It is proven that one endmarker can be eliminated from a stack acceptor without affecting recognition power. It is also noted that both endmarkers can be eliminated from deterministic linear bounded acceptors. (Author)

Comparison of the amino acid sequences of three different proteoglycan core proteins reveals a 12-amino acid sequence that is about 50% homologous among these proteoglycans. In each of the proteoglycans, this sequence surrounds the serine-glycine dipeptide in which the serine is known or presumed to be substituted with a chondroitin/dermatan sulfate glycosaminoglycan chain. Peptides containing ...

BackgroundFor splice site recognition, one has to solve two classification problems: discriminating true from decoy splice sites for both acceptor and donor sites. Gene finding systems typically rely on Markov Chains to solve these tasks.ResultsIn this work we consider Support Vector Machines ...

The enzymatic transfer of activated mannose yields mannosides in glycoconjugates and oligo- and polysaccharides. Yet, despite its biological necessity, the mechanism by which glycosyltransferases recognize mannose and catalyze its transfer to acceptor molecules is poorly understood. Here, we report broad high-throughput screening and kinetic analyses of both natural and ...

A highly colored polystyrene derivative bearing side chain chromophores composed of dialkylanilino donor and cyano-based acceptor groups, prepared by atom-economic click postfunctionalization, displays the dual colorimetric detection behavior of several metal ions based on the specific interactions with different nitrogen atoms. Hard to borderline metal ions, such as Fe(3+) , ...

Noncovalent interactions are significant in facilitating molecular recognition and charge transfer in many enzymatic redox processes at protein-protein interfaces. The design of guest (G) and host (H) molecules, which undergo molecular recognition in solution using hydrogen bonding interactions, provides a means of understanding and controlling the nature ...

Accommodation of donor and acceptor substrates is critical to the catalysis of (thio)phosphoryl group transfer, but there has been no systematic study of donor nucleotide recognition by kinase ribozymes, and there is relatively little known about the structural requirements for phosphorylating internal 2?OH. To address these questions, new ...

222 donor and 222 acceptor (including 206 pairs) non-homologous splicing sites were studied. Well known features of these were confirmed and some novel observations were made. It is (1) cCAGGGag signal in (-60)-(-58) region of acceptor sites; (2) strong complementarity between regions (-69)-(-55) and (-36)-(-22) of ...

The removal of organic compounds from ground water during bioremediation at wood-preserving sites is a function of the stoichiometric demand for electron acceptors (oxygen, nitrate, and sulfate) to metabolize the organic contaminants and the supply of the electron acceptors in th...

BackgroundOne of the challenges of bioinformatics remains the recognition of short signal sequences in genomic DNA such as donor or acceptor splice sites, splicing enhancers or silencers, translation initiation sites, transcription start sites, transcription factor binding ...

A nonconjugated fluorescent molecule with a triarylboron acceptor and an alkylamine donor has been found to display bright green fluorescence due to charge transfer through space, which can be reversibly deactivated by blocking either the donor or acceptor site. Binding of the fluoride ion to boron switches the fluorescence color to ...

Multidrug resistance related to the increased expression of P-glycoprotein (P-gp) by cancer cells is the major contributor for the failure of chemotherapeutic treatments. Starting from pharmacophores and data already published and in macrocyclic diterpenes isolated from Euphorbia species, a comprehensive study of pharmacophore definitions of features was performed in order to obtain a new improved ...

To explore the possibility of using restriction enzymes in a synthetic biology based on artificially expanded genetic information systems (AEGIS), 24 type-II restriction endonucleases (REases) were challenged to digest DNA duplexes containing recognition sites where individual Cs and Gs were replaced by the AEGIS nucleotides Z and P [respectively, ...

To explore the possibility of using restriction enzymes in a synthetic biology based on artificially expanded genetic information systems (AEGIS), 24 type-II restriction endonucleases (REases) were challenged to digest DNA duplexes containing recognition sites where individual Cs and Gs were replaced by the AEGIS nucleotides Z and P [respectively, ...

Transferases of the Fem family catalyse peptide-bond formation by using aminoacyl-tRNAs and peptidoglycan precursors as donor and acceptor substrates, respectively. The specificity of Fem transferases is essential since mis-incorporated amino acids could act as chain terminators thereby preventing formation of a functional stress-bearing peptidoglycan network. Here we have ...

Cholate extracts of murine lymphocytes were shown to contain haemagglutinating activity against autologous erythrocytes. The species specificity and sugar inhibition pattern of the haemagglutinin closely paralleled the specificity of autorosetting, an interaction that had been shown previously to involve the recognition by lymphocytes of carbohydrate structures on autologous ...

This study demonstrates a critical role for N-methylation in cyclosporin biosynthesis and maintenance of the biologically active cyclosporin conformation. The structural requirements for the AdoMet binding to CySyn were defined. N-methylation of specific amide positions in the cyclosporin backbone is critical for the complete assembly and cyclization of the cyclosporin peptide. A maximum of two ...

Ten derivatives of {beta}-carbolines with known affinities to the GABA{sub A}/BDZ (benzodiazepine) receptor were studied using the Am 1 and MNDO/H Semiempirical techniques to identify and characterize molecular modulators of receptor recognition. Steric, lipophilic, and electrostatic properties of these compounds were calculated and examined for their possible role in ...

