Electrophoretic variation between class II molecules expressed on HLA-DRw8 homozygous typing cells reveals multiple distinct haplotypes

Two-dimensional (2D) gel electrophoresis of immunoprecipitated HLA-DR antigens from eight homozygous typing cells (HTC) expressing the HLA-DRw8 specificity revealed a clustering of polymorphic chain patterns into distinct electrophoretic variants. The variant patterns correlate with three discrete HLA-D clusters that are defined in the mixed leukocyte culture reaction (MLR) using DRw8-positive HTC. These HLA-D clusters have been provisionally designated Dw8.1, detected primarily in Caucasoids, Dw8.2, detected primarily in American Indians, and Dw8.3, detected predominantly in Orientals. All three HLA-Dw8.1 cell lines express a single DR-locus product as defined by immunoprecipitation with a DR-specific monoclonal antibody, P4.1. This DR chain is identical among the Dw8.1 cell lines and different from the DR chains of the Dw8.2 and Dw8.3 cell lines. Two separate Dw8.2 HTC express a shared DR chain that is slightly more basic than the 8.1 DR molecule; interestingly, one of these lines also expresses an additional DR-like chain not found in the other cells. Thus, the two lines defining the Dw8.2 cluster share one distinct class 11 molecule, but differ in another and therefore are not biochemically HLA-identical. Cells from the Dw8.3 cluster are likewise distinct from all other Dw8 clusters. One additional DRw8-positive HTC has been analyzed and found to be distinct from the Dw8.1, 8.2 and 8.3 clusters by both MLR and 2D gels. lmmunoprecipitates using monoclonal antibody 1B5 [anti-DR and anti-DQ(DS)] identify additional polymorphic class II variants among the cell lines tested. These data indicate that HLA-DRw8 is a public serologic specificity present on class II molecules expressed on multiple distinct haplotypes. These haplotypes differ from each other in expression of polymorphic class II molecules encoded by at least two HLA loci. They also differ in HLA-D, even though they all type as HLA-DRw8 homozygous. In Dw8.2, variation in expressed chains is not reflected in variation in HLA-D, indicating that MLR, as well as serologic typing, does not detect the full degree of allelic polymorphism within HLA.     

Unique sequences for two HLA-DRB1 genes expressed on distinct DRw6 haplotypes

We have used restriction fragment length polymorphism (RFLP) analysis and DNA sequencing to characterize two distinct DRB1 alleles expressed on DRw52 and DQw7-associated haplotypes but not readily defined by conventional DR serology. These two haplotypes, designated HLA-D HAG and PEV, react variably with DRw13(w6), DRw14(w6), and the more broad DR 3+6 antisera. Analysis of RFLP revealed that HLA-D HAG and PEV are associated with different DRw52 variants, and that HAG is indistinguishable from DRw18(3) haplotypes. Sequencing of the HAG and PEV DRB1 genes showed each to represent novel alleles. Nevertheless, these sequences show similarities with the other alleles of the DR5, w6, and w8 family. HAG (DRB1*1303) appears to have arisen either from two recombinational events involving at least three DRB1 sequences (DRB1*1101, DRB1*0803, DRB1*0401) or from a single recombinational event together with multiple point mutational events. PEV appears to represent a DRB1*1301-1302/DRB1*1101 recombinant allele, with recombination having occured in the region of bases 175 – 198. The results of this study suggest that the DRw52 family haplotypes is derived from a relatively restricted number of ancestral sequences, with diversity among DRB1 alleles within this family arising through gene conversion or recombination events.     

Human aorta collagens: evidence for three distinct species

Three different molecular species of collagen and a soluble form of elastin were obtained by digestion of human aortas with pepsin. Two of the three collagens contain $\text{1}\text{2}$ cystine, present in interchain disulfide crosslinkages, and appear to represent type IV collagen previously described in basement membranes and type III collagen, recently found in fetal skin. The third collagen species is type I, the molecule found in a wide variety of connective tissues including skin, bone, tendon and ligaments.     

