that the oligomerization state of native Hcs is dependent on the crab environment. The investigation of these different non-covalent self-assemblies is very important for the life history of crabs, since they are directly related with different oxygen binding abilities and thus, with their ability to colonize habitats with different oxygen contents.

Animals↗

Direct analysis of an oligomeric hindered amine light stabilizer in polypropylene materials by MALDI-MS using a solid sampling technique to study its photostabilizing action.

A novel method for the direct analysis of small amounts of an oligomeric hindered amine light stabilizer (HALS) occluded in polypropylene (PP) material was developed to study its photostabilizing action on the basis of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) using a solid sampling technique while avoiding troublesome solvent extraction. In this sampling protocol, the powdered mixture of PP composite sample containing trace amounts of an oligomeric HALS, Adekastab LA-68LD (MW = 1900), and the matrix reagent (dithranol) was spotted on the sample plate, then ion exchanged water was deposited onto the mixture to make a suspension, and finally, the dried mixture adhered on the plate was subjected to MALDI-MS measurement. On the mass spectrum thus obtained by the solid sampling MALDI, the molecular ions of the HALS desorbed from the PP composite were clearly observed as three major series of the HALS components in the range up to about m/z 7000 with little interference by the PP substrate and the other additives. Moreover, in the MALDI-MS spectra for the UV-exposed sample, the satellite peaks around the major HALS components proved to enhance significantly, reflecting the oxidized HALS species at the tetramethylpiperidine units to cause the photostabilizing action. In addition, hydrolyzed HALS species were also observed for the irradiated sample. These results suggest that not only the oxidation reaction but also the hydrolysis or decomposition of the oligomeric HALS components competitively proceed in the PP composites during UV exposure.

Journal Article↗

Oligomeric fluorescent labels for DNA.

In an effort to find fluorescent labels that have large Stokes shifts and increased emission intensity, a strategy for fluorescence labeling of DNA was explored in which multiple individual fluorophores are incorporated at adjacent positions at the end of a DNA probe. To encourage close interactions, hydrocarbon and heterocycle fluorophores were substituted at C-1 of deoxyribose, replacing the DNA base. The C-glycosides studied contained the well-known fluorophores terphenyl, pyrene, and terthiophene. For comparison, a commercial fluorescein-dU nucleotide was examined. Oligomeric labels containing up to five fluorophores were tested. Interestingly, all four dyes behaved differently on multiple substitution. Fluorescein displayed strong self-quenching properties, with the quantum yield dropping severalfold with each additional substitution and with a constant, small Stokes shift. In contrast, pyrene showed increases in quantum yield on addition of more than one fluorophore and yielded efficient long-wavelength emission on multiple substitution, with Stokes shifts of >130 nm. Oligomeric terphenyl labels gave a small progressive red shift in absorption and a marked red shift in emission wavelength and showed a strong increase in brightness with more monomers. Finally, terthiophene oligomers showed self-quenching combined with increasing Stokes shifts. Overall, the results suggest that some oligomeric fluorescent labels exhibit properties not available in common fluorescein class (or other commercial) labels, such as large Stokes shifts and increasing brightness with increasing substitution.

Absorption↗

Modulation of smooth muscle myosin light chain kinase activity by Ca2+/calmodulin-dependent, oligomeric-type modifications.

Oligomerization of turkey gizzard myosin light chain kinase (MLCKase) was demonstrated by a zero-length cross-linker, 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide hydrochloride (EDC), a standard reagent used in investigations of specific protein-protein interaction [Mornet et al. (1989) J. Muscle Res. Cell Motil. 10, 10-24]. This approach revealed that in solution the kinase was not monomeric but the monomers were in equilibrium with the kinase dimeric and oligomeric forms. Addition of Ca2+/calmodulin (CM) shifted this equilibrium in the direction of the kinase dimers, accompanied by a 2-fold decrease of the kinase catalytic activity, in addition to a 2-fold decrease of its apparent affinity for CM [Sobieszek et al. (1993) Biochem. J. 295, 405-411]. The dimer (and/or oligomer) formation was shown to result from an interaction of the kinase autoinhibitory domain with its 24 kDa tryptic fragment containing titin-like domain II-3. The possible significance of the oligomerization in regulation of MLCKase activity is discussed.

Animals↗

Pig heart CoA transferase exists as two oligomeric forms separated by a large kinetic barrier.