, but the specific ADP-ribose acceptor sites have remained enigmatic. Here, we show that PARP1 co- valently ADP of H3, as well as K16 of H4 as ADP-ribose acceptor sites. Multiple explicit water molecular dynamics or at their unstructured amino-terminals tails. Moreover, unconfirmed ADP- ribose ...

Propofol is the most widely used injectable general anesthetic. Its targets include ligand-gated ion channels such as the GABA{sub A} receptor, but such receptor-channel complexes remain challenging to study at atomic resolution. Until structural biology methods advance to the point of being able to deal with systems such as the GABA{sub A} receptor, it will be necessary to use more tractable ...

Defining the conditions for coherent site-directed transport from an electron donor to a specific acceptor through tunneling barriers in a network of multiple donor/acceptors sites is an important step toward controlling electronic processes in molecular networks. The required analysis is most challenging since the ...

A scanning-tunneling-microscopy-substitution technique is used to incorporate single Mn atoms into Ga sites in GaAs (110) surfaces. The electronic states near a single Mn in the acceptor configuration produce a strong in-gap resonance associated with the acceptor level. The isolated Mn acceptor is probed in both ...

Oligosaccharyltransferase (OST), an integral component of the endoplasmic-reticulum membrane, catalyses the transfer of dolichyl diphosphate-linked oligosaccharides to specific asparagine residues forming part of the Asn-Xaa-Thr/Ser sequence. We have studied the binding and catalytic properties of the enzyme from pig liver using peptide analogues derived from the acceptor ...

BackgroundWe present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined) weight matrices. Matrices are refined by adding experimentally-defined binding ...

The light chain of botulinum neurotoxin A (BoNT/A-LC) is a zinc-metalloprotease that requires two extended exosites for optimal substrate binding and recognition of its intracellular target SNAP25. CFP and YFP connected through SNAP25 peptide (141�206) containing both exosites (CsY) has been used in a FRET-based assay for BoNT/A. To further improve the FRET efficiency in ...

When human DNA(cytosine-5)methyltransferase was used to methylate a series of snapback oligodeoxy-nucleotides of differing stem lengths, each containing a centrally located CG dinucleotide recognition site, the enzyme required a minimum of 22 base pairs in the stem for maximum activity. Extrahelical cytosines in slipped duplexes that were 30 base pairs in ...

BackgroundVariations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of splice site recognition inconsistently identifies intron-exon boundaries, and cassette exons (CEs) are often caused by variable ...

Ab initio quantum mechanical calculations are used to explore the interaction of dimaprit, a histamine H,-receptor agonist, with a molecular complex designed to model the specific recognition of histamine, and the H{sub 2}-receptor activation mechanism triggered by the binding of the ligand. The stabilization of several isomeric forms of the isothiourea moiety of dimaprit in ...

The steroid receptor interactions in vitro with specific acceptor sites composed of acceptor protein-DNA complexes fulfill many of the criteria of a physiologically significant binding system. Chromatin acceptor sites for many steroid receptors (especially for the progesterone and estrogen ...

Treatment of bovine brain myelin basic protein with 42-kDa mitogen-activated protein kinase [p42 MAPK or extracellular signal-regulated kinase 2 (ERK2)] in the presence of ATP and Mg2+ results in phosphorylation of Thr94 and Thr97. Thr94 is not previously known to be an ERK2 phosphorylation site. Both residues are phosphorylated to about the same extent and are in the highly ...

UDP-GalNAc:polypeptide ?-N-acetylgalactosaminyltransferases (ppGaNTases) initiate the formation of mucin-type, O-linked glycans by catalyzing the transfer of ?-N-acetylgalactosamine from UDP-GalNAc to Ser or Thr residues of core proteins to form the Tn antigen (GalNAc-?-1-O-Ser/Thr). ppGaNTases are unique among glycosyltransferases in containing a C-terminal lectin domain. We present the x-ray ...

azide using a Staudinger ligation with a phosphine conjugate to the FLAG peptide (Figure 4).25 Product-Az by Staudinger ligation. PhBL was used to ligate DTB-Az to p67 acceptor protein. The introduced azide ligation of biotin onto a lysine side chain of a 15-amino acid recognition sequence called the "acceptor

The present invention generally relates to organic polymers able to participate in an analyte-recognition process, where an analyte facilitates an energy transfer between an energy donor and an energy acceptor. Certain embodiments of the invention make us...

... In the test procedure section of this report will discuss the scaling and simplifying assumptions used to go from the full scale Machrihanish site to a ...

... alternate electron acceptors/by-products (NO)-, 5042-, Fe3+, CHa, ethene, and ethane), total organic carbon, alkalinity, chloride, dissolved ...

... the vadose zone and phreatic soils serves as ... Site history and the results of soil and groundwater ... Comparison of BTEX, CAH, electron acceptor, and ...

... general request for potentially interested parties in real-time Ada kernels on the ... the most likely acceptor sites (those who may use the Kernel in their ...

that the glucose binds at the acceptor site of the free enzyme in this case. The binding site for the acceptor in the active site of Escherichia coli -galactosidase was studied by X-ray crystallography and enzyme kinetics. Binding of the competitive inhibitor isopropyl thio- -D-galactoside ...

The FemX_Wv aminoacyl transferase of Weissella viridescens initiates the synthesis of the side chain of peptidoglycan precursors by transferring l-Ala from Ala-tRNA^Ala to UDP-MurNAc-pentadepsipeptide. FemX_Wv is an attractive target for the development of novel antibiotics, since the side chain is essential for the last ...

