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PubMed1981

Reaction of C-type cytochromes with the iron hexacyanides. Mechanistic implications.

The reaction of c-cytochromes with iron hexacyanides is similar in mechanism to the interaction of cytochromes with their physiological oxidants and reductants in that the formation of complexes precedes electron transfer. Analysis of the kinetics of oxidation and reduction of a number of c-cytochromes by solving the simultaneous differential equations defining the mechanism is possible, and allows assignment of all six rate constants describing a minimum three-step mechanism [cyto(Fe(+3)) + Fe(+2) right harpoon over left harpoon cyto (Fe(+3)) - Fe(+2) right harpoon over left harpoon cyto(Fe(+2)) - Fe(+3) right harpoon over left harpoon cyto(Fe(+2)) + Fe(+3)]. We find that the usual steady-state approximations are not valid. Furthermore, the ratio of first-order rate constants for electron transfer was approximately 1.0, and no correlation was found between any of the six rate constants and the differences in oxidation-reduction potential of the iron-hexacyanides and different cytochromes c. However, it was found that the ratio of the rate constants for complex formation between ferricytochrome c and potassium ferrocyanide and ferrocytochrome c and potassium ferricyanide was proportional to the difference in oxidation-reduction potentials. Thus the minimum three-step mechanism given above accurately describes the observed kinetic data. However, this mechanism leads to a number of conceptual difficulties. Specifically, the mechanism requires that the collision complexes formed [cyto(Fe(+3)) - Fe(CN)(6) (-4) and cyto(Fe(+2)) - Fe(CN)(6) (-3)] have very different equilibrium constants, and further requires that formation of the collision complexes be accompanied by "chemistry" to make the intermediates isoenergetic. A more complex five-step mechanism which requires that the reactants [Fe(CN)(6) (-4) and ferricytochrome c or Fe(CN)(6) (-3) and ferrocytochrome c] form a collision complex followed by a first-order process before electron transfer, was found to yield results similar to those of the three-step mechanism. However, describing the formation of the collision complex in terms of a rapid equilibrium circumvents conceptual difficulties and leads to a physically reasonable mechanism. In this mechanism the reactants are in rapid equilibrium with the collision complexes and the rate constants for complex formation are controlled by diffusion and accessibility. The collision complexes then rearrange, possibly through conformational changes and/or solvent reorganization, to yield isoenergetic intermediates that can undergo rapid reversible electron transfer. The five-step mechanism can be described by the same rate constants obtained from the three-step mechanism with the appropriate adjustments to account for rapid equilibrium. This more complex analysis associates the oxidation-reduction potential of a particular cytochrome with the relative magnitude of the first-order conversion of the oxidant and reductant collision complexes to their respective intermediates. Thus the cytochromes c control their oxidation-reduction potential by chemical and/or structural alterations. This mechanism appears to be general in that it is consistent with the observed kinetics of 11 different cytochromes c from a wide variety of sources with a range of oxidation-reduction potentials.

Animals↗
PubMed2002

Activation of CFTR Cl(-) channel by tyrphostins via a protein tyrosine kinase-independent pathway in forskolin-stimulated renal epithelial A6 cells.

We studied effects of tyrphostin A23 (an inhibitor of protein tyrosine kinase; PTK) and tyrphostin A63 (an inactive analog of tyrphostin A23) on forskolin-activated cystic fibrosis transmembrane conductance regulator (CFTR) Cl(-) channels and Cl(-) secretion in renal epithelial A6 cells. Tyrphostin A23 and A63 had no effects on the basal CFTR Cl(-) channel and Cl(-) secretion. However, under the forskolin-stimulated condition, tyrphostin A23 and A63 stimulated Cl(-) secretion by activating CFTR Cl(-) channels. These observations suggest that: 1) tyrphostin A23 and A63 stimulate the cAMP-activated CFTR Cl(-) channel via a PTK-independent, structure-dependent mechanism, and 2) tyrphostin A23 and A63 do not stimulate the basal CFTR Cl(-) channel. These lead us to an idea that: 1) cAMP might cause a conformational change of CFTR Cl(-) channel which is accessible by tyrphostins, and 2) tyrphostins would stimulate translocation of the cAMP-modified channel to the apical membrane by binding to the channel.