Pig heart CoA transferase (EC 2.8.3.5) has been shown previously to adopt a homodimeric structure, in which each subunit has a molecular weight of 52 197 and consists of N- and C-domains linked by a hydrophilic linker or "hinge". Here we identify and characterize a second oligomeric form constituent in purified enzyme preparations, albeit at low concentrations. Both species catalyze the transfer of CoA with similar values for k(cat) and K(M). This second form sediments more rapidly than the homodimer under the conditions of conventional sedimentation velocity and active enzyme centrifugation. Apparent molecular weight values determined by sedimentation equilibrium and gel filtration chromatography are 4-fold greater than the subunit molecular weight, confirming that this form is a homotetramer. The subunits of both oligomeric forms are indistinguishable with respect to molecular mass, far-UV CD, intrinsic tryptophan fluorescence, and equilibrium unfolding. Dissociation of the homotetramer to the homodimer occurs very slowly in benign solutions containing high salt concentrations (0.25-2.0 M KCl). The homotetramer is fully converted to homodimer during refolding from denaturant at low protein concentrations. Disruption of the hydrophilic linker between the N- and C-domains by mutagenesis or mild proteolysis causes a decrease in the relative amount of the larger conformer. The homotetramer is stabilized by interactions involving the helical hinge region, and a substantial kinetic barrier hinders interconversion of the two oligomeric species under nondenaturing conditions.

Animals↗

Protonation of histidine-132 promotes oligomerization of the channel-forming toxin aerolysin.

Aerolysin is a bacterial toxin that binds to a receptor on eukaryotic cells and oligomerizes to form stable, SDS-resistant, noncovalent oligomers that insert into the plasma membrane and produce well-defined channels. Little is known about the mechanisms controlling this process. Here we show that the protonation of a single histidine is required for oligomerization of aerolysin in solution. First we have investigated the effect of pH on the activity of aerolysin. The toxin's ability to disrupt human erythrocytes declined as the pH increased above 7.4. Experiments with receptor-free planar lipid bilayers demonstrated that the rate at which aerolysin formed channels also decreased with increasing pH, although the conductance of preexisting channels was not affected. The reduction in the rate of channel formation was shown to be due to a decrease in the toxin's ability to oligomerize. Our data indicate that the pH effect on activity is due to the deprotonation of a single residue rather than a global effect of pH on the protein. In agreement with our previous site-directed mutagenesis studies, His-132 is most likely to be the target of this pH effect. This conclusion was reinforced by the fact that we could shift the pH dependence of the activity to lower pH values by mutating Asp-139, a residue less than 3 A away from His-132 and likely to contribute to the usually high pKa of this histidine.

Bacterial Toxins↗

Solution oligomerization of the rev protein of HIV-1: implications for function.

rev is an RNA-binding protein of human immunodeficiency virus-1 and is required for the expression of incompletely spliced viral transcripts. Oligomerization of rev is thought to be associated with RNA binding and rev function. Here, we have characterized the oligomerization of rev using equilibrium analytical centrifugation. rev is predominantly monomeric at low concentrations, but reversibly polymerizes to produce large aggregates at higher concentrations. The data fit well to an unlimited isodesmic self-association model in which the association constants for the addition of a monomer to each aggregate are equal [K = 1.08 x 10(6) M-1 at 4 degrees C]. The association constant is essentially independent of monovalent salt concentration from 0.15 to 2 M at pH 6-9. Thermodynamic parameters derived from the temperature dependence of the association constant over the limited range of 0-30 degrees C reveal that the primary contribution to the free energy of oligomerization is a large negative enthalpy. Binding of rev to the rev-responsive element of RNA was characterized under the same conditions as the centrifugation experiments using a nitrocellulose filter assay. rev binds to the RRE at a protein concentration where rev is predominantly monomeric, suggesting that solution multimerization of rev is not required for rev function.

Cloning, Molecular↗

Oligomeric states of the insulin receptor: binding and autophosphorylation properties.

Properties of oligomeric states of the insulin receptor were analyzed by polyacrylamide gel electrophoresis in nondenaturing buffer conditions (ND-PAGE). Partially purified insulin receptors resolve in ND-PAGE as three distinct species: (i) the fast electrophoretic mobility, low molecular mass form manifests intense labeling by iodinated insulin and shows basal and insulin-stimulated autophosphorylation; (ii) the middle, intermediate mobility form exhibits strong labeling by iodinated ligand but does not possess the capacity to be autophosphorylated; (iii) the slow mobility, highest molecular mass form necessitates covalent binding with iodinated hormone to withstand electrophoresis and shows autophosphorylation enhanced by insulin. This receptor form is more heavily labeled by phosphorylation than the low form. At 22 degrees C, binding and autophosphorylation do not appear to be time dependent. At 37 degrees C, binding and autophosphorylation of low and high species attain a maximum after 15 min and then decrease as time of incubation with insulin is prolonged to 120 min; the middle species exhibits a much slower association rate, and its labeling by iodinated hormone becomes more intense with time. Our data show that in cell-free systems insulin receptors appear in various oligomeric states and that the highest molecular mass oligomer exhibits the most pronounced autophosphorylation. This is compatible with the concept that insulin receptor oligomerization provides a mechanism for transmembrane signaling.

Animals↗