To maintain functional conformations of DNA and RNA in high-temperature environments, an extremely thermophilic bacterium, Thermus thermophilus, employs a unique polyamine biosynthetic pathway and produces more than 16 types of polyamines. In the thermophile genome, only one spermidine synthase homolog (SpeE) was found and it was shown to be a key enzyme in the pathway. The catalytic assay of the ...

Three cases of MTBE contamination of ground water are presented. Each case site had its own characteristics and different geochemical condition. The first case site was where dissolved oxygen was the dominant electron acceptor, while the sites of the seco...

Three cases of MTBE contamination of ground water are presented. Each case site had own characteristics and different geochemical condition. The first case site was where dissolved oxygen was the dominant electron acceptor, while the sites of the second and third cases were und...

Phosphatidyl-myo-inositol mannosyltransferase A (PimA) is an essential glycosyltransferase (GT) involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIMs), which are key components of the mycobacterial cell envelope. PimA is the paradigm of a large family of peripheral membrane-binding GTs for which the molecular mechanism of substrate/membrane recognition and ...

... of the sites that met his standards for reliability and accuracy. NBC's Today Show (September 30, 2008), " ...

ABSTRACT: BACKGROUND: Cytosine is a biologically important compound owing to its natural occurrence as a component of nucleic acids. Cytosine plays a crucial role in DNA/RNA base pairing, through several hydrogen-bonding patterns, and controls the essential features of life as it is involved in genetic codon of 17 amino acids. The molecular recognition among cytosines, and the ...

Fluorescence resonance energy transfer (FRET) is a process in which energy is transferred nonradiatively from one fluorophore (the donor) in an excited electron state to another, the chromophore (the acceptor). FRET is distinctive in its ability to reveal the presence of specific recognition of select targets such as the nerve agent stimulant Methyl ...

The recognition properties of DNA duplexes containing single or triple incorporations of eight different donor-modified (OMe, NH(2)) and acceptor-modified (NO(2)) biphenyl residues as base replacements in opposite positions were probed by UV-melting and by CD and fluorescence spectroscopy. We found a remarkable dependence of duplex stability on the natures ...

BackgroundThe splicing of pre-mRNAs is conspicuously often variable and produces multiple alternatively spliced (AS) isoforms that encode different messages from one gene locus. Computational studies uncovered a class of highly similar isoforms, which were related to tandem 5'-splice sites (5'ss) and 3'-splice sites (3'ss), yet with very sparse anecdotal ...

Sucrose phosphorylase catalyzes the O-glucosylation of a wide range of acceptor substrates. Acceptors presenting a suitable 1,2-diol moiety are glucosylated exclusively at the secondary hydroxyl. Production of the naturally occurring compatible solute, 2-O-alpha-d-glucopyranosyl-sn-glycerol, from sucrose and glycerol is a notable industrial realization of ...

Photoluminescence spectroscopy of nitrogen-related emissions in ZnO is used to establish the ionization energy of the substitutional nitrogen acceptor. The temperature dependence of the nitrogen-related electron-acceptor (e,A0) emission band has been monitored in as-grown single crystals of ZnO. Line shape analysis of this band is used to determine the ...

Chiral discrimination in electronic energy-transfer processes is investigated for a series of systems in which the energy donors and acceptors are dissymmetric metal complexes. The sample systems contain a racemic mixture of luminescent donor complexes in solution with an enantiomerically resolved concentration of nonluminescent acceptor complexes. Chiral ...

We studied the doping with Si and Be of GaAs nanowires (NWRs) grown by molecular beam epitaxy. Regarding the NW morphology, no influence was observed for Si doping but high Be doping concentrations cause a kinking and tapering of the NWRs. We investigated local vibrational modes by means of resonant Raman scattering to determine the incorporation sites of the dopant atoms. For ...

We report herein a method for the ultra-trace detection of TNT on p-aminothiophenol-functionalized silver nanoparticles coated on silver molybdate nanowires based on surface-enhanced Raman scattering (SERS). The method relies on ?-donor-acceptor interactions between the ?-acceptor TNT and the ?-donor p,p'-dimercaptoazobenzene (DMAB), with the latter ...

Facial Recognition. Face Perception and Recognition Laboratories � Face Lab - UWA Department of Psychology � The Noh Mask Effect: An Illusion of Facial ...

... 3H]ACh recognition sites in brain. Repeated injections of nicotine for 5-21 days increase the number of [ 3H]ACh recognition ...

... DTIC Online - This search queries the DTIC Online Public Web site. ... Title : Learning and Recognition of US, Soviet and Pictographic Military ...

... laboratory community or other sites identified as related to S & T organizations. ... Title : Distortion-Invariant Pattern Recognition in Non-Random Noise ...

... S&T - Allows users to query the DoD laboratory community or other sites identified as related to S ... Title : Distance Measures for Speech Recognition. ...

UDP-GalNAc:polypeptide alpha-N-acetylgalactosaminyltransferases (GalNAc-Ts) constitute a family of up to 20 transferases that initiate mucin-type O-glycosylation. The transferases are structurally composed of catalytic and lectin domains. Two modes have been identified for the selection of glycosylation sites by GalNAc-Ts: confined sequence recognition by ...

UDP-GalNAc:polypeptide ?-N-acetylgalactosaminyltransferases (GalNAc-Ts) constitute a family of up to 20 transferases that initiate mucin-type O-glycosylation. The transferases are structurally composed of catalytic and lectin domains. Two modes have been identified for the selection of glycosylation sites by GalNAc-Ts: confined sequence recognition by the ...

