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At least 469 records · Page 26Linked to original sources

PubMed2005

Tailoring the optical property by a three-dimensional epitaxial heterostructure: a case of ZnO/SnO2.

Epitaxial growth, as a best strategy to attain a heterostructure with a well-defined and clean interface, usually takes place on a planar substrate. In this paper, using a ZnO/SnO2 core-shell heterostructure as an example, we demonstrate the possibility of establishing a three-dimensional epitaxial interface between two materials with different crystal systems for the first time and show possible tailoring optical properties by building the heteroepitaxial crystal interface. The characterization results of element mapping, high-resolution transmission electron microscopy, and selected area electric diffraction reveal that the as-prepared ZnO/SnO2 heterostructure has a tetrapod-like ZnO core and a SnO2 shell with 15-30 nm, and their special epitaxial relation is (010)SnO2//(010)ZnO and [100]SnO2//[0001]ZnO. Such three-dimensional epitaxy between the ZnO core and SnO2 shell is quite different from the usual planar epitaxy or three-dimensional epitaxy between materials having the same crystal structure. A rational model of such complicated epitaxy has been proposed through investigating the certain structural comparability between the wurtzite ZnO and rutile SnO2 crystals. The as-prepared T-ZnO/SnO2 epitaxial heterostructure exhibits unique luminescence properties in contrast with individual tetrapod ZnO and SnO2 nanostructures, in which the epitaxial interface induces new luminescence properties. This result may inspire great interest in exploring other complicated epitaxy systems and their potential applications in laser, gas sensor, solar energy conversion, photo catalysis, and nanodevices in the future.

Crystallization↗

PubMed2006

Systems interface biology.

The field of systems biology has attracted the attention of biologists, engineers, mathematicians, physicists, chemists and others in an endeavour to create systems-level understanding of complex biological networks. In particular, systems engineering methods are finding unique opportunities in characterizing the rich behaviour exhibited by biological systems. In the same manner, these new classes of biological problems are motivating novel developments in theoretical systems approaches. Hence, the interface between systems and biology is of mutual benefit to both disciplines.

Gene Expression Regulation↗

PubMed2006

Supramolecular assemblies of a new series of gemini-type schiff base amphiphiles at the air/water interface: in situ coordination, interfacial nanoarchitectures, and spacer effect.

Great interest has been devoted to the gemini amphiphiles because of their unique properties. In this article, we report some interesting properties of the interfacial films formed by a series of newly designed gemini amphiphiles containing the Schiff base moiety. This novel series of gemini amphiphiles with their Schiff base headgroups linked by a hydrophobic alkyl spacer (BisSBC18Cn, n = 2, 4, 6, 8, 10) could be spread to form stable monolayers and coordinated with Cu(Ac)(2) in situ in the monolayer. The alkyl spacer in the amphiphiles has a great effect on the regulation of the properties of the Langmuir monolayers. A maximum limiting molecular area was observed for the monolayers of the gemini amphiphile with the spacer length of hexa- or octamethylene groups. Both the monolayers on water and on the aqueous Cu(Ac)(2) subphase were transferred onto solid substrates, and different morphologies were observed for films with different spacers. Nanonail and tapelike morphologies were observed for amphiphile films with shorter spacers (n = 2 and 4) on the water surface. Wormlike morphologies were observed for gemini films with longer spacers of C(8) and C(10) when coordinated with Cu(Ac)(2). An interdigitated layer structure was supposed to form in the multilayer films transferred from water or the aqueous Cu(Ac)(2) subphase.

Journal Article↗

PubMedDate not supplied

The application of the acoustic spectrophonometer to biomolecular spectrometry: a step towards acoustic "fingerprinting".

