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An integrated methodology is described to establish ligand requirements for heparan sulfate (HS) binding proteins based on a workflow in which HS octasaccharides are produced by partial enzymatic degradation of natural HS followed by size exclusion purification, affinity enrichment using an immobilized HS-binding protein of interest, putative structure determination of isolated compounds by a hydrophilic interaction chromatography-high-resolution mass spectrometry platform, and chemical synthesis of well-defined HS oligosaccharides for structure-activity relationship studies. The methodology was used to establish the ligand requirements of human Roundabout receptor 1 (Robo1), which is involved in a number of developmental processes. Mass spectrometric analysis of the starting octasaccharide mixture and the Robo1-bound fraction indicated that Robo1 has a preference for a specific set of structures. Further analysis was performed by sequential permethylation, desulfation, and pertrideuteroacetylation followed by online separation and structural analysis by MS/MS. Sequences of tetrasaccharides could be deduced from the data, and by combining the compositional and sequence data, a putative octasaccharide ligand could be proposed (GlA-GlcNS6S-IdoA-GlcNS-IdoA2S-GlcNS6S-IdoA-GlcNAc6S). A modular synthetic approach was employed to prepare the target compound, and binding studies by surface plasmon resonance (SPR) confirmed it to be a high affinity ligand for Robo1. Further studies with a number of tetrasaccharides confirmed that sulfate esters at C-6 are critical for binding, whereas such functionalities at C-2 substantially reduce binding. High affinity ligands were able to reverse a reduction in endothelial cell migration induced by Slit2-Robo1 signaling.

Age-related diseases, like Alzheimer's disease and type 2 diabetes mellitus, are characterized by protein misfolding and the subsequent pathological deposition of fibrillized protein, also called amyloid. Several classes of amyloid-inhibitors have recently been tested, traditionally under bulk conditions. However, it has become apparent that amyloid fibrils and oligomers assemble and exert their cytotoxic effect at cellular membranes, rather than in bulk solution. Knowledge is therefore required of inhibitor activity specifically at the phospholipid membrane interface. Here we show, using surface-specific sum-frequency generation (SFG) spectroscopy and atomic force microscopy (AFM), that the commonly used (-)-epigallocatechin gallate (EGCG) is a much less efficient amyloid inhibitor at a phospholipid interface than in bulk solution. Moreover, EGCG is not able to disaggregate existing amyloid fibrils at a phospholipid interface, in contrast to its behavior in bulk. Our results show that interfaces significantly affect the efficiency of inhibition by EGCG inhibitors and should therefore be considered during the design and testing of amyloid inhibitors. © 2012 American Chemical Society.

Luminescence temperature antiquenching (LTAQ) is observed for water-soluble CdTe quantum dots (QDs) capped with aminoethanethiol (AET). The efficient exciton emission (quantum efficiency of approximately 40% at 300 K) is quenched almost completely as the QD solutions are cooled to below 230 K and is fully recovered around 270 K upon warming up to room temperature (LTAQ). Temperature-dependent lifetime measurements show that the quenching rate is high, resulting in an on/off behavior. No LTAQ is observed for CdTe QDs capped with aminoundecanethiol (AUT). The LTAQ is explained by the influence of solvent freezing on the surface of the QD core. Freezing of the solvation water molecules surrounding the QD will induce strain in the capping shell, due to the interaction between water and the charged heads of the capping molecules. Short carbon chains (AET) will propagate the strain to the QD surface, creating surface quenching states, whereas long and flexible chains (AUT) will dissipate the strain, thus avoiding surface distortion. Freezing-point depression by the addition of methanol results in a lowering of the transition temperature. Additional support is provided by the size dependence of the LTAQ: smaller particles, with higher local ionic strength due to a higher density of charged NH(3)(+) surface groups, experience a lower transition temperature due to stronger local freezing-point depression.

