Analyzing protein-protein interactions in cell membranes

Interactions among membrane proteins regulate numerous cellular processes, including cell growth, cell differentiation and apoptosis. We need to understand which proteins interact, where they interact and to which extent they interact. This article describes a set of novel approaches to measure, on the surface of living cells, the number of clusters of proteins, the number of proteins per cluster, the number of clusters or membrane domains that contain pairs of interacting proteins and the fraction of one protein species that interacts with another protein within these domains. These data can then be interpreted in terms of the function of the protein-protein interactions.     

Purification,Cloning and Functional Expression of hydroxyphenylpyruvate Reductase Involved in Rosmarinic Acid Biosynthesis in Cell Cultures of Coleus Blumei

Hydroxyphenylpyruvate reductase (HPPR) is an enzyme involved in the biosynthesis of rosmarinic acid in Lamiaceae reducing hydroxyphenylpyruvates in dependence of NAD(P)H to the corresponding hydroxyphenyllactates. The HPPR protein was purified from suspension cells of Coleus blumei accumulating high levels of rosmarinic acid by ammonium sulfate precipitation, anion exchange chromatography, hydroxylapatite chromatography, chromatography on 2',5'-ADP-Sepharose 4B and SDS-polyacrylamide gel electrophoresis. The protein was tryptically digested and the peptides sequenced. Sequence information was used to isolate a full-length cDNA-clone for HPPR (EMBL accession number AJ507733) by RT-PCR, screening of a C. blumei cDNA-library and 5'-RACE-PCR. The open reading frame of the HPPR-cDNA consists of 939 nucleotides encoding a protein of 313 amino acid residues. The sequence showed that HPPR belongs to the family of D-isomer-specific 2-hydroxyacid dehydrogenases. The HPPR-cDNA was heterologously expressed in Escherichia coli and the protein was shown to catalyse the NAD(P)H-dependent reduction of 4-hydroxyphenylpyruvate to 4-hydroxyphenyllactate and 3,4-dihydroxyphenylpyruvate to 3,4-dihydroxyphenyllactate.     

Mannopeptimycin esters and carbonates, potent antibiotic agents against drug-resistant bacteria

A series of ester and carbonate derivatives of the glycopeptide mannopeptimycin alpha (1) with potent activity against G+ bacteria, including the methicillin-resistant staphylococci and vancomycin-resistant enterococci, was synthesized. The SAR data obtained from natural and semisynthetic compounds demonstrated the importance of a hydrophobic group in the terminal mannosyl moiety for antibacterial activity.     

Comparison of species diversity of arbuscular mycorrhizal fungi in winter-rainfall areas of South Africa and summer-rainfall areas of Namibia

Arbuscular mycorrhizal fungi and their mycorrhizae were studied in winter rainfall areas of western South Africa. The species composition, spore numbers, and mycorrhization were attempted to correlate with various abiotic factors. Mycorrhization of grasses was significantly correlated with pH and spore numbers and negatively correlated with electric conductivity, total N-content, and total P-content of the soils. Spore numbers were negatively correlated with electric conductivity and total N-content. These relationships observed for the winter rainfall area were compared to data available for summer rainfall areas in Namibia, where the same amount of rain falls. Factors influencing species distribution were geographic distance and to a lesser extent rainfall. Rainfall was a stronger determinant of species composition in the summer rainfall area than in the winter rainfall area. These findings show that abiotic factors alone are not sufficient in explaining species distribution, and that other factors (e.g. the availability of suitable host plants) have to be taken into account when comparing different study sites.     

Carbohydrate moieties can induce mediator release: a detailed characterization of two major timothy grass pollen allergens

Specific IgE binding to carbohydrate moieties of glycosylated allergens has been known for years, but the importance of these structures for the elicitation of allergic reactions is still a matter of debate. Because of their conserved carbohydrate structures, especially N-glycans have always been prime candidates for IgE cross-reactivity between allergens from unrelated species. The aim of our study was to determine whether carbohydrate structures on glycoproteins can by themselves elucidate allergic reactions. We characterized in detail the carbohydrate moieties of the major allergens Phl p 1 and Phl p 13 of timothy grass pollen (Phleum pratense L.) by performing tryptic digests followed by HPLC, N-terminal sequencing, sugar analysis, MALDI-TOF- and ESI-ICRFT-MS. Phl p 1 contains one N-glycan with one of the two glycoforms MMXF3 and M0XF3 and a single furanosidic arabinose, which is bound to a hydroxyproline residue in direct vicinity to the N-glycan. This O-glycosylation is probably due to an arabinosylation consensus sequence found in the N-terminal part of Phl p 1 and other group 1 allergens, but displayed no IgE-reactivity. Thus, Phl p 1 is monovalent with respect to its IgE-binding carbohydrate epitopes and showed no mediator release. In contrast, the carbohydrate moiety of Phl p 13, which carries four of the same N-glycans (like Phl p 1), can cross-link IgE-receptors via carbohydrate chains and elicits IL-4 release from basophils.     