A tunable acoustic biosensor for investigating the properties of biomolecules at the solid-liquid interfaces is described. In its current, format the device can be tuned to frequencies between 6.5 MHz and 1.1 GHz in order to provide a unique detection feature: a variable evanescent wave thickness at the sensor surface. The key to its successful implementation required the careful selection of antennae designs that could induce shear acoustic waves at the solid-liquid interface. This non-contact format makes it possible to recover resonant shear acoustic waves over 100 different harmonic frequencies as a result of the electrical characteristics of the spiral coil. For testing this multifrequency sensing concept the surface of a quartz disc was exposed to solutions of immunoglobulin G (IgG) to form an adsorbed monolayer, whence protein A and IgG were added again in order to form multilayers. Spectra at frequencies between 6 and 600 MHz were generated for each successive layer and revealed two characteristic phases: an initial phase at the low megahertz frequencies consistent with the conventional Sauerbrey relation, and a possible additional phase towards the high megahertz to gigahertz frequencies, that we believe relates to the structure of the biomolecular film. This two-phase behaviour evident from differences between high and low frequencies, rather than from any distinct frequency transition, was anticipated from the reduction in evanescent wave thickness down to nanometre dimensions, and thin film resonance phenomena that are known to occur for film and fluid systems. These measurements suggested that the single element acoustic biosensor we present here may form the basis from which to generate acoustic molecular spectra, or "acoustic fingerprints", in a manner akin to optical spectroscopy.

Acoustics↗

PubMed2005

Blood-brain barrier genomics, proteomics, and new transporter discovery.

The blood-brain barrier (BBB) is an impermeable cellular interface that physically separates the blood from the interstices of the brain. The endothelial cells lining the brain blood vessels form the principle barrier, and their unique phenotype is a consequence of dynamic interactions with several perivascular cell types present in the brain parenchyma. In addition, BBB dysfunction has been observed in the large majority of neurological diseases, but the causes of aberrant vascular behavior are generally unknown. Because of its barrier phenotype, drug delivery to the brain has also proven to be a very difficult task. Global genomics and proteomics analyses are currently being used to examine BBB function in healthy and diseased brain to better characterize this dynamic interface. It is becoming increasingly evident that these approaches have the potential to clarify the unique attributes of a healthy BBB, to identify therapeutic targets in diseased brain, and to identify novel conduits for noninvasive delivery of drugs against these targets. This review will discuss the application of genomics and proteomics to blood-brain barrier research and will offer views on the prospects of such approaches.

Animals↗

PubMed1999

In vitro assessment of endothelial cell adhesion mechanism on vascular patches.

Endothelial cell (EC) seeding of small caliber vascular grafts prior to their implantation has proved to significantly improve long-term patency in humans. We have previously demonstrated that a monolayer of EC could be obtained on type I collagen-coated knitted ultrathin polyster grafts (InterVascular, La Ciotat, France). Thus, the aim of the present work was to understand the nature of cell adhesion mechanisms involved in the cell /biomaterial interface, using HemaCarotid (InterVascular) patches made of type I collagen-coated knitted ultrathin polyster (type I collagen is used to coat patches to attain low permeability). By means of quantitative attachment tests, adhesion blocking assays, RT-PCR for the expression of beta1 integrin mRNA, indirect immunofluorescence with antivinculin antibody, we were able to show that EC are able to adhere to such surfaces by the means (non-unique) of cell surface receptors of the beta1 integrin group. However, the latter are probably downregulated at the cell/biomaterial interface.

Journal Article↗

PubMed2003

Mapping the binding interface between human eukaryotic initiation factors 1A and 5B: a new interaction between old partners.