Amiloride↗
PubMed1998

Apomyoglobin folding intermediates characterized by the hydrophobic fluorescent probe 8-anilino-1-naphthalene sulfonate.

Folding apomyoglobin intermediates were investigated by optical techniques including steady-state fluorescence, frequency domain fluorometry, and absorption spectroscopy. The investigated chromophores were the aromatic residues, i.e., tyrosyl and tryptophanyl residues, and the extrinsic probe (8-anilino-1-naphthalenesulfonate, ANS) which is particularly useful for studying partly structured forms appearing in the early stage of protein folding. The emission decay of the extrinsic probe as well as resonance energy transfer from tryptophanyl residues to ANS permitted to identify and characterize partly folded forms obtained under different experimental conditions. The results indicate that the intermediates so far detected (I-1 and I-2 states) are distinct structural states. The differences concern the solvent accessibility to the aromatic side chains and the conformational dynamics of the protein region forming the binding site for the extrinsic fluorophore.

Anilino Naphthalenesulfonates↗
PubMed1991

The association with receptors regulates the Na+,K(+)-ATPase inhibitory potency of some cardioactive steroids.

The onset of inhibition of Na+,K(+)-ATPase from guinea-pig myocardium was quantified with pseudo-first-order rate constants in a series of 14 cardioactive steroids. From these data the association and dissociation rate constants of the steroid-receptor complex were calculated. It was then found that the association of the steroids with receptors but not the dissociation of the steroid-receptor complex determined the largely different inhibitory potencies. Consistent with this finding, at equieffective steroid concentrations the rates of inhibition varied only slightly. The correlation of the association rate with the hydrophobicity of the compounds suggests that hydrophobic interactions facilitate the access of the steroid to the receptor. A conformational transition of the vicinity of the receptor subsequent to the formation of the steroid-receptor complex seems to alter the hydrophobic properties of the receptor environment to make the dissociation rate independent from hydrophobicity.

Animals↗
PubMed2003

Chemoenzymatic route to macrocyclic hybrid peptide/polyketide-like molecules.

Hybrid peptide-polyketides are a class of medically and biologically important natural products characterized by stereochemical and functional diversity. In their biosynthesis, hybrids are often macrocyclized to achieve rigid structures that populate bioactive conformations. We herein present a chemoenzymatic strategy to access the stereochemical and functional diversity found in macrocyclic hybrid natural products in a manner amenable to efficient library synthesis. Our method makes use of small building blocks in the form of Fmoc-protected epsilon-amino acids containing embedded polyketide functionality. The building block approach allows for combinatorial synthesis of linear molecules that can be activated as soluble thioesters or tethered to a solid-phase resin. We demonstrate that these linear molecules are substrates for macrocyclization by a tolerant catalyst, TycC TE, derived from a nonribosomal peptide synthetase. The method should allow for access to diverse structures with hybrid peptide-polyketide character that can be screened for improved or novel activities.

Amides↗
PubMed1999

IcePick: a flexible surface-based system for molecular diversity.

IcePick is a system for computationally selecting diverse sets of molecules. It computes the dissimilarity of the surface-accessible features of two molecules, taking into account conformational flexibility. Then, the intrinsic diversity of an entire set of molecules is calculated from a spanning tree over the pairwise dissimilarities. IcePick's dissimilarity measure is compared against traditional 2D topological approaches, and the spanning tree diversity measure is compared against commonly used variance techniques. The method has proven easy to implement and is fast enough to be used in selection of reactants for numerous production-sized combinatorial libraries.

Drug Design↗
PubMed2006

Protein-GAG interactions: new surface-based techniques, spectroscopies and nanotechnology probes.

