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Diversity of T cell receptor-alpha chain transcripts from hyperimmune alloreactive T cells.

Alloreactive T cells represent a relatively large fraction of the T cell population compared with the fraction of T cells that are specific for other foreign Ag. Recent findings indicate that most alloreactive T cells recognize endogenous peptides in association with a non-self MHC product. In light of these observations, it is perhaps not surprising that previous studies of the size of the TCR-alpha beta repertoire among alloreactive cells showed that they express many different V alpha and V beta genes. To further access the extent of diversity among alloreactive cells, we examined V alpha J alpha combinatorial diversity in polyclonal populations of a BALB/c anti-BALB.B mixed lymphocyte response. A long term culture from naive mice contained a diverse repertoire of V alpha J alpha combinations that was similar to the diversity present among unstimulated splenic T cells. In contrast, long term cultures from hyperimmunized animals contained "dominant" clones of T cells that expressed a restricted repertoire of V alpha J alpha combinations. Examination of the nucleotide sequences of these alpha-chains suggested that there was selective expansion of T cells with identical alpha-chains. In addition, T cells that express the same V alpha J alpha combination but different junctions were also identified. Consistent with previous results, the isolates from hyperimmune animals did not contain somatic mutations in the CDR3 region of the alpha-chains. Nevertheless, the results suggest that T cells may be subject to in vivo selection and clonal expansion analogous to the process of affinity maturation of Ig.

Animals↗

Molecular dynamics analysis of a second phosphate site in the hemoglobins of the seabird, south polar skua. Is there a site-site migratory mechanism along the central cavity?

Hemoglobin function is modulated by several non-heme ligands; among these effectors, organic phosphates generally bind to heterotropic sites with a one-to-one stoichiometry. The phosphate binding site of human hemoglobin is located at the interface between the two beta chains. An additional binding site for polyanions has been studied at the molecular level (Tamburrini, M., A. Riccio, M. Romano, B. Giardina, and G. di Prisco. 2000. Eur. J. Biochem. 267:6089-6098) in the hemoglobins of the south polar skua (Catharacta maccormicki). It is formed by a cluster of six positive charges of both alpha chains (Val-1, Lys-99, Arg-141); the two Lys-99alpha have an essential role in the site structure. The present investigation, carried out on skua deoxyhemoglobins by using a molecular dynamics approach, confirms the structural feasibility of the additional site, possibly having the role of an entry-leaving site, and leads to the proposal of a novel migration pathway for phosphate along the central cavity of hemoglobin from one binding site to the other, occurring according to the hypothesis of a site-site migratory mechanism, which may assign a functional role to the central cavity. The role of Lys-99alpha was further confirmed by molecular dynamics experiments on the mutant Lys-99alpha-->Ala in which, at the end of the simulation, the phosphate was external to the additional site.

Animals↗

Polymerase chain reaction for Mycobacterium tuberculosis: impact on clinical management of refugees with pulmonary infiltrates.

STUDY OBJECTIVES: Screening for pulmonary tuberculosis (TB) in war refugees entering low-prevalence countries for TB is a common policy, but workup strategies are difficult and expensive. DESIGN: Prospective screening of war refugees for TB by chest radiograph and evaluation of the impact of additional polymerase chain reaction (PCR) testing for Mycobacterium tuberculosis complex (MTB) on clinical management in case of pulmonary infiltrates suspicious for TB. SETTING: Academic university medical center. PATIENTS: A total of 3,119 adult war refugees from the Kosovo war were screened by chest radiograph on arrival. Refugees with pulmonary infiltrates suspicious for TB were hospitalized, and a standardized diagnostic workup was performed. MEASUREMENTS AND RESULTS: Of 3,119 adult war refugees screened for TB, 29 patients (0.9%) were identified with pulmonary infiltrates suspicious for TB; 103 specimens (76 sputa; 27 BAL fluids) were collected for acid-fast smear (AFS), PCR, and culture. The prevalence of culture-proven TB infection in this population was 27.6%. Sensitivity for PCR was higher compared with AFS for all specimens (64% vs 20%; p < 0.01) and also for each refugee with at least one positive specimen finding (100% vs 37.5%; p = 0.025). More important, the negative predictive value for three consecutive PCRs (in two sputa and one BAL) was 100%. CONCLUSIONS: Repeated PCR testing for MTB in a population of asymptomatic war refugees with pulmonary infiltrates highly suggestive of TB is significantly more sensitive than AFS. Three negative PCR results allow discharge from isolation, thus reducing the economic burden of isolation strategies.

