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PDK1 activates AKT suggesting that PDK1 inhibition might suppress tumor development. However, while PDK1 has been investigated intensively as an oncology target, selective inhibitors suitable for in vivo studies have remained elusive. In this study we present the results of in vivo PDK1 inhibition through a universally applicable RNAi approach for functional drug target validation in oncogenic pathway contexts. This approach, which relies on doxycycline-inducible shRNA expression from the Rosa26 locus, is ideal for functional studies of genes like PDK1 where constitutive mouse models lead to strong developmental phenotypes or embryonic lethality. We achieved more than 90% PDK1 knockdown in vivo, a level sufficient to impact physiological functions resulting in hyperinsulinemia and hyperglycemia. This phenotype was reversible on PDK1 reexpression. Unexpectedly, long-term PDK1 knockdown revealed a lack of potent antitumor efficacy in 3 different mouse models of PTEN-deficient cancer. Thus, despite efficient PDK1 knockdown, inhibition of the PI3K pathway was marginal suggesting that PDK1 was not a rate limiting factor. Ex vivo analysis of pharmacological inhibitors revealed that AKT and mTOR inhibitors undergoing clinical development are more effective than PDK1 inhibitors at blocking activated PI3K pathway signaling. Taken together our findings weaken the widely held expectation that PDK1 represents an appealing oncology target., (©2011 AACR.)

The adsorption of ammonia on multilayers of well-ordered, flat-lying iron phthalocyanine (FePc) molecules on a Au(111) support was investigated by x-ray photoelectron spectroscopy. We find that the electron-donating ammonia molecules coordinate to the metal centers of iron phthlalocyanine. The coordination of ammonia induces changes of the electronic structure of the iron phthalocyanine layer, which, in particular, lead to a modification of the FePc valence electron spin.

The adsorption of ammonia on Au(111)-supported monolayers of iron phthalocyanine has been investigated by x-ray photoelectron spectroscopy, x-ray absorption spectroscopy, and density functional theory calculations. The ammonia-induced changes of the x-ray photoemission lines show that a dative bond is formed between ammonia and the iron center of the phthalocyanine molecules, and that the local spin on the iron atom is quenched. This is confirmed by density functional theory, which also shows that the bond between the iron center of the metalorganic complex and the Au(111) substrate is weakened upon adsorption of ammonia. The experimental results further show that additional adsorption sites exist for ammonia on the iron phthalocyanine monolayer.

Recent advances in genome technologies and the ensuing outpouring of genomic information related to cancer have accelerated the convergence of discovery science and clinical medicine. Successful examples of translating cancer genomics into therapeutics and diagnostics reinforce its potential to make possible personalized cancer medicine. However, the bottlenecks along the path of converting a genome discovery into a tangible clinical endpoint are numerous and formidable. In this Perspective, we emphasize the importance of establishing the biological relevance of a cancer genomic discovery in realizing its clinical potential and discuss some of the major obstacles to moving from the bench to the bedside.

Phosphoinositide-dependent kinase 1 (PDK1) is a critical activator of multiple prosurvival and oncogenic protein kinases and has garnered considerable interest as an oncology drug target. Despite progress characterizing PDK1 as a therapeutic target, pharmacological support is lacking due to the prevalence of nonspecific inhibitors. Here, we benchmark literature and newly developed inhibitors and conduct parallel genetic and pharmacological queries into PDK1 function in cancer cells. Through kinase selectivity profiling and x-ray crystallographic studies, we identify an exquisitely selective PDK1 inhibitor (compound 7) that uniquely binds to the inactive kinase conformation (DFG-out). In contrast to compounds 1-5, which are classical ATP-competitive kinase inhibitors (DFG-in), compound 7 specifically inhibits cellular PDK1 T-loop phosphorylation (Ser-241), supporting its unique binding mode. Interfering with PDK1 activity has minimal antiproliferative effect on cells growing as plastic-attached monolayer cultures (i.e. standard tissue culture conditions) despite reduced phosphorylation of AKT, RSK, and S6RP. However, selective PDK1 inhibition impairs anchorage-independent growth, invasion, and cancer cell migration. Compound 7 inhibits colony formation in a subset of cancer cell lines (four of 10) and primary xenograft tumor lines (nine of 57). RNAi-mediated knockdown corroborates the PDK1 dependence in cell lines and identifies candidate biomarkers of drug response. In summary, our profiling studies define a uniquely selective and cell-potent PDK1 inhibitor, and the convergence of genetic and pharmacological phenotypes supports a role of PDK1 in tumorigenesis in the context of three-dimensional in vitro culture systems.

