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PubMed2000

Highly stable oligomerization forms of HIV-1 Tat detected by monoclonal antibodies and requirement of monomeric forms for the transactivating function on the HIV-1 LTR.

The use of newly generated murine monoclonal antibodies directed against distinct epitopes of a functionally active, chemically synthesized HIV-1 Tat protein has permitted the identification of several molecular forms including monomers, dimers and trimers. Dimers and trimers are particularly stable and resistant to strong reducing conditions. Through epitope mapping it has been possible to demonstrate that the major immunodominant epitope is contained within the basic region of the Tat protein and is lost after oligomerization of the molecule. In contrast, N-terminal, C-terminal and conformation-dependent epitopes are still accessible to mAb specific recognition after Tat oligomerization. Moreover, by using a quantitative HIV-LTR transactivation assay depending upon exogenous Tat, we could extrapolate the amount of functional Tat produced by cell lines stably transfected with the viral transactivator. More importantly, we could show that only the monomeric form of exogenous Tat is the relevant functional form acting in cells harbouring the HIV-1 LTR promoter.

Alkylation↗
PubMed2001

News on the Maillard reaction of oligomeric carbohydrates: a survey.

The reaction behaviour of monosaccharides in the Maillard reaction is well investigated. Amadori compounds, for instance, form deoxyhexosuloses which are responsible for the formation of volatile flavour substances and melanoidins. These intermediates can be quantified by a trapping reaction with o-phenylendiamine as stable quinoxalines. However the reaction behaviour of oligo and polymeric carbohydrates in non-enzymatic browning reactions are hardly known. Therefore maltooligosaccharides and in some cases starch were used together with glycine as model substances to investigate the Maillard reaction mechanism of oligo and polysaccharides. In quasi waterfree reaction systems oligosaccharides form alpha-dicarbonyl compounds via a "peeling off" mechanism. The Maillard reaction with the amino compound starts at the reducing end of an alpha-glucane residue and results in the formation of 1,4-dideoxyhexosulose. This is the main alpha-dicarbonyl compound found by trapping reaction with o-phenylendiamine during thermally induced degradation of maltooligosaccharides. The thermal reaction of maltooligosaccharides is accompanied by transglycosylations leading to formation of branched carbohydrate structures and by dehydrations forming anhydrosugars. The reaction mechanism which is responsible for degradation of oligomeric carbohydrates in aqueous model systems differs significantly from pathways mentioned above for water free reaction conditions. As the main alpha-dicarbonyl compound 3-deoxypentosulose is formed which can be proved also by trapping reactions. Under aqueous reaction conditions the formation of other alpha-dicarbonyls plays only a marginal role in the Maillard reaction of oligomeric carbohydrates. In an aqueous system transglycosylation and dehydration of maltooligosaccharides are not important.

Hot Temperature↗
PubMed1994

Reovirus protein sigma 1: from cell attachment to protein oligomerization and folding mechanisms.

The reovirus cell attachment protein sigma 1 is a lollipop-shaped structure with the fibrous tail anchored to the virion. Since it interacts with the cell receptor, sigma 1 is a major determinant of reovirus infectivity and tissue tropism. Studies on its structure-function relationships have been facilitated by the fact that protein sigma 1 produced in any expression system is capable of binding to cell receptors. The use of site-specific and deletion mutants has led to the identification and characterization of its virion anchorage and receptor binding domains. Studies on the oligomeric status of sigma 1 have revealed that sigma 1 is a homotrimer and that two independent trimerization events at different loci (the N- and C-terminal halves, respectively) of the protein, are involved in its generation. This also accounts for a clearly demonstrable dominant negative effect by a mutant subunit in a wild-type/mutant sigma 1 heterotrimer. Current efforts are focused on the involvement of chaperones in the generation of sigma 1 and on events that take place upon sigma 1 binding to the cell receptor. Protein sigma 1 has therefore become an excellent model system for the study of both virus attachment and protein oligomerization and folding mechanisms.

Animals↗
PubMed2002

Fourier transform IR study of aggregational behavior of N-acetyl-L- and N-butyloxycarbonyl-L-glutamic acid oligomeric benzyl esters in dioxane and benzene: beta-turn --> antiparallel beta-sheet transition.