Adult↗

TGF-beta receptors.

The nature and role of cell surface proteins that bind members of the TGF-beta family has been investigated. TGF-beta, activins, and BMPs each bind to receptors of 55 kDa (type I) and 70 kDa (type II). In the TGF-beta system, these receptors are implicated in the mediation of multiple responses. A member of the type II receptor family has been cloned that encodes four alternatively spliced versions of a transmembrane serine/threonin kinase receptor related to the recently cloned mouse activin receptor and C-elegans daf-1 gene. Inhibitors of serine/threonine kinase activity block transcriptional and growth inhibitory responses to TGF-beta. In addition to the signaling receptors, many cell types express the TGF-beta binding proteoglycan betaglycan. Betaglycan has been purified, molecularly cloned, and shown to bind TGF-beta via its core protein and basic fibroblast growth factor via its heparan sulfate chains. In addition to receptors I and II and betaglycan, some cells express a newly identified set of membrane proteins that specifically bind either TGF-beta 1 or TGF-beta 2. Three of the four isoform-restricted binding proteins are bound to the membrane via phospholipid anchors. Like betaglycan, these proteins might function to regulate the interaction between TGF-beta and their target cells.

Amino Acid Sequence↗

New concepts on the role of ubiquinone in the mitochondrial respiratory chain.

Ubiquinone participates in the oxidation-reduction reactions of the mitochondrial respiratory chain. In addition, this molecule possesses the necessary properties to function as a hydrogen carrier, thereby stoichiometrically coupling proton translocation to respiration by a direct chemiosmotic mechanism. This review discusses recent experimental evidence and new concepts relating to ubiquinone function in the mitochondrial respiratory chain. Emphasis is placed on possible protonmotive mechanisms of ubiquinone function, recent evidence implicating stable forms of ubisemiquinone in the respiratory chain, and properties of the ubiquinone molecule which may relate to its biological function.

Animals↗

Development of chicken lymphoid system. I. Synthesis and secretion of immunoglobulins by chicken lymphoid cells.

Synthesis and secretion of Ig by chicken lymphoid cells was studied. Both spleen and bursa cells synthesize and secrete IgM and IgG whereas Ig was not detected in thymus cells. In contrast to the spleen cells which synthesize H and L chains in balanced quantities, the bursa cells synthesize and secrete free L chains. In addition to the lymphoid cells which secrete IgM or IgG, the bursa appears to contain a cell population which synthesizes nonsecretory Ig. The structure of this Ig was studied by specific serological precipitation and by SDS-acrylamide gel electrophoresis. The H chains of this nonsecretory Ig are serologically related to micro-chains and exhibit a smaller molecular weight (i.e., approximately 50,000) in SDS-acrylamide gel electrophoresis than H chains of IgG and IgM synthesized by the spleen cells (i.e., approximately 70,000).

Animals↗

Studies on incorporation of mannose into rat alpha 1-acid glycoprotein: evidence for precursor forms in rough membranes.

Rats were given pulse injections of D-[14C]mannose and were killed at various times up to 60 min after injection. Rough, smooth, and Golgi fractions were prepared from liver, and alpha 1-acid glycoprotein was isolated from Lubrol extracts of the fractions. The kinetics of incorporation of D-[14C]mannose into total protein, Lubrol protein, and alpha 1-acid glycoprotein showed that proteins associated with rough fractions had particularly high specific radioactivities at early times of incorporation. One explanation for the kinetic data is that glycoproteins contain a high mannose content at early times of assembly of oligosaccharide chains. This idea was confirmed in the case of alpha 1-acid glycoprotein by isolation of a high mannose containing precursor species of alpha 1-acid glycoprotein from rough fractions of liver. This species contained 56 residues of hexose (mainly mannose) compared with 35 residues of hexose (roughly equal amounts of mannose and galactose) which are found in the native protein. It is proposed that the high mannose precursor is a form of alpha 1-acid glycoprotein that exists at an early stage in assembly of the glycoprotein and which contains largely unprocessed carbohydrate chains. In addition, evidence is presented from amino acid analyses and gel electrophoresis of the high mannose precursor and another fraction from which it is formed by limited tryptic treatment, that pro-forms of alpha 1-acid glycoprotein with extensions of the polypeptide chain may also exist.