Hemes (iron porphyrins) are involved in a range of functions in biology, including electron transfer, small-molecule binding and transport, and O2 activation. The delocalization of the Fe d-electrons into the porphyrin ring and its effect on the redox chemistry and reactivity of these systems has been difficult to study by optical spectroscopies due to the dominant porphyrin pi--pi(*) transitions, which obscure the metal center. Recently, we have developed a methodology that allows for the interpretation of the multiplet structure of Fe L-edges in terms of differential orbital covalency (i.e., differences in mixing of the d-orbitals with ligand orbitals) using a valence bond configuration interaction (VBCI) model. Applied to low-spin heme systems, this methodology allows experimental determination of the delocalization of the Fe d-electrons into the porphyrin (P) ring in terms of both P--Fe sigma and pi-donation and Fe--P pi back-bonding. We find that pi-donation to Fe(III) is much larger than pi back-bonding from Fe(II), indicating that a hole superexchange pathway dominates electron transfer. The implications of the results are also discussed in terms of the differences between heme and non-heme oxygen activation chemistry.

This article describes the synthesis and binding properties of highly selective noncovalent molecular receptors 1(3).(DEB)6 and 3(3).(DEB)6 for different hydroxyl functionalized anthraquinones 2. These receptors are formed by the self-assembly of three calix[4]arene dimelamine derivative molecules (1 or 3) and six diethylbarbiturate (DEB) molecules to give 1(3).(DEB)6 or 3(3).(DEB)6. Encapsulation of 2 occurs in a highly organized manner; that is, a noncovalent hydrogen-bonded trimer of 2 is formed within the hydrogen-bonded receptors 1(3).(DEB)6 and 3(3).(DEB)6. Both receptors 1(3).(DEB)6 and 3(3).(DEB)6 change conformation from staggered to eclipsed upon complexation to afford a better fit for the 2(3) trimer. The receptor selectivity toward different anthraquinone derivatives 2 has been studied using 1H NMR spectroscopy, X-ray crystallography, UV spectroscopy, and isothermal microcalorimetry (ITC). The pi-pi stacking between the electron-deficient center ring of the anthraquinone derivatives 2a-c and 2e-g and the relatively electron-poor melamine units of the receptor is the driving force for the encapsulation of the guest molecules. The selectivity of the hydrogen-bonded host for the anthraquinone derivatives is the result of steric interactions between the guest molecules and the calix[4]arene aromatic rings of the host.

We present a method that significantly enhances the robustness of (automated) NMR structure determination by allowing the NOE data corresponding to unassigned NMR resonances to be used directly in the calculations. The unassigned resonances are represented by additional atoms or groups of atoms that have no interaction with the regular protein atoms except through distance restraints. These so-called "proxy" residues can be used to generate NOE-based distance restraints in a similar fashion as for the assigned part of the protein. If sufficient NOE information is available, the restraints are expected to place the proxies at positions close to the correct atoms for the unassigned resonance, which can facilitate subsequent assignment. Convergence can be further improved by supplying additional information about the possible identities of the unassigned resonances. We have implemented this approach in the widely used automated assignment and structure calculation protocols ARIA and CANDID. We find that it significantly increases the robustness of structure calculations with regard to missing assignments and yields structures of higher quality. Our approach is still able to find correctly folded structures with up to 30% randomly missing resonance assignments, and even when only backbone and beta resonances are present! This should be of significant value to NMR-based structural proteomics initiatives.

The structure determination of protein-protein complexes is a rather tedious and lengthy process, by both NMR and X-ray crystallography. Several methods based on docking to study protein complexes have also been well developed over the past few years. Most of these approaches are not driven by experimental data but are based on a combination of energetics and shape complementarity. Here, we present an approach called HADDOCK (High Ambiguity Driven protein-protein Docking) that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments or mutagenesis data. This information is introduced as Ambiguous Interaction Restraints (AIRs) to drive the docking process. An AIR is defined as an ambiguous distance between all residues shown to be involved in the interaction. The accuracy of our approach is demonstrated with three molecular complexes. For two of these complexes, for which both the complex and the free protein structures have been solved, NMR titration data were available. Mutagenesis data were used in the last example. In all cases, the best structures generated by HADDOCK, that is, the structures with the lowest intermolecular energies, were the closest to the published structure of the respective complexes (within 2.0 Å backbone RMSD).