Oligomeric N-acetyl-L-glutamic acid benzyl esters (AN(p)Z) with exact residue numbers (N(p) = 2, 3, 4, and 5) and N-butyloxycarbonyl-L-glutamic acid benzyl esters (BOCN(p)Z) with exact residue numbers (N(p) = 4, 5, 6, and 8) are synthesized by a stepwise procedure in a liquid phase. The aggregational behavior of these oligomeric molecules in dioxane and benzene is examined by Fourier transform IR spectra. In particular, the concentration dependence of the IR spectra for the AN(p)Z solutions with N(p) values of 4 (A4Z) and 5 (A5Z) shows that the predominant antiparallel beta-sheet structure is stabilized above the critical aggregation concentration (cac), while other conformations including beta-turns may coexist below the cac. This fact provides evidence that aggregation induces the conformational transition from other conformers (probably beta-turns) to an antiparallel beta-sheet form. The IR results for the A3Z and A2Z solutions indicate that specific conformers (beta-turns), which are different from the beta-sheet structure, may be preferentially stabilized upon aggregation. Thus, the critical residue number of the AN(p)Z oligopeptides, which is essential for formation of a rodlike aggregate in dioxane and benzene, is 4 or 5.

Amino Acid Sequence↗
PubMed2006

Sodium chloride enhanced oligomerization of L-arginine.

NaCl significantly enhanced the longer oligoarginine formation in the oligomerization of L-arginine activated by N,N'-carbonyldiimidazole (CDI) in homogeneous aqueous solution. The optimal concentration of NaCl for the highest yield of longer oligoarginine formation is around 1M. It is suggested that the weak interactions of Cl(-) with the positive-charged guanidinium group of the oligoarginines formed in the oligomerization of L-arginine are responsible for the enhancement by NaCl.

Arginine↗
PubMed1995

A new mode of size-dependent separation of proteins by capillary electrophoresis in presence of sodium dodecyl sulfate and concentrated oligomeric dextran.

Capillary electrophoresis in presence of sodium dodecyl sulfate (SDS) and 10% w/v of oligomeric dextran with molecular weight of just above 1000 was found to be an efficient medium for size-dependent separation of proteins (Karim, M. R., Janson, J.-C., Takagi, T., Electrophoresis 1994, 15, 1531-1534). The separations were found to be highly reproducible, both with respect to the position and relative amounts of the peaks. No evidence for a network structure in the medium could be found on examination of the effect of dextran concentration and viscosity measurements. The separation mechanism appears to be different from sieving by a polymer network structure. In free solution, SDS-protein complexes with molecular weights > 10,000 migrate with almost the same mobilities, irrespective of their molecular weight (this behavior is called free draining). Such SDS-complexes of proteins or peptides with molecular weights < 10,000, however, tend to increase their negatively signed mobilities with decreasing molecular weight (Karim, M. R., Shinagawa, S., Takagi, T., Electrophoresis 1994, 15, 1141-1146). Our working hypothesis is that in presence of the oligomeric dextran, the range of deviation from the free-draining electrophoretic behavior extends to higher molecular weights, resulting in a novel separation made.

Circular Dichroism↗
PubMed1994

p53 oligomerization and DNA looping are linked with transcriptional activation.

We examined the role of p53 oligomerization in DNA binding and in transactivation. By conventional electron microscopy (EM) and scanning transmission EM, we find that wild-type tetramers contact 18-20 bp at single or tandem 19 bp consensus sequences and also stack in apparent register, tetramer on top of tetramer. Stacked tetramers link separated DNA binding sites with DNA loops. Interestingly, the p53(1-320) segment, which lacks the C-terminal tetramerization domain, binds DNA consensus sites as stacked oligomers. Although the truncated protein binds DNA with reduced efficiency, it nevertheless induces DNA looping by self-association. p53, therefore, has a C-terminal tetramerization domain that enhances DNA binding and a non-tetrameric oligomerization domain that stacks p53 at consensus sites and loops separated consensus sites via protein-protein interactions. Using model promoters, we demonstrate that wild-type and tetramerization-deficient p53s activate transcription well when tandem consensus sites are proximal to TATA sequences and poorly when tandem sites are distal. In the presence of proximal sites, however, stimulation by distal sites increases 25-fold. Tetramerization and stacking of tetramers, therefore, provide dual mechanisms to augment the number of p53 molecules available for activation through p53 response elements. DNA looping between separated response elements further increases the concentration of local p53 by translocating distally bound protein to the promoter.

Animals↗
PubMed1989

Temperature-dependent oligomerization of hsp85 in vitro.