Amino Acids↗

Exhaustive Metropolis Monte Carlo sampling and analysis of polyalanine conformations adopted under the influence of hydrogen bonds.

We propose a novel Metropolis Monte Carlo procedure for protein modeling and analyze the influence of hydrogen bonding on the distribution of polyalanine conformations. We use an atomistic model of the polyalanine chain with rigid and planar polypeptide bonds, and elastic alpha carbon valence geometry. We adopt a simplified energy function in which only hard-sphere repulsion and hydrogen bonding interactions between the atoms are considered. Our Metropolis Monte Carlo procedure utilizes local crankshaft moves and is combined with parallel tempering to exhaustively sample the conformations of 16-mer polyalanine. We confirm that Flory's isolated-pair hypothesis (the steric independence between the dihedral angles of individual amino acids) does not hold true in long polypeptide chains. In addition to 3(10)- and alpha-helices, we identify a kink stabilized by 2 hydrogen bonds with a shared acceptor as a common structural motif. Varying the strength of hydrogen bonds, we induce the helix-coil transition in the model polypeptide chain. We compare the propensities for various hydrogen bonding patterns and determine the degree of cooperativity of hydrogen bond formation in terms of the Hill coefficient. The observed helix-coil transition is also quantified according to Zimm-Bragg theory.

Hydrogen Bonding↗

[Branched-chain amino acids in the treatment of latent porto-systemic encephalopathy. A placebo-controlled double-blind cross-over study].

In a doubleblind cross-over placebo-controlled trial the efficiency of oral treatment with branched chain amino acids was investigated in 22 inpatients with liver cirrhosis. In all patients evidence of latent (subclinical) portalsystemic encephalopathy was obtained by using an extensive psychometric test programme. Patients received a defined diet of 35 cal/kg/day containing 1 g of protein. In addition, branched chain amino acids or casein in a dosage of 0.25 g/kg/day was administered in a cross-over fashion, each for 1 week. Semiquantitative nitrogen balance increased during both treatments, with a tendency towards a larger increase during branched chain amino acid treatment. At the same time ammonia concentration tended to decrease during branched chain amino acid treatment. Taking into account the cross-over design, significant improvements attributable to branched chain amino acid treatment could be demonstrated in psychomotor functions (line tracing, tapping, steadiness, auditory reaction time), attention (digit table), and practical intelligence (digit symbol, number connection test).

Administration, Oral↗

Raman spectra of some saturated, unsaturated and deuterated C18 fatty acids in the HCH-deformation and CH-stretching regions.

We have analyzed the Raman spectra of stearic acid and two deuterated derivatives thereof, 2,2-dideutero stearic acid and 18,18,18-trideutero stearic acid, as well as of four unsaturated, C18 acids, (cis,-9; cis, cis-9,12, cis, cis, cis-9,12,15; and trans, trans-9,12) in their solid and liquid states. The different spectra of stearic acid and the two deuterated derivatives exhibit distinctive HCH-deformation and CH-stretching features for CH2 residues adjacent to CO2H or CH3 residues. Unsaturated hydrocarbon chains reveal additional features attributed to CH2 residues adjacent to one or two HC=CH groups. The spectra of the various fatty acids in their solic or liquid states show that both the HCH-deformation and CH-stretching regions are very sensitive to chain architecture, the CH-stretching region most dramatically so. Evaluation of the spectral features in the two regions indicates that the detailed structure of the CH-stretching region depends strongly upon interaction, enhanced by Fermiresonance, between CH-stretching fundamentals and HCH-deformation overtones. The data further suggest that the differences between HCH-deformation, in the solid and liquid states, and the resulting altered interactions between CH-stretching fundamentals and HCH-deformation overtones, produce the large modifications of the CH-stretching region that accompany solid-liquid transitions. The results thus provide a basis for the changes in the CH-stretching region, that accompany order-disorder transitions in model and biological membranes.

