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At least 19 recordsLinked to original sources
PubMed2001

Effect of enzyme inhibitors on protein quaternary structure determined by on-line size exclusion chromatography-microelectrospray ionization mass spectrometry.

Aldehyde dehydrogenases (ALDH) are a family of enzymes primarily involved in the oxidation of various aldehydes. Most ALDH enzymes derived from mammalian sources have been shown to exist as homotetramers, consisting of four identical subunits of approximately 54 kDa. The presence of the homotetramer appears to be necessary for enzyme activity. In this study, recombinant rat liver mitochondrial ALDH (rmALDH) was inhibited in vitro with four different inhibitors, namely, disulfiram (MW, 296.5), prunetin (MW, 284.3), benomyl (MW, 290.3), and N-tosyl-L-phenylalanine chloromethyl ketone (TPCK) (MW, 351.8). Subsequently, inhibited rmALDH was analyzed by a novel approach of on-line size exclusion chromatography-microelectrospray ionization-mass spectrometry (SEC-muESI-MS) to examine the noncovalent quaternary structural stability of the inhibited enzyme. Analysis of native rmALDH by SEC-muESI-MS revealed predominantly the homotetramer (Mr = approximately 217,457 Da, +/- 0.01%) with some in-source, skimmer-induced dissociation to afford monomer (Mr = approximately 54,360 Da, +/- 0.01%). Both disulfiram and prunetin inhibited rmALDH by >70% and >90%, respectively, but did not disrupt the quaternary structure of rmALDH. Furthermore, there was no detectable change within experimental error (+/- 0.01%) of the disulfiram or the prunetin homotetramers (Mr = approximately 217,448 Da and Mr = approximately 217,446 Da). This may possibly indicate that inhibition occurred via formation of intramolecular disulfide bond at the enzyme active site, or weak affinity noncovalent binding. In contrast, benomyl-inhibited rmALDH homotetramer (>90% inhibition) exhibited a Mr = approximately 217,650 Da (+/- 0.01%) corresponding to two butylcarbamoyl adducts on two of the four enzyme subunits. The skimmer-induced monomer afforded a mixture of unmodified rmALDH (Mr = approximately 54,365 Da, +/- 0.01%) and butylcarbamoylated enzyme (Mr = approximately 54,459 Da, +/- 0.01%). Finally, TPCK (>90% inhibition) modified all four subunits of rmALDH to give Mr = approximately 218,646 Da (+/- 0.01%). In all four cases while significant enzyme inhibition occurred, no destabilization of the quaternary complex was detected.

Aldehyde Dehydrogenase↗
PubMed1986

Co-operativity value of DNA RecA protein interaction. Influence of the protein quaternary structure on the binding analysis.

We show that an erroneous estimation of the quaternary structure of free protein distorts the quantitative analysis of its interaction with DNA, affecting especially the co-operativity value found. This could explain the discrepancy reported for the co-operativity value of the RecA-DNA interaction. The large cluster observed by electron microscopy indicates a very high co-operativity, whereas analysis of the binding isotherm indicates a moderate one, on the assumption of monomer. But if RecA is a large oligomer, the latter analysis would give a much higher co-operativity value and the former a smaller one, and they would be in accordance. Our sedimentation and light-scattering experiments suggest an oligomerization of about 30-mer or more, and support this explanation.

Allosteric Regulation↗
PubMed1993

Deficient antigen processing of a protein quaternary structure can be overcome by receptor-mediated uptake.