Pharmacodynamic (PD) biomarkers are an increasingly valuable tool for decision-making and prioritization of lead compounds during preclinical and clinical studies as they link drug-target inhibition in cells with biological activity. They are of particular importance for novel, first-in-class mechanisms, where the ability of a targeted therapeutic to impact disease outcome is often unknown. By definition, proximal PD biomarkers aim to measure the interaction of a drug with its biological target. For kinase drug discovery, protein substrate phosphorylation sites represent candidate PD biomarkers. However, substrate phosphorylation is often controlled by input from multiple converging pathways complicating assessment of how potently a small molecule drug hits its target based on substrate phoshorylation measurements alone. Here, we report the use of quantitative, differential mass-spectrometry to identify and monitor novel drug-regulated phosphorylation sites on target kinases. Autophosphorylation sites constitute clinically validated biomarkers for select protein tyrosine kinase inhibitors. The present study extends this principle to phosphorylation sites in serine/threonine kinases looking beyond the T-loop autophosphorylation site. Specifically, for the 3'-phosphoinositide-dependent protein kinase 1 (PDK1), two phospho-residues p-PDK1(Ser410) and p-PDK1(Thr513) are modulated by small-molecule PDK1 inhibitors, and their degree of dephosphorylation correlates with inhibitor potency. We note that classical, ATP-competitive PDK1 inhibitors do not modulate PDK1 T-loop phosphorylation (p-PDK1(Ser241)), highlighting the value of an unbiased approach to identify drug target-regulated phosphorylation sites as these are complementary to pathway PD biomarkers. Finally, we extend our analysis to another protein Ser/Thr kinase, highlighting a broader utility of our approach for identification of kinase drug-target engagement biomarkers.

The dynamic behavior of surface accommodated chlorine atoms on RuO(2)(110) was studied by a variety of experimental methods including high resolution core level shift, thermal desorption-, and in situ infrared spectroscopy as well as in situ surface X-ray diffraction in combination with state-of-the-art density functional theory calculations. On the chlorinated RuO(2)(110) surface the undercoordinated oxygen atoms have been selectively replaced by chlorine. These strongly bound surface chlorine atoms shift from bridging to on-top sites when the sample is annealed in oxygen, while the reverse shift of Cl from on-top into bridge positions is observed during CO exposure; the vacant bridge position is then occupied by either chlorine or CO. For the CO oxidation reaction over chlorinated RuO(2)(110), the reactant induced site switching of chlorine causes a site-blocking of the catalytically active one-fold coordinatively unsaturated (1f-cus) Ru sites. This site blocking reduces the number of active sites and, even more important, on-top Cl blocks the free migration of the adsorbed reactants along the one-dimensional 1f-cus Ru rows, thus leading to a loss of catalytic activity.

The future use of single-molecule magnets in applications will require the ability to control and manipulate the spin state and magnetization of the magnets by external means. There are different approaches to this control, one being the modification of the magnets by adsorption of small ligand molecules. In this paper we use iron phthalocyanine supported by an Au(111) surface as a model compound and demonstrate, using x-ray photoelectron spectroscopy and density functional theory, that the spin state of the molecule can be tuned to different values (S ∼ 0, [Formula: see text], 1) by adsorption of ammonia, pyridine, carbon monoxide or nitric oxide on the iron ion. The interaction also leads to electronic decoupling of the iron phthalocyanine from the Au(111) support.

From an interplay between scanning tunneling microscopy, temperature programmed desorption, X-ray photoelectron spectroscopy, and density functional theory calculations we have studied low-temperature CO oxidation on Au/Ni(111) surface alloys and on Ni(111). We show that an oxide is formed on both the Ni(111) and the Au/Ni(111) surfaces when oxygen is dosed at 100 K, and that CO can be oxidized at 100 K on both of these surfaces in the presence of weakly bound oxygen. We suggest that low-temperature CO oxidation can be rationalized by CO oxidation on O(2)-saturated NiO(111) surfaces, and show that the main effect of Au in the Au/Ni(111) surface alloy is to block the formation of carbonate and thereby increase the low-temperature CO(2) production.

Although we have made great progress in understanding the complex genetic alterations that underlie human cancer, it has proven difficult to identify which molecularly targeted therapeutics will benefit which patients. Drug-specific modulation of oncogenic signaling pathways in specific patient subpopulations can predict responsiveness to targeted therapy. Here, we report a pathway-based phosphoprofiling approach to identify and quantify clinically relevant, drug-specific biomarkers for phosphatidylinositol 3-kinase (PI3K) pathway inhibitors that target AKT, phosphoinositide-dependent kinase 1 (PDK1), and PI3K-mammalian target of rapamycin (mTOR). We quantified 375 nonredundant PI3K pathway-relevant phosphopeptides, all containing AKT, PDK1, or mitogen-activated protein kinase substrate recognition motifs. Of these phosphopeptides, 71 were drug-regulated, 11 of them by all three inhibitors. Drug-modulated phosphoproteins were enriched for involvement in cytoskeletal reorganization (filamin, stathmin, dynamin, PAK4, and PTPN14), vesicle transport (LARP1, VPS13D, and SLC20A1), and protein translation (S6RP and PRAS40). We then generated phosphospecific antibodies against selected, drug-regulated phosphorylation sites that would be suitable as biomarker tools for PI3K pathway inhibitors. As proof of concept, we show clinical translation feasibility for an antibody against phospho-PRAS40(Thr246). Evaluation of binding of this antibody in human cancer cell lines, a PTEN (phosphatase and tensin homolog deleted from chromosome 10)-deficient mouse prostate tumor model, and triple-negative breast tumor tissues showed that phospho-PRAS40(Thr246) positively correlates with PI3K pathway activation and predicts AKT inhibitor sensitivity. In contrast to phosphorylation of AKT(Thr308), the phospho-PRAS40(Thr246) epitope is highly stable in tissue samples and thus is ideal for immunohistochemistry. In summary, our study illustrates a rational approach for discovery of drug-specific biomarkers toward development of patient-tailored treatments.

