Crystallographic studies of 3-ketoacylCoA thiolase from yeast Saccharomyces cerevisiae

Good diffracting crystals of 3-ketoacylCoA thiolase (EC 2.3.1.16) from yeast Saccharomyces cerevisiae have been obtained. The crystals diffract to at least 2.4 A. The space group of these crystals is P2(1)2(1)2(1), with cell dimensions a = 71.8 A, b = 93.8 A and c = 119.9 A. There is one dimer per asymmetric unit.     

Isolation of hemopoietic pluripotent stem cells from spleens of thiamphenicol-pretreated mice

The present report describes the bulk isolation of pluripotent stem cells (PSC) (assayed as day-9 CFU-S, colony-forming-units-spleen). As starting material, spleens, highly enriched with PSC, were used from mice that were bled and treated with thiamphenicol (TAP). In subjecting the spleen cells to a two-stage centrifugal elutriation procedure and a subsequent Percoll gradient centrifugation stage a 30-fold enrichment in the CFU-S concentration was achieved. The splenic PSC seeded with a characteristic low efficiency in the spleens of irradiated mice (f = 2%). Correcting the colony number for this, we obtained a cell mixture consisting of 88% PSC, contaminated with 4% committed precursor cells and about 10% ganuloid cells.     

Synthesis of a Gene Coding for Vasoactive intestinal Peptide (VIP)

Abstract

A solid phase phosphoramidite triester coupling approach was used for the synthesis of the 16 fragments of a gene coding for human/porcine VIP. The design, synthesis, purification, subcloning and sequencing of the gene will be described.     

Quantitative variability of 342 plasma proteins in a human twin population

The degree and the origins of quantitative variability of most human plasma proteins are largely unknown. Because the twin study design provides a natural opportunity to estimate the relative contribution of heritability and environment to different traits in human population, we applied here the highly accurate and reproducible SWATH mass spectrometry technique to quantify 1,904 peptides defining 342 unique plasma proteins in 232 plasma samples collected longitudinally from pairs of monozygotic and dizygotic twins at intervals of 2–7 years, and proportioned the observed total quantitative variability to its root causes, genes, and environmental and longitudinal factors. The data indicate that different proteins show vastly different patterns of abundance variability among humans and that genetic control and longitudinal variation affect protein levels and biological processes to different degrees. The data further strongly suggest that the plasma concentrations of clinical biomarkers need to be calibrated against genetic and temporal factors. Moreover, we identified 13 cis‐SNPs significantly influencing the level of specific plasma proteins. These results therefore have immediate implications for the effective design of blood‐based biomarker studies.     

Sec-Mediated Transport of Posttranslationally Dehydrated Peptides in Lactococcus lactis

Nisin is a lanthionine-containing antimicrobial peptide produced by Lactococcus lactis. Its (methyl)lanthionines are introduced by two posttranslational enzymatic steps involving the dehydratase NisB, which dehydrates serine and threonine residues, and the cyclase NisC, which couples these dehydrated residues to cysteines, yielding thioether-bridged amino acids called lanthionines. The prenisin is subsequently exported by the ABC transporter NisT and extracellularly processed by the peptidase NisP. L. lactis expressing the nisBTC genes can modify and secrete a wide range of nonlantibiotic peptides. Here we demonstrate that in the absence of NisT and NisC, the Sec pathway of L. lactis can be exploited for the secretion of dehydrated variants of therapeutic peptides. Furthermore, posttranslational modifications by NisB and NisC still occur even when the nisin leader is preceded by a Sec signal peptide or a Tat signal peptide 27 or 44 amino acids long, respectively. However, transport of fully modified prenisin via the Sec pathway is impaired. The extent of NisB-mediated dehydration could be improved by raising the intracellular concentration NisB or by modulating the export efficiency through altering the signal sequence. These data demonstrate that besides the traditional lantibiotic transporter NisT, the Sec pathway with an established broad substrate range can be utilized for the improved export of lantibiotic enzyme-modified (poly)peptides.     