Bacterial dd-peptidases, the targets of beta-lactam antibiotics, are believed to catalyze d-alanyl-d-alanine carboxypeptidase and transpeptidase reactions in vivo. To date, however, there have been few concerted attempts to explore the kinetic and thermodynamic specificities of the active sites of these enzymes. We have shown that the peptidoglycan-mimetic peptide, ...

Processes occurring during mechanochemical activation (MA) of {gamma}-Al{sub 2}O{sub 3} are studied by physicochemical methods. As a result of MA, the surface concentration of coordinatively unsaturated aluminum ions falls. The concentration of strong Lewis acid sites decreases by two orders of magnitude, and that of weak Lewis centers falls several times, whereas the bulk ...

Proton-coupled electron transfer (PCET) reactions occur in many biological and artificial solar energy conversion processes. In these reactions the electron is often transferred to a site distant to the proton acceptor site. In this work, we employ the dual descriptor and the electrophilic Fukui function from density functional ...

We examined the catalytic cycle of transaldolase (TAL) from Thermoplasma acidophilum by cryocrystallography and were able to structurally characterize-for the first time, to our knowledge-different genuine TAL reaction intermediates. These include the Schiff base adducts formed between the catalytic lysine and the donor ketose substrates fructose-6-phosphate and sedoheptulose-7-phosphate as well ...

Endocytosis is, besides secretion, the most prominent membrane transport pathway in eukaryotic cells. In membrane transport, defined areas of the donor membranes engulf solutes of the compartment they are bordering and bud off with the aid of coat proteins to form vesicles. These transport vehicles are guided along cytoskeletal paths, often matured and, finally, fuse to the ...

Halogen bonding has been extensively described in the context of a variety of self-assembled supramolecular systems and efficiently utilized in the rational design of materials with specific structural properties. However, it has so far received only little recognition for its possible role in the stabilization of small molecule-protein complexes. In this tutorial review, we ...

Sialyltransferases (STs) represent an important group of enzymes that transfer N-acetylneuraminic acid (Neu5Ac) from cytidine monophosphate-Neu5Ac to various acceptor substrates. In higher animals, sialylated oligosaccharide structures play crucial roles in many biological processes but also in diseases, notably in microbial infection and cancer. Cell surface sialic acids have ...

In the past, the concentrations of iron II in monitoring wells has been used to evaluate natural attenuation processes at hazardous waste sites. Changes in the aqueous concentrations of electron acceptors/products are important to the evaluation of natural biological attenuation...

We analyze the protein�RNA interfaces in 81 transient binary complexes taken from the Protein Data Bank. Those with tRNA or duplex RNA are larger than with single-stranded RNA, and comparable in size to protein�DNA interfaces. The protein side bears a strong positive electrostatic potential and resembles protein�DNA interfaces in its amino acid composition. On the RNA side, the phosphate ...

Chemists strive for the wherewithal to express a great deal of control over the compounds they make. In supramolecular science and the molecular chemistry of the mechanical bond, there is a degree of complexity, expressed either by dynamic equilibria or the relative motions of mechanically bonded components, that does not typically exist in more traditional molecular settings. Although both of ...

Hydrogen-bond interaction in donor-acceptor charge-transfer complexes of TTF-imidazole demonstrated the electronic effects in terms of control of component ratio and redox activation. These unprecedented effects of hydrogen bonds renewed the criteria giving "a high probability of being organic metals" and produced a number of highly conductive complexes with various ...

We report on the control of the energy transfer pathway in individual donor-acceptor dyads by proper timing of light pulses matching the donor and acceptor transition frequencies, respectively. Excitation of both chromophores at virtually the same time induces efficient singlet-singlet annihilation, whereby excitation energy effectively flows from the ...

Riboswitches are a type of natural genetic control element that use untranslated sequence in the RNA to recognize and bind to small molecules that regulate expression of that gene. Creation of synthetic riboswitches to novel ligands depends on the ability to screen for analyte binding sensitivity and specificity. In our work, we have coupled a synthetic riboswitch to an optical reporter assay ...

The modified nucleosides N(2)-methylguanosine and -dimethylguanosine in transfer RNA occur at five positions in the D and anticodon arms, and at positions G6 and G7 in the acceptor stem. Trm1 and Trm11 enzymes are known to be responsible for several of the D/anticodon arm modifications, but methylases catalyzing post-transcriptional m(2)G synthesis in the ...

The modified nucleosides N²-methylguanosine and N22-dimethylguanosine in transfer RNA occur at five positions in the D and anticodon arms, and at positions G6 and G7 in the acceptor stem. Trm1 and Trm11 enzymes are known to be responsible for several of the D/anticodon arm modifications, but methylases catalyzing post-transcriptional ...

Fructosyltransferases catalyze the transfer of a fructose unit from one sucrose/fructan to another and are engaged in the production of fructooligosaccharide/fructan. The enzymes belong to the glycoside hydrolase family 32 (GH32) with a retaining catalytic mechanism. Here we describe the crystal structures of recombinant fructosyltransferase (AjFT) from Aspergillus japonicus CB05 and its mutant ...

Nicotinamide N-methyltransferase (NNMT) catalyzes the N-methylation of nicotinamide, pyridines and other analogs using S-adenosyl-L-methionine as donor. NNMT plays a significant role in the regulation of metabolic pathways and is expressed at markedly high levels in several kinds of cancers, presenting it as a potential molecular target for cancer therapy. We have determined the crystal structure ...