The phosphoinositide 3-kinase/AKT signaling pathway plays a key role in cancer cell growth, survival, and angiogenesis. Phosphoinositide-dependent protein kinase-1 (PDK1) acts at a focal point in this pathway immediately downstream of phosphoinositide 3-kinase and PTEN, where it phosphorylates numerous AGC kinases. The PDK1 kinase domain has at least three ligand-binding sites: the ATP-binding pocket, the peptide substrate-binding site, and a groove in the N-terminal lobe that binds the C-terminal hydrophobic motif of its kinase substrates. Based on the unique PDK1 substrate recognition system, ultrahigh throughput TR-FRET and Alphascreen screening assays were developed using a biotinylated version of the PDK1-tide substrate containing the activation loop of AKT fused to a pseudo-activated hydrophobic motif peptide. Using full-length PDK1, K(m) values were determined as 5.6 mum for ATP and 40 nm for the fusion peptide, revealing 50-fold higher affinity compared with the classical AKT(Thr-308)-tide. Kinetic and biophysical studies confirmed the PDK1 catalytic mechanism as a rapid equilibrium random bireactant reaction. Following an ultrahigh throughput screen of a large library, 2,000 compounds were selected from the reconfirmed hits by computational analysis with a focus on novel scaffolds. ATP-competitive hits were deconvoluted by dose-response studies at 1x and 10x K(m) concentrations of ATP, and specificity of binding was assessed in thermal shift assay. Inhibition studies using fusion PDK1-tide1 substrate versus AKT(Thr-308)-tide and kinase selectivity profiling revealed a novel selective alkaloid scaffold that evidently binds to the PDK1-interacting fragment pocket. Molecular modeling suggests a structural paradigm for the design of inhibitory versus activating allosteric ligands of PDK1.

The adsorption of water and coadsorption with oxygen on Rh{111} under ultrahigh vacuum conditions was studied using synchrotron-based photoemission and photoabsorption spectroscopy. Water adsorbs intact on the clean surface at temperatures below 154 K. Irradiation with x-rays, however, induces fast dissociation and the formation of a mixed OH+H(2)O layer indicating that the partially dissociated layer is thermodynamically more stable. Coadsorption of water and oxygen at a coverage below 0.3 monolayers has a similar effect, leading to the formation of a hydrogen-bonded network of water and hydroxyl molecules at a ratio of 3:2. The partially dissociated layers are more stable than chemisorbed intact water with the maximum desorption temperatures up to 30 K higher. For higher oxygen coverage, up to 0.5 monolayers, water does not dissociate and an intact water species is observed above 160 K, which is characterized by an O 1s binding energy 0.6 eV higher than that of chemisorbed water and a high desorption temperature similar to the partially dissociated layer. The extra stabilization is most likely due to hydrogen bonds with atomic oxygen.

The nature of the intermolecular and substrate bonds of iron phthalocyanine adsorbed on highly oriented pyrolitic graphite has been investigated by x-ray photoelectron spectroscopy and x-ray absorption spectroscopy. We find that the molecules grow in a highly ordered fashion with the molecules essentially plane-parallel to the surface in both the mono- and multilayers. The spectra obtained on both types of film are virtually identical, which shows that the bonds both between the adsorbate and substrate and between the molecular layers have a pure van der Waals nature. Supporting density functional theory results indicate that the layers are stabilized by weak hydrogen bonds within the molecular layers.

We report the first experiments carried out on a new imaging setup, which combines the high spatial resolution of a photoemission electron microscope (PEEM) with the temporal resolution of extreme ultraviolet (XUV) attosecond pulse trains. The very short pulses were provided by high-harmonic generation and used to illuminate lithographic structures and Au nanoparticles, which, in turn, were imaged with a PEEM resolving features below 300 nm. We argue that the spatial resolution is limited by the lack of electron energy filtering in this particular demonstration experiment. Problems with extensive space charge effects, which can occur due to the low probe pulse repetition rate and extremely short duration, are solved by reducing peak intensity while maintaining a sufficient average intensity to allow imaging. Finally, a powerful femtosecond infrared (IR) beam was combined with the XUV beam in a pump-probe setup where delays could be varied from subfemtoseconds to picoseconds. The IR pump beam could induce multiphoton electron emission in resonant features on the surface. The interaction between the electrons emitted by the pump and probe pulses could be observed.

The PI3K/Akt signaling pathway plays a key role in cancer cell growth, survival, and tumor angiogenesis. 3-Phosphoinositide-dependent protein kinase 1 (PDK1) is a Ser/Thr protein kinase, which catalyzes the phosphorylation of a conserved residue in the activation loop of a number of AGC kinases, including proto-oncogenes Akt, p70S6K, and RSK kinases. To find new small-molecule inhibitors of this important regulator kinase, the authors have developed PDK1-specific high-throughput enzymatic assays in time-resolved fluorescence resonance energy transfer (TR-FRET) and AlphaScreen formats, monitoring phosphorylation of a biotinylated peptide substrate derived from the activation loop of Akt. Development of homogeneous assays enabled screening of a focused kinase library of approximately 21,500 compounds in 1536-well TR-FRET format in duplicate. Upon validation of hits in an alternative 384-well AlphaScreen assay, several classes of structurally diverse PDK1 inhibitors, including tetracyclics, tricyclics, azaindoles, indazoles, and indenylpyrazoles, were identified, thus confirming the utility and sensitivity of the developed assays. Further testing in PC3 prostate cancer cells confirmed that representatives of the tetracyclic series showed intracellular modulation of the PDK1 activity, as evident from decreased phosphorylation levels of AKT, RSK, and S6-ribosomal protein.

