Structural repertoire of immunoglobulin λ light chains

The immunoglobulin λ isotype is present in nearly all vertebrates and plays an important role in the human immune system. Despite its importance, few systematic studies have been performed to analyze the structural conformation of its variable regions, contrary to what is the case for κ and heavy chains. We show here that an analysis of the structures of λ chains allows the definition of a discrete set of recurring conformations (canonical structures) of their hypervariable loops and, most importantly, the identification of sequence constraints that can be used to predict their structure. We also show that the structural repertoire of λ chains is different and more varied than that of the κ chains, consistently with the current view of the involvement of the two major light-chain families in complementary strategies of the immune system to ensure a fine tuning between diversity and stability in antigen recognition.     

Identification of β-aggregate sites in protein chains

The problem of amyloidoses is pressing and have recently attracted special attention throughout the world because of epidemics of prion diseases such as mad cow disease and human Creutzfeldt-Jacob disease. These diseases result from the conversion of a native protein or peptide into a highly stable pathological form. Molecules having a pathological conformation aggregate to form amyloid fibrils, capable of unlimited growth. It is important to study the molecular mechanisms of prion diseases and to identify the protein regions responsible for their development. The review considers theoretical and experimental works focusing on the formation of amyloid fibrils.     

Sequence analysis of sheep T-cell receptor β chains

The nucleotide sequences reported in this paper have been submitted to the GenBank database and have been assigned the accession numbers M94181-M94183.     

Isolation of monotreme T-cell receptor α and β chains

Monotremes are an ancient mammalian lineage that last shared a common ancestor with the marsupial and eutherian (placental) mammals about 170 million years ago. Characterization of their immune genes is allowing us to gain insights into the evolutionary processes that lead to the mammalian immune response. Here we describe the characterization of the first cDNA clones encoding T-cell receptors from a monotreme. Two TCR -chain cDNAs (TCRA) from the short-beaked echidna, Tachyglossus aculeatus, containing complete variable, joining and constant regions were isolated. The echidna TCRA constant region shares approximately 37% amino acid identity with other mammalian TCRA constant region sequences. The two variable regions belong to the TCRAV group C, which also contains V genes from humans, mice, cattle and chickens. One echidna TCR -chain cDNA (TCRB) containing the entire constant region was isolated and sequenced. It shares about 63% identity with other mammalian TCRB constant region sequences. The echidna TCRBV belongs to TCRBV group A, which also contains V genes from various eutherian species. Southern blot analysis indicates that, like in other mammalian species, there is only one TCRA constant region copy in the echidna genome, but at least two TCRB constant regions.     

Preassembly and ligand-induced restructuring of the chains of the IFN-γ receptor complex： the roles of Jak kinases, Statl and the receptor chains

We previously demonstrated using noninvasive technologies that the interferon-gamma （IFN-γ） receptor complex is preassembled [ 1 ]. In this report we determined how the receptor complex is preassembled and how the ligand-mediated conformational changes occur. The interaction of Statl with IFN-γR1 results in a conformational change localized to IFN- γR1. Jakl but not Jak2 is required for the two chains of the IFN-γ receptor complex （IFN-γR1 and IFN-γR2） to interact; however, the presence of both Jakl and Jak2 is required to see any ligand-dependant conformational change. Two IFN- γR2 chains interact through species-specific determinants in their extracellular domains. Finally, these determinants also participate in the interaction of IFN-γR2 with IFN-γR1. These results agree with a detailed model of the IFN-γ receptor that requires the receptor chains to be pre-associated constitutively for the receptor to be active.     

The specificity of chain interactions among immunoglobulins. Combinations of γ chains with κ chains of the same subgroup as in the parent immunoglobulin G

1. The specificity of combination of heavy and light chains from selected human immunoglobulins was examined in the light of greater structural information than in previous studies. Heavy (gamma) chains from immunoglobulin G (kappa) myeloma proteins were allowed to combine with their homologous light (kappa) chains or with other kappa chains of the same variable-region subgroup. The affinity of each such pairing was assessed by having the test kappa chain compete with a standard population of normal light chains. 2. There was a spread of affinities among the heavy-light pairings with the homologous pairings having an average affinity significantly higher than the heterologous pairings. 3. It follows that (a) the preference shown for homologous heavy-light pairings is not explicable simply in terms of the known subdivisions of the variable and constant regions of the chains, and (b) it is unlikely that those residues specifying the subgroups of kappa-chain variable regions have a predominant role in the formation of interchain bonds with the gamma-chain variable regions.     