Deuterium↗

Proteolytic interactions of factor IXa with human factor VIII and factor VIIIa.

Factor IXa was shown to inactivate both factor VIII and factor VIIIa in a phospholipid-dependent reaction that could be blocked by an antifactor IX antibody. Factor IXa-catalyzed inactivation correlated with proteolytic cleavages within the A1 subunit of factor VIIIa and within the heavy chain (contiguous A1-A2-B domains) of factor VIII. Furthermore, a relatively slow conversion of factor VIII light chain to a 68-Kd fragment was observed after prolonged incubation. Sites of cleavage were identified within the A1 domain at Arg336-Met337 and within the factor VIII light chain at Arg1719-Asn1720. Factor IXa failed to cleave isolated factor VIII heavy chains, yet cleaved isolated factor VIII light chain. In addition, the purified A1/A3-C1-C2 dimer derived from factor VIIIa was a substrate for factor IXa; however, cleavage of the A1 subunit occurred at less than 30% the rate of cleavage of A1 in trimeric factor VIIIa. These data suggest that factor VIII light chain contributes to the binding site for factor IXa and also support a role for a heavy chain determinant located within the A2 subunit in the association of factor VIIIa with factor IXa. Furthermore, the capacity of factor IXa to proteolytically inactivate its cofactor, factor VIIIa, suggests a mode of regulation within the intrinsic tenase complex.

Amino Acid Sequence↗

Dynamics of the core tryptophan during the formation of a productive molten globule intermediate of barstar.

The evolution of the nanosecond dynamics of the core tryptophan, Trp53, of barstar has been monitored during the induction of collapse and structure formation in the denatured D form at pH 12, by addition of increasing concentrations of the stabilizing salt Na(2)SO(4). Time-resolved fluorescence methods have been used to monitor the dynamics of Trp53 in the intermediates that are populated during the salt-induced transition of the D form to the molten globule B form. The D form approximates a random coil and displays two rotational correlation times. A long rotational correlation time of 2.54 ns originates from segmental mobility, and a short correlation time of 0.26 ns originates from independent motion of the tryptophan side chain. Upon addition of approximately 0.1 M Na(2)SO(4), the long rotational correlation time increases to approximately 6.4 ns, as the chain collapses and the segmental motions merge to reflect the global tumbling motion of a pre-molten globule P form. The P form exists as an expanded form with approximately 30% greater volume than the native (N) state. The persistence of an approximately 50% contribution to anisotropy decay by the short rotational correlation time suggests that the core of the P form is highly molten and permits free rotation of the Trp side chain. With increasing salt concentrations, tight core packing is achieved before secondary and tertiary structure formation is complete, an observation which agrees well with earlier kinetic folding studies. Thus, the equilibrium model developed here for describing the formation of structure during folding faithfully captures snapshots of transient kinetic intermediates observed on the folding pathway of barstar. A comparison of the refolding kinetics at pH 7, when refolding is initiated from the D, P, and B forms, suggests that formation of a collapsed state with a rigid core and approximately 30% secondary and tertiary structure, which presumably defines a coarse native-like topology, constitutes the intrinsic barrier in the folding of barstar.

Bacterial Proteins↗

Secretion of a soluble, chimeric gamma delta T-cell receptor-immunoglobulin heterodimer.