The failure of conventional subcellular fractionation methods to identify interactions between the bulk of hsp85 and other cellular structures suggested that critical stress protein interactions might be detectable only at elevated temperatures. This was confirmed by showing that incorporation of hsp85 and grp95 into sedimentable complexes in Triton X-100 extracts of L929 cells increased progressively over the 30 degrees C-43 degrees C temperature range. Whereas several other proteins, including hsp110 and hsp69, became sedimentable under these conditions, this effect required temperatures of approximately 43 degrees C and was only partially detergent-dependent. In contrast, hsp85 became sedimentable at temperatures as low as 33 degrees C, and this effect was highly detergent-dependent. Temperature-dependent conversion of purified hsp85 to a sedimentable form was shown to result from limited oligomerization of the protein, which occurred in the presence of detergent. Since the detergent requirement could be met by a variety of compounds, including sphingosine, these findings suggest that hsp85 oligomerization may occur when intact cells are exposed to elevated temperature.

Animals↗
PubMed2006

Simultaneous separation and identification of oligomeric procyanidins and anthocyanin-derived pigments in raw red wine by HPLC-UV-ESI-MSn.

Samples of raw red wine (Primitivo di Manduria, Apulia, Southern Italy) were analysed without any pre-treatment (except 1:2 dilution with water) using HPLC with detection based on UV absorbance and Electrospray Ionisation Sequential Mass Spectrometry (ESI-MSn, with n = 1-3) in a series configuration. In particular, absorbance at 520 nm was monitored for UV detection in order to identify pigments responsible for wine colour. On the other hand, two subsequent stages of MS detection based on positive ions were adopted. The first consisted of an explorative MS acquisition, aimed at the individuation of the m/z ratios for positively charged compounds; the second was based on fragmentation of the detected ions within an ion trap analyser, followed by MS/MS and, if required, MS3 acquisitions. The synergy between UV detection and MSn analysis led to the identification of 41 pigments, which can be classified into five groups: grape anthocyanins, pyranoanthocyanins, vinyl-linked anthocyanin-flavanol pigments, ethyl-bridged anthocyanin-flavanol pigments and flavanol-anthocyanin compounds. Many isomeric and oligomeric structures were found within each group. A further class of compounds, not absorbing in the visible spectrum, could be also characterised by ESI-MSn and corresponded to B-type procyanidins, i.e. proanthocyanidins arising from C4-->C8/C4-->C6 couplings between catechin or epicatechin units. In particular, oligomeric structures (from dimers to pentamers), often present with several isomers, were identified and their fragmentation patterns clarified.

Anthocyanins↗
PubMed2002

Paradigm shifts in Alzheimer's disease and other neurodegenerative disorders: the emerging role of oligomeric assemblies.

Alzheimer's disease (AD) is a progressive, neurodegenerative disorder characterized by amyloid deposition in the cerebral neuropil and vasculature. These amyloid deposits comprise predominantly fragments and full-length (40 or 42 residue) forms of the amyloid beta-protein (Abeta) organized into fibrillar assemblies. Compelling evidence indicates that factors that increase overall Abeta production or the ratio of longer to shorter forms, or which facilitate deposition or inhibit elimination of amyloid deposits, cause AD or are risk factors for the disease. In vitro studies have demonstrated that fibrillar Abeta has potent neurotoxic effects on cultured neurons. In vivo experiments in non-human primates have demonstrated that Abeta fibrils directly cause pathologic changes, including tau hyperphosphorylation. In concert with histologic studies revealing a lack of tissue injury in areas of the neuropil in which non-fibrillar deposits were found, these data suggested that fibril assembly was a prerequisite for Abeta-mediated neurotoxicity in vivo. Recently, however, both in vitro and in vivo studies have revealed that soluble, oligomeric forms of Abeta also have potent neurotoxic activities, and in fact, may be the proximate effectors of the neuronal injury and death occurring in AD. A paradigm shift is thus emerging that necessitates the reevaluation of the relative importance of polymeric (fibrillar) vs. oligomeric assemblies in the pathobiology of AD. In addition to AD, an increasing number of neurodegenerative disorders, including Parkinson's disease, familial British dementia, familial amyloid polyneuropathy, amyotrophic lateral sclerosis, and prion diseases, are associated with abnormal protein assembly processes. The archetypal features of the assembly-dependent neuropathogenetic effects of Abeta may thus be of relevance not only to AD but to these other disorders as well.

Alzheimer Disease↗
PubMed1995

Backbone dynamics of the oligomerization domain of p53 determined from 15N NMR relaxation measurements.