In microseconds after photoexcitation, rhodopsin forms the Meta I intermediate from lumirhodopsin. In this conversion, contacts between retinal and the apoprotein are formed, which result in a defined arrangement of donor and acceptor groups for proton translocations. A system of protonation-dependent coupled equilibria is now adopted, comprising Meta intermediates I, II and ...

Basics About Attack Recognition How does one recognize an attack? Not just a Denial of Service attack, but any attack? Before we can start applying solutions, we need to have a discussion of attack recognition techniques. So let's first look at the two main methods of attack recognition - pattern recognition and ...

Disulfiram (tetraethylthiuram disulfide), a metal chelator, inhibits photosynthetic electron transport in broken chloroplasts. A major site of inhibition is detected on the electron-acceptor side of photosystem II between Q_A, the first plastoquinone electron-acceptor, and the second plastoquinone ...

Substitutional carbon on an arsenic lattice site is the shallowest and one of the most dominant acceptors in semi-insulating Liquid Encapsulated Czochralski (LEC) GaAs. However, the role of this acceptor in determining the well known ''W'' shape spatial v...

The role of the accessary bacteriochlorophyll bridging the gap between the primary donor and bacteriopheophytin acceptor is examined. Experimental data based on magnetic interactions in the radical pair formed between primary donor and primary acceptor is presented which is consistent with the bridging bacteriochlorophyll providing a ...

The effects of co-implantation on the electrical activity of C acceptors have been studied using a series of elements as co-implants. A variety of electrical and structural techniques were used for characterization. It is found that although co-implantation with heavy ions improves the substitutionally of C atoms on As sites, a high electrical activity of ...

We report a Li-Fraumeni syndrome family in which we have detected a splice acceptor mutation in intron 3 of TP53. The mutation affects one of the invariant residues at the splice acceptor site, as a result of which two aberrant transcripts are produced. A child with Wilms' tumour aged 3 years in this family was shown not to be a ...

There remains considerable interest in the behavior of acceptors in ZnO, the ultimate goal being the realization of device grade p-type material. Silver is a candidate acceptor, and, in this study, in situ doping of silver was performed during plasma-assisted molecular beam epitaxy. Silver concentrations, as determined by ion beam analysis, ranged between ...

Employing a Koopmans corrected density functional method, we find that the metal-site acceptors Mg, Be, and Zn in GaN and Li in ZnO bind holes in deep levels that are largely localized at single anion ligand atoms. In addition to this deep ground state (DGS), we observe an effective-masslike delocalized state that can exist as a short lived shallow ...

The flavin mononucleotide in complex I (NADH:ubiquinone oxidoreductase) catalyzes NADH oxidation, O(2) reduction to superoxide, and the reduction of several 'artificial' electron acceptors. Here, we show that the positively-charged electron acceptors paraquat and hexaammineruthenium(III) react with the nucleotide-bound reduced flavin in complex I, by an ...

... followed by a thrombin cleavage recognition site (GE Healthcare UK Ltd, UK). The BamHI-HindIII cDNA fragment ... followed by a PreScission cleavage recognition site (GE Healthcare). Troponin expression ve...

Interactions of the polymerase X of African swine fever virus with the double-stranded DNA (dsDNA) have been studied with fluorescent dsDNA oligomers, using quantitative fluorescence titrations, analytical ultracentrifugation, and fluorescence energy transfer techniques. Studies with unmodified dsDNAs were performed, using competition titration method. ASV pol X binds the dsDNA with a ...

BackgroundFructans � ?-D-fructofuranosyl polymers with a sucrose starter unit � constitute a carbohydrate reservoir synthesised by a considerable number of bacteria and plant species. Biosynthesis of levan (?Glc(1�2)?Fru [(2�6)?Fru]_n), an abundant form of bacterial fructan, is catalysed by levansucrase (sucrose:2,6-?-D-fructan-6-?-D-fructosyl transferase), utilizing ...

A common feature in the structures of GT-A-fold-type glycosyltransferases is a mobile polypeptide loop that has been observed to participate in substrate recognition and enclose the active site upon substrate binding. This is the case for the human ABO(H) blood group B glycosyltransferase GTB, where amino acid residues 177�195 display significantly ...

Sialic acids play important roles in various biological processes and typically terminate the oligosaccharide chains on the cell surfaces of a wide range of organisms including mammals and bacteria. Their attachment is catalyzed by a set of sialyltransferases with defined specificities both for their acceptor sugars and the position of attachment. However, little is known of ...

... Current HLA matching guidelines for unrelated HCT recommend avoidance of mismatches only within the antigen recognition site (ARS). ...

... from the primary tumor site and infiltrating distal tissues, is dependant on cell movement and shape, which in turn are controlled by the cytoskeleton. ...

and oviposition site recognition by the dragonfly Aeshna juncea (L.): an experimental approach in natural habitats

... Title : Determination of the Structural Basis ... designed for protein antigen recognition ... ANTIBODIES, *MOLECULAR STRUCTURE, PROTEINS, SITES ...

A detailed and comprehensive overview is presented about the design, modeling, and synthesis, as well as spectroscopic characterization, of a new class of beta-sheet ligands. The characteristic feature of these compounds is a peptidic chimeric structure formed from a specific combination of aminopyrazolecarboxylic acids with naturally occurring alpha-amino acids. These hybrid peptides are designed ...