Soluble derivatives of T-cell antigen receptors (TCRs) should prove invaluable for studying the interaction of these receptors with antigens and major histocompatibility complex molecules, for structural studies, and for the identification of unknown ligands. We have engineered chimeric proteins, containing the extracellular domains of the mouse V gamma 1.1-C gamma 4 and V delta 6.2-C delta (V, variable; C, constant) TCR chains fused to the hinge region, CH2 (H, heavy), and CH3 domains of human IgG1 heavy chain, and expressed them by transient transfection in COS cells. We show here that TCR gamma-IgH and TCR delta-IgH chimeric chains are produced intracellularly in significant amounts, that the two chains can assemble correctly to form disulfide-linked, glycosylated heterodimers, and that a selective mechanism allows secretion of correctly paired receptor chains into the medium. Identity of the chimeric secreted TCR gamma delta-IgH heterodimer was confirmed by immunoblot analysis using V gamma 1-specific anti-peptide antiserum and immunoprecipitation analysis using the monoclonal antibody UC7, which is shown to be specific for the TCR delta chain. In addition, the soluble TCR gamma delta-IgH heterodimer can be immunoprecipitated with the anti-clonotypic monoclonal antibody F10/56, which suggests that the fusion protein likely has a structural conformation similar to that of the native TCR. The COS cell expression system may prove useful for the production of additional TCR-IgH fusion proteins.

Animals↗

Tissue specificity of glycosphingolipids as expressed in pancreas and small intestine of blood group A and B human individuals.

A chemical investigation has been done on blood group active glycosphingolipids of both small intestine and pancreas from two individuals, one blood group A and one blood group B. Total non-acid glycolipid fractions were prepared and the major blood group fucolipids present were purified and structurally characterized by mass spectrometry, proton NMR spectroscopy, and degradation methods. The glycolipid structures identified were a blood group Leb hexaglycosylceramide, a B-hexaglycosylceramide with a type 1 (Gal beta 1 leads to 3GlcNAc) carbohydrate chain, A-hexaglycosylceramides with types 1 and 2 (Gal beta 1 leads to 4GlcNAc) carbohydrate chains, a B-heptaglycosylceramide with a type 1 carbohydrate chain, and A-heptaglycosylceramides with type 1 and 2 carbohydrate chains. In addition several minor glycolipids having more than seven sugar residues were detected by thin-layer chromatography. The small intestine and pancreas had some distinct differences in their expression of the major fucolipids. The small intestine contained only glycolipids based upon type 1 carbohydrate chain while the pancreas had both type 1 and type 2 structures. The intestines contained mainly difucosyl compounds while the pancreas tissues contained both mono- and difucosyl glycolipids. Monofucosylglycolipids based on both types 1 and 2 saccharides were present in one pancreas while the other one contained only monofucosylcomponents based on type 1 chain. The ceramides of the intestinal glycolipids were found to be more hydroxylated (trihydroxy long-chain base, hydroxy fatty acids) compared to the pancreas glycolipids (dihydroxy long-chain base, non-hydroxy fatty acids).

ABO Blood-Group System↗

Inhibition of enzymic and non-enzymic lipid peroxidation of flounder muscle sarcoplasmic reticulum by pretreatment with phospholipase A2.

Sarcoplasmic reticulum, isolated from the muscle of winter flounder (Pseudopleuronectes americanus), was preincubated with phospholipase A2 to determine the effects of enzymic and non-enzymic lipid-peroxidation systems. Eicosapentaenoic acid (20:5) was preferentially released by phospholipase A2, but the percentage of docosahexaenoic acid (22:6) in the free fatty acids was similar to the percentage in membrane total fatty acids. A decrease in the production of both thiobarbituric acid-reactive substances and lipid hydroperoxides was observed in both the enzymic and non-enzymic peroxidation systems upon preincubation with phospholipase A2. Addition of palmitic acid or lysophosphatidylcholine did not inhibit either peroxidation system. Non-enzymic peroxidation was inhibited by the addition of beta-glycerophosphate, but enzymic peroxidation was apparently unaffected. A model is proposed to explain the inhibitory effect of phospholipid hydrolysis on lipid peroxidation in both systems, suggesting that fatty acids are structurally realigned upon hydrolysis, leading to decreased free-radical chain propagation. Additional factors appear to contribute to inhibition of enzymic peroxidation.

Animals↗

Reversed-phase liquid chromatography as a tool in the determination of the hydrophilicity/hydrophobicity of amino acid side-chains at a ligand-receptor interface in the presence of different aqueous environments. II. Effect of varying peptide ligand hydrophobicity.