New approaches, rooted in the physical sciences, have been developed to gain a more fundamental understanding of protein-GAG (glycosaminoglycan) interactions. DPI (dual polarization interferometry) is an optical technique, which measures real-time changes in the mass of molecules bound at a surface and the geometry of the bound molecules. QCM-D (quartz crystal microbalance-dissipation), an acoustic technique, measures the mass and the viscoelastic properties of adsorbates. The FTIR (Fourier-transform IR) amide bands I, II and III, resulting from the peptide bond, provide insight into protein secondary structure. Synchrotron radiation CD goes to much shorter wavelengths than laboratory CD, allowing access to chromophores that provide insights into the conformation of the GAG chain and of beta-strand structures of proteins. To tackle the diversity of GAG structure, we are developing noble metal nanoparticle probes, which can be detected at the level of single particles and so enable single molecule biochemistry and analytical chemistry. These new approaches are enabling new insights into structure-function relationships in GAGs and together they will resolve many of the outstanding problems in this field.

Animals↗
PubMed2005

Fcp1 directly recognizes the C-terminal domain (CTD) and interacts with a site on RNA polymerase II distinct from the CTD.

Fcp1 is an essential protein phosphatase that hydrolyzes phosphoserines within the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II). Fcp1 plays a major role in the regulation of CTD phosphorylation and, hence, critically influences the function of Pol II throughout the transcription cycle. The basic understanding of Fcp1-CTD interaction has remained ambiguous because two different modes have been proposed: the "dockingsite" model versus the "distributive" mechanism. Here we demonstrate biochemically that Fcp1 recognizes and dephosphorylates the CTD directly, independent of the globular non-CTD part of the Pol II structure. We point out that the recognition of CTD by the phosphatase is based on random access and is not driven by Pol II conformation. Results from three different types of experiments reveal that the overall interaction between Fcp1 and Pol II is not stable but dynamic. In addition, we show that Fcp1 also interacts with a region on the polymerase distinct from the CTD. We emphasize that this non-CTD site is functionally distinct from the docking site invoked previously as essential for the CTD phosphatase activity of Fcp1. We speculate that Fcp1 interaction with the non-CTD site may mediate its stimulatory effect on transcription elongation reported previously.

Chromatography, Gel↗
PubMed2002

UDP-Glc:glycoprotein glucosyltransferase recognizes structured and solvent accessible hydrophobic patches in molten globule-like folding intermediates.

Protein folding in the cell involves the action of different molecular chaperones and folding-facilitating enzymes. In the endoplasmic reticulum (ER), the folding status of glycoproteins is stringently controlled by a glucosyltranferase enzyme (GT) that creates monoglucosylated structures recognized by ER resident lectins (calnexincalreticulin, CNXCRT). GT serves as a folding sensor because it only glucosylates misfolded or partly folded glycoproteins. Nevertheless, the molecular mechanism behind this recognition process remains largely unknown. In this paper we explore the structural determinants for GT recognition by using a single domain model protein. For this purpose we used a family of chemically glycosylated proteins derived from chymotrypsin inhibitor-2 as GT substrates. Structural characterization of species showing higher glucose acceptor capacity suggests that GT recognizes solvent accessible hydrophobic patches in molten globule-like conformers mimicking intermediate folding stages of nascent glycoproteins. It was further confirmed that BiP (binding protein, a chaperone of the heat shock protein 70 family) preferentially recognized neoglycoproteins displaying extended conformations, thus providing a molecular rationale for the sequential BiP-CNXCRT interaction with folding glycoproteins observed in vivo.

Amino Acid Sequence↗
PubMed1984

Quantitation of aflatoxin B1 adduction within the ribosomal RNA gene sequences of rat liver DNA.