Human chorionic gonadotropin (hCG) is a dimer of non-covalently associated alpha (hCG-alpha) and beta (hCG-beta) subunits. This molecule was used to study whether receptor-mediated uptake influences the presentation of a protein quaternary structure. Unprimed splenocytes and a B cell lymphoma were capable of presenting only the free (hCG-alpha) but not the combined (hCG) alpha subunit to hCG-alpha T cell hybridomas, while hCG-alpha-primed lymph node cells (LNC) responded to both hCG-alpha and hCG. As antigen (Ag)-specific antigen-presenting cells (APC) present in the hCG-alpha-primed LNC population may be potentially effective for presenting hCG, we investigated the role of specific Ag capture, through mIg and Fc gamma R, in the processing and presentation of hCG and hCG-alpha to HAG5, a T cell hybridoma directed against the immunodominant region (amino acids 61-81) of hCG-alpha. Results showed that only B cells bearing membrane immunoglobulin capable of recognizing hCG-alpha and hCG, and present in hCG-alpha-primed mice, were extremely effective in presenting the free as well as the combined alpha subunit. The effect of FcR-mediated uptake was analyzed using a B cell line transfected with the Fc gamma RII-B2 gene to present immune complexes of either hCG-alpha or hCG. We found that hCG-alpha and hCG were presented equally well, whatever the Ag-binding site of each antibody to hCG or its alpha subunit. Using HBG 6, an hCG-beta T cell hybridoma, we performed similar experiments with the Fc gamma RII-B2 cell line and determined that the potentiation of hCG presentation to HBG 6 was similar to that observed with HAG 5. Then kinetic experiments were performed to examine the effect of Ag uptake through FcR on processing. Results demonstrated that the uptake pathway drastically influenced the expression of alpha T cell determinants in the alpha/beta dimer. In addition, treatment with cycloheximide, a protein synthesis inhibitor, only impaired the ability of APC to present specifically captured Ag. Thus, the processing pathway for specifically captured Ag might be different from the pathway used to process nonspecifically captured Ag. This observation might explain why receptor-enhanced uptake bypasses the inefficient processing of the hCG quaternary structure and enables similar efficiency in the presentation of alpha and beta T cell specificities. These findings provide new insight into the antigenicity of oligomeric molecules, which is modified whether antigen capture is specific or not.

Animals↗
PubMed1993

Influence of protein-quaternary structure on antigen processing.

T cell recognition of the quaternary structure of human chorionic gonadotropin (hCG), resulting from the association between its alpha (hCG-alpha) and beta (hCG-beta) subunits, was analyzed using hCG-alpha and hCG-beta T cell hybridomas produced in BALB/c mice. First, the fine specificity of these T cell hybridomas was determined, enabling us to divide hCG-alpha-specific T cell hybridomas into two groups. Group I recognized the hCG-alpha(61-81) region, and group II responded to the hCG-alpha(50-70) part of the molecule. Two groups of hCG-beta-specific T cell hybridomas, designated groups III and IV, were analyzed and found to respond to the C- and the N-terminal parts of the hCG-beta(1-22) peptide, respectively. Moreover, we observed that the nature of APC influenced Ag recognition by hCG-beta T cell hybridomas from group IV, but not by other selected T cell hybridomas. We then showed that recognition of the hCG alpha/beta dimer by alpha-specific T cell hybridomas was dramatically reduced compared to both free hCG-alpha and heat-dissociated hCG alpha/beta molecules. In contrast, hCG-beta hybridomas exhibited comparable responses to the free beta subunit and the hCG dimer. Experiments using a dimeric molecule assembled from the alpha-subunit of human follicle-stimulating hormone, which is identical to hCG-alpha, and the beta-subunit of human follicle-stimulating hormone, which is homologous to hCG-beta, confirmed that the three-dimensional structure of the complex rather than the primary structure of the beta-subunit plays a critical role in the processing pathway. Finally, kinetic experiments showed that the presentation of hCG-alpha T cell epitopes differed depending upon whether the alpha-subunit was in its free or combined form. In contrast, the kinetic expression of hCG-beta T cell epitopes appeared to be independent of the quaternary structure of hCG. Thus, conformational alterations resulting from the alpha/beta subunit association mainly influenced processing of the alpha-subunit in its complexed form, rather than processing of the combined beta-subunit. The effect of protein-quaternary structure on T cell recognition may represent a new element in our understanding of the processing and presentation of oligomeric molecules.

Animals↗
PubMedDate not supplied

[Role of surface distribution of hydrophobic groups in the assembly of protein quaternary structure].

