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Biomedical subjects

J Frank

Publications and source records attributed to J Frank.

At least 55 records · Page 3Linked to original sources
PubMed2001

Towards functional group-specific detection in high-performance liquid chromatography using mid-infrared quantum cascade lasers.

A distributed feedback quantum cascade laser was applied for the first time as a powerful light source for mid-infrared (MIR) detection in liquid chromatography. Fructose and glucose in red wine were separated with an isocratic HPLC system, which was connected to a custom-made flow cell. This flow cell was constructed of two diamond windows with adjustable spacing and two hollow wave-guides for guiding the incoming and outgoing light. The HPLC column based on an ion-exchange resin with calcium(II) counter ion was run at 80 degrees C with 0.04% formic acid as the mobile phase. Under these conditions the carbohydrates could not be completely separated from the organic acids also present in wine. However, the emission of the laser at 1067 cm(-1) matches the absorption maximum of fructose and glucose, whereas the organic acids do not absorb appreciably at this wavenumber. Thus group-specific detection could be achieved. Additionally, the optical path length could be increased from 25 to 125 microm, which is very promising in gaining enhanced sensitivity compared to Fourier transform IR detection.

Calibration↗
PubMed2001

Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.

A cryo-EM reconstruction of the translating yeast 80S ribosome was analyzed. Computationally separated rRNA and protein densities were used for docking of appropriately modified rRNA models and homology models of yeast ribosomal proteins. The core of the ribosome shows a remarkable degree of conservation. However, some significant differences in functionally important regions and dramatic changes in the periphery due to expansion segments and additional ribosomal proteins are evident. As in the bacterial ribosome, bridges between the subunits are mainly formed by RNA contacts. Four new bridges are present at the periphery. The position of the P site tRNA coincides precisely with its prokaryotic counterpart, with mainly rRNA contributing to its molecular environment. This analysis presents an exhaustive inventory of an eukaryotic ribosome at the molecular level.

Base Sequence↗
PubMed2001

Architecture of the protein-conducting channel associated with the translating 80S ribosome.

In vitro assembled yeast ribosome-nascent chain complexes (RNCs) containing a signal sequence in the nascent chain were immunopurified and reconstituted with the purified protein-conducting channel (PCC) of yeast endoplasmic reticulum, the Sec61 complex. A cryo-EM reconstruction of the RNC-Sec61 complex at 15.4 A resolution shows a tRNA in the P site. Distinct rRNA elements and proteins of the large ribosomal subunit form four connections with the PCC across a gap of about 10-20 A. Binding of the PCC influences the position of the highly dynamic rRNA expansion segment 27. The RNC-bound Sec61 complex has a compact appearance and was estimated to be a trimer. We propose a binary model of cotranslational translocation entailing only two basic functional states of the translating ribosome-channel complex.

Base Sequence↗
PubMed2001

Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA.

S1 is the largest ribosomal protein, present in the small subunit of the bacterial ribosome. It has a pivotal role in stabilizing the mRNA on the ribosome. Thus far, S1 has eluded structural determination. We have identified the S1 protein mass in the cryo-electron microscopic map of the Escherichia coli ribosome by comparing the map with a recent x-ray crystallographic structure of the 30S subunit, which lacks S1. According to our finding, S1 is located at the junction of head, platform, and main body of the 30S subunit, thus explaining all existing biochemical and crosslinking data. Protein S1 as identified in our map has a complex, elongated shape with two holes in its central portion. The N-terminal domain, forming one of the extensions, penetrates into the head of the 30S subunit. Evidence for direct interaction of S1 with 11 nucleotides of the mRNA, immediately upstream of the Shine-Dalgarno sequence, explains the protein's role in the recognition of the 5' region of mRNA.

Cryoelectron Microscopy↗
PubMed2001

Influence of allosteric effectors on the kinetics and equilibrium binding of phosphoenolpyruvate (PEP) to phosphoenolpyruvate carboxylase (PEPC) from Zea mays.