The in vivo formation of covalent aflatoxin B1 (AFB1)-DNA adducts within the rRNA gene sequences of nuclear DNA has been studied in AFB1-treated rats. Liver nuclear DNA, enriched in ribosomal DNA (rDNA) by one round of cesium salt density gradient centrifugation, was treated under buffered alkaline conditions to convert unstable AFB1-N7-guanine adducts to stable AFB1-formamidopyrimidine derivatives. The alkali-treated DNA was hybridized to 18S and 28S rRNA in 70% formamide buffer to form rRNA X rDNA hybrids. These hybrids were separated from the bulk of nuclear DNA by two rounds of centrifugation in CsCl, and the level of AFB1 adduction to rDNA versus total nuclear DNA was compared as a function of dose 2 hr after AFB1 administration. Over an 8-fold dose range (0.25-2.0 mg of AFB1 per kg of body weight), rDNA contained 4- to 5-fold more AFB1 residues than nuclear DNA, indicating that rDNA is preferentially accessible to carcinogen modification in vivo. While aflatoxin B1 forms adducts with DNA principally at guanine residues, the guanine enrichment of rDNA was insufficient to explain the magnitude of observed preferential AFB1 modification of rDNA. These results support the hypothesis that rDNA regions are preferentially accessible to carcinogen modification because of the diffuse conformation maintained within transcribed genes. This experimental approach permits the quantitative description of carcinogen modification within a defined gene sequence; further refinement of this approach may be useful in defining the precise relationships between covalent chemical-DNA interactions and the alterations in gene expression that result.

Aflatoxin B1↗
PubMed1997

Binding of mammalian ribosomal protein complex P0.P1.P2 and protein L12 to the GTPase-associated domain of 28 S ribosomal RNA and effect on the accessibility to anti-28 S RNA autoantibody.

We have investigated binding of rat ribosomal proteins to the "GTPase domain" of 28 S rRNA and its effect on accessibility to the anti-28 S autoantibody, which recognizes a unique tertiary structure of this RNA domain. Ribosomal protein L12 and P protein complex (P complex) consisting of P0, P1, and P2 both bound to the GTPase domain of rat 28 S rRNA in a buffer containing Mg2. Chemical footprinting analysis of their binding sites revealed that the P complex mainly protected a conserved internal loop region comprising residues 1855-1861 and 1920-1922, whereas L12 protected an adjacent helix region encompassing residues 1867-1878 and 1887-1899. These sites are close to but distinct from the binding site for anti-28 S antibody determined previously. The bindings of P complex and L12 increased the anti-28 S accessibility, as revealed by gel retardation and quantitative immunoprecipitation analyses. In a Mg2+-eliminated condition, the RNA failed to bind to either anti-28 S or L12 but assembled into a complex under their coexistence. However, the RNA retained a property of binding to the P complex even in the absence of Mg2+, and this binding conferred high anti-28 S accessibility. These results indicated that the bindings of the P complex and L12 to their respective sites influenced the GTPase domain to increase the accessibility to anti-28 S. A possible RNA conformation adjusted by the protein bindings is discussed.

Animals↗
PubMed2003

Serines 260 and 288 are involved in sulfate transport by hNaSi-1.

The low affinity Na+/sulfate cotransporter, NaSi-1, belongs to the SLC13 family that also includes the Na+/dicarboxylate cotransporters, NaDC. Two serine residues in hNaSi-1, at positions 260 and 288, are conserved in all of the sulfate transporters in the family whereas the NaDC contain alanine or threonine at those positions. Therefore, the functional roles of serines 260 and 288 in substrate and cation binding by hNaSi-1 were investigated. These two serine residues were first mutated to alanine and the mutants were characterized in Xenopus oocytes. Alanine substitution of Ser-260 resulted in increased Km values for both substrate and Na+ whereas alanine replacement at Ser-288 resulted in a broadened cation selectivity, indicating that these two serines might play important roles in cation and/or substrate binding of hNaSi-1. The two serines and 12 surrounding residues were further mutated to cysteine and studied using a thiol-reactive compound, [2-(trimethylammonium)ethyl]methane-thiosulfonate (MTSET). Four mutants surrounding Ser-260 (T257C, T259C, T261C, and L263C) were sensitive to MTSET inhibition. The sensitivity to MTSET was dependent on the presence of substrate, suggesting that the accessibility of these substituted cysteines depends on the conformational state of the transporter. Because the four residues are located in transmembrane domain 5, this transmembrane domain is likely to participate in the conformational movements during the transport cycle of hNaSi-1.

