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Substrate Interactions (substrate + interaction)

Distribution by Scientific Domains

Chemistry	42%
Polymers and Materials Science	26%
Life Sciences	21%
Medical Sciences	10%

Selected Abstracts

Balancing Intermolecular and Molecule,Substrate Interactions in Supramolecular Assemblies

ADVANCED FUNCTIONAL MATERIALS, Issue 2 2009
Dimas G. de Oteyza
Abstract Self-assembly of functional supra-molecular nanostructures is among the most promising strategies for further development of organic electronics. However, a poor control of the interactions driving the assembling phenomena still hampers the tailored growth of designed structures. Here exploration of how non-covalent molecule-substrate interactions can be modified on a molecular level is described. For that, mixtures of DIP and F16CuPc, two molecules with donor and acceptor character, respectively are investigated. A detailed study of their structural and electronic properties is performed. In reference to the associated single-component layers, the growth of binary layers results in films with strongly enhanced intermolecular interactions and consequently reduced molecule-substrate interactions. This new insight into the interplay among the aforementioned interactions provides a novel strategy to balance the critical interactions in the assembly processes by the appropriate choice of molecular species in binary supra-molecular assemblies, and thereby control the self-assembly of functional organic nanostructures. [source]

Cell Shape Normalization, Dendrite Orientation, and Melanin Production of Normal and Genetically Altered (Haploinsufficient NF1)-Melanocytes by Microstructured Substrate Interactions

CHEMPHYSCHEM, Issue 1 2004
Simon Jungbauer
Abstract Little is known about how functional regulation failure in genetically altered cells is influenced by topographical confinement of cells, a situation often present in tissues in vivo. We used cultured melanocytes derived from human skin samples as a model system for such investigations. Normal melanocytes have a very well defined shape consisting of a cell body and two dendrites arranged 180° relative to each other. In contrast, neurofibromin 1-melanocytes (NF1-melanocytes) have up to a 50,% reduction of neurofibromin 1, which results in an altered morphology that can be easily measured. NF1-melanocytes deviate from the defined structure of normal melanocytes by forming more than two dendrites per cell. We show that morphology consequences of genetically altered melanocytes can be canceled if cells interact with substrates microstructured by stripes that apply mechanophysical signals in the form of physical topography. The strength of the mechanophysical signal was varied systematically by increasing the height of the microstructures. Melanocytes respond to surface topographical features that are larger than 50 nm and have lateral confinements smaller 4 ,m. The response of normal and NF1-melanocytes to different topographies was analyzed quantitatively by determining density distributions for the number of dendrites per cell, the angles between dendrites, and the orientation imprinted in the substrate. The synthesis of melanin, a pigment produced by melanocytes, differs in the case of genetically altered NF1- and normal melanocytes. In both cases, the interaction with microstripes enhanced melanin production significantly. This enhanced melanin production is speculated to be caused by the mechanical stabilization of the dendrites by substrate guidance. [source]

Substrate interactions of the electroneutral Na+ -coupled inorganic phosphate cotransporter (NaPi-IIc)

THE JOURNAL OF PHYSIOLOGY, Issue 17 2009
Chiara Ghezzi
The SLC34 solute carrier family comprises the electrogenic NaPi-IIa/b and the electroneutral NaPi-IIc, which display Na+ : Pi cotransport stoichiometries of 3 : 1 and 2 : 1, respectively. We previously proposed that NaPi-IIc lacks one of the three Na+ interaction sites hypothesised for the electrogenic isoforms, but, unlike NaPi-IIa/b, its substrate binding order is undetermined. By expressing NaPi-IIc in Xenopus oocytes, isotope influx and efflux assays gave results consistent with Na+ being the first and last substrate to bind. To further investigate substrate interactions, we applied a fluorometry-based technique that uses site-specific labelling with a fluorophore to characterize substrate-induced conformational changes. A novel Cys was introduced in the third extracellular loop of NaPi-IIc that could be labelled with a reporter fluorophore (MTS-TAMRA). Although labelling resulted in suppression of cotransport as previously reported for the electrogenic isoforms, changes in fluorescence were induced by changes in extracellular Na+ concentration in the absence of Pi and by changes in extracellular Pi concentration in presence of Na+. These data, combined with 32P uptake data, also support a binding scheme in which Na+ is the first substrate to interact. Moreover, the apparent Pi affinity from fluorometry agreed with that from 32P uptake, confirming the applicability of the fluorometric technique for kinetic studies of electroneutral carriers. Analysis of the fluorescence data showed that like the electrogenic NaPi-IIb, 2 Na+ ions interact cooperatively with NaPi-IIc before Pi binding, which implies that only one of these is translocated. This result provides compelling evidence that SLC34 proteins share common motifs for substrate interaction and that cotransport and substrate binding stoichiometries are not necessarily equivalent. [source]