Method for the complete separation of radioactively labeled human γ-globin chains from pre-βA chains on CM-cellulose chromatography: Use of cold carrier globin chains

Carboxymethyl (CM)-cellulose chromatography of globins is the technique used most frequently in analysis of hemoglobin synthesis. However, if this method is to be reliable in cases where only small amounts of fetal hemoglobin (α₂γ₂) compared to adult hemoglobin (α₂β₂^A) are synthesized, it is important to obtain a clean separation of γ chains from pre-β^A chains. In the past, it has been found that small amounts of pre-β^A chains tend to elute with the γ chains. Radioactively labeled γ chains can be completely and reproducibly separated from small amounts of labeled pre-β^A chains by the addition of unlabeled β^J chains (Hb J Baltimore = β16 Gly → Asp) which elute at the same position as the pre β^A chains, thus increasing the quantity of this peak and allowing a clean separation from the γ chains.     

Subgroups of Tcr α chains and correlation with T-cell function

T-cell receptor (Tcr) chains are classified into four subgroups (I, II, III, and miscellaneous) based on the amino acid residues at positions 61 and 62. Subgroup I has Gly Phe at these positions, subgroup II has Arg Phe, subgroup III has Arg Leu, and subgroup miscellaneous has several other combinations. Variability plots for subgroups I, II, and III sequences show higher values around positions 93–103, 105, 108, 111, 113, and 115, suggesting that these positions may interact with the processed antigen molecules. Smaller peaks are present at various other regions which may bind the major histocompatibility complex class I or II molecules. The patterns of variability within one subgroup are similar for all species, for human alone, and for mouse alone. These subgroup patterns appear much less complicated than patterns for sequences in all subgroups taken together, implying that subgroups may be related to Tcr functions. Among 83 mouse chains, 15 are from cytotoxic cells and 40 from helper cells. Of the 15 from cytotoxic cells, 11, 2, 0, and 2 are in subgroups I, II, III, and miscellaneous; and of the 40 from helper cells, 9, 16, 12, ans 3 are in subgroups I, II, III, and miscellaneous, respectively. Thus, a correlation between sequence and function of Tcr chains seems possible. Address correspondence and offprint requests to: M. Schiffer.     

Effect of parity on productivity and sustainability of Lotka–Volterra food chains

Hairston, Slobodkin, and Smith conjectured that top down forces act on food chains, which opposed the previously accepted theory that bottom up forces exclusively dictate the dynamics of populations. We model food chains using the Lotka–Volterra predation model and derive sustainability constants which determine which species will persist or go extinct. Further, we show that the productivity of a sustainable food chain with even trophic levels is predator regulated, or top down, while a sustainable food chain with odd trophic levels is resource limited, which is bottom up, which is consistent with current ecological theory.     

Determination of the structure of the carbohydrate chains of acid α-glucosidase from human placenta

Acid α-glucosidase (α-d-glucoside glucohydrolase, EC 3.2.1.20) from human placenta (70 and 76 kDa) was found to contain 4 N-glycosidic carbohydrate chains per molecule. Sugar analysis of purified enzyme revealed the presence of mannose, N-acetylglucosamine and fucose at a molar ratio of 5.0:2.0:0.6. In addition, trace amounts of galactose and N-acetylneuraminic acid were detected. The sugar chains were liberated from the polypeptides by the hydrazinolysis procedure and subsequently fractionated by gel filtration and HPLC. Purified compounds were investigated by 500-MHz ¹H-NMR spectroscopy. Oligomannoside-type chains of intermediate size, e.g., Man₅GlcNAcGlcNAc-ol and Man₇GlcNAcGlcNAc-ol, and N-type chains of smaller size e.g., Man_2–3GlcNAc[Fuc]_0–1GlcNAc-ol, were demonstrated to be present at a ratio of 2:3. In addition, a small amount of sialylated N-acetyllactosamine-type chains has been found. The possible biosynthetic route of the fucose-containing small-size chains is discussed.     

The amino acid sequences of the Fd fragments of two human γ heavy chains

The amino acid sequences of the Fd fragments of two human pathological immunoglobulins of the immunoglobulin G1 class are reported. Comparison of the two sequences shows that the heavy-chain variable regions are similar in length to those of the light chains. The existence of heavy chain variable region subgroups is also deduced, from a comparison of these two sequences with those of another gamma 1 chain, Eu, a mu chain, Ou, and the partial sequence of a fourth gamma 1 chain, Ste. Carbohydrate has been found to be linked to an aspartic acid residue in the variable region of one of the gamma 1 chains, Cor.     

Structural assessment of β-glucuronidase carbohydrate chains by lectin affinity chromatography

Rat liver -glucuronidase was studied by sequential lectin affinity chromatography. -Glucuronidase glycopeptides were obtained by extensive Pronase digestion followed byN-[¹⁴C]acetylation and desialylation by neuraminidase treatment. According to the distribution of the radioactivity in the various fractions obtained by chromatography on different lectins, and on the assumption that all glycopeptides were acetylated to the same specific radioactivity, a relative distribution of glycan structure types is proposed. The presence of complex biantennary and oligomannose type glycans (56.8% and 42.7%, respectively) was indicated by Concanavalin A-Sepharose chromatography.Ulex europaeus agglutinin-agarose chromatography revealed the presence of (1-3) linked fucose in some of the complex biantennary type glycans (16.6% of the total glycopeptides). Wheat germ agglutinin chromatography indicated that the minority (0.5%) were hybrid or poly (N-acetyllactosamine) type glycans. Furthermore, the absence of O-glycans, tri-, tetra- and bisected biantennary type glycans was demonstrated by analysis of Concanavalin A-Sepharose unbound fraction by chromatography on immobilized soybean agglutinin,Ricinus communis agglutinin andPhaseolus vulgaris erythroagglutinin.     