Constitutive activation of one or more kinase signaling pathways is a hallmark of many cancers. Here we extend the previously described mass spectrometry-based KAYAK approach by monitoring kinase activities from multiple signaling pathways simultaneously. This improved single-reaction strategy, which quantifies the phosphorylation of 90 synthetic peptides in a single mass spectrometry run, is compatible with nanogram to microgram amounts of cell lysate. Furthermore, the approach enhances kinase monospecificity through substrate competition effects, faithfully reporting the signatures of many signaling pathways after mitogen stimulation or of basal pathway activation differences across a panel of well-studied cancer cell lines. Hierarchical clustering of activities from related experiments groups peptides phosphorylated by similar kinases together and, when combined with pathway alteration using pharmacological inhibitors, distinguishes underlying differences in potency, off-target effects and genetic backgrounds. Finally, we introduce a strategy to identify the kinase, and even associated protein complex members, responsible for phosphorylation events of interest.

Ga diffusion from focused ion beam (FIB) milled grooves has been studied using x-ray photoemission electron microscopy (XPEEM) and mirror electron microscopy (MEM). We analyze the surface chemistry of the FIB structures measuring the Ga presence in the top layers of the milled grooves and morphological defects inside the grooves. The Ga is initially strictly confined to the grooves. However, annealing at temperatures as low as 150 degrees C leads to rapid and significant Ga surface diffusion from the FIB structures. The out-diffused Ga forms a thin layer extending up to several microns laterally in a non-regular pattern. The diffusion is significantly enhanced at small crystallites at the edges of the grooves. We explain the general behavior with an atomic scale model in which interstitial Ga in the milled areas diffuses out and substitutes silanol groups on the surface.

We establish a new mechanism for self-propelled motion of droplets, in which ordering of the nanoscale step morphology by sublimation beneath the droplets themselves acts to drive them perpendicular and up the surface steps. The mechanism is demonstrated and explored for Ga droplets on GaP(111)B, using several experimental techniques allowing studies of the structure and dynamics from micrometers to the atomic scale. We argue that the simple assumptions underlying the propulsion mechanism make it relevant for a wide variety of materials systems.

Using scanning tunneling microscopy and density functional theory, we have studied the initial oxidation of Rh(111) surfaces with two types of straight steps, having {100} and {111} microfacets. The one-dimensional (1D) oxide initially formed at the steps acts as a barrier impeding formation of the 2D oxide on the (111) terrace behind it. We demonstrate that the details of the structure of the 1D oxide govern the rate of 2D oxidation and discuss implications for oxidation of nanoparticles.

The (1 X 1) --> quasihexagonal (HEX) phase transition on a clean Pt(100) surface was investigated by monitoring the time evolution of the Pt4f(72) core level photoemission spectra. The spectral component originating from the atoms forming the (1x1) metastable unreconstructed surface was found at -570+/-20 meV with respect to the bulk peak. Ab initio calculations based on density functional theory confirmed the experimental assignment. At temperatures above 370 K, the (1 X 1) phase irreversibly reverts to the more stable HEX phase, characterized by a surface core level shifted component at -185 +/ -40 meV. By analyzing the intensity evolution of the core level components, measured at different temperatures in the range of 393 - 475 K, we determined the activation energy of the phase transformation, E = 0.76 +/- 0.04 eV. This value is considerably lower than the one previously determined by means of low energy electron diffraction. Possible reasons for this discrepancy are discussed.

The properties of bimetallic Ni-Rh nanowires, fabricated by decorating the steps of vicinal Rh(111) surfaces by stripes of self-assembled Ni adatoms, have been probed by STM, photoemission, and ab initio density functional theory calculations. These Ni-Rh nanowires have specific electronic properties that lead to a significantly enhanced chemical reactivity towards oxygen. As a result, the Ni-Rh nanowires can be oxidized exclusively, generating novel quasi-one-dimensional oxide structures.

The reduction mechanism of the RuO(2)(110) surface by molecular hydrogen exposure is unraveled to an unprecedented level by a combination of temperature programmed reaction, scanning tunneling microscopy, high-resolution core level shift spectroscopy, and density functional theory calculations. We demonstrate that even at room temperature hydrogen exposure to the RuO(2)(110) surface leads to the formation of water. In a two-step process, hydrogen saturates first the bridging oxygen atoms to form (O(br)-H) species and subsequently part of these O(br)-H groups move to the undercoordinated Ru atoms where they form adsorbed water. This latter process is driven by thermodynamics leaving vacancies in the bridging O rows.