Physical attachment of fluorescent protein particles to atomic force microscopy probes in aqueous media: Implications for surface pH, fluorescence, and mechanical properties studies

MICROSCOPY RESEARCH AND TECHNIQUE, Issue 8 2010
Susana Moreno-Flores
Abstract Transfer of a fluorescently labeled protein particle from a surface to a microsized scanning probe has been induced by repetitive scanning in aqueous medium. The so-attached particle can in turn act as a probing tool to study particle,substrate and particle,particle interactions. Attachment of the fluorescent particle occurs at the apical region of an atomic force microscope (AFM) cantilever tip and it endures repetitive loading,unloading cycles against the sample surface. Fluorescence microscopy has been used to address the exact location of the attached particle in the cantilever and to identify the moment when the particle contacts the sample. Moreover, we have observed that fluorescence intensity at the contact point is lower when the probing particle contacts another fluorescent particle than when it contacts the nonfluorescent substrate. The change in fluorescence is attributed to local changes of pH and interparticle-quenching of fluorophores in the contact region. These findings are promising since they constitute a chemical-free way to attach bioparticles to AFM probes under fisiological conditions. The atomic force microscopy combined with fluorescence microscopy provides a straight forward method to study particle/particle and particle/substrate interactions, as well as to investigate mechanical properties of biocolloids. Microsc. Res. Tech. 73:746,751, 2010. © 2009 Wiley-Liss, Inc. [source]

Silver Nanoparticles with Controlled Dispersity and Their Assembly into Superstructures

ADVANCED ENGINEERING MATERIALS, Issue 5 2010
Karsten Moh
In this paper we report on the influence of particle size distribution, particle substrate interaction, and drying behavior on the self-assembly process using ligand stabilized silver particles. Two-dimensional particle arrays were characterized using transmission electron microscopy and extensive image analysis. The formation of such structures was observed in situ using an environmental scanning electron microscope in WET-STEM mode. The results confirm that a small particle size distribution is crucial for the formation of regular particle patterns with long range order, but also the particle substrate interaction and the particle density have an influence on the degree of ordering. Additionally, we find that separated binary particle assemblies keep the orientation of their two-dimensional hexagonal lattices over alternating domains of small and big particles. This is probably enabled due to the formation of dislocations and a small change of the course of the lattice lines within the respective boundary. [source]

Intracellular signaling involved in macrophage adhesion and FBGC formation as mediated by ligand,substrate interaction

JOURNAL OF BIOMEDICAL MATERIALS RESEARCH, Issue 4 2002
Weiyuan John Kao
Abstract Fibronectin and RGD- and/or PHSRN-containing oligopeptides were preadsorbed onto physicochemically distinct substrata: polyethyleneglycol-based networks or tissue culture polystyrene (TCPS). The role of selected signaling kinases (namely protein tyrosine kinases, protein serine/threonine kinases, PI3-kinase, Src, and MAPK) in the adhesion of human primary blood-derived macrophages and the formation of foreign-body giant cells (FBGC) on these modified substrata was investigated. The involvement of individual intracellular signaling molecules in mediating macrophage adhesion dynamically varied with the culture time, substrate, and ligand. For example, fibronectin on TCPS or networks involved similar signaling events for macrophage adhesion; however, fibronectin and G3RGDG6PHSRNG, but not peptides with other RGD and/or PHSRN orientations, mediated similar signaling events for macrophage adhesion on TCPS but mediated different signaling events on networks. Depending on the substrate, a specific molecule (i.e., Src, protein kinase C) within the protein tyrosine kinase or protein serine/threonine kinase family was either an antagonist or agonist in mediating FBGC formation. © 2002 Wiley Periodicals, Inc. J Biomed Mater Res 62: 478,487, 2002 [source]