Amino Acid Sequence↗
PubMed1987

Cleavage fragments of the retrovirus surface protein gp70 during virus entry.

The surface protein gp70 of an ecotropic murine retrovirus was followed during entry of [3H]glucosamine-labelled virions into SC-1 mouse fibroblasts. Upon entry, gp70 was cleaved into fragments with molecular weights 35K, 30K and 17K. The 35K and 17K fragments were also observed after trypsin or thermolysin cleavage of the virion, indicating that certain locations on the gp70 molecule are easily accessible from the outside of the virion. The conformation of gp70 on the membrane was shown to have a major effect on the cleavage. This protein is known to be important for early interactions with the cell (binding and membrane fusion). The results indicate that gp70 cleavage may be important for membrane fusion.

Animals↗
PubMed1989

A nucleoprotein complex mediates the integration of retroviral DNA.

The integration of viral DNA into the host genome is an essential step in the retrovirus life cycle. To understand this process better, we have examined the native state of viral DNA in cells acutely infected by murine leukemia virus (MLV), using both a physical assay for viral DNA and a functional assay for integration activity (Brown et al. 1987). The viral DNA and integration activity copurify during velocity sedimentation, gel filtration, and density equilibrium centrifugation, indicating that viral DNA is in a large (approximately 160S) nucleoprotein complex that includes all functions required for integration activity in vitro. Analysis by immunoprecipitation shows that the viral capsid protein is part of the active nucleoprotein complex, but recognition of the complex by only a subset of anti-capsid sera implies that the protein is constrained conformationally. The viral DNA within this structure is accessible to nucleases; the effects of nucleases on the integrity of the complex suggest that the integration-competent particle is derived from and similar to the core of extracellular virions.

Animals↗
PubMed1998

A broadband multimedia collaborative system for advanced teleradiology and medical imaging diagnosis.

This paper presents a new telemedicine system currently in routine clinical usage, developed within the European Union (EU) ACTS BONAPARTE project (1). The telemedicine system is developed on an asynchronous transfer mode (ATM) multimedia hardware/software platform comprising the following set of telemedicine services: synchronous cooperative work, high-quality video conference, multimedia mail, medical image digitizing, processing, storing and printing, and local and remote transparent database access. The medical information handled by the platform conforms to the Digital Imaging and Communications in Medicine (DICOM) 3.0 medical imaging standard. The telemedicine system has been installed for clinical routines in three Spanish hospitals since November 1997 and has been used in an average of one/two clinical sessions per week. At each clinical session, a usability and clinical evaluation of the system was carried out. Evaluation is carried out through direct observation of interactions and questionnaire-based subjective data. The usability evaluation methodology and the results of the system usability study are also presented in this article. The experience gained from the design, development, and evaluation of the telemedicine system is providing an indepth knowledge of the benefits and difficulties involved in the installation and clinical usage of this type of high-usability and advanced multimedia telemedicine system in the field of teleradiology and collaborative medical imaging diagnosis.

Diagnostic Imaging↗
PubMed2005

In vitro culture of skin-homing T lymphocytes from inflammatory skin diseases.