We studied the mechanism of CO oxidation on O-precovered Pd(111) surfaces by means of fast x-ray photoelectron spectroscopy (XPS). The oxygen overlayer is compressed upon CO coadsorption from a p(2 x 2) structure into a (square root(3) x square root(3))R30 degrees structure and then into a p(2 x 1) structure with increasing CO coverage. These three O phases exhibit distinctly different reactivities. (1) The p(2 x 2) phase does not react with CO unless the surface temperature is sufficiently high (<290 K). (2) In the square root(3) x square root(3))R30 degrees phase, the reaction occurs exclusively at island peripheries. CO molecules in a high-density phase formed under CO exposure react with oxygen atoms, leading to quite a small apparent activation energy. (3) The reaction proceeds uniformly over the islands in the p(2 x 1) phase.

The reduction of the surface oxide on Rh(111) by H(2) was observed in situ by scanning tunneling microscopy (STM) and high-resolution core level spectroscopy (HRCLS). At room temperature, H(2) does not adsorb on the oxide, only in reduced areas. Reduction starts in very few sites, almost exclusively in stepped areas. One can also initiate the reduction process by deliberately creating defects with the STM tip allowing us to examine the reduction kinetics in detail. Depending on the size of the reduced area and the hydrogen pressure, two growth regimes were found. At low H(2) pressures or small reduced areas, the reduction rate is limited by hydrogen adsorption on the reduced area. For large reduced areas, the reduction rate is limited by the processes at the border of the reduced area. Since a near-random distribution of the reduction nuclei was found and the reduction process at defects starts at a random time, one can use Johnson-Mehl-Avrami-Kolmogoroff (JMAK) theory to describe the process of reduction. The microscopic data from STM agree well with spatially averaged data from HRCLS measurements.

The structure of the oxygen-induced p(4 x 4) reconstruction of Ag(111) is determined by a combination of scanning tunneling microscopy, surface x-ray diffraction, core level spectroscopy, and density functional theory. We demonstrate that all previous models of this surface structure are incorrect and propose a new model which is able to explain all our experimental findings but has no resemblance to bulk silver oxide. We also shed some light on the limitations of current density functional theories and the potential role of van der Waals interactions in the stabilization of oxygen-induced surface reconstructions of noble metals.

Using core-level spectroscopy and density functional theory we show that a one-dimensional (1D) oxide structure forms at the steps of the Pt(332) surface after exposure. The 1D oxide is found to be stable in an oxygen pressure range, where bulk oxides are only metastable, and is therefore argued to be a precursor to the Pt oxidation. As an example of the consequences of such a precursor exclusively present at the steps, we investigate the reaction of CO with oxygen covered Pt(332). Albeit more strongly bound, the oxidic oxygen is found to react more easily with CO than oxygen chemisorbed on the Pt terraces.

The structural phases of Al(x)Na(1-x) surface alloys have been investigated theoretically and experimentally. We describe the system using a lattice-gas Hamiltonian, determined from density functional theory, together with Monte Carlo (MC) calculations. The obtained phase diagram reproduces the experiment on a quantitative level. From calculation of the (configurational) density of states by the recently introduced Wang-Landau MC algorithm, we derive thermodynamic quantities, such as the free energy and entropy, which are not directly accessible from conventional MC simulations. We accurately reproduce the stoichiometry, as well as the temperature at which an order-disorder phase transition occurs, and demonstrate the crucial role, and magnitude, of the configurational entropy.

The oxidation of Pd(100) and the formation of PdO was studied in situ using surface x-ray diffraction. A bulklike, epitaxial PdO film is formed at oxygen partial pressures beyond 1 mbar and sample temperatures exceeding 650 K. The main orientation is PdO(001)/Pd(001), based upon bulk reflections from the PdO film. By comparing with measurements from the Pd crystal truncation rods, we estimate an rms surface roughness of 6 A, in good agreement with previous high pressure scanning tunneling microscopy measurements. Finally, we observed the transformation from the (radical5 x radical5) surface oxide to PdO bulk oxide at 675 K and 50 mbar O(2) pressure., ((c) 2005 American Institute of Physics.)

The exponential growth of sequence data has become a challenge to database curators and end-users alike and biologists seeking to utilize the data effectively are faced with numerous analysis methods. Here, with practical examples from our bioinformatics analysis of the protein tyrosine phosphatases (PTPs), we show how computational analysis can be exploited to fuel hypothesis-driven experimental research through the exploration of online databases. We cover the following elements: (i) similarity searches and strategies to collect a non-redundant database of tyrosine-specific PTP domains; (ii) utilization of this database to classify human, fly, and worm PTPs (based on alignments and phylogenetic analysis); (iii) three-dimensional structural analysis to identify conserved regions (structure-function) and non-conserved selectivity-determining regions (substrate specificity); and (iv) genomic analysis, including mapping of exon structure, identification of pseudogenes, and exploration of disease databases. We discuss the importance of manual curation, illustrating examples in which pseudogenes give rise to predicted proteins in GenBank and note that domain servers, such as PFAM and SMART, erroneously include dual-specificity and lipid phosphatases in their collection of tyrosine-specific PTPs. To capitalize on our annotated set of 402 PTP domains (from 47 species and five phyla), we identify sequence conservation across taxonomic categories and explore structure-function relationships among tandem domain receptor-like PTPs. We define three Src homology 2 domain-containing PTP genes in stingray, zebrafish, and fugu and speculate on their evolutionary relationship with human pseudogenes. Our annotated sequences, along with a web service for phylogenetic classification of PTP domains, are available online (http://ptp.cshl.edu and http://science.novonordisk.com/ptp).