Insights into the anthrax lethal factor,substrate interaction and selectivity using docking and molecular dynamics simulations

PROTEIN SCIENCE, Issue 8 2009
Georgios A. Dalkas
Abstract The anthrax toxin of the bacterium Bacillus anthracis consists of three distinct proteins, one of which is the anthrax lethal factor (LF). LF is a gluzincin Zn-dependent, highly specific metalloprotease with a molecular mass of ,90 kDa that cleaves most isoforms of the family of mitogen-activated protein kinase kinases (MEKs/MKKs) close to their amino termini, resulting in the inhibition of one or more signaling pathways. Previous studies on the crystal structures of uncomplexed LF and LF complexed with the substrate MEK2 or a MKK-based synthetic peptide provided structure-activity correlations and the basis for the rational design of efficient inhibitors. However, in the crystallographic structures, the substrate peptide was not properly oriented in the active site because of the absence of the catalytic zinc atom. In the current study, docking and molecular dynamics calculations were employed to examine the LF-MEK/MKK interaction along the catalytic channel up to a distance of 20 Å from the zinc atom. This residue-specific view of the enzyme-substrate interaction provides valuable information about: (i) the substrate selectivity of LF and its inactivation of MEKs/MKKs (an issue highly important not only to anthrax infection but also to the pathogenesis of cancer), and (ii) the discovery of new, previously unexploited, hot-spots of the LF catalytic channel that are important in the enzyme/substrate binding and interaction. [source]

Substrate interactions of the electroneutral Na+ -coupled inorganic phosphate cotransporter (NaPi-IIc)

Modification of Supramolecular Binding Motifs Induced By Substrate Registry: Formation of Self-Assembled Macrocycles and Chain-Like Patterns

CHEMISTRY - A EUROPEAN JOURNAL, Issue 42 2009
Leslie-Anne Fendt
Abstract The self-assembly properties of two ZnII porphyrin isomers on Cu(111) are studied at different coverage by means of scanning tunneling microscopy (STM). Both isomers are substituted in their meso -positions by two voluminous 3,5-di(tert -butyl)phenyl and two rod-like 4,-cyanobiphenyl groups, respectively. In the trans -isomer, the two 4,-cyanobiphenyl groups are opposite to each other, whereas they are located at right angle in the cis -isomer. For coverage up to one monolayer, the cis- substituted porphyrins self-assemble to form oligomeric macrocycles held together by antiparallel CN,,,CN dipolar interactions and CN,,,H-C(sp2) hydrogen bonding. Cyclic trimers and tetramers occur most frequently but everything from cyclic dimers to hexamers can be observed. Upon annealing of the samples at temperatures >150,°C, dimeric macrocyclic structures are observed, in which the two porphyrins are bridged by Cu atoms, originating from the surface, under formation of two CN,,,Cu,,,NC coordination bonds. The trans -isomer builds up linear chains on Cu(111) at low coverage, whereas for higher coverage the molecules assemble in a periodic, densely packed structure. Both cis - and trans -bis(4,-cyanobiphenyl)-substituted ZnII porphyrins behave very differently on Cu(111) compared to similar porphyrins in literature on less reactive surfaces such as Au(111) and Ag(111). On the latter surfaces, there is no signal visible between molecular orientation and the crystal directions of the substrate, whereas on Cu(111), very strong adsorbate,substrate interactions have a dominating influence on all observed structures. This strong porphyrin,substrate interaction enables a much broader variety of structures, including also less favorable intermolecular bonding motifs and geometries. [source]

Transition-State Energy and Position along the Reaction Coordinate in an Extended Activation Strain Model,