Phosphoenolpyruvate carboxylase (PEPC) the carbon dioxide processing enzyme of C(4) plants, shows the features of an allosteric enzyme. Allosteric activators such as D-glucose-6-phosphate and glycine increase the affinity of PEPC for its substrate PEP at pH 8.0 and pH 7.0. Allosteric inhibitors like L-malate and L-aspartate predominantly decrease the affinity of the carboxylase for PEP at pH 7.0. This was demonstrated by determination of the enzymatic activity and stopped flow (SF) fluorimetry. The binding reaction of PEP to PEPC from Zea mays was measured using the fluorescence probe 2-p-toluidinonaphthalene-6-sulfonate (TNS). The kinetics are described by an allosteric mechanism with a fast reversible bimolecular binding step of PEP to a high affinity (tensed) form of PEPC, which is in equilibrium with its low affinity (relaxed) form. The influence of allosteric effectors on the conformational transition step is demonstrated in support of the description of the kinetics of PEPC by applying a concerted allosteric mechanism as introduced by Monod, Wyman and Changeux. In summary, we present data for the influence of allosteric activators on the kinetics of PEP binding to PEPC and on the concentration dependence of the isomerisation reaction between two allosteric forms of PEPC.

Algorithms↗
PubMed2001

Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G-dependent translocation.

L11 protein is located at the base of the L7/L12 stalk of the 50 S subunit of the Escherichia coli ribosome. Because of the flexible nature of the region, recent X-ray crystallographic studies of the 50 S subunit failed to locate the N-terminal domain of the protein. We have determined the position of the complete L11 protein by comparing a three-dimensional cryo-EM reconstruction of the 70 S ribosome, isolated from a mutant lacking ribosomal protein L11, with the three-dimensional map of the wild-type ribosome. Fitting of the X-ray coordinates of L11-23 S RNA complex and EF-G into the cryo-EM maps combined with molecular modeling, reveals that, following EF-G-dependent GTP hydrolysis, domain V of EF-G intrudes into the cleft between the 23 S ribosomal RNA and the N-terminal domain of L11 (where the antibiotic thiostrepton binds), causing the N-terminal domain to move and thereby inducing the formation of the arc-like connection with the G' domain of EF-G. The results provide a new insight into the mechanism of EF-G-dependent translocation.

Cryoelectron Microscopy↗
PubMed2001

Design, simulation and application of a new micromixing device for time resolved infrared spectroscopy of chemical reactions in solution.

We present a novel micromachined fast diffusion based mixing unit for the study of rapid chemical reactions in solution with stopped-flow time resolved Fourier transform infrared spectroscopy (TR-FTIR). The presented approach is based on a chip for achieving lamination of two liquid sheets of 10 microm thickness and approximately 1 mm width on top of each other and operation in the stopped-flow mode. The microstructure is made on infrared transmitting calcium fluoride discs and built up with two epoxy negative photoresist layers and one silver layer in between. Due to the highly laminar flow conditions and the short residence time in the mixer there is hardly any mixing when the two liquid streamlines pass through the mixing unit, which allows one to record a mid-IR transmission spectrum of the analytes prior to reaction. When the flow is stopped, the reactant streams are arrested in the flow-cell and rapidly mixed by diffusion due to the reduced interstream distances and the reaction can be directly followed with hardly any dead time. On the basis of two model reactions-neutralisation of acetic acid with sodium hydroxide as well as saponification of methyl monochloroacetate-the performance of the mixing device was tested revealing proper functioning of the device with a time for complete mixing of less than 100 ms. The experimental results were supported by numerical simulations using computational fluid dynamics (CFD), which allowed a reliable, quantitative analysis of concentration, pressure and flow profiles in the course of the mixing process.

Journal Article↗
PubMed2001

Interaction of fluorescence labeled single-stranded DNA with hexameric DNA-helicase RepA: a photon and fluorescence correlation spectroscopy study.

Fluorescence correlation spectroscopy (FCS) was used to characterize the interaction of fluorescence labeled single-stranded DNA (ssDNA) with hexameric RepA DNA-helicase (hRepA) encoded by plasmid RSF1010. The apparent dissociation constants, Kd(app), for the equilibrium binding of 12mer, 30mer, and 45mer ssDNA 5'-labeled with BFL to hRepA dimer in the presence of 0.5 mM ATPgammaS at pH 5.8 and 25 degrees C were determined to be 0.58 +/- 0.12, 0.52 +/- 0.07, and 1.66 +/- 0.32 microM, respectively. Binding curves are compatible with one binding site for ssDNA present on hRepA dimer, with no indication of cooperativity. At pH 7.6 in the presence of ATPgammaS and at pH 5.8 in the absence of ATPgammaS, complex formation between ssDNA and hRepA was too weak for measuring complete binding curves by FCS. Under these conditions, the dissociation constant, Kd(app), is in the range between 10 and 250 microM. The kinetics of complex formation at pH 5.8 are faster than the time resolution (approximately 10-20 s) of FCS experiments under pseudo-first-order conditions, with respect to BFL-ssDNA. Photon correlation spectroscopy (PCS) experiments yielded, within the experimental error range, the same values for the apparent hydrodynamic radii, R(h), of hRepA dimer and its complex with ssDNA as determined by FCS (R(h) = 6.6 +/- 1 nm). hRepA starts to aggregate under acidic conditions (<pH 6.0) which are optimal for ssDNA binding. CD spectra taken at pH 5.8 in the presence of ATPgammaS showed a structural change induced by ssDNA binding to hRepA which is not visible at pH 7.6 and with ADP as nucleotide cofactor.