The backbone dynamics of the tetrameric p53 oligomerization domain (residues 319-360) have been investigated by two-dimensional inverse detected heteronuclear 1H-15N NMR spectroscopy at 500 and 600 MHz. 15N T1, T2, and heteronuclear NOEs were measured for 39 of 40 non-proline backbone NH vectors at both field strengths. The overall correlation time for the tetramer, calculated from the T1/T2 ratios, was found to be 14.8 ns at 35 degrees C. The correlation times and amplitudes of the internal motions were extracted from the relaxation data using the model-free formalism (Lipari G, Szabo A, 1982, J Am Chem Soc 104:4546-4559). The internal dynamics of the structural core of the p53 oligomerization domain are uniform and fairly rigid, with residues 327-354 exhibiting an average generalized order parameter (S2) of 0.88 +/- 0.08. The N- and C-termini exhibit substantial mobility and are unstructured in the solution structure of p53. Residues located at the N- and C-termini, in the beta-sheet, in the turn between the alpha-helix and beta-sheet, and at the C-terminal end of the alpha-helix display two distinct internal motions that are faster than the overall correlation time. Fast internal motions (< or = 20 ps) are within the extreme narrowing limit and are of uniform amplitude. The slower motions (0.6-2.2 ns) are outside the extreme narrowing limit and vary in amplitude.(ABSTRACT TRUNCATED AT 250 WORDS)

Computer Graphics↗
PubMed1997

Oligomerization properties of GCN4 leucine zipper e and g position mutants.

Putative intersubunit electrostatic interactions between charged amino acids on the surfaces of the dimer interfaces of leucine zippers (g-e' ion pairs) have been implicated as determinants of dimerization specificity. To evaluate the importance of these ionic interactions in determining the specificity of dimer formation, we constructed a pool of > 65,000 GCN4 leucine zipper mutants in which all the e and g positions are occupied by different combinations of alanine, glutamic acid, lysine, or threonine. The oligomerization properties of these mutants were evaluated based on the phenotypes of cells expressing lambda repressor-leucine zipper fusion proteins. About 90% of the mutants do not form stable homooligomers. Surprisingly, approximately 8% of the mutant sequences have phenotypes consistent with the formation of higher-order (> dimer) oligomers, which can be classified into three types based on sequence features. The oligomerization states of mutants from two of these types were determined by characterizing purified fusion proteins. The Type I mutant behaved as a tetramer under all tested conditions, whereas the Type III mutant formed a variety of higher-order oligomers, depending on the solution conditions. Stable homodimers comprise less than 3% of the pool; several g-e' positions in these mutants could form attractive ion pairs. Putative repulsive ion pairs are not found among the homodimeric mutants. However, patterns of charged residues at the e and g positions do not seem to be sufficient to predict either homodimer or heterodimer formation among the mutants.

Amino Acid Sequence↗
PubMed2005

Oligomerization states of Bowman-Birk inhibitor by atomic force microscopy and computational approaches.

Several methods have been applied to study protein-protein interaction from structural and thermodynamic point of view. The present study reveals that atomic force microscopy (AFM), molecular modeling, and docking approaches represent alternative methods offering new strategy to investigate structural aspects in oligomerization process of proteinase inhibitors. The topography of the black-eyed pea trypsin/chymotrypsin inhibitor (BTCI) was recorded by AFM and compared with computational rigid-bodies docking approaches. Multimeric states of BTCI identified from AFM analysis showed globular-ellipsoidal shapes. Monomers, dimers, trimers, and hexamers were the most prominent molecular arrays observed in AFM images as evaluated by molecular volume calculations and corroborated by in silico docking and theoretical approaches. We therefore propose that BTCI adopts stable and well-packed self-assembled states in monomer-dimer-trimer-hexamer equilibrium. Although there are no correlation between specificity and packing efficiency among proteinases and proteinase inhibitors, the AFM and docked BTCI analyses suggest that these assemblies may exist in situ to play their potential function in oligomerization process.

Computational Biology↗
PubMed2001

High-performance liquid chromatography analysis of spectrin oligomerization.

Gel filtration chromatography has been used to analyze the oligomerization of human erythrocyte spectrin. By applying an exponentially modified Gaussian function we have been able to resolve overlapping elution peaks. From these peaks it was possible to calculate the equilibrium composition of each spectrin concentration and thus also the dissociation constants describing the oligomeric process. The determined dissociation constants for tetramer formation (1.3 microM) and for hexamer formation (24 microM) agree well with other measurements.