CHEMPHYSCHEM, Issue 8 2007
G. Theodoor de Jong Dr.
Abstract We investigate palladium-induced activation of the CH, CC, CF, and CCl bonds in methane, ethane, cyclopropane, fluoromethane, and chloromethane, using relativistic density functional theory (DFT) at ZORA-BLYP/TZ2P. Our purpose is to arrive at a qualitative understanding, based on accurate calculations, of the trends in activation barriers and transition state (TS) geometries (e.g. early or late along the reaction coordinate) in terms of the reactants' properties. To this end, we extend the activation strain model (in which the activation energy ,E, is decomposed into the activation strain ,E,strain of the reactants and the stabilizing TS interaction ,E,int between the reactants) from a single-point analysis of the TS to an analysis along the reaction coordinate ,, that is, ,E(,)=,Estrain(,)+,Eint(,). This extension enables us to understand qualitatively, trends in the position of the TS along , and, therefore, the values of the activation strain ,E,strain=,Estrain(,TS) and TS interaction ,E,int=,Eint(,TS) and trends therein. An interesting insight that emerges is that the much higher barrier of metal-mediated CC versus CH activation originates from steric shielding of the CC bond in ethane by CH bonds. Thus, before a favorable stabilizing interaction with the CC bond can occur, the CH bonds must be bent away, which causes the metal,substrate interaction ,Eint(,) in CC activation to lag behind. Such steric shielding is not present in the metal-mediated activation of the CH bond, which is always accessible from the hydrogen side. Other phenomena that are addressed are anion assistance, competition between direct oxidative insertion (OxIn) versus the alternative SN2 pathway, and the effect of ring strain. [source]

Advanced glycation endproducts: what is their relevance to diabetic complications?

DIABETES OBESITY & METABOLISM, Issue 3 2007
N. Ahmed
Glycation is a major cause of spontaneous damage to proteins in physiological systems. This is exacerbated in diabetes as a consequence of the increase in glucose and other saccharides derivatives in plasma and at the sites of vascular complications. Protein damage by the formation of early glycation adducts is limited to lysine side chain and N-terminal amino groups whereas later stage adducts, advanced glycation endproducts (AGEs), modify these and also arginine and cysteine residues. Metabolic dysfunction in vascular cells leads to the increased formation of methylglyoxal which adds disproportionately to the glycation damage in hyperglycaemia. AGE-modified proteins undergo cellular proteolysis leading to the formation and urinary excretion of glycation free adducts. AGEs may potentiate the development of diabetic complications by activation of cell responses by AGE-modified proteins interacting with specific cell surface receptors, activation of cell responses by AGE free adducts, impairment of protein,protein and enzyme,substrate interactions by AGE residue formation, and increasing resistance to proteolysis of extracellular matrix proteins. The formation of AGEs is suppressed by intensive glycaemic control, and may in future be suppressed by thiamine and pyridoxamine supplementation, and several other pharmacological agents. Increasing expression of enzymes of the enzymatic defence against glycation provides a novel and potentially effective future therapeutic strategy to suppress protein glycation. [source]

Customized Electronic Coupling in Self-Assembled Donor,Acceptor Nanostructures

ADVANCED FUNCTIONAL MATERIALS, Issue 22 2009
Dimas G. de Oteyza
Abstract Charge transfer processes between donor,acceptor complexes and metallic electrodes are at the heart of novel organic optoelectronic devices such as solar cells. Here, a combined approach of surface-sensitive microscopy, synchrotron radiation spectroscopy, and state-of-the-art ab initio calculations is used to demonstrate the delicate balance that exists between intermolecular and molecule,substrate interactions, hybridization, and charge transfer in model donor,acceptor assemblies at metal-organic interfaces. It is shown that charge transfer and chemical properties of interfaces based on single component layers cannot be naively extrapolated to binary donor,acceptor assemblies. In particular, studying the self-assembly of supramolecular nanostructures on Cu(111), composed of fluorinated copper-phthalocyanines (F16CuPc) and diindenoperylene (DIP), it is found that, in reference to the associated single component layers, the donor (DIP) decouples electronically from the metal surface, while the acceptor (F16CuPc) suffers strong hybridization with the substrate. [source]