A new O induced structure on Rh(111) displaying a (2 sqaureroot[3] x 2sqaureroot[3])R30 degrees periodicity with an oxygen coverage of 2/3 has been studied by high resolution core level spectroscopy, scanning tunneling microscopy, and density functional theory. Although O favors fcc hollow sites in all other known phases, it occupies both fcc and hcp sites in this structure, which cannot be explained by pairwise adsorbate repulsion only. Both the (2sqaureroot[3] x 2sqaureroot[3])R30 degrees and (2 x 2)-3O structures also exemplify that density-of-states contrast can lead to oxygen adatoms appearing as protrusions in scanning tunneling microscopy images.

Core-level photoelectron spectra, in excellent agreement with ab initio calculations, confirm that the stable wetting layer of water on Ru[0001] contains O-H and H2O in roughly 3:5 proportion, for OHx coverages between 0.25 and 0.7 ML, and T<170 K. Proton disorder explains why the wetting structure looks to low energy electron diffraction (LEED) to be an ordered p(square root of 3 x square root of 3)R30 degrees adlayer, even though approximately 3/8 of its molecules are dissociated. Complete dissociation to atomic oxygen starts near 190 K. Low photon flux in the synchrotron experiments ensured that the diagnosis of the nature of the wetting structure quantified by LEED is free of beam-induced damage.

Semiconductor nanowires are expected to be important components in future nano-electronics and photonics. Already a wide range of applications has been realized, such as high-performance field-effect transistors, bio/chemical sensors, diode logics and single-nanowire lasers. As nanowires have small cross-sections and large surface-to-bulk ratios, their properties can be significantly influenced by individual atomic-scale structural features, and they can have properties or even atomic arrangements with no bulk counterparts. Hence, experimental methods capable of directly addressing the atomic-scale structure of nanowires are highly desirable. One such method is scanning tunnelling microscopy (STM), which, by direct imaging of the atomic and electronic structure of surfaces has revolutionized the perception of nanoscale objects and low-dimensional systems. Here we demonstrate how combining STM with an embedding scheme allows us to image the interior of semiconductor nanowires with atomic resolution. Defect structures such as planar twin segments and single-atom impurities are imaged inside a GaAs nanowire. Further, we image an intriguing GaAs nanowire that is separated into two distinct nanocrystallites along the growth direction of the wire.

The oxidation of the Rh(111) surface at oxygen pressures from 10(-10) mbar to 0.5 bar and temperatures between 300 and 900 K has been studied on the atomic scale using a multimethod approach of experimental and theoretical techniques. Oxidation starts at the steps, resulting in a trilayer O-Rh-O surface oxide which, although not thermodynamically stable, prevents further oxidation at intermediate pressures. A thick corundum like Rh2O3 bulk oxide is formed only at significantly higher pressures and temperatures.

The oxidation of the Pd(100) surface at oxygen pressures in the 10(-6) to 10(3) mbar range and temperatures up to 1000 K has been studied in situ by surface x-ray diffraction (SXRD). The results provide direct structural information on the phases present in the surface region and on the kinetics of the oxide formation. Depending on the (T,p) environmental conditions, we observe either a thin (sqrt[5]xsqrt[5])R27 degrees surface oxide or the growth of a rough, poorly ordered bulk oxide film of PdO predominantly with (001) orientation. By either comparison to the surface phase diagram from first-principles atomistic thermodynamics or by explicit time-resolved measurements we identify a strong kinetic hindrance to the bulk oxide formation even at temperatures as high as 675 K.

The protein tyrosine phosphatases (PTPs) are now recognized as critical regulators of signal transduction under normal and pathophysiological conditions. In this analysis we have explored the sequence of the human genome to define the composition of the PTP family. Using public and proprietary sequence databases, we discovered one novel human PTP gene and defined chromosomal loci and exon structure of the additional 37 genes encoding known PTP transcripts. Direct orthologs were present in the mouse genome for all 38 human PTP genes. In addition, we identified 12 PTP pseudogenes unique to humans that have probably contaminated previous bioinformatics analysis of this gene family. PCR amplification and transcript sequencing indicate that some PTP pseudogenes are expressed, but their function (if any) is unknown. Furthermore, we analyzed the enhanced diversity generated by alternative splicing and provide predicted amino acid sequences for four human PTPs that are currently defined by fragments only. Finally, we correlated each PTP locus with genetic disease markers and identified 4 PTPs that map to known susceptibility loci for type 2 diabetes and 19 PTPs that map to regions frequently deleted in human cancers. We have made our analysis available at http://ptp.cshl.edu or http://science.novonordisk.com/ptp and we hope this resource will facilitate the functional characterization of these key enzymes.