Molecular dynamics (MD) simulations are used to show that a spherical zinc blende (ZB) nanocrystal (NC) can transform into a tetrapod or an octapod as a result of heating, by a local zincblende-to-wurtzite phase transformation taking place in the NC. The partial sphere-to-tetrapod or sphere-to-octapod transition occurs within simulation times of 30 ns and depends on both temperature and NC size. Surprisingly, the wurtzite (WZ) subdomains are not formed through a slip mechanism but are mediated by the formation of highly mobile Cd vacancies on the ZB{111} Cd atomic planes. The total potential energy of a tetrapod is found to be lower than that of a ZB sphere at the same numbers of atoms. The simulation results are in good agreement with experimental high-resolution transmission electron microscopy (HR-TEM) data obtained on heated colloidal CdSe NCs.

Technologies that can visualize, capture, and identify subsets of biomolecules that are not encoded by the genome in the context of healthy and diseased cells will offer unique opportunities to uncover the molecular mechanism of a multitude of physiological and disease processes. We describe here a chemical reporter strategy for labeling of cell surface glycoconjugates that takes advantage of recombinant glycosyltransferases and a corresponding sugar nucleotide functionalized by biotin. The exceptional efficiency of this method, termed one-step selective exoenzymatic labeling, or SEEL, greatly improved the ability to enrich and identify large numbers of tagged glycoproteins by LC–MS/MS. We further demonstrated that this labeling method resulted in far superior enrichment and detection of glycoproteins at the plasma membrane compared to a sulfo-NHS-activated biotinylation or two-step SEEL. This new methodology will make it possible to profile cell surface glycoproteomes with unprecedented sensitivity in the context of physiological and disease states.

Anomeric sulfonium ions are attractive glycosyl donors for the stereoselective installation of 1,2-cis glycosides. Although these donors are receiving increasing attention, their mechanism of glycosylation remains controversial. We have investigated the reaction mechanism of glycosylation of a donor modified at C-2 with a (1S)-phenyl-2-(phenylsulfanyl)ethyl chiral auxiliary. Preactivation of this donor results in the formation of a bicyclic β-sulfonium ion that after addition of an alcohol undergoes 1,2-cis-glycosylation. To probe the importance of the thiophenyl moiety, analogs were prepared in which this moiety was replaced by an anisoyl or benzyl moiety. Furthermore, the auxiliaries were installed as S- and R-stereoisomers. It was found that the nature of the heteroatom and chirality of the auxiliary greatly influenced the anomeric outcome and only the one containing a thiophenyl moiety and having S-configuration gave consistently α-anomeric products. The sulfonium ions are sufficiently stable at a temperature at which glycosylations proceed indicating that they are viable glycosylation agents. Time-course NMR experiments with the latter donor showed that the initial rates of glycosylations increase with increases in acceptor concentration and the rate curves could be fitted to a second order rate equation. Collectively, these observations support a mechanism by which a sulfonium ion intermediate is formed as a trans-decalin ring system that can undergo glycosylation through a bimolecular mechanism. DFT calculations have provided further insight into the reaction path of glycosylation and indicate that initially a hydrogen-bonded complex is formed between sulfonium ion and acceptor that undergoes SN2-like glycosylation to give an α-anomeric product.

We have developed a united atom force field able to accurately describe the adsorption properties of linear alkanes in the sodium form of FAU-type zeolites. This force field successfully reproduces experimental adsorption properties of n-alkanes over a wide range of sodium cation densities, temperatures, and pressures. The force field reproduces the sodium positions in dehydrated FAU-type zeolites known from crystallography, and it predicts how the sodium cations redistribute when n-alkanes adsorb. The cations in the sodalite cages are significantly more sensitive to the n-alkane loading than those in the supercages. We provide a simple expression that adequately describes the n-alkane Henry coefficient and adsorption enthalpy as a function of sodium density and temperature at low coverage. This expression affords an adequate substitute for complex configurational-bias Monte Carlo simulations. The applicability of the force field is by no means limited to low pressure and pure adsorbates, for it also successfully reproduces the adsorption from binary mixtures at high pressure.