Definition of gene content for nine common group B haplotypes of the Caucasoid population: KIR haplotypes contain between seven and eleven KIR genes

The segregation of killer cell immunoglobulin-like receptor ( KIR) genes was determined for a panel of 21 Caucasoid families: 23 different KIR gene patterns were found and could be assigned to combinations of 16 different haplotypes. Four loci were held in common by all haplotypes: KIR2DL4, KIR3DL2, the putative pseudogene KIR3DL3 and KIR2DL2/KIR2DL3, the latter likely being alleles of one gene. Group A haplotypes, which have a unique combination of seven KIR genes, were found at 80% frequency in the family panel, the polygenic group B haplotypes at 65% frequency. KIR gene segregation was fully determined for the nine group B haplotypes, which occurred at highest frequencies in both the family panel and a panel of unrelated individuals. The group B haplotypes carried between seven and 11 KIR genes and encoded inhibitory KIR for one, two, or all three major HLA class I epitopes. Analysis of human leucocyte antigen (HLA) class I genotypes revealed that most, but not all, individuals possess an inhibitory KIR for a self HLA class I epitope. The number of stimulatory KIR genes in group B haplotypes varied considerably between one and five. The data show that group B haplotypes possess a broad spectrum of KIR gene patterns, which is largely complementary to the KIR gene set of group A haplotypes. The results suggest that rapid diversification of group B haplotypes is the result of pathogen-mediated selection for KIR genotypes that have more than the set of KIR genes provided by the group A haplotype.     

Platelet-collagen adhesion: evidence for participation of antigenically distinct entities

Univalent antibody fragments prepared from a rabbit antiserum raised against whole human platelets completely inhibited adhesion of platelets to immobilized trimeric collagen in a defined, Mg2+- dependent, adhesion assay. An octylglucoside extract of whole platelets completely neutralized this antibody, and all neutralizing activity bound to immobilized wheat germ agglutinin. Further fractionation on concanavalin A gave rise to subfractions that each neutralized only partially at saturation, when tested against antibody concentrations that inhibit 50% of platelet-collagen adhesion. When tested against higher antibody concentrations that completely inhibited adhesion, each subfraction had no detectable neutralizing effect, although the combined subfractions neutralized completely. This and other evidence suggests that more than one platelet entity participates in platelet- collagen adhesion. Although distinct, they appear to play interdependent roles in a single adhesion process.     

Toward understanding MHC disease associations: partial resequencing of 46 distinct HLA haplotypes

We carried out a resequencing project that examined 552 kb of sequence from each of 46 individual HLA haplotypes representing a diversity of HLA allele types, generating nearly 27 Mb of fully phased genomic sequence. Haplotype blocks were defined extending from telomeric of HLA-F to centromeric of HLA-DP including in total 5186 MHC SNPs. To investigate basic questions about the evolutionary origin of common HLA haplotypes, and to obtain an estimate of rare variation in the MHC, we similarly examined two additional sets of samples. In 19 independent HLA-A1, B8, DR3 chromosomes, the most common HLA haplotype in Northern European Caucasians, variation was found at 11 SNP positions in the 3600-kb region from HLA-A to DR. Partial resequencing of 282 individuals in the gene-dense class III region identified significant variability beyond what could have been detected by linkage to common SNPs.     

Complement C7 deficiency: seven further molecular defects and their associated marker haplotypes

Seven further molecular bases of C7 deficiency are described. All these new molecular defects involve single-nucleotide events, deletions and substitutions, some of which alter splice sites, and others codons. They are distributed along the C7 gene, but predominantly towards the 3′ end. All were found in compound heterozygous individuals. The C6/C7 marker haplotypes associated with most C7 defects are tabulated. Received: 30 March 1998 / Accepted: 3 July 1998     

Biochemistry of Coxiella burnetii: 6-phosphogluconic acid dehydrogenase

Purified preparations of the rickettsial agent, Coxiella burnetii, have been examined for their ability to decarboxylate 6-phosphogluconate. The enzyme 6-phosphogluconic acid dehydrogenase [6-phospho-d-gluconate: NADP (nicotinamide adenine dinucleotide phosphate) oxidoreductase (decarboxylating), EC 1.1.1.44] was detected in extracts, but not in whole-cell preparations of C. burnetii. Both extracts and whole cells were shown to be free from contaminating host enzyme activity. Partial characterization of the enzyme has shown that it is substrate-dependent, specific for NADP, and requires magnesium for activity. The pH optimum of the rickettsial enzyme is 8.0.     