We, in this study, describe how T lymphocytes in a skin biopsy can proliferate in vitro for up to 3 months by using T-cell growth factors - interleukin-2 (IL-2) and IL-4 yielding approximately 100-160 million T lymphocytes within 1 month. We established cell lines from three tuberculin skin tests, four positive patch tests, 15 of 16 biopsies from atopic dermatitis (AD), 15 of 19 biopsies from mycosis fungoides (MF), 12 of 24 biopsies from psoriasis vulgaris, which was significantly less than AD (P < 0.05), and with a reduced cumulative number of lymphocytes (P < 0.05). Omitting IL-2 and IL-4 led to immediate halt of proliferation. Blood mononuclear cells from patients and biopsies from healthy persons never gave cell lines. All cells were T lymphocytes expressing CD45RO+, HLA-DR+ and CD150. The CD7 expression was significantly increased in cell lines from AD (P < 0.05). T-cell receptor beta-chain studies by using reverse transcription-polymerase chain reaction showed that all T lymphocytes had access to the skin compartment. Single-stranded conformational analysis showed clonally expanded T cells numbering between 40 and 60 clones. After approximately 2 months of growth, the mean CD4+ : CD8+ ratio was for AD 1.20, MF 0.65 and psoriasis 0.85. Patients with AD treated with cyclosporin-A had almost no growth of CD8+ cells in vitro. Our findings indicate a changed homeostasis among skin-homing lymphocytes for in vitro culture. Our culture system of skin-homing T lymphocytes leads to a prominent cellular expansion allowing for a range of studies of in vivo activated skin T lymphocytes.

Adolescent↗
PubMed2004

Interaction between dopamine and its transporter: role of intracellular sodium ions and membrane potential.

The present study addresses the effect of intracellular Na(+) and membrane potential on the binding of dopamine (DA) to the dopamine transporter (DAT). Perforation of plasma membranes of DAT-expressing cells with gramicidin diminished DA uptake and decreased the potency (increases K(i)) of DA in inhibiting the binding of cocaine analog [(3)H]2beta-carbomethoxy-3beta-(4-fluorophenyl)tropane (CFT). It also compromised the ability of external Na(+) to reduce DA K(i). No substantial effect on DA K(i) was observed upon gramicidin treatment in Na(+)-free buffer, membrane depolarization with high [K(+)](o), or elevation of [Na(+)](i) with monensin under non-depolarizing conditions. Elevation of DA K(i) was greater at more positive potentials when [Na(+)](i) was raised to a similar level, or at higher [Na(+)](i) when the membrane was depolarized to a similar level. In cells expressing D313N DAT, DA K(i) was significantly higher but less sensitive to gramicidin than that in wild-type (WT) cells. In contrast, DA K(i) in cell-free membranes was insensitive to Na(+), gramicidin, and D313N mutation. The data suggest that (i) intracellular Na(+) plays a role in affecting the external access to DA binding sites at DAT on depolarized plasma membranes of cells, and (ii) access to DA binding sites in cell-free membranes may occur from the intracellular side of the membrane. Unlike DA binding, CFT binding to both cells and membranes was sensitive to Na(+) and D313N mutation but insensitive to gramicidin, consistent with exclusively external access to sites that are different from but conformationally linked to those for DA.

Cell Line↗
PubMed1980

Transport ATPases in anion and proton transport.

Studies in our laboratory have shown that the anion-sensitive Mg-ATPase is located in mitochondria, but not in the plasma membrane of rabbit gastric mucosa, trout gill, rabbit kidney and rat pancreas; whereas in rabbit erythrocyte membrane, it is part of the Ca-Mg activated ATPase system. These findings appear to rule out a function of the anion-sensitive ATPase in the transport of anions and protons across the plasma membrane in these tissues. On the other hand, the K-activated ATPase in a gradient-purified vesicle fraction of pig gastric mucosa mediates proton uptake in exchange for K+ in the presence of ATP, in agreement with earlier findings of other investigators. The enzyme requires a phospholipid environment for its activity. Studies of arginine modification with butanedione in the presence or absence of ATP and its analogues, and of activating cations indicate that the enzyme contains an essential arginine group involved in ATP binding; and that K+ induces a conformational change, which leads to decreased ATP binding and probably coincides with enzyme dephosphorylation. Similar studies of sulfhydryl modification with DTNB indicate that the enzyme contains an essential sulfhydryl group, which does not appear to be directly involved in ATP binding, but rather that ATP binding may induce a conformational change which makes the sulfhydryl group less accessible.

Adenosine Triphosphatases↗