The present study represents a continuation of our development of a chromatographic model for studying the hydrophobic interactions which characterize the way a ligand binds to its receptor. We have designed 18-residue amphipathic alpha-helical peptides (representing the hydrophobic binding domain of a ligand), where the non-polar face interacts with the non-polar face of a reversed-phase stationary phase (representing a receptor protein with a hydrophobic binding pocket). Two series of amphipathic alpha-helical peptides were subjected to reversed-phase liquid chromatography at pH 2.0, where the "native" Ala-face peptide contains seven Ala residues in its non-polar face and the "native" Leu-face series contains seven Leu residues in its non-polar face. Mutants of the two series were then prepared by replacing one residue in the centre of the non-polar face in both series of peptides, resulting in amino acid side-chains being exposed to a moderately non-polar environment (Ala series) or a very hydrophobic environment (Leu series) surrounding the substitution site. With this model, we have demonstrated that an increase in non-polarity of the ligand enhances hydrophilicity (decreases hydrophobicity) of all amino acids at the ligand-receptor interface, this effect being dependent on the intrinsic hydrophilicity/hydrophobicity of the side-chain. The addition of salt to the aqueous environment surrounding the binding site of the ligand and receptor was also shown to affect the hydrophilicity/hydrophobicity of amino acids in the binding interface. For the Ala-face mutants, the majority of the non-polar side-chains and the three positively charged residues (Arg, His, Lys) showed significant enhancement of hydrophobicity in the presence of salt; in contrast, in the much more hydrophobic environment of the Leu-face mutants, there was a trend of lesser hydrophobicity enhancement and/or significantly more hydrophilicity enhancement in the presence of salt. Our results should have major implications for the understanding of the hydrophilicity/ hydrophobicity of side-chains in varying hydrophobic and aqueous environments.

Amino Acids↗

Determination of the location of fluorescent probes attached to fatty acids using parallax analysis of fluorescence quenching: effect of carboxyl ionization state and environment on depth.

In this report, parallax analysis of fluorescence quenching (see the preceding paper in this issue) was used to determine the location (depth) of anthroyloxy and carbazole probes attached to model membrane inserted fatty acids. A monotonic increase in depth was found as the number of carbon atoms between the attachment site of the probe and the fatty acyl carboxyl group is increased. It was also found that depth is sensitive to pH, with an increase in probe depth upon protonation of the fatty acid carboxyl group of around 0.5-2.5 A, depending on probe location and identity. This result shows that carboxyl protonation causes an increase in depth all along a fatty acid chain. In addition, it indicates that parallax analysis is very sensitive to small changes in depth. At a given pH, no significant change in probe depth was observed in vesicles containing anionic phospholipid or at various ionic strengths, suggesting these parameters do not strongly regulate fatty acyl chain location. It was also found that there is a decrease of the apparent depth of each of the fatty acyl attached probes both at longer excitation wavelengths and at longer emission wavelengths. This is consistent with there being a distribution of depth for each fluorophore, with shallower fluorophore dominating the fluorescence at red-shifted wavelengths. Solvent relaxation effects also appear to contribute to this wavelength dependence.

Electrochemistry↗

Synthesis and aggregation behavior of four-arm star amphiphilic block copolymers in water.

We report the first synthesis of amphiphilic four-arm star diblock copolymers consisting of styrene (STY) and acrylic acid (AA) made using reversible addition-fragmentation chain transfer (RAFT; Z group approach with no star-star coupling). The polymerization proceeded in an ideal "living" manner. The size of the poly(AA(132)-STY(m)4 stars in DMF were small and close to 7 nm, suggesting no star aggregation. Slow addition of water (pH = 6.8) to this mixture resulted in aggregates of 15 stars per micelle with core-shell morphology. Calculations showed that the polyAA blocks were slightly extended with a shell thickness of 15 nm. Treatment of these micelles with piperidine to cleave the block arms from the core resulted in little or no change on micelle size or morphology, but the polyAA shell thickness was close to 29 nm (33 nm is the maximum at full extension) suggesting a release of entropy when the arms are detached from the core molecule. In this work we showed through the use of star amphiphilic polymers that the micelle size, aggregation number, and morphology could be controlled.

Acrylates↗