The method for two-dimensional representation of protein surfaces, based on the analogy with geographic map, and the algorithm for the search of the most favourable regions of izologous intermolecular interactions are proposed. It is assumed that the most favourable izologous interaction corresponds to an izologous contact of subunits which maximally dehydrates surface hydrophobic groups. The subunits are approximated by ellipsoids of revolution. The hydrophobic groups are assumed to be dehydrated if their C beta-atoms are inside the surface regions of the contacting ellipsoids inaccessible for contact with the sphere representing a water molecule. Using the proposed methods it is shown that for all izologous structures, known to atomic resolution, general shape of the molecule and distribution of hydrophobic groups on its surface: 1) provide a rough intersubunit recognition during assembly (deviation of the center of the experimentally localized contact region from the center of one of two-three regions obtained by us does not exceed 6--7 A); 2) choose only a few most favourable mutual orientations of the contacting regions; 3) can determine the pathway of the assembly.

Macromolecular Substances↗
PubMed1992

Membrane fusion process of Semliki Forest virus. I: Low pH-induced rearrangement in spike protein quaternary structure precedes virus penetration into cells.

The Semliki Forest virus (SFV) directs the synthesis of a heterodimeric membrane protein complex which is used for virus membrane assembly during budding at the surface of the infected cell, as well as for low pH-induced membrane fusion in the endosomes when particles enter new host cells. Existing evidence suggests that the E1 protein subunit carries the fusion potential of the heterodimer, whereas the E2 subunit, or its intracellular precursor p62, is required for binding to the nucleocapsid. We show here that during virus uptake into acidic endosomes the original E2E1 heterodimer is destabilized and the E1 proteins form new oligomers, presumably homooligomers, with altered E1 structure. This altered structure of E1 is specifically recognized by a monoclonal antibody which can also inhibit penetration of SFV into host cells as well as SFV-mediated cell-cell fusion, thus suggesting that the altered E1 structure is important for the membrane fusion. These results give further support for a membrane protein oligomerization-mediated control mechanism for the membrane fusion potential in alphaviruses.

Animals↗
PubMed1976

Interactions of oxytocin and vasopressin with bovine neurophysins I and II. Effects of hormone binding on the protein quaternary structure: a simple model.

The effects of hormone binding on the reversible monomer in equilibrium dimer equilibrium of bovine neurophysins I or II in solution have been studied by sedimentation equilibrium measurements performed in conjunction with equilibrium dialysis experiments. Under normal solution conditions saturating amounts of oxytocin displace the neurophysin dimerization equilibrium toward the associated form of the protein to give a dimeric complex with two oxytocin molecules bound per dimer. Vasopressin exerts different influences on this oligomerization process. At low fractional saturation this ligand exhibits a behavior similar to oxytocin with a higher affinity for the neurophysin dimer than the monomer. But in contrast, at higher fractional saturation, vasopressin strongly displaces the aggregation equilibrium toward a monomeric complex bearing two vasopressin molecules. However, in the presence of a high concentration of LiCl two oxytocin molecules are bound per neurophysin protomer (10,000 daltons). These observations, together with earlier data for vasopressin binding, suggest that each neurophysin molecule possesses two structurally distinct hormone binding sites. These observations can be rationalized in a simple schematic model of hormone binding to neurophysin in which oxytocin favors a dimeric form with one hormone binding site available per 10,000 daltons while vasopressin favors the monomeric form with two hormone binding sites available per 10,000 daltons.

Animals↗
PubMed1993

Inactivation of glyceraldehyde-3-phosphate dehydrogenase with SH-reagents and its relationship to the protein quaternary structure.

Inactivation of mung bean glyceraldehyde-3-phosphate dehydrogenase (GPDH) with excess iodoacetate or N-ethylmaleimide exhibits pseudo-first order kinetics at pH 7.3 and 8.6 in the absence and presence of NAD+, suggesting that all the reactive SH groups (four per tetrameric GPDH molecule) have equivalent reactivity towards these reagents. This is similar to the D2-symmetry conformation proposed on the basis of thermal inactivation data [Malhotra and Srinivasan, Arch. Biochem. Biophys. 236, 775-781 (1985)]. With p-chloromercury benzoate (p-CMB), the inactivation of GPDH is very fast and its kinetics can be monitored at low reagent concentration only. Keeping a high molar p-CMB: enzyme ratio (= 47), the kinetics were found to be biphasic, with half of the activity being lost in a fast and the remaining in a slow phase, characteristic of C2-symmetry conformation and half site reactivity. The p-CMB inactivation could be largely reversed on the addition of excess cysteine. A comparison of these data with literature reports on this and other GPDHs reveals that all reagents having large non-polar moieties exhibit half site reactivity with this enzyme.