Specific donor and acceptor pairs have been assembled in bovine serum albumin (BSA), at neutral pH and room temperature, and these dye-protein complexes indicated efficient donor to acceptor singlet-singlet energy transfer. For example, pyrene-1-butyric acid served as the donor and Coumarin 540A served as the acceptor. Both the donor ...

The defective Suppressor-mutator (dSpm)-induced allele bronze1-mutable 13 (bz1-m13) and many of its derivative alleles are leaky mutants with measurable levels of flavonol O3-glucosyltransferase activity. This activity results from splicing at acceptor site-1, one of two cryptic 3' splice sites within the dSpm insertion in bz1-m13. In ...

The defective Suppressor-mutator (dSpm)-induced allele bronze1-mutable 13 (bz1-m13) and many of its derivative alleles are leaky mutants with measurable levels of flavonol O3-glucosyltransferase activity. This activity results from splicing at acceptor site-1, one of two cryptic 3' splice sites within the dSpm insertion in bz1-m13. In ...

Resources Management Division DOE Employment Recognition and Awards Program Gold Awards Silver Award Federal Employees Union (AFGE Local 788) Work Schedules / Pay and Leave...

Resources Management Division DOE Employment Recognition and Awards Program Gold Awards Silver Award Federal Employees Union (AFGE Local 788) Work Schedules / Pay and Leave...

BackgroundCytosine is a biologically important compound owing to its natural occurrence as a component of nucleic acids. Cytosine plays a crucial role in DNA/RNA base pairing, through several hydrogen-bonding patterns, and controls the essential features of life as it is involved in genetic codon of 17 amino acids. The molecular recognition among cytosines, and the molecular ...

We have done a systematic study on the contribution of the single-stranded NCCA end (where N is any nucleotide) to the stability of the aminoacyl stem of tRNA. A 7-bp RNA duplex with the single-strand ACCA 3' terminus derived from the aminoacyl stem of Escherichia coli tRNA(Ala) and several chemically synthesized sequence variants are characterized by proton NMR and thermodynamic parameters. The ...

Alternative splicing at tandem splice sites (wobble splicing) is widespread in many species, but the mechanisms specifying the tandem sites remain poorly understood. Here, we used synaptotagmin I as a model to analyze the phylogeny of wobble splicing spanning more than 300 My of insect evolution. Phylogenetic analysis indicated that the occurrence of ...

Background and purpose:The human organic cation transporter-1 (hOCT1) is a polyspecific transporter that plays a role in drug distribution, metabolism and excretion. Previous studies have demonstrated that hOCT1 binding can be stereoselective, but the mechanism for stereochemical recognition has not been described. The purpose of this study was to develop a pharmacophore model ...

Dephosphocoenzyme A kinase performs the transfer of the ?-phosphate of ATP to dephosphocoenzyme A, catalyzing the last step of coenzyme A biosynthesis. This enzyme belongs to the P-loop-containing NTP hydrolase superfamily, all members of which posses a three domain topology consisting of a CoA domain that binds the acceptor substrate, the nucleotide binding domain and the lid ...

Reorganization and degradation of the wall crosslinking and seed storage polysaccharide xyloglucan by glycoside hydrolase family 16 (GH16) endo-transglycosylases and hydrolases are crucial to the growth of the majority of land plants, affecting processes as diverse as germination, morphogenesis, and fruit ripening. A high-resolution, three-dimensional structure of a nasturtium (Tropaeolum majus) ...

Bioremediation is a technology that uses microorganisms to treat contaminants through natural biodegradation mechanisms through the addition of microbes, nutrients, electron donors, and/or electron acceptors (enhanced bioremediation). This technology, per...

... of the myristoylation acceptor site in gag leads to a ... we developed or adapted utilizing 1) acute HIV-l infection ... 10 amino acids) to gp4l lead to greatly ...

Technical protocols for evaluating natural attenuation at petroleum hydrocarbon and chlorinated solvent contaminated sites specify the analysis of electron acceptors and metabolic by-products for identifying and quantifying natural attenuation processes. However, these protocols ...

This report continues the study of chloroplast aging and rate limitations in the photosynthetic electron transport system. It was confirmed that the photosystem II acceptor, phenylenediamine, accepts electrons from two sites in the electron transport chai...

identified such a mechanism as the origin of the mild to asymptomatic phenotype observed in cystic fibrosis membrane of epithelial cells, cause cystic fibrosis (CF). CF is the most common severe autosomal recessive for the centers that contributed the data to the French Cystic Fibrosis registry and particularly Prof. Yves

Intron A of the human growth hormone gene does not contain an A residue within 56 nucleotides preceding the 3' splice site. The analysis of the excised intron lariat revealed a C residue 28 nucleotides upstream from the 3' splice site as the major branch acceptor nucleotide. Two additional minor branched nucleotides ...

This work aims at describing the water structure characteristics that influence the electron transfer superexchange mechanism by explicitly calculating the solvent mediated conductance between the donor and acceptor in a generic pair. The method employed here is based on the non-equilibrium Green function formalism for calculating the conductance over solvent trajectories ...

This work aims at describing the water structure characteristics that influence the electron transfer superexchange mechanism by explicitly calculating the solvent mediated conductance between the donor and acceptor in a generic pair. The method employed here is based on the non-equilibrium Green function formalism for calculating the conductance over solvent trajectories ...