A Computational Study of the Sub-monolayer Growth of Pentacene

ADVANCED FUNCTIONAL MATERIALS, Issue 13 2006
D. Choudhary
Abstract A computational study of organic thin-film growth using a combination of ab,initio based energy calculations and kinetic Monte Carlo (KMC) simulations is provided. A lattice-based KMC model is used in which binding energies determine the relative rates of diffusion of the molecules. This KMC approach is used to present "landscapes" or "maps" that illustrate the possible structural outcomes of growing a thin film of small organic molecules, represented as a two-site dimer, on a substrate in which the strength of organic,substrate interactions is allowed to vary. KMC provides a mesoscopic-scale view of sub-monolayer deposition of organic thin films on model substrates, mapped out as a function of the flux of depositing molecules and the temperature of the substrate. The morphology of the crystalline thin films is shown to be a strong function of the molecule,molecule and molecule,substrate interactions. A rich variety of maps is shown to occur in which the small organic molecules either stand up or lie down in a variety of different patterns depending on the nature of the binding to the surface. In this way, it is possible to suggest how to tailor the substrate or the small organic molecule in order to create a desired growth habit. In order to demonstrate how this set of allowable maps is reduced in the case where the set of energy barriers between substrate and organic molecule are reliably known, we have used Gaussian,98 calculations to establish binding energies for the weak van der Waals interactions between a),pairs of pentacene molecules as a function of orientation and b),pentacene and two substrates, silicon surfaces passivated with cyclopentene molecules and a crystalline model of silicon dioxide. The critical nucleation size and the mode of diffusion of this idealized two-site dimer model for pentacene molecules are found to be in good agreement with experimental data. [source]

Vinculin, VASP, and profilin are coordinately regulated during actin remodeling in epithelial cells, which requires de novo protein synthesis and protein kinase signal transduction pathways

JOURNAL OF CELLULAR PHYSIOLOGY, Issue 2 2004
Margaret P. Quinlan
Transformation progression of epithelial cells involves alterations in their morphology, polarity, and adhesive characteristics, all of which are associated with the loss and/or reorganization of actin structures. To identify the underlying mechanism of formation of the adhesion-dependent, circumferential actin network, the expression and localization of the actin binding and regulating proteins (ABPs), vinculin, VASP, and profilin were evaluated. Experimental depolarization of epithelial cells results in the loss of normal F-actin structures and the transient upregulation of vinculin, VASP, and profilin. This response is due to the loss of cell,cell, and not cell,substrate interactions, since cells that no longer express focal adhesions or stress fibers are still sensitive to changes in adhesion and manifest this in the altered profile of expression of these ABPs. Transient upregulation is dependent upon de novo protein synthesis, and protein kinase-, but not phosphatase-sensitive signal transduction pathway(s). Inhibition of the synthesis of these proteins is accompanied by dephosphorylation of the ribosomal S6 protein, but does not involve inhibition of the PI3-kinase-Akt-mTOR pathway. Constitutive expression of VASP results in altered cell morphology and adhesion and F-actin and vinculin structures. V12rac1 expressing epithelial cells are constitutively nonadhesive, malignantly transformed, and constitutively express high levels of these ABPs, with altered subcellular localizations. Transformation suppression is accompanied by the restoration of normal levels of the three ABPs, actin structures, adhesion, and epithelial morphology. Thus, vinculin, VASP, and profilin are coordinately regulated by signal transduction pathways that effect a translational response. Additionally, their expression profile maybe indicative of the adhesion and transformation status of epithelial cells. J. Cell. Physiol. 200: 277,290, 2004. © 2004 Wiley-Liss, Inc. [source]

Ribonucleotide activation by enzyme ribonucleotide reductase: Understanding the role of the enzyme