Binding Sites↗
PubMed2001

Miniaturized electrospraying as a technique for the production of microarrays of reproducible micrometer-sized protein spots.

Electrospraying in a stable cone-jet mode at <400 microm above a substrate is shown to be a powerful technique to produce arrays of identical micrometer-sized spots consisting of biologically active substances. Aqueous solutions with a surface tension of 0.04 N m(-1) and conductivities ranging from 0.04 to 2.2 S m(-1) were sprayed at ultralow flow rates ranging from 100 to 300 pL s(-1). The charged jet that emanates from the cone tip breaks up into a spray of charged droplets that are deposited in the form of a uniform spot of 130-350 microm in diameter by spraying during 0.5-3 s at 220-400 microm above a substrate, respectively. After a spot was deposited, spraying was stopped instantaneously by increasing the distance between the capillary tip and the substrate by an additional 100 microm using a computer-controlled x-y-z table. This was immediately followed by a rapid shift of the substrate 400 microm sideways and 100 microm upward, thus causing spraying to resume instantaneously because of the increased electric field strength, which resulted in the deposition of the next spot. It is shown here that spraying of lactate dehydrogenase (LDH), glucose-6-phosphate dehydrogenase (G6P-DH), and pyruvate kinase (PK) on a liquid layer resulted in the complete preservation of their activities despite the high solution conductivity of 3.3 S m(-1) and high currents ranging from 300 to 500 nA. LDH and PK activities were fully preserved after spraying onto dry aluminum by adding 0.05 M buffer and 0.5 and 1 wt % of trehalose, respectively, to the spray solutions. Electrospraying allows for accurate dispensing of liquid volumes as small as 50 pL. Enzymatic activities of LDH and PK are fully preserved after spraying.

Electrochemistry↗
PubMed2001

Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit.

Initiation of protein synthesis in eukaryotes requires recruitment of the 40S ribosomal subunit to the messenger RNA (mRNA). In most cases, this depends on recognition of a modified nucleotide cap on the 5' end of the mRNA. However, an alternate pathway uses a structured RNA element in the 5' untranslated region of the messenger or viral RNA called an internal ribosomal entry site (IRES). Here, we present a cryo-electron microscopy map of the hepatitis C virus (HCV) IRES bound to the 40S ribosomal subunit at about 20 A resolution. IRES binding induces a pronounced conformational change in the 40S subunit and closes the mRNA binding cleft, suggesting a mechanism for IRES-mediated positioning of mRNA in the ribosomal decoding center.

5' Untranslated Regions↗
PubMed2001

Human equivalent of the mouse Nude/SCID phenotype: long-term evaluation of immunologic reconstitution after bone marrow transplantation.

Human Nude/SCID (severe combined immunodeficiency) is the first severe combined immunodeficiency caused by mutation of the winged-helix-nude (WHN) gene, which is expressed in the thymus but not in the hematopoietic lineage. The disease is characterized by a T-cell defect, congenital alopecia, and nail dystrophy. A Nude/SCID patient who underwent bone marrow transplantation from the human leukocyte antigen-identical heterozygote brother was studied to investigate, in this unique model, the role of the thymus in immunologic reconstitution. Despite an increase in CD3(+), CD4(+), and CD8(+) cells, CD4(+) CD45 RA naive lymphocytes were not regenerated. Conversely, naive CD8(+) cells were normal. After an initial recovery, lymphocyte proliferation to mitogens progressively declined compared with controls and genotypically identical donor cells grown in the WHN(+/-) environment. Analysis of the T-cell receptor (TCR) repertoire of CD4(+) cells revealed that only 3 of 18 Vbeta families had an altered CDR3 heterogeneity length profile. Conversely, CD8(+) lymphocytes showed an abnormal distribution in most Vbeta families. These data indicate that the thymus is differentially required in the reconstitution of CD4(+) and CD8(+) naive subsets and in the maintenance of their TCR repertoire complexity. Taken together, these findings suggest that bone marrow transplantation is ineffective in the long-term cure of this form of SCID.