Thermostability of alcohol dehydrogenase: evidence for distinct subunits with different deactivation properties

Several independent experimental techniques, including nondenaturing and denaturing isoelectric focusing, spin labeling, and enzyme immobilization, indicate that four ethanol-active subunits of horse liver alcohol dehydrogenase (LADH) can be classified as one of two types, designated E(1) and E(2). Thermal inactivation studies of LADH in solution and immobilized to two different supports demonstrate that the first-order rate constants of deactivation of E(1) and E(2) differ by more than an order of magnitude. Furthermore, E(1), and E (2) can be distinguished by EPR spectroscopy, with the less stable subunit type, E(2), appearing to have the less compactly structured active-site environment. The less stable enzyme form also loses catalytic activity upon covalent attachment to CNBr-Sepharose but remains active when adsorbed to Octyl-Sepharose. Moreover, the immobilization results in conjunction with lysine modification studies suggest that E(2) immobilized to CNBr-Sepharose cannot bind coenyzme. Overall, these results illustrate how EPR measurements in concert with activity assays can pro vide insights into the molecular mechanisms of enzyme stabilization.     

Hydrogen-exchange evidence for distinct structural classes in globular proteins

Exchange-rate probability-density functions (pdf) have been calculated for lysozyme hydrogen-exchange data by numerical Laplace inversion over the temperature range 5–45°C. The smoothest numerical solutions show three broad overlapping peaks. Analysis of the temperature dependence of the cumulative exchange-rate distributions provides the model-independent probability-density function for the activation energies. For the most rapidly exchanging protons, the activation energies are low, consistent with hydroxyl-ion catalysis in the protein–water interface. The second peak of the exchange-rate pdf's contains those protons located in regions of lower motility we call “matrices,” for which exchange rates are limited by gated-diffusion of the hydroxyl-ion catalyst. The most slowly exchanging protons are located on groups forming strong, dense “knot” structures, identified by neutron-diffraction and nmr data as clustered segments of β-sheet with well-organized hydrogen bonding and sections of the internal faces of α-helices. Exchange from knot structures occurs through local disordering with little loss of strength or stability to expose one or more protons at a time for exchange. Knots appear to be responsible for the two-state character of thermal unfolding that occurs by cooperative disruption of the dominant structures of this type. Below about 55°C, all protons exchange from folded states. Contributions to exchange from unfolding processes occur only at temperatures above 55°C. There is a qualitative difference between the two types of structures indicated by the appearance of two and only two enthalpy–entropy compensation patterns. The compensation temperature, T_c, for the matrices is about 470 K; that for the knots, about 360 K. The preservation of rank-order with temperature change is shown to be a consequence of the fact that all exchange rates in the slow and very slow peaks of the pdf lie on one or the other of the two compensation lines. Although the same electrostatic factors are present in all parts of the protein, we have been forced to conclude that given certain necessary geometric possibilities, these factors cooperate to produce the knots. The knots appear to be the most significant structural element in globular proteins responsible for the structural form of the matrix regions and the dynamic behavior of the protein interior. The knots have high density and low permeability to water, hydroxyl ion, etc., and are probably the explanation for the very low compressibilities, the matrices being nearly mechanically transparent. The knots must make some contribution to folded stability, but it is not clear that this contribution is large. Their major thermodynamic function is to establish kinetic stability; that is, to make the activation free energy for unfolding high. The most important factor in the existence of knots appears to be the ease with which hydrogen bonds adapt in length, angle, and strength to local electrostatic conditions. In proteins, as in water, adaptation is cooperative in local groups of hydrogen bonds, and as in water, this cooperation is enhanced by contact with aromatic and aliphatic groups.     

Two distinct visual motion mechanisms for smooth pursuit: evidence from individual differences

Smooth-pursuit eye velocity to a moving target is more accurate after an initial catch-up saccade than before, an enhancement that is poorly understood. We present an individual-differences-based method for identifying mechanisms underlying a physiological response and use it to test whether visual motion signals driving pursuit differ pre- and postsaccade. Correlating moment-to-moment measurements of pursuit over time with two psychophysical measures of speed estimation during fixation, we find two independent associations across individuals. Presaccadic pursuit acceleration is predicted by the precision of low-level (motion-energy-based) speed estimation, and postsaccadic pursuit precision is predicted by the precision of high-level (position-tracking) speed estimation. These results provide evidence that a low-level motion signal influences presaccadic acceleration and an independent high-level motion signal influences postsaccadic precision, thus presenting a plausible mechanism for postsaccadic enhancement of pursuit.     