Electronic tunneling in a complex molecular network of N(>2) donor/acceptor sites, connected by molecular bridges, is analyzed. The 'deep' tunneling dynamics is formulated using a recursive perturbation expansion, yielding a McConnell-type reduced N-level model Hamiltonian. Applications to models of molecular junctions demonstrate ...

Fluorescence resonance energy transfer was used to measure the distances between three nucleotide binding sites on solubilized chloroplast coupling factor from spinach and between each nucleotide site and two tyrosine residues which are important for catalytic activity. The nucleotide energy donor was 1,N/sup 6/-ethernoadenosine di- or triphosphate, and ...

New polymeric colloids functionalized with 2,4-diaminotriazine residues have been prepared. The functionalities provide a triple hydrogen bond motif with a donor-acceptor-donor (DAD) pattern. The colloids are based on cross-linked poly-4-methoxymethyl styrene and polymerized by means of surfactant free emulsion polymerization. The reaction pathway including five steps was ...

The human holocarboxylase synthetase (HCS) catalyzes transfer of biotin to biotin-dependent carboxylases, and the enzyme is therefore of fundamental importance for many physiological processes, including fatty acid synthesis, gluconeogenesis, and amino acid catabolism. In addition, the enzyme functions in regulating transcription initiation at several genes that code for proteins involved in ...

Having learned from failed family planning (FP) incentive schemes in other countries, Indonesia implemented a reward system designed to popularize FP in the community. In order to overcome cultural opposition to FP, many countries in the 1970s opted to give incentives--money, materials, etc.--to new contraceptive acceptors and the FP workers who successfully recruited ...

A negatively charged region on the surface of photosystem II (PSII) near Q(A) has been identified as a docking site for cationic exogenous electron acceptors. Oxygen evolution activity, which is inhibited in the presence of the herbicide 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), is recovered by adding Co(III) complexes. Thus, a new electron-transfer ...

Pre-mRNA splicing is carried out by the spliceosome, which identifies exons and removes intervening introns. In vertebrates, most splice sites are initially recognized by the spliceosome across the exon, because most exons are small and surrounded by large introns. This gene architecture predicts that efficient exon recognition depends largely on the ...

Nanocrystalline TiO(2) (anatase) is an essential oxide for environment and energy applications. A combination of EXAFS spectroscopy and DFT calculations on a series of dopants with quite similar ion radius, but increasing ion charge, show boundary space charge segregation of acceptor cations. The picture illustrates the Fourier-transformed EXAFS spectrum for Sn(4+)-doped ...

We report the neutralization of the shallow acceptors boron and gallium in p-type silicon to a depth >1 ..mu..m after exposure to a H/sub 2/O plasma for 3 h at temperatures as low as 80 /sup 0/C. The fact that uncompensated n-type silicon is unaffected by the plasma treatment means that donor formation is excluded. Exposure to either O/sub 2/ or H/sub 2/ plasmas does not ...

In natural photosynthesis, organisms optimize solar energy conversion through organized assemblies of photofunctional chromophores and catalysts within proteins that provide specifically tailored environments for chemical reactions. As with their natural counterparts, artificial photosynthetic systems for practical solar fuels production must collect light energy, separate charge, and transport ...

Recently, a novel family of methyltransferases was identified in plants. Some members of this newly discovered and recently characterized methyltransferase family catalyze the formation of small-molecule methyl esters using S-adenosyl-L-Met (SAM) as a methyl donor and carboxylic acid-bearing substrates as methyl acceptors. These enzymes include SAMT (SAM:salicylic acid ...

Recently, a novel family of methyltransferases was identified in plants. Some members of this newly discovered and recently characterized methyltransferase family catalyze the formation of small-molecule methyl esters using S-adenosyl-l-Met (SAM) as a methyl donor and carboxylic acid�bearing substrates as methyl acceptors. These enzymes include SAMT (SAM:salicylic acid ...

Virus capsids find increasing use as nanoparticulate platforms for the surface display of heterologous ligands, including as multivalent vaccine carriers. Presentation on the icosahedral hepatitis B virus capsid (HBcAg) is known to strongly enhance immunogenicity of foreign sequences, most efficiently if they are inserted into the dominant c/e1 B cell epitope, a surface-exposed loop in the ...

Caspases-3 is a kind of cysteine proteases and plays an important role in cell apoptosis. It has been reported that caspase-3 activation can be real-time detected in living cells by fluorescence resonance energy transfer (FRET) between an enhanced cyan fluorescent protein and enhanced yellow fluorescent protein. However, the large spectral overlap between cyan fluorescent protein (CFP) and yellow ...

The branch point (BP) is one of the three obligatory signals required for pre-mRNA splicing. In mammals, the degeneracy of the motif combined with the lack of a large set of experimentally verified BPs complicates the task of modeling it in silico, and therefore of predicting the location of natural BPs. Consequently, BPs have been disregarded in a considerable fraction of the genome-wide studies ...

Escherichia coli alanyl-tRNA synthetase contains the sequence Cys-X2-Cys-X6-His-X2-His. This motif is distinct from the zinc fingers of DNA-binding proteins but has some similarity to the Cys-X2-Cys-X4-His-X4-Cys zinc-binding motif of retroviral gag proteins, where it has a role in RNA packaging. In Ala-tRNA synthetase, this sequence is located in an amino-terminal domain which has the ...