The translation initiation factors (IFs) IF1/eIF1A and IF2e/IF5B have been conserved throughout all kingdoms. Although the central roles of the bacterial factors IF1 and IF2 were established long ago, the importance of their eukaryotic homologs, eukaryotic IFs (eIFs) eIF1A and eIF5B, has only recently become evident. The translation machinery in eukaryotes is more complex and accordingly, eIF1A and eIF5B seem to have acquired a number of new functions while also retaining many of the roles of bacterial IF1 and IF2. IF1 and IF2 have been shown to interact on the ribosome but no binding has been detected for the free factors. In contrast, yeast eIF1A and eIF5B have been reported to interact in the absence of ribosomes. Here, we have identified the binding interface between human eIF1A and the C-terminal domain of eIF5B by using solution NMR. That interaction interface involves the C termini of the two proteins, which are not present in bacterial IF1 and IF2. The interaction is, therefore, unique to eukaryotes. A structural model for the interaction of eIF1A and eIF5B in the context of the ribosome is presented. We propose that eIF1A and eIF5B simultaneously interact at two sites that are >50 A apart: through their C termini as reported here, and through an interface previously identified in bacterial IF1 and IF2. The binding between the C termini of eIF1A and eIF5B has implications for eukaryote-specific mechanisms of recruitment and release of translation IFs from the ribosome.

Binding Sites↗

PubMed1997

The use of on-line capillary electrophoresis/electrospray ionization with detection via an ion trap storage/reflectron time-of-flight mass spectrometer for rapid mutation-site analysis of hemoglobin variants.

Capillary electrophoresis/electrospray ionization using an ion trap storage/reflectron time-of-flight mass spectrometer detector (CE/ESI-IT/reTOF) is used to provide a rapid and sensitive method for analyzing structural variants in the hemoglobin (Hb) beta-chain. The Hb alpha- and beta-chains are separated and the beta-chain is digested by trypsin. The digest is analyzed by CE/ESI-IT/reTOF where a comparison of the total ion electrophorograms and mass spectra of the mutant and normal hemoglobins (Hbs) can detect the presence of a mutation site. In addition, collision-induced dissociation in the vacuum interface-skimmer region can be used to pinpoint the identity of such a site. The unique capability of the CE/ESI-IT/reTOF system for accurately detecting fast separations with narrow peaks that may be under 1 s full width at half maximum is demonstrated. The speed of this system is essential for resolution of the large number of peaks that are separated in a short time duration using CE separations.

Amino Acid Sequence↗

PubMedDate not supplied

The role of liquid chromatography-mass spectrometry in the determination of heroin and related opioids in biological fluids.

The opioid most commonly sold in the illicit market is heroin. This substance, classified as an analgesic narcotic drug, has an extremely short half-life, and it is rapidly metabolized to 6-monoacetyl-morphine and further to morphine. Morphine is principally metabolized by conjugation to morphine-3 and morphine-6 glucuronides. Morphine itself is a potent analgesic that is frequently used in the pharmacological intervention of cancer pain. The toxicological and clinical evaluation of heroin and morphine have stimulated pharmacokinetic studies in human and animal models. Although a number of methods exist to determine opiates and their metabolites, liquid chromatography (LC) appears to be the technique that can separate without any pretreatment the lipophilic and the hydrophilic analytes of the complete metabolic profile of heroin and/or morphine. Moreover, mass spectrometry (MS) used as a detector for liquid chromatography is unique, because it offers universality and selectivity. Furthermore, efforts have been made to develop LC/MS interfaces that could overcome the previous problem of poor sensitivity. For this reason, in recent years LC combined with MS has been applied to the analysis of opiates--parent drugs and metabolites--in biological fluids. This article reviews the existing literature on the determination, using liquid chromatography coupled to mass spectrometry, of opiate metabolites found in different biological matrices after the administration of the parent compounds.

Body Fluids↗

PubMed1987

Neuropeptide Y, somatostatin, and reduced nicotinamide adenine dinucleotide phosphate diaphorase in the human striatum: a combined immunocytochemical and enzyme histochemical study.