The N,C,N'-bonded arylruthenium 2,2':6',2''-terpyridine (tpy) complex salts [Ru(NCN)(tpy)](Cl) ([1a](Cl), NCN = 2,6-bis[(dimethylamino)methyl]phenyl) and [Ru(N--C--N)(tpy)](PF(6)), ([2a](PF(6)), N--C--N = 2,6-bis(2-pyridyl)phenyl) can be halogenated under very mild conditions by oxidation with copper(II) halogen salts. Halogenation occurs exclusively para to the site of metalation and yields the cations [Ru(4-R-NCN)(tpy)](+) (R = Cl, [1b](+) and R = Br [1c](+)) and [Ru(4-R-N--C--N)(tpy)](+) (R = Cl, [2b](+) and R = Br [2c](+)). In the presence of an excess of oxidant relative to [1a](+), the halogenation reaction follows first order kinetics in the oxidized ruthenium complex. However, by using a small excess of copper(II) compared to [1a](+), dimerization of the complex cation to [{Ru(tpy)}(2)(mu-NCN-NCN)](4+) ([3](4+)) is observed, which obeys second order kinetics. Both halogenation (C-X coupling) and dimerization (C-C coupling) are a result of the unique properties of the ruthenium(III) complexes compared to their parent ruthenium(II) species. According to the nature of the highest occupied spin orbital (HOSO) in DFT calculations the unpaired electron in [1a](2+) and [2a](2+) is partially localized on the para position. The involvement of the cyclometalated ligand in the HOSO is supported by redox data and electronic absorption spectroscopy. The ruthenium(III) species can best be considered a persistent organometallic radical.

We measured the lateral mobility of integral membrane proteins reconstituted in giant unilamellar vesicles (GUVs), using fluorescence correlation spectroscopy. Receptor, channel, and transporter proteins with 1-36 transmembrane segments (lateral radii ranging from 0.5 to 4 nm) and a alpha-helical peptide (radius of 0.5 nm) were fluorescently labeled and incorporated into GUVs. At low protein-to-lipid ratios (i.e., 10-100 proteins per microm(2) of membrane surface), the diffusion coefficient D displayed a weak dependence on the hydrodynamic radius (R) of the proteins [D scaled with ln(1/R)], consistent with the Saffman-Delbruck model. At higher protein-to lipid ratios (up to 3000 microm(-2)), the lateral diffusion coefficient of the molecules decreased linearly with increasing the protein concentration in the membrane. The implications of our findings for protein mobility in biological membranes (protein crowding of approximately 25,000 microm(-2)) and use of diffusion measurements for protein geometry (size, oligomerization) determinations are discussed.

A synthesis strategy to obtain monodisperse hexanethiolate-protected Au38 clusters based on their resistance to etching upon exposure to a hyperexcess of thiol is reported. The reduction time in the standard Brust-Schiffrin two-phase synthesis was optimized such that Au38 were the only clusters that were fully passivated by the thiol monolayer which leaves larger particles vulnerable to etching by excess thiol. The isolated Au38 was characterized by mass spectrometry, thermogravimetric analysis, optical spectroscopy, and electrochemical techniques giving Au38(SC6)22 as the molecular formula for the cluster. These ultrasmall Au clusters behave analogously to molecules with a wide energy gap between occupied (HOMO) and unoccupied levels (LUMO) and undergo single-electron charging at room temperature in electrochemical experiments. Electrochemistry provides an elegant means to study the electronic structure and the chemical stability of the clusters at different charge states. We used cyclic voltammetry and scanning electrochemical microscopy to unequivocally demonstrate that Au38 can be reversibly oxidized to charge states z = +1 or +2; however, reduction to z = -1 leads to desorption of the protecting thiolate monolayer. Although this reductive desorption of thiol from the cluster surface is superficially analogous to electrochemical desorption of planar self-assembled monolayers (SAMs) from macroscopic electrodes, the molecular details of the process are likely to be complicated based on the current view that the thiolate monolayer in clusters is in fact composed of polymeric Au-S complexes.

Stable dispersions of molecularlike aggregates of CdTe quantum dots are prepared by chemical cross-linking. Cryo-TEM images confirm the presence of cross-linked quantum dots and show that the size of the small aggregates can be controlled by the amount of cross-linker added. Optical measurements reveal two types of interdot interactions within these quantum-dot molecules: exciton energy transfer and electronic coupling. Quantitative information on the energy transfer rates in quantum-dot molecules is obtained by photoluminescence lifetime measurements. The degree of electronic coupling is dependent on the size of the quantum dots, which is supported by quantum mechanical calculations.