Alopecia↗
PubMed2001

New approaches for fabrication of microfluidic capillary electrophoresis devices with on-chip conductivity detection.

In practice, microfluidic systems are based on the principles of capillary electrophoresis (CE), for a large part due to the simplicity of electroosmotic pumping. In this contribution, a universal conductivity detector is presented that allows detection of charged species down to the microM level. Additionally, powderblasting is presented as a novel technique for direct etching of microfluidic networks. This method allows creation of features down to 50 microm with a total processing time (design to device) of less than one day. The performance of powderblasted devices with integrated conductivity detection is illustrated by the separation of lithium, sodium, and potassium ions and that of fumaric, malic, and citric acid.

Acids↗
PubMed2001

Cryo-electron microscopy as an investigative tool: the ribosome as an example.

Cryo-electron microscopy allows the visualization of macromolecules in their native state. Combined with techniques of three-dimensional reconstruction, cryo-EM images of single molecules can be used to study macromolecular interactions. The ribosome, a large RNA-protein complex with multiple binding interactions, is an excellent test case illustrating the power of these new techniques. Conformational changes during the binding of tRNA and protein factors to the ribosome can now be studied without the interference of crystal packing. Now that the first X-ray structures of ribosomal subunits have become available, conformational changes observed by cryo-EM in different functional states can be traced back to internal rearrangements of the underlying structural framework. Electron microscopy, X-ray crystallography, and modeling should be used together in the endeavor to understand the functioning of the translational machinery.

Animals↗
PubMed2001

Ribosomal dynamics explored by cryo-electron microscopy.

Cryo-electron microscopy has furnished direct evidence for conformational changes of the ribosome as it proceeds, in a cyclic manner, through different functional states. Strategies to explore the ribosome dynamics include trapping of particular functionally meaningful states by chemical, genetic, or physical means. The new atomic information obtained by X-ray crystallography should make it possible to track conformational changes observed by cryo-electron microscopy to changes of the underlying structural framework of the ribosome.

Cryoelectron Microscopy↗
PubMed2001

Detecting the effect of medical care on mortality.

OBJECTIVES: To demonstrate an important limitation of empirical tests of the proposition that medical care has contributed to long-term declines in mortality. Quasi-experiments cannot detect the effect of care that sustain, rather than change, a downward trajectory. We demonstrate this limitation by testing two hypotheses. One is that isolation of patients and antibiotic treatment coincided with declines in tuberculosis (TB) mortality in Massachusetts between 1850 and 1950. Another is that the introduction of Medicare in the 1960s increased life expectancy at age 65. RESULTS: The first hypothesis is supported, for both patient isolation and streptomycin. The second is not. The circumstances that could yield such results are explored. CONCLUSIONS: Epidemiologists and historians should cooperate to devise methods that can resolve the issue of whether medical care has sustained the steady downward trend in mortality witnessed over the last century-and-a-half.

Aged↗
PubMed2001

Electron tomographic and other approaches for imaging molecular machines.

Two new methods, single-particle cryo-electron microscopy reconstruction and electron tomography, are increasingly used to visualize molecular machines in vitro and in the cellular context, respectively. Current efforts focus on the development of methods capable of visualizing molecular signatures in the cell, and first progress in this direction has now been made.

Animals↗
PubMed2001

Localization of the ribosomal protection protein Tet(O) on the ribosome and the mechanism of tetracycline resistance.

Tet(O) belongs to a class of ribosomal protection proteins that mediate tetracycline resistance. It is a G protein that shows significant sequence similarity to elongation factor EF-G. Here we present a cryo-electron microscopic reconstruction, at 16 A resolution, of its complex with the E. coli 70S ribosome. Tet(O) was bound in the presence of a noncleavable GTP analog to programmed ribosomal complexes carrying fMet-tRNA in the P site. Tet(O) is directly visible as a mass close to the A-site region, similar in shape and binding position to EF-G. However, there are important differences. One of them is the different location of the tip of domain IV, which in the Tet(O) case, does not overlap with the ribosomal A site but is directly adjacent to the primary tetracycline binding site. Our findings give insights into the mechanism of tetracycline resistance.

Bacterial Proteins↗