Animals↗
PubMed2000

Solubility of fluoromethemoglobin S: effect of phosphate and temperature on polymerization.

The polymerization properties of the fully liganded fluoromet derivative of hemoglobin S (FmetHb S) were investigated by electron microscopy and absorption spectroscopy. Polymerization progress curves, as measured by increasing sample turbidity at 700 nm, exhibit a delay time (t(d)) consistent with the double nucleation mechanism. The pattern of fiber growth, as monitored by electron microscopy, is also indicative of a heterogeneous nucleation process, and dimensions of the fibers were found to be comparable to that of deoxyHb S. The polymerization rate constant (1/t(d)) depends exponentially on Hb S concentration, and the size of the homogeneous and heterogeneous nuclei also depend on FmetHb S concentration. As for deoxyHb S, higher concentrations of protein and phosphate favor fiber formation, while lower temperatures inhibit polymerization. Solubility experiments reveal, however, that eight times more FmetHb S is required for polymerization. The current studies further show that reaction order is independent of phosphate concentration if Hb S activity and not concentration is considered. The allosteric effector, inositol hexaphosphate (IHP), promotes fiber formation, and temperature-dependent reaggregation of FmetHb S suggests that IHP stabilizes pregelation aggregates. These studies show that FmetHb S resembles deoxyHb S in many of its polymerization properties; however, IHP-bound FmetHb S potentially provides a unique avenue for future studies of the early stages of Hb S polymerization and the effect of tertiary and quaternary protein structure on the polymerization process.

Allosteric Regulation↗
PubMed2000

Native quaternary structure of bovine alpha-crystallin.

Alpha-crystallin is the most important soluble protein in the eye lens. It is responsible for creating a high refractive index and is known to be a small heat-shock protein. We have used static and dynamic light scattering to study its quaternary structure as a function of isolation conditions, temperature, time, and concentration. We have used tryptophan fluorescence to study the temperature dependence of the tertiary structure and its reversibility. Gel filtration, analytical ultracentrifugation, polyacrylamide gel electrophoretic analysis, and absorption measurements were used to study the chaperone-like activity of alpha-crystallin in the presence of destabilized lysozyme. We have demonstrated that the molecular mass of the in vivo alpha-crystallin oligomer is about 700 kDa (alpha(native)) while the 550 kDa molecule (alpha(37 degrees C),diluted), which is often found in vitro, is a product of prolonged storage at 37 degrees C of low concentrated alpha-crystallin solutions. We have proven that the molecular mass of the alpha-crystallin oligomer is concentration dependent at 37 degrees C. We have found strong indications that, during chaperoning, the alpha-crystallin oligomer undergoes a drastic rearrangement of its peptides during the process of complex formation with destabilized lysozyme. We propose the hypothesis that all these processes are governed by the phenomenon of subunit exchange, which is well-known to be strongly temperature-dependent.

Animals↗
PubMed1995

Calcium-induced dimerization of troponin C: mode of interaction and use of trifluoroethanol as a denaturant of quaternary structure.

Protein aggregation can be a problem, especially as a large number of proteins become available for structural studies at fairly high concentrations using solution techniques such as NMR spectroscopy. The muscle regulatory protein troponin C (TnC) undergoes a calcium-induced dimerization at neutral pH with a dissociation constant for the dimerization of 0.4 mM at 20 degrees C. The present study indicates that the mode of dimerization involves the N-domain of one monomer interacting with the N-domain of another monomer. Addition of the solvent trifluoroethanol (TFE) to a concentration of 15%, v/v, results in a 10-fold increase in the dimer dissociation constant of calcium-saturated TnC (4 mM at 20 degrees C), making TnC predominantly a monomer for spectroscopic studies. Further, TFE, at the concentrations used herein, acts to perturb the quaternary structure of TnC without adversely affecting the secondary or tertiary structure as evidenced by minimal changes to its CD spectra and 1H, 13C, and 15N NMR chemical shifts.