Protein tyrosine phosphatase 1B (PTP1B) is implicated as a negative regulator of insulin receptor (IR) signaling and a potential drug target for the treatment of type 2 diabetes and other associated metabolic syndromes. To further define the role of PTP1B in insulin signaling and to test the hypothesis that blocking the activity of PTP1B would augment the action of insulin, we prepared several cell permeable, potent and selective, small molecule PTP1B inhibitors, and evaluated their biological effects in several insulin sensitive cell lines. Our data indicate that PTP1B inhibitors bind to and colocalize with PTP1B on the surface of the endoplasmic reticulum and PTP1B exerts its negative effect on insulin signaling upstream of phosphatidylinositol 3-kinase and MEK1. Treatment of cells with PTP1B inhibitors, both in the presence and in the absence of insulin, markedly enhances IRbeta and IRS-1 phosphorylation, Akt and ERK1/2 activation, Glut4 translocation, glucose uptake, and Elk1 transcriptional activation and cell proliferation. These results indicate that small molecule inhibitors targeted to PTP1B can act as both insulin mimetics and insulin sensitizers. Taken together, our findings combined with results from PTP1B knockout, antisense, and biochemical studies provide strong evidence that PTP1B negatively regulates insulin signaling and that small molecule PTP1B inhibitors have the ability to potentiate and augment the action of insulin.

Background: Induction of pneumoperitoneum can be a difficult, time-consuming, and occasionally hazardous task in a morbidly obese patient., Methods: We have induced pneumoperitoneum in 600 consecutive morbidly obese patients using a 120 mm Veress needle inserted <1 mm beneath the left costal margin, between the mid-clavicular and anterior axillary lines. Absolute muscular relaxation was necessary., Results: A distinct "pop" was felt on entering the peritoneal cavity. The expected intraperitoneal pressure was 7-14 mmHg. A pressure >20 mmHg indicated that the Veress needle was in the abdominal wall. CO2 infusion began at a flow of <1 L/min. "Shaking" the Veress needle to-and-fro improved flow to 1-2 L/min. Complete filling of the abdomen occurred at 4.0 L or more at a pressure limit of 15 mmHg. Increasing the pressure limit to 17 mmHg did not change the rate or final volume of CO(2) infusion. After initial trocar placement, the Veress needle was observed. Frequently it was in the omentum and there was CO(2) beneath the omentum. There was one visceral injury in the 600 patients--a puncture wound to the muscularis, but not the lumen, of the transverse colon. It was repaired laparoscopically with a single stitch. There have been no episodes of perforation of a hollow viscus, no unusual bleeding from the abdominal wall or viscera, and no injuries to the liver or spleen., Conclusion: Percutaneous induction of a pneumoperitoneum with the Veress needle in the left upper quadrant is a safe and effective technique in morbidly obese patients.

Vicinal Rh(111) surfaces are studied with high resolution core level photoemission. We demonstrate the possibility to distinguish between the different kinds of surface atoms on these surfaces by virtue of their 3d core level binding energies. In particular, the low coordinated step atoms are found to exhibit a clear fingerprint in Rh 3d spectra. We demonstrate how this may be used to show that initial oxygen adsorption occurs on the steps and not on the terraces of the vicinal surfaces.

The second messenger hydrogen peroxide is required for optimal activation of numerous signal transduction pathways, particularly those mediated by protein tyrosine kinases. One mechanism by which hydrogen peroxide regulates cellular processes is the transient inhibition of protein tyrosine phosphatases through the reversible oxidization of their catalytic cysteine, which suppresses protein dephosphorylation. Here we describe a structural analysis of the redox-dependent regulation of protein tyrosine phosphatase 1B (PTP1B), which is reversibly inhibited by oxidation after cells are stimulated with insulin and epidermal growth factor. The sulphenic acid intermediate produced in response to PTP1B oxidation is rapidly converted into a previously unknown sulphenyl-amide species, in which the sulphur atom of the catalytic cysteine is covalently linked to the main chain nitrogen of an adjacent residue. Oxidation of PTP1B to the sulphenyl-amide form is accompanied by large conformational changes in the catalytic site that inhibit substrate binding. We propose that this unusual protein modification both protects the active-site cysteine residue of PTP1B from irreversible oxidation to sulphonic acid and permits redox regulation of the enzyme by promoting its reversible reduction by thiols.

Protein tyrosine phosphatases (PTPs) play a central role in cellular signaling processes, resulting in an increased interest in modulating the activities of PTPs. We therefore decided to undertake a detailed enzyme kinetic evaluation of various transmembrane and cytosolic PTPs (PTPalpha, PTPbeta, PTPepsilon, CD45, LAR, PTP1B and SHP-1), using pNPP as substrate. Most noticeable is the increase in the turnover number for PTPbeta with increasing pH and the weak pH-dependence of the turnover number of CD45. The kinetic data for PTPalpha-D1 and PTPalpha-D1D2 suggest that D2 affects the catalysis of pNPP. PTPepsilon and the closely homologous PTPalpha behave differently. The K(m) data were lower for PTPepsilon than those for PTPalpha, while the inverse was observed for the catalytic efficiencies.

The oxidation of Pd(111) leads to an incommensurate surface oxide, which was studied by the use of scanning tunneling microscopy, surface x-ray diffraction, high resolution core level spectroscopy, and density functional calculations. A combination of these methods reveals a two-dimensional structure having no resemblance to bulk oxides of Pd. Our study also demonstrates how the atomic arrangement of a nontrivial incommensurate surface can be solved by molecular dynamics in a case where experimental techniques alone give no solution.