Isolation and characterization of the erythroid progenitor cell: CFU-E

Erythroid progenitor cells, CFU-E (colony-forming-unit-erythroid), were isolated to practical homogeneity by a combination of three enrichment procedures. CFU-E were generated in large amounts in spleens of mice previously bled and treated with the erythropoiesis-suppressing drug thiamphenicol. The average CFU-E concentration in spleens from mice 4 d after the thiamphenicol-treatment was 10%. These CFU-E were separated from lymphocytes, erythrocytes, and granulocytes and their progenitor cells by centrifugal elutriation and Percoll density gradient centrifugation. A three- to five-fold enrichment was obtained by elutriation, leading to a CFU-E concentration of 45%. With the Percoll gradient another twofold enrichment was achieved, providing us with a 80-100% CFU-E cell population. The overall recovery of CFU-E was 60- 70%. This is a cheap, rapid, and highly efficient method of obtaining large quantities of viable CFU-E. The sequential formation of two-, four-, and eight-cell colonies from CFU-E cultured in vitro was studied. These cells enable us to study the biochemical changes occurring in the differentiation process of an erythroid progenitor cell induced by the hormone erythropoietin. The morphological and some physical and biological properties of these cells are presented.     

Biogenesis of the red cell membrane and cytoskeletal proteins during erythropoiesis in vitro

Purified erythroid progenitor cells (CFU-E) were used to study in vitro the production of the proteins present in the plasma membrane and the membrane skeleton. At different stages of erythropoiesis incorporation of [35S]methionine was measured and membranes were isolated. Whereas incorporation in the total protein mass of the cells increased during erythropoiesis, the labeling of the membrane protein fraction decreased. The major erythrocyte membrane proteins were synthesized already in the CFU-E and continued to be made till the orthochromatic erythroblast stage. Band 3 protein, however, was made at a much lower rate. The incorporation in the late stages was only 5% of that in the CFU-E. The major changes in the protein composition of the membrane and its adherent skeleton occurred at the enucleation step.     

Quirks of dye nomenclature. 6. Malachite green

Malachite green was discovered independently by two researchers in Germany in the 19^th century and found immediate employment as a dye and a pigment. Subsequently, other uses, such as staining biological specimens, emerged. A much later application was the control of fungal and protozoan infections in fish, for which the dye remains popular, although illegal in many countries owing to a variety of toxicity problems. In solution, malachite green can exist as five different species depending on the pH. The location of the positive charge of the colored cation on a carbon atom or a nitrogen atom is still debated. The original names of this dye, and their origins, are briefly surveyed.     

Immunodominant CD4+ T-cell epitope within nonstructural protein 3 in acute hepatitis C virus infection.

In acute hepatitis C virus infection, 50 to 70% of patients develop chronic disease. Considering the low rate of spontaneous viral clearance during chronic hepatitis C infection, the first few months of interaction between the patient's immune system and the viral population seem to be crucial in determining the outcome of infection. We previously reported the association between a strong and sustained CD4+ T-cell response to nonstructural protein 3 (NS3) of the hepatitis C virus and a self-limited course of acute hepatitis C infection. In this study, we identify an immunodominant CD4+ T-cell epitope (amino acids 1248 to 1261) that was recognized by the majority (14 of 23) of NS3-specific CD4+ T-cell clones from four of five patients with acute hepatitis C infection. This epitope can be presented to CD4+ T cells by HLA-DR4, -DR11, -DR12, -DR13, and -DR16. HLA-binding studies revealed a high binding affinity for 10 of 13 common HLA-DR alleles. Two additional CD4+ T-cell epitopes, amino acids 1388 to 1407 and amino acids 1450 to 1469, showed a very narrow pattern of binding to individual HLA-DR alleles. Our data suggest that the NS3-specific CD4+ T-cell response in acute hepatitis C infection is dominated by a single, promiscuous peptide epitope which could become a promising candidate for the development of a CD4+ T-cell vaccine.     

The planar conformation of a strained proline ring: a QM/MM study

QM and QM/MM energy calculations have been carried out on an atomic resolution structure of liganded triosephosphate isomerase (TIM) that has an active site proline (Pro168) in a planar conformation. The origin of the planarity of this proline has been identified. Steric interactions between the atoms of the proline ring and a tyrosine ring (Tyr166) on one side of the proline prevent the ring from adopting the up pucker (chi1 is approximately -30 degrees), while the side chain of a nearby alanine (Ala171) forbids the down pucker (chi1 is approximately +30 degrees). To obtain a proline conformation that is in agreement with the experimentally observed planar state, a quantum system of sufficient size is required and should at least include the nearby side chains of Tyr166, Ala171, and Glu129 to provide enough stabilization. It is argued that the current force fields for structure optimization do not describe strained protein fragments correctly. The proline is part of a catalytic loop that closes upon ligand binding. Comparison of the proline conformation in different TIM X-ray structures, indicates that in the closed conformation of TIM the proline is planar or nearly planar, while in the open conformation it is down puckered. This suggests that the planarity possibly plays a role in the overall catalytic cycle of TIM, presumable acting as a reservoir of energy that becomes available upon loop opening.