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2004
Nuno M. F. S. A. Cerqueira
Abstract This article focuses on the first step of the catalytic mechanism for the reduction of ribonucleotides catalyzed by the enzyme Ribonucleotide Reductase (RNR). This corresponds to the activation of the substrate. In this work a large model of the active site region involving 130 atoms was used instead of the minimal gas phase models used in previous works. The ONIOM method was employed to deal with such a large system. The results gave additional information, which previous small models could not provide, allowing a much clearer evaluation of the role of the enzyme in this step. Enzyme,substrate interaction energies, specific transition state stabilization, and substrate steric strain energies were obtained. It was concluded that the transition state is stabilized in 4.0 kcal/mol by specific enzyme,substrate interactions. However, this stabilization is cancelled by the cost in conformational energy for the enzyme to adopt the transition state geometry; the overall result is that the enzyme machinery does not lead to a rate enhancement in this step. It was also found that the substrate binds to the active site with almost no steric strain, emphasizing the complementarity and specificity of the RNR active site for nucleotide binding. The main role of the enzyme at the very beginning of the catalytic cycle was concluded to be to impose stereospecifity upon substrate activation and to protect the enzyme radical from the solvent, rather than to be an reaction rate enhancement. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 2031,2037, 2004 [source]

Substrate interactions of the electroneutral Na+ -coupled inorganic phosphate cotransporter (NaPi-IIc)

Self-Assembled Monolayers of Alkoxy-Substituted Octadehydrodibenzo[12]annulenes on a Graphite Surface: Attempts at peri -Benzopolyacene Formation by On-Surface Polymerization

CHEMISTRY - A EUROPEAN JOURNAL, Issue 28 2010
Kazukuni Tahara Dr.
Abstract Self-assembled monolayers of a series of tetraalkoxy-substituted octadehydrodibenzo[12]annulene (DBA) derivatives 1,c,g possessing butadiyne linkages were studied at the 1,2,4-trichlorobenzene (TCB) or 1-phenyloctane/graphite interface by scanning tunneling microscopy (STM). The purpose of this research is not only to investigate the structural variation of two-dimensional (2D) monolayers, but also to assess a possibility for peri -benzopolyacene formation by two-dimensionally controlled polymerization on a surface. As a result, the formation of three structures, porous, linear, and lamella structures, were observed by changing the alkyl chain length and the solute concentration. The formation of multilayers of the lamella structure was often observed for all compounds. The selection of molecular networks is basically ascribed to intermolecular and molecule,substrate interactions per unit area and network density. The selective appearance of the linear structure of 1,d is attributed to favorable epitaxial registry matching between the substrate lattice and the overlayer lattice. Even though the closest interatomic distance between the diacetylenic units of the DBAs in the lamella structure (,0.6,nm) is slightly larger compared to the typical distances necessary for topochemical polymerization, the reactivity toward external stimuli (electronic-pulse irradiation from an STM tip and UV irradiation) was investigated. Unfortunately, no evidence for polymerization of the DBAs on the surface was observed. The present results indicate the necessity for further designing a suitable system for the on-surface construction of structurally novel conjugated polymers, which are otherwise difficult to prepare. [source]

Modification of Supramolecular Binding Motifs Induced By Substrate Registry: Formation of Self-Assembled Macrocycles and Chain-Like Patterns

Bifunctional Catalysis by Natural Cinchona Alkaloids: A Mechanism Explained

CHEMISTRY - A EUROPEAN JOURNAL, Issue 32 2009
Clotilde
Abstract The use of bifunctional chiral catalysts, which are able to simultaneously bind and activate two reacting partners, currently represents an efficient and reliable strategy for the stereoselective preparation of valuable chiral compounds. Cinchona alkaloids such as quinine and quinidine, simple organic molecules generously provided by Nature, were the first compounds to be proposed to operate through a cooperative catalysis. To date, a full mechanistic characterization of the dual catalysis mode of cinchona alkaloids has proven a challenging objective, due to the transient, non-covalent nature of the involved catalyst,substrate interactions. Here, we propose a mechanistic rationale on how natural cinchona alkaloids act as efficient bifunctional catalysts by using a broad range of computational methods, including classical molecular dynamics, a mixed quantum mechanical/molecular mechanics (QM/MM) approach, and correlated ab-initio calculations. We also unravel the origin of enantio- and diastereoselectivity, which is due to a specific network of hydrogen bonds that stabilize the transition state of the rate-determining step. The results are validated by experimental evidence. [source]