We present a structural determination of the surface reconstruction of the Sm(0001) surface using surface x-ray diffraction, scanning tunneling microscopy, and ab initio calculations. The reconstruction is associated with a large (22%) expansion of the atomic radius for the top monolayer surface Sm atoms. The mechanism driving the surface reconstruction in Sm is unique among all elements and is connected to the strong correlations of the 4f electrons in Sm and the intermediate valence observed in certain Sm compounds. The atoms constituting the top monolayer of Sm(0001) have vastly different chemical properties compared to the layer underneath and behave as if they were an adsorbate of a different chemical species.

The reversible tyrosine phosphorylation of proteins, modulated by the coordinated actions of protein-tyrosine kinases and protein-tyrosine phosphatases (PTPs), regulates the cellular response to a wide variety of stimuli. It is established that protein kinases possess discrete sets of substrates and that substrate recognition is often dictated by the presence of consensus phosphorylation sites. Here, we have extended this concept to the PTPs and demonstrated that (E/D)-pY-pY-(R/K) is a consensus substrate recognition motif for PTP1B. We have shown that JAK2 and TYK2 are substrates of PTP1B and that the substrate recognition site within theses kinases is similar to the site of dephosphorylation previously identified within the insulin receptor. A substrate-trapping mutant of PTP1B formed a stable interaction with JAK2 and TYK2 in response to interferon stimulation. Expression of wild type or substrate-trapping mutant PTP1B inhibited interferon-dependent transcriptional activation. Finally, mouse embryo fibroblasts deficient in PTP1B displayed subtle changes in tyrosine phosphorylation, including hyperphosphorylation of JAK2. The closely related JAK family member, JAK1, which does not match the consensus dephosphorylation site, was not recognized as a substrate. These data illustrate that PTP1B may be an important physiological regulator of cytokine signaling and that it may be possible to derive consensus substrate recognition motifs for other members of the PTP family, which may then be used to predict novel physiological substrates.

An unusual multilayer surface alloy is formed by adsorption of one monolayer Li on Al(100). It is shown by low energy electron diffraction that the first three layers consist of a mixed Al-Li layer, a pure Al layer, and a second Al-Li layer. Thus the alloy has the same layer stoichiometry as the (100) surface of the metastable Al(3)Li bulk alloy. However, the relative orientation of the two mixed layers is the same as that in the Al(3)Ti-type structure. These findings are confirmed by total-energy calculations, which lead further to the prediction that the bulk Al(3)Li alloy has a faulted, Al(3)Ti-type surface.

The Be 1s core level photoemission line from metallic Be is shown to contain unexpected internal fine structure. We argue that this fine structure is caused by intrinsic excitation of a narrow band of optical phonons in the 1s photoemission process. The general importance of the present results for high resolution core level photoemission investigations of metals is pointed out.

To study the influence of subcellular localization as a determinant of signal transduction specificity, we assessed the effects of wild-type transmembrane and cytoplasmic protein tyrosine phosphatase (PTP) epsilon on tyrosine kinase signalling in baby hamster kidney (BHK) cells overexpressing the insulin receptor (BHK-IR). The efficiency by which differently localized PTPepsilon and PTPalpha variants attenuated insulin-induced cell rounding and detachment was determined in a functional clonal-selection assay and in stable cell lines. Compared with the corresponding receptor-type PTPs, the cytoplasmic PTPs (cytPTPs) were considerably less efficient in generating insulin-resistant clones, and exceptionally high compensatory expression levels were required to counteract phosphotyrosine-based signal transduction. Targeting of cytPTPepsilon to the plasma membrane via the Lck-tyrosine kinase dual acylation motif restored high rescue efficiency and abolished the need for high cytPTPepsilon levels. Consistent with these results, expression levels and subcellular localization of PTPepsilon were also found to determine the phosphorylation level of cellular proteins including focal adhesion kinase (FAK). Furthermore, PTPepsilon stabilized binding of phosphorylated FAK to Src, suggesting this complex as a possible mediator of the PTPepsilon inhibitory response to insulin-induced cell rounding and detachment in BHK-IR cells. Taken together, the present localization-function study indicates that transcriptional control of the subcellular localization of PTPepsilon may provide a molecular mechanism that determines PTPepsilon substrate selectivity and isoform-specific function.

The protein tyrosine phosphatase PTP1B is responsible for negatively regulating insulin signaling by dephosphorylating the phosphotyrosine residues of the insulin receptor kinase (IRK) activation segment. Here, by integrating crystallographic, kinetic, and PTP1B peptide binding studies, we define the molecular specificity of this reaction. Extensive interactions are formed between PTP1B and the IRK sequence encompassing the tandem pTyr residues at 1162 and 1163 such that pTyr-1162 is selected at the catalytic site and pTyr-1163 is located within an adjacent pTyr recognition site. This selectivity is attributed to the 70-fold greater affinity for tandem pTyr-containing peptides relative to mono-pTyr peptides and predicts a hierarchical dephosphorylation process. Many elements of the PTP1B-IRK interaction are unique to PTP1B, indicating that it may be feasible to generate specific, small molecule inhibitors of this interaction to treat diabetes and obesity.