The synthesis of a variety of benzophosphepine complexes [R = Ph, t-Bu, Me; ML(n )()= W(CO)(5), Mo(CO)(5), Cr(CO)(5), Mn(CO)(2)Cp] by two successive hydrophosphinations of 1,2-diethynylbenzene is discussed in detail. The first hydrophosphination step proceeds at ambient temperature without additional promoters, and subsequent addition of base allows full conversion to benzophosphepines. Novel benzeno-1,4-diphosphinanes were isolated as side products. The benzophosphepine complexes themselves serve as convenient phosphinidene precursors at elevated, substituent-dependent temperatures (>55 degrees C). Kinetic and computational analyses support the proposal that the phosphepine-phosphanorcaradiene isomerization is the rate-determining step. In the absence of substrate, addition of the transient phosphinidene to another benzophosphepine molecule is observed, and addition to 1,2-diethynylbenzene furnishes a delicate bidentate diphosphirene complex.

Bifunctional 2-ureido-4[1H]-pyrimidinone (UPy) derivatives can form small cyclic oligomers as well as long supramolecular polymers in chloroform solutions using the quadruple hydrogen-bonding motif. Ring-chain equilibria of a set of supramolecular monomers containing methyl-substituted alkyl linkers between the hydrogen-bonding UPy moieties were investigated by (1)H NMR spectroscopy and viscometry. The data were characterized in terms of critical concentration (CC, denoting the onset of polymerization) and equilibrium cyclic dimer concentration (EDC, representing preorganization of the monomer toward selective formation of cyclic dimer). Methyl substituents in the monomer were found to promote conformations favorable for cyclic dimerization, leading to an increase in both the EDC and the CC with respect to unsubstituted monomer. Furthermore, we observed an odd-even effect in the CC and EDC with increasing length of the linker between the hydrogen-bonding units. The combined results allow tuning of the critical concentration over a broad range and offer detailed information on the correlation between monomer structure, conformation, and polymerizability which may provide new insights for the study and design of other ring-chain equilibria or helix-random coil transitions.

The reactivity of the bifunctionalized ligand NC(Br)N-I 1 [IC(6)H(2)(CH(2)NMe(2))(2)-3,5-Br-4] has been studied as a versatile synthon for organic and/or organometallic synthesis. Chemoselective metalation (M = Pd, Pt, Li) at the C(aryl)-I or C(aryl)-Br bonds was achieved by choosing the appropriate metal precursors. In this way a series of Pt(II) and Pd(II) complexes were prepared that have a second functional group available for further reactions. These Pt(II) and Pd(II) complexes were subjected to a wide range of organic and organometallic reactions, revealing the remarkable stability of their M-C sigma-bond and opening an easy route for the synthesis of mono- and (hetero)bimetallic building blocks. The scope of the chemistry of such building blocks shows that they are good candidates for use in the synthesis of dendrimers, bioorganometallic systems, or polymetallic materials. The X-ray crystal structures of the most representative complexes (2, 3a, 19, 20, and 24) are also reported.

The effects of metal particle size in catalysis are of prime scientific and industrial importance and call for a better understanding. In this paper the origin of the cobalt particle size effects in Fischer-Tropsch (FT) catalysis was studied. Steady-State Isotopic Transient Kinetic Analysis (SSITKA) was applied to provide surface residence times and coverages of reaction intermediates as a function of Co particle size (2.6-16 nm). For carbon nanofiber supported cobalt catalysts at 210 degrees C and H(2)/CO = 10 v/v, it appeared that the surface residence times of reversibly bonded CH(x) and OH(x) intermediates increased, whereas that of CO decreased for small (6 nm) Co particles. A higher coverage of irreversibly bonded CO was found for small Co particles that was ascribed to a larger fraction of low-coordinated surface sites. The coverages and residence times obtained from SSITKA were used to describe the surface-specific activity (TOF) quantitatively and the CH(4) selectivity qualitatively as a function of Co particle size for the FT reaction (220 degrees C, H(2)/CO = 2). The lower TOF of Co particles6 nm is caused by both blocking of edge/corner sites and a lower intrinsic activity at the small terraces. The higher methane selectivity of small Co particles is mainly brought about by their higher hydrogen coverages.