Neuropeptide Y and somatostatin immunoreactive neurons and processes were examined in human striatum using both immunofluorescence and avidin biotin immunoperoxidase methods. Reduced nicotinamide adenine dinucleotide phosphate diaphorase activity was histochemically determined by the reduction of nitro blue tetrazolium. Immunofluorescence using a monoclonal anti-somatostatin antibody and a polyclonal anti-neuropeptide Y antibody, followed by diaphorase histochemistry, showed that these three neurochemical markers are co-localized in a single population of medium-sized aspiny intrinsic neurons. Cells were evenly distributed in clusters throughout the striatum, but fiber density was higher in the nucleus accumbens and ventromedial regions of the caudate and putamen. Double-stained reduced nicotinamide adenine dinucleotide phosphate diaphorase-acetylcholinesterase sections demonstrated that these neurons are located in zones of high acetylcholinesterase activity, often at the interface of these zones with regions of low enzyme activity. These biochemically distinctive neurons are uniquely situated to modulate activity between striatal compartments. Our findings provide new information about the modular organization of the striatum and extend these observations in human brain.

Aged↗

PubMed1995

Complexity and complicity in eclampsia: barriers or bridges?

The aetiology of pre-eclampsia-eclampsia remains largely unclarified, despite over 100 years of systematic study. The assumption that the triggering event is linear and amenable to reductionist techniques has characterized these efforts. The main purpose of this paper is to show that complexity and complicity characterize most pathophysiological processes in pre-eclampsia-eclampsia, a situation suggesting that similar mechanisms must exist at the origin of the disease. The unique configuration of the intervillous space and the intensity of energy transference through the fetomaternal interface offer many dysfunctional possibilities, even in clinically normal pregnancies. The most characteristic seem to be: the shedding and deportation of trophoblast, the fragmentation of villi, the escape of fetal blood, and events associated with trophoblast damage, degeneration and death. The pathogenic potential of these natural processes seems to depend on the association with amplifiers and permissive factors, which vary from person to person and from time to time. Thus, considering the convergence of multiple factors and the presence of nonlinearity in some of their interactions as a plausible working hypothesis, further exploration on this subject should adhere to the rules of this different reality. To find the best possible method of inquiry and to recognize its limitations will be the surest way to avoid failure.

Chorionic Villi↗

PubMed1999

Helianthus tuberosus lectin reveals a widespread scaffold for mannose-binding lectins.

BACKGROUND: Heltuba, a tuber lectin from the Jerusalem artichoke Helianthus tuberosus, belongs to the mannose-binding subgroup of the family of jacalin-related plant lectins. Heltuba is highly specific for the disaccharides Man alpha 1-3Man or Man alpha 1-2Man, two carbohydrates that are particularly abundant in the glycoconjugates exposed on the surface of viruses, bacteria and fungi, and on the epithelial cells along the gastrointestinal tract of lower animals. Heltuba is therefore a good candidate as a defense protein against plant pathogens or predators. RESULTS: The 2.0 A resolution structure of Heltuba exhibits a threefold symmetric beta-prism fold made up of three four-stranded beta sheets. The crystal structures of Heltuba in complex with Man alpha 1-3Man and Man alpha 1-2Man, solved at 2.35 A and 2.45 A resolution respectively, reveal the carbohydrate-binding site and the residues required for the specificity towards alpha 1-3 or alpha 1-2 mannose linkages. In addition, the crystal packing reveals a remarkable, donut-shaped, octahedral assembly of subunits with the mannose moieties at the periphery, suggesting possible cross-linking interactions with branched oligomannosides. CONCLUSIONS: The structure of Heltuba, which is the prototype for an extended family of mannose-binding agglutinins, shares the carbohydrate-binding site and beta-prism topology of its galactose-binding counterparts jacalin and Maclura pomifera lectin. However, the beta-prism elements recruited to form the octameric interface of Heltuba, and the strategy used to forge the mannose-binding site, are unique and markedly dissimilar to those described for jacalin. The present structure highlights a hitherto unrecognized adaptability of the beta-prism building block in the evolution of plant proteins.

Agglutinins↗

PubMed1995

Monovalent cations affect dynamic and functional properties of the tryptophan synthase alpha 2 beta 2 complex.