Protein targeting by tyrosine- and di-leucine-based signals: evidence for distinct saturable components

Targeting of transmembrane proteins to lysosomes, endosomal compartments, or the trans-Golgi network is largely dependent upon cytoplasmically exposed sorting signals. Among the most widely used signals are those that conform to the tyrosine-based motif, YXXO (where Y is tyrosine, X is any amino acid, and O is an amino acid with a bulky hydrophobic group), and to the di-leucine (or LL) motif. Signals conforming to both motifs have been implicated in protein localization to similar post-Golgi compartments. We have exploited the saturability of sorting to ask whether different YXXO or LL signals use shared components of the targeting machinery. Chimeric proteins containing various cytoplasmic domains and/or targeting signals were overexpressed in HeLa cells by transient transfection. Endogenous transferrin receptor and lysosomal proteins accumulated at the cell surface upon overexpression of chimeric proteins containing functional YXXO targeting signals, regardless of the compartmental destination imparted by the signal. Furthermore, overexpression of these chimeric proteins compromised YXXO-mediated endocytosis and lysosomal delivery. These activities were ablated by mutating the signals or by appending sequences that conformed to the YXXO motif but lacked targeting activity. Interestingly, overexpression of chimeric proteins containing cytoplasmic LL signals failed to induce surface displacement of endogenous YXXO-containing proteins, but did displace other proteins containing LL motifs. Our data demonstrate that: (a) Protein targeting and internalization mediated by either YXXO or LL motifs are saturable processes; (b) common saturable components are used in YXXO-mediated protein internalization and targeting to different post-Golgi compartments; and (c) YXXO- and LL-mediated targeting mechanisms use distinct saturable components.     

Genetic analysis of Escherichia coli urease genes: evidence for two distinct loci.

Studies with two uropathogenic urease-producing Escherichia coli strains, 1021 and 1440, indicated that the urease genes of each are distinct. Recombinant plasmids encoding urease activity from E. coli 1021 and 1440 differed in their restriction endonuclease cleavage sites and showed minimal DNA hybridization under stringent conditions. The polypeptides encoded by the DNA fragments containing the 1021 and 1440 urease loci differed in electrophoretic mobility under reducing conditions. Regulation of urease gene expression differed in the two ureolytic E. coli. The E. coli 1021 locus is probably chromosomally encoded and has DNA homology to Klebsiella, Citrobacter, Enterobacter, and Serratia species and to about one-half of the urease-producing E. coli tested. The E. coli 1440 locus is plasmid encoded; plasmids with DNA homology to the 1440 locus probe were found in urease-producing Salmonella spp., Providencia stuartii, and two E. coli isolates. In addition, the 1440 urease probe was homologous to Proteus mirabilis DNA.     

Editorial board page for “Preparative Biochemistry”, Volume 6, Number 6

This is a scanned image of the original Editorial Board page(s) for this issue.     

Structural definition of a family of Ld-like molecules distributed among four of seven haplotypes compared

Comparative tryptic peptide analyses were performed on 12 different D region molecules representing seven different haplotypes. The Dd, Dq, and Dw16 regions were shown to encode multiple, antigenically distinct molecules (Dd Ld, Dq Lq Rq, and Dw16 Lw16, respectively). In addition, each of these molecules was found to have a unique primary structure, implying that they are the products of separate genes. However the previously described Rd molecule, which was identified by sequential immuno-precipitation and 2-D gel analyses, was indistinguishable from Ld by tryptic peptide mapping, implying that these two molecules may be products of the same gene. The Db, Ddx, Dk, and Dp regions were found to determine a single molecule with the reagents tested. Intra- and/or inter-haplotype comparisons of the peptide maps of each of these D region molecules revealed widely disparate structural relationships. For example, the Db, Dq, Lq, Rq, Dw16, and Lw16 molecules all showed striking homology with the Ld molecule. Members of this family share between 43 to 55% peptide homology with Ld, indicating a high conservation of primary structure (greater than 90%). However, because Dq and Dw16 region-encoded molecules show no exceptional relationship to each other, the portion of the conserved sequence is not the same for each of these Ld-like molecules. By contrast, comparisons of the Dk, Dd, Ddx, and Dp molecules with Ld or with each other revealed tryptic peptide homologies ranging from 22 to 38%, suggesting a sequence homology of 70 to 85%. When compared with the Kb molecule, each of the D region molecules showed between 21 to 36% peptide map homology (70 to 85% sequence homology). These studies indicate, therefore, that there is a family of Ld-like molecules representing several distinct haplotypes. This definition of a highly homologous family of D region molecules suggests that many D-region molecules have evolved from an Ld-like primordial gene and that in different haplotypes different portions of this prototypic structure have been maintained.