Animals↗
PubMed2001

Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus.

Single-stranded DNA binding proteins (SSBs) play central roles in cellular and viral processes involving the generation of single-stranded DNA. These include DNA replication, homologous recombination and DNA repair pathways. SSBs bind DNA using four 'OB-fold' (oligonucleotide/oligosaccharide binding fold) domains that can be organised in a variety of overall quaternary structures. Thus eubacterial SSBs are homotetrameric whilst the eucaryal RPA protein is a heterotrimer and euryarchaeal proteins vary significantly in their subunit compositions. We demonstrate that the crenarchaeal SSB protein is an abundant protein with a unique structural organisation, existing as a monomer in solution and multimerising on DNA binding. The protein binds single-stranded DNA distributively with a binding site size of approximately 5 nt per monomer. Sulfolobus SSB lacks the zinc finger motif found in the eucaryal and euryarchaeal proteins, possessing instead a flexible C-terminal tail, sensitive to trypsin digestion, that is not required for DNA binding. In comparison with Escherichia coli SSB, the tail may play a role in protein-protein interactions during DNA replication and repair.

Amino Acid Sequence↗
PubMed2000

Expression, purification, and initial structural characterization of YadQ, a bacterial homolog of mammalian ClC chloride channel proteins.

YadQ of Escherichia coli is a homolog of the mammalian chloride channels of the ClC family. The yadQ gene was cloned as a fusion protein with a hexahistidine tag and tobacco etch virus protease site for the removal of the tag. The protein was expressed in the membrane of E. coli and extracted with decylmaltoside. Purification was achieved by metal affinity chromatography followed by cation exchange. Circular dichroism revealed a high alpha-helical content. Size exclusion chromatography suggests that YadQ forms dimers. The similarity in primary, secondary, and quaternary structure and the ability to recombinantly express YadQ in the cell membrane make the protein a good candidate for the structural study of ClC chloride channels.

Amino Acid Sequence↗
PubMed2000

Direct association of ligand-binding and pore domains in homo- and heterotetrameric inositol 1,4,5-trisphosphate receptors.

Inositol 1,4,5-trisphosphate receptors (IP(3)Rs) are a family of intracellular Ca(2+) channels that exist as homo- or heterotetramers. In order to determine whether the N-terminal ligand-binding domain is in close physical proximity to the C-terminal pore domain, we prepared microsomal membranes from COS-7 cells expressing recombinant type I and type III IP(3)R isoforms. Trypsin digestion followed by cross-linking and co-immunoprecipitation of peptide fragments suggested an inter-subunit N- and C-terminal interaction in both homo- and heterotetramers. This observation was further supported by the ability of in vitro translated C-terminal peptides to interact specifically with an N-terminal fusion protein. Using a (45)Ca(2+) flux assay, we provide functional evidence that the ligand-binding domain of one subunit can gate the pore domain of an adjacent subunit. We conclude that common structural motifs are shared between the type I and type III IP(3)Rs and propose that the gating mechanism of IP(3)R Ca(2+) channels involves the association of the N-terminus of one subunit with the C-terminus of an adjacent subunit in both homo- and heterotetrameric complexes.

Animals↗
PubMed2000

Trypsin sheds light on the singular case of seminal RNase, a dimer with two quaternary conformations.

Dimeric seminal RNase presents the singular case of a dimer with access at equilibrium to two conformations: one in which the subunits exchange, or swap, their NH(2)-terminal arms; the other with no exchange. Thus a continuous unfolding/refolding of structural elements into two alternative conformations takes place in the native protein at equilibrium. The phenomenon was investigated by kinetic and mass spectrometric analyses of the effects of trypsin on the native protein, on its isolated quaternary forms, as well as on a monomeric derivative of the protein and on homologous dimeric RNase A. The kinetics of tryptic action on the protein forms and on the protein derivatives, as well as the location of the tryptic cleavage sites, and their chronological sequence, led to the identification of relevant interconversion intermediates, to the description of a model for the interconversion process, and to a hypothesis for the unique phenomenon of the dual quaternary conformation of seminal RNase.

Animals↗