NMR structure determination of a modified DNA oligonucleotide containing a new intercalating nucleic acid

The intercalating nucleic acid (INA) presented in this paper is a novel 1-O-(1-pyrenylmethyl)glycerol DNA intercalator that induces high thermal affinity for complementary DNA. The duplex examined contained two INA intercalators, denoted X, inserted directly opposite each other: d(C(1)T(2)C(3)A(4)A(5)C(6)X(7)C(8)A(9)A(10)G(11)C(12)T(13)):d(A(14)G(15)C(16)T(17)-T(18)G(19)X(20)G(21)T(22)T(23)G(24)A(25)G(26)). Unlike most other nucleotide analogues, DNA with INA inserted has a lower affinity for hybridizing to complementary DNA with an INA inserted directly opposite than to complementary unmodified DNA. In this study we used two-dimensional (1)H NMR spectroscopy to determine a high-resolution solution structure of the weak INA-INA duplex. A modified ISPA approach was used to obtain interproton distance bounds from NOESY cross-peak intensities. These distance bounds were used as restraints in molecular dynamics (rMD) calculations. Twenty final structures were generated for the duplex from a B-type DNA starting structure. The root-mean-square deviation (RMSD) of the coordinates for the 20 structures of the complex was 1.95 A. This rather large value, together with broad lines in the area of insertion, reflect the high degree of internal motion in the complex. The determination of the structure revealed that both intercalators were situated in the center of the helix, stacking with each other and the neighboring nucleobases. The intercalation of the INAs caused an unwinding of the helix in the insertion area, creating a ladderlike structure. The structural changes observed upon intercalation were mainly of local character; however, a broadening of the minor groove was found throughout the helix.     

Modelling zinc-binding proteins with GADGET: genetic algorithm and distance geometry for exploring topology

A novel combination of optimization methods (Genetic Algorithm with Distance Geometry) has been developed and shown to find near-optimal solutions to a set of imposed structural constraints. With this modelling tool (GADGET), the fold-space of a variety of small zinc-binding proteins was investigated under the constraints required to form a zinc-binding site (or pair of sites). Analysis of the results concentrated on the ring-finger domain as the "classic" zinc-finger domains were too constrained to provide much topological variety, whilst the TFIIH domain (which has large unstructured loops) did not behave well. The intermediate ring-finger domain, however, was found to adopt a variety of different folds, many of which had near-optimal scores under the fitness function employed in GADGET (forming good secondary structures and zinc-coordination). Although the native fold was dominant amongst the solutions, the discovery of good alternate folds shows that even the eight residues constrained to form two zinc-binding sites was not sufficient to uniquely determine the native fold. Despite this, the fold-space of 48 theoretically possible folds was greatly reduced with just six topologies found in significant numbers.     

Human serum albumin and its structural variants mediate cholesterol efflux from cultured endothelial cells

In the present study, we used the human EA.hy926 endothelial cell line as the model system to investigate the effect of human serum albumin (HSA) and its structural variants on cholesterol efflux. Initial studies showed that HSA promoted cholesterol efflux in a dose- and time-dependent manner, reaching a plateau at 10 mg/ml at 90 min. As a control, gelatin displayed no significant effect on efflux, while HSA was significantly more efficient than ovalbumin and bovine serum albumin (BSA) in promoting cholesterol efflux. Equal molar concentrations of HSA and apolipoprotein A-I (apoA-I) showed that apoA-I had considerably higher efficiency in efflux. However, the prevailing high plasma concentrations of HSA may compensate for its lower efflux rate compared to apoA-I. To characterize the mechanism of HSA-mediated cholesterol efflux, we studied the effects of cAMP and temperature on efflux using both EA.hy926 endothelial cells and murine RAW 264.7 macrophages. We found that HSA-mediated efflux occurred via a cAMP-independent and relatively temperature-insensitive pathway. We next examined the nature of HSA-cholesterol interaction by comparing the effects of various HSA mutants to wild-type HSA on cholesterol efflux. We found specific interactions between subdomains 2A and 3A and cholesterol, as indicated by the changes in the efflux rate of various HSA mutants. In conclusion, our study provides evidence for the role of HSA in cholesterol efflux, and shows that the substitution of specific amino acid residues in subdomains of 2A and 3A may be important structural determinants in its ability to bind to cholesterol and participate in cholesterol efflux.     

Genetic variation in the midcontinental population of sandhill cranes,Grus canadensis

Three subspecies of sandhill crane (Grus canadensis) are recognized in the Midcontinental population, the lesser (Grus c. canadensis), Canadian (G. c. rowani), and greater (G. c. tabida). Blood samples collected on the population's primary spring staging area in Nebraska, U.S.A., were used to resolve the genetic relationship among these subspecies. Phylogenetic analysis of 27 G. canadensis, by DNA sequencing of a 675 bp region of the mtDNA, supports the subspecies designations of G. c. canadensis and G. c. tabida. G. c. rowani individuals were intermediate with each of the other two subspecies. Genetic divergence ranged from 6.5 to 14.5% between G. c. canadensis and G. c. tabida, 0.5 to 6.6% within G. c. canadensis, and 0.1 to 6.0% within G. c. tabida. Sufficient DNA for analysis was obtained from shed feathers indicating a source of genetic material that does not require the capture or sacrifice of the birds. Other genetic markers and methods, including satellite telemetry, are required for obtaining detailed information on crane distributions as needed to establish effective management units for the MCP.