Monovalent cations affect both conformational and catalytic properties of the tryptophan synthase alpha 2 beta 2 complex from Salmonella typhimurium. Their influence on the dynamic properties of the enzyme was probed by monitoring the phosphorescence decay of the unique Trp-177 beta, a residue located near the beta-active site, at the interface between alpha- and beta-subunits. In the presence of either Li+, Na+, Cs+, or NH4+, the phosphorescence decay is biphasic and the average lifetime increases indicating a decrease in the flexibility of the N-terminal domain of the beta-subunit. Since amplitudes but not lifetimes are affected, cations appear to shift the equilibrium between preexisting enzyme conformations. The effect on the reaction between indole and L-serine was studied by steady state kinetic methods at room temperature. We found that cations: (i) bind to the L-serine--enzyme derivatives with an apparent dissociation constant, measured as the concentration of cation corresponding to one-half of the maximal activity, that is in the millimolar range and decreases with ion size; (ii) increase kcat with the order of efficacy Cs+ > K+ > Li+ > Na+; (iii) decrease KM for indole, Na+ being the most effective and causing a 30-fold decrease; and (iv) cause an increase of the kcat/KM ratio by 20-40-fold. The influence on the equilibrium distribution between the external aldimine and the alpha-aminoacrylate, intermediates in the reaction of L-serine with the beta-subunits of the enzyme, was found to be cation-specific.(ABSTRACT TRUNCATED AT 250 WORDS)

Ammonia↗

PubMed1992

The major piscine liver alcohol dehydrogenase has class-mixed properties in relation to mammalian alcohol dehydrogenases of classes I and III.

The major alcohol dehydrogenase of cod liver has been purified, enzymatically characterized, and structurally analyzed in order to establish original functions and relationships among the deviating classes of the enzyme in mammalian tissues. Interestingly, the cod enzyme exhibits mixed properties--many positional identities with a class III protein, but functionally a class I enzyme--blurring the distinction among the classes of alcohol dehydrogenase. The two domain interfaces, affected by movements upon coenzyme binding, both exhibit substitutions in a manner thus far unique to the cod enzyme. In contrast, coenzyme-binding residues are highly conserved. At the active site, inner and outer parts of the substrate pocket show different extents of amino acid replacement. In total, no less than 7-10 residues of 11 in the substrate binding pocket differ from those of all the mammalian classes, explaining the substrate specificities. However, the inner part of the substrate pocket is very similar to that of the class I enzymes, which is compatible with the observed characteristics of the cod enzyme: ethanol is an excellent substrate (Km = 1.2 mM) and 4-methylpyrazole is a strong inhibitor (Ki = 0.1 microM). These values are about as low as those typical for the ethanol-active class I mammalian enzyme and do not at all resemble those for class III, for which ethanol is hardly a substrate and pyrazole is hardly an inhibitor. Further out in the substrate pocket, several residues differ from the mammalian classes, affecting large substrates.(ABSTRACT TRUNCATED AT 250 WORDS)

Alcohol Dehydrogenase↗

PubMed2005

Localized influence of 2'-hydroxyl groups and helix geometry on protein recognition in the RNA major groove.

The local geometry of a DNA helix can influence protein recognition, but the sequence-specific features that contribute to helix structure are not fully understood, and even less is known about how RNA helix geometry may affect protein recognition. To begin to understand how local or global helix structure may influence binding in an RNA model system, we generated a series of DNA analogues of HIV and BIV TAR RNAs in which ribose sugars were systematically substituted in and around the known binding sites for argininamide and a BIV Tat arginine-rich peptide, respectively, and measured their corresponding binding affinities. For each TAR interaction, binding occurs in the RNA major groove with high specificity, whereas binding to the all-DNA analogue is weak and nonspecific. Relatively few substitutions are needed to convert either DNA analogue of TAR into a high-affinity binder, with the ribose requirements being restricted largely to regions that directly contact the ligand. Substitutions at individual positions show up to 70-fold differences in binding affinity, even at adjacent base pairs, while two base pairs at the core of the BIV Tat peptide-RNA interface are largely unaffected by deoxyribose substitution. These results suggest that the helix geometries and unique conformational features required for binding are established locally and are relatively insulated from effects more than one base pair away. It seems plausible that arginine-rich peptides are able to adapt to a mosaic helical architecture in which segments as small as single base steps may be considered as modular recognition units.