PCR amplification of cDNAs of fish hemoglobin β chains using a consensus primer: cDNA-derived amino acid sequences of β chains from the catfishParasilurus asotus and the scadDecapterus maruadsi

Hemoglobinβ chains were isolated from the catfishParasilurus asotus, the scadDecapterus maruadsi, the filefishThamnaconus modestus, and the scorpaenoidSebastiscus marmoratus by reverse-phase chromatography, and the N-terminal sequences were determined. To obtain the complete amino acid sequence, a 20-meric redundant consensus primer based on the N-terminal amino acid sequences of theβ chains was designed. Using this primer and oligo-dT adaptor, we amplified successfully the β-chain cDNAs of about 600 bp from the four fishes. The amplified products fromParasilurus andDecapterus were subcloned in theSmaI site of pUC18 and cDNA-derived amino acid sequences of 147 residues were determined, of which 69 and 76 residues, respectively, were identified by the chemical amino acid sequencing of internal peptides. Thus this PCR methodology using the consensus primer should be widely applicable for amplifying hemoglobinβ chains from teleosts.     

Biophysical consequences of remodeling the neutral side chains of rhamnogalacturonan I in tubers of transgenic potatoes

Two lines of transgenic potato (Solanum tuberosum L.) plants modified in their cell wall structure were characterized and compared to wild type with regard to biomechanical properties in order to assign functional roles to the particular cell wall polysaccharides that were targeted by the genetic changes. The targeted polymer was rhamnogalacturonan I (RG-I), a complex pectic polysaccharide comprised of mainly neutral oligosaccharide side chains attached to a backbone of alternating rhamnosyl and galacturonosyl units. Tuber rhamnogalacturonan I molecules from the two transformed lines are reduced in linear galactans and branched arabinans, respectively. The transformed tuber tissues were found to be more brittle when subjected to uniaxial compression and the side-chain truncation was found to be correlated with the physical properties of the tissue. Interpretation of the force–deflection curves was aided by a mathematical model that describes the contribution of the cellulose microfibrils, and the results lead to the proposition that the pectic matrix plays a role in transmitting stresses to the load-bearing cellulose microfibrils and that even small changes to the rheological properties of the matrix have consequences for the biophysical properties of the wall.     

Purification of β-glucuronidase and structural assessment of the carbohydrate chains by lectin affinity immunoelectrophoresis

The purification of rat liver -glucuronidase from a lysosomal fraction by methods including affinity chromatography, chromatofocusing and preparative PAGE steps is described. Molecular weights of 300 000 and 150 000 were estimated by two dimensional gradient PAGE/immunoelectrophoresis of the lysosomal extract. Isoelectrofocusing in agarose gel followed by immunoelectrophoresis in the second dimension revealed the presence of at least five maxima in the range pH 4.3–7.4.The structural assessment of the carbohydrate chains of lysosomal and microsomal -glucuronidase was performed by lectin affinity immunoelectrophoresis. Reaction with Concanavalin A indicated the presence of bi-antennary complex, oligomannosidic and hybrid type structures, whereas the absence of tri- and tetra-antennary complex type structures was deduced from the lack of interaction with phytohemagglutinin-L. The reaction withLens culinaris agglutinin, Pisum sativum agglutinin andLotus tetragonolobus lectin revealed that part of the glycans contained a fucose (1-6)-linked to theN-acetylglucosamine attached to asparagine. The presence of terminal (1-4)-galactose residues was detected withRicinus communis agglutinin I.     

Characterization of human αβTCR repertoire and discovery of D-D fusion in TCRβ chains

The characterization of the human T-cell receptor (TCR) repertoire has made remarkable progress, with most of the work focusing on the TCRβ chains. Here, we analyzed the diversity and complexity of both the TCRα and TCRβ repertoires of three healthy donors. We found that the diversity of the TCRα repertoire is higher than that of the TCRβ repertoire, whereas the usages of the V and J genes tended to be preferential with similar TRAV and TRAJ patterns in all three donors. The V-J pairings, like the V and J gene usages, were slightly preferential. We also found that the TRDV1 gene rearranges with the majority of TRAJ genes, suggesting that TRDV1 is a shared TRAV/DV gene (TRAV42/DV1). Moreover, we uncovered the presence of tandem TRBD (TRB D gene) usage in ～2% of the productive human TCRβ CDR3 sequences.