We show that water-edited solid-state NMR spectroscopy allows for probing global protein conformation and residue-specific solvent accessibility in a lipid bilayer environment. The transfer dynamics can be well described by a general time constant, irrespective of protein topology and lipid environment. This approach was used to follow structural changes in response to protein function in the chimeric potassium channel KcsA-Kv1.3. Data obtained as a function of pH link earlier biochemical data to changes in protein structure in a functional bilayer setting.

anti-W(CO)(5)-complexed 9-methyl-9-phosphabicyclo[6.1.0]nonatriene represents a covalently interlocked molecular bevel gear. Correlated movement of the phosphorus atom and the eight-membered ring by way of a "walk" rearrangement makes gear slippage impossible. The gearing motion is transferred to the four-toothed W(CO)(5) propeller connected to the rotating phosphorus atom, enabling a gearing ratio of 2:1 according to B3LYP and Car-Parrinello Molecular Dynamics calculations. Methyl substitution of the eight-membered ring tempers the gearing process, with the PMeW(CO)(5) entity passing the substituted carbon atom only at temperatures above 50 degrees C.

A special in situ PEM fuel cell has been developed to allow X-ray absorption measurements during real fuel cell operation. Variations in both the coverage of O[H] (O[H] indicates O and/or OH) and CO (applying a novel Deltamu(L3) = mu(L3)(V) - mu(L3)(ref) difference technique), as well as in the geometric (EXAFS) and electronic (atomic XAFS) structure of the anode catalyst, are monitored as a function of the current. In hydrogen, the N(Pt)(-)(Ru) coordination number increases much slower than the N(Pt)(-)(Pt) with increasing current, indicating a more reluctant reduction of the surface Pt atoms near the hydrous Ru oxide islands. In methanol, both O[H] and CO adsorption are separately visible with the Deltamu technique and reveal a drop in CO and an increase in OH coverage in the range of 65-90 mA/cm(2). With increasing OH coverage, the Pt-O coordination number and the AXAFS intensity increase. The data allow the direct observation of the preignition and ignition regions for OH formation and CO oxidation, during the methanol fuel cell operation. It can be concluded that both a bifunctional mechanism and an electronic ligand effect are active in CO oxidation from a PtRu surface in a PEM fuel cell.

As-grown single-crystal InP nanowires, covered with a surface oxide, show a photoluminescence efficiency that strongly varies from wire to wire. We show that the luminescence efficiency of single-crystal InP nanowires can be improved by photoassisted wet chemical etching in a butanol solution containing HF and the indium-coordinating ligand trioctylphosphine oxide. Electron-hole photogeneration, electron scavenging, and oxidative dissolution combined with surface passivation by the indium-coordinating ligand are essential elements to improve the luminescence efficiency. Time traces of the luminescence of surface-passivated wires show strong oscillations resembling the on-off blinking observed with single quantum dots. These results reflect the strong influence of a single or a few nonradiative recombination center(s) on the luminescence properties of an entire wire. © 2005 American Chemical Society. U7 - Export Date: 2 August 2010 U7 - Source: Scopus

Selective incorporation of bisurea guests in thermoplastic elastomers with poly(tetrahydrofuran) soft blocks and bisurea containing hard blocks is observed when the distances between the urea groups of host and guest match. The incorporation leads to significant modulation of mechanical properties. With bisurea-functionalized dyes as guests, a strong difference in extractability by detergent solution was shown between dyes differing by just one methylene unit between urea groups. Upon elongation of elastomer films, strong differences in alignability of matching and nonmatching dyes were observed.

X-ray absorption fine structure (XAFS) spectroscopy is used to unravel the structure of homogeneous catalysts in their catalytically active phase (solution), for which other characterization techniques failed in providing detailed structural information. Application of in situ EXAFS shows that the conformation of the allylic fragment of (P-P)Pd(1,1-dimethylallyl) catalytic intermediate complexes in solution (i.e., reaction medium) differs from that in the solid state, dependent on the bidentate ligand. The change in orientation directly explains differences in regioselectivity in the allylic alkylation reaction, displayed by the distinct complexes.