Amino Acid Motifs↗

PubMed1996

Flavin reductase P: structure of a dimeric enzyme that reduces flavin.

We report the structure of an NADPH:FMN oxidoreductase (flavin reductase P) that is involved in bioluminescence by providing reduced FMN to luciferase. The 1.8 A crystal structure of flavin reductase P from Vibrio harveyi was solved by multiple isomorphous replacement and reveals that the enzyme is a unique dimer of interlocking subunits, with 9352 A2 of surface area buried in the dimer interface. Each subunit comprises two domains. The first domain consists of a four-stranded antiparallel beta-sheet flanked by helices on either side. The second domain reaches out from one subunit and embraces the other subunit and is responsible for interlocking the two subunits. Our structure explains why flavin reductase P is specific for FMN as cofactor. FMN is recognized and tightly bound by a network of 16 hydrogen bonds, while steric considerations prevent the binding of FAD. A flexible loop containing a Lys and an Arg could account for the NADPH specificity. The structure reveals information about several aspects of the catalytic mechanism. For example, we show that the first step in catalysis, which is hydride transfer from C4 of NADPH to cofactor FMN, involves addition to the re face of the FMN, probably at the N5 position. The limited accessibility of the FMN binding pocket and the extensive FMN-protein hydrogen bond network are consistent with the observed ping-pong bisubstrate--biproduct reaction kinetics. Finally, we propose a model for how flavin reductase P might shuttle electrons between NADPH and luciferase.

Binding Sites↗

PubMed2001

Explosions and blast injuries.

Powerful explosions have the potential to inflict many different types of injuries on victims, some of which may be initially occult. Flying debris and high winds commonly cause conventional blunt and penetrating trauma. Injuries caused by blast pressures alone result from complex interactions on living tissues. Interfaces between tissues of different densities or those between tissues and trapped air result in unique patterns of organ damage. These challenge out-of-hospital personnel, emergency physicians, and trauma surgeons to specifically seek evidence of these internal injuries in individuals with multiple trauma, adjust management considerations to avoid exacerbation of life-threatening problems caused by the blast wave itself, and ensure appropriate disposition of these patients in possible mass-casualty situations. Knowledge of the potential mechanisms of injury, early signs and symptoms, and natural courses of these problems will greatly aid the management of blast-injured patients.

Biomechanical Phenomena↗

PubMed1978

Interactive computer surface graphics approach to study of the active site of bovine trypsin.

A descriptive medium for the presentation of protein structure has been developed and used to evaluate the structure of the active site of bovine trypsin (EC 3.4.21.4). This technique, involving advanced computer graphics technology, permits the facile display of a representation of the molecular surface of proteins of known structure and employs color to code the structural or chemical features of this surface. Benzamidine derivatives were inserted into the benzamidine-binding site of trypsin and the binary inhibitor-trypsin complex was evaluated by using the computer-generated structure. On the basis of qualitative assessments of the contribution of electrostatic and hydrophobic forces to the binding energy associated with complex formation, we made predictions concerning the effects of interaction of benzamidine substituents and amino acid side chains upon the binding energy associated with inhibitor-protein binding. The computer display of the molecular surfaces of the binary complex of substituted benzamidines and trypsin permitted unique insight into the identity and chemical properties of the atoms that participate at the interface of the molecular surfaces of the inhibitor and the protein. The computer-generated molecular surface display can potentially be combined with quantitative definition of the physical forces involved in the interaction of molecular surfaces. This technology should facilitate the study of the structure-activity relationship of substrates, inhibitors, and drugs that bind to proteins of known three-dimensional structure.

Animals↗