Chromatography, Gel↗
PubMed1995

Cell cycle phase-dependent changes of localization and oligomerization states of nucleophosmin / B23.

Nucleophosmin / B23, an abundant nucleolar phosphoprotein, accumulates in the nucleoplasm of cells during the stationary phase of growth or after exposure to selected cytotoxic drugs [Chan, P.K. (1992) Exp. Cell Res. 203, 174-181]. Monomeric and hexameric forms of nucleophosmin / B23 are present in cells [Yung, B.Y.M. and Chan, P.K. (1987) Biochim. Biophys. Acta. 925, 74-82]. Using indirect immunofluorescence, here we show that there are changes in nucleophosmin / B23's cellular localizations throughout the cell cycle. The alternation of the nuclear and nucleolar localizations of nucleophosmin / B23 is most frequently observed in cells of G1 and G1/S phases. The incidence of the changes of localizations of nucleophosmin / B23 decreases as cells enter into S and G2 phases. In parallel, using Western blotting, the reversible change of oligomerization states between the hexameric and monomeric forms of nucleophosmin / B23 is also found to occur most frequently in cells of G1 and G1/S phases. As cells progressed into S, G2 and M phases, the frequency of the reversible change of hexameric and monomeric forms of nucleophosmin / B23 decreases. These findings suggest that nucleophosmin / B23 being possibly involved in rRNA processing and transport, is highly active at G1 and G1/S phases as demonstrated by the dynamic, reversible changes of localization and oligomerization states of nucleophosmin / B23.

Biological Transport, Active↗
PubMed1998

LonR9 carrying a single Glu614 to Lys mutation inhibits the ATP-dependent protease La (Lon) by forming mixed oligomeric complexes.

An unusual lon mutation (called lonR9) is dominant over the wild-type gene, which encodes the ATP-dependent protease La (Lon) in Escherichia coli, when present in multicopy plasmids. Here, we cloned and sequenced lonR9, and showed that the mutant gene carries a single point mutation in its open reading frame, which leads to replacement of Glu614 by Lys. The LonR9 protein and its poly-His-tagged form were purified to apparent homogeneity. Both of the purified proteins were capable of inhibiting the ATP-dependent proteolysis and the protein-activated ATP hydrolysis by protease La. Furthermore, the His-tagged LonR9 protein was found to form mixed oligomeric complexes with protease La, upon analysis by chromatography on a metal-chelating column. These results suggest that the phenotypic dominance of the lonR9 mutant is due to the formation of mixed oligomeric complexes between LonR9 and protease La, in which the defective components prevent the function of the wild-type subunits.

ATP-Dependent Proteases↗
PubMed1999

Biophysical characterization of the oligomeric state of Bax and its complex formation with Bcl-XL.

The overexpression of Bax, a member of the Bcl-2 family, promotes cell death and the dimerization (or oligomerization) of Bax has been shown to be important for its function. Using size-exclusion chromatography and in vitro cross-linking experiments, we demonstrated that Bax exists mainly as a large oligomer of approximately 30 monomeric units. Furthermore, several binding assays demonstrated that Bcl-XL, an anti-apoptotic member of the Bcl-2 family, can bind to the oligomeric form of Bax without requiring Bax to dissociate to monomers.

Apoptosis↗
PubMed2000

An N-terminal 33-amino-acid-deletion variant of hsp25 retains oligomerization and functional properties.

The mechanism(s) by which heat shock protein 25 (hsp25) protects cells from stress may involve one or more of the biochemical properties attributed to hsp25 and other small M(r) hsp. In this report, structural and functional properties of an N-terminal 33 amino acid deletion variant of hsp25 (termed hsp25.c) were considered by comparison with hsp25. 6-His tagged recombinant hsp25 and hsp25.c (termed (H6)hsp25.a and (H6)hsp25.c) were expressed and purified. Oligomeric proteins formed and possessed properties previously attributed to hsp25. The 33 amino acid deletion represented by hsp27.c did not affect the ability of the recombinant protein to act as an inhibitor of elastase, as a molecular chaperone in the refolding of denatured citrate synthase, or as an actin-binding protein. The overexpression of either hsp25 or hsp25.c, enhanced the stress resistance of stable transformed eukaryotic cells. This N-terminal variant protein may be used in further cellular and biochemical assessment of hsp25 oligomerization and function.

Actins↗