The economics of affinity-tagging technologies, particularly at preparative scales, depends in part on the cost and efficiency of the bioprocessing step used to remove the affinity tag and obtain the final purified product (Lowe et al., J Biochem Biophys Methods. 2001;49:561-574). When CBM9, the family 9 cellulose binding module from Thermotoga maritima, serves as the affinity tag, the overall ...

Trametes cervina lignin peroxidase (LiP) is a unique enzyme lacking the catalytic tryptophan strictly conserved in all other LiPs and versatile peroxidases (more than 30 sequences available). Recombinant T. cervina LiP and site-directed variants were investigated by crystallographic, kinetic, and spectroscopic techniques. The crystal structure shows three substrate oxidation ...

Oligosaccharyl transferase (OT) is a multi-subunit enzyme that catalyzes N-linked glycosylation of nascent polypeptides in the lumen of the endoplasmic reticulum. In the case of Saccharomyces cerevisiae, OT is composed of nine integral membrane protein subunits. Defects in N-linked glycosylation cause a series of disorders known as congenital disorders of glycosylation (CDG). The C-terminal domain ...

There is an increasing concern for the effects of toxicants expressed during embryonic development. This paper considers the teratogenicity of polychlorocycloalkane insecticides. They are neurotoxicants which act at the convulsant recognition site(s) of the GABA receptor-chloride ionophore and antagonize GABA-mediated inhibitory neurotransmission. This ...

Fructosyltransferases catalyze the transfer of a fructose unit from one sucrose/fructan to another and are engaged in the production of fructooligosaccharide/fructan. The enzymes belong to the glycoside hydrolase family 32 (GH32) with a retaining catalytic mechanism. Here we describe the crystal structures of recombinant fructosyltransferase (AjFT) from Aspergillus japonicus CB05 and its mutant ...

This project utilized the zinc enzyme human carbonic anhydrase II (CAII) as a paradigm for dissecting and understanding the structural basis of protein-transition metal recognition and discrimination. We have successfully redesigned the zinc binding site ...

SummaryOne obstacle to achieving complete understanding of the principles underlying sequence-dependent recognition of DNA is the paucity of structural data for DNA recognition sequences in their free (unbound) state. Here we carried out crystallization screening of 50 DNA duplexes containing cognate protein binding sites and obtained ...

The purpose of this project is to use molecular recognition strategies to develop sensor technology based on luminescent, conductive polymers that contain sites for binding specific molecules or ions in the presence of related molecules or ions. Selective...

This program integrates three individual, highly interactive projects that will use molecular recognition strategies to develop sensor technology based on luminescent, conductive polymers that contain sites for binding specific molecules or ions in the presence of related molecul...

ARTICLES Acoustic recognition in macaroni penguins: an original signature system AMANDA SEARBY: 7572) Penguins use vocal signatures as cues to identify their kin in dense colonies. Experimental ecology of the birds. Penguins that have a meeting site for pair members and chicks (genus Pygoscelis

Cyclodextrin-glycosyltransferases (CGTases) (EC ) preferably catalyze transglycosylation reactions with glucosyl residues as acceptor, whereas the homologous alpha-amylases catalyze hydrolysis reactions using water as acceptor. This difference in reaction specificity is most likely caused by the acceptor binding ...

A robust analysis and discovery platform for antibiotics targeting the bacterial rRNA A-site has been developed by incorporating a new emissive U surrogate into the RNA and labeling the aminoglycosides with an appropriate fluorescence acceptor. Specifically, a 5-methoxyquinazoline-2,4(1H,3H)-dione-based emissive uracil analogue was identified to be an ...

Hydrogen bonding affects the partitioning of organic compounds between environmental and biological compartments as well as the three-dimensional shape of macromolecules. Using the semiempirical quantum chemical AM1 level of calculation, we have developed a model to predict the site-specific hydrogen bond (HB) acceptor strength from ground-state properties ...

Hydrogen bonding affects the partitioning of organic compounds between environmental and biological compartments as well as the three-dimensional shape of macromolecules. Using the semiempirical quantum chemical AM1 level of calculation, we have developed a model to predict the site-specific hydrogen bond (HB) acceptor strength from ground-state properties ...

The difference in the resistance degradation behavior was investigated between fixed valence acceptor (Mg) and the variable valence acceptor (Mn)-doped BaTiO3 ceramics with an increase of each acceptor concentration. Coarse-grained specimens with uniform grain sizes and different acceptor concentrations were ...

G-quadruplex represents a suitable scaffold for FRET (fluorescence resonance energy transfer) since its two external quartets offer two well-defined binding sites for concomitant trapping of donor/acceptor partners. Combining selective G-quadruplex binders (macrocyclic bis(quinacridine) BOQ(1) or monomeric quinacridine MMQ(1), donor) with a highly ...

This article indicates that one can use NMR to study the structure of the combining sites of monoclonal antibodies. These combining site structures involve both the protein folding problem, the 'module assembly problem', and the molecular complementarity ...

FRET between the zinc porphyrin (ZnP) chromophore in zinc-substituted cytochrome c (Zn-cyt c) and an Alexa Fluor dye attached to specific surface sites was used to characterize Zn-cyt c unfolding. The use of ZnP as a fluorescent acceptor eliminates the need to doubly label the protein with exogenous dyes to perform FRET experiments in which both donor and ...

An intense infrared absorption band has been observed in a hydrothermally grown ZnO crystal. At 12 K, the band peaks near 3577.3 cm-1 and has a half width of 0.40 cm-1, and at 300 K, the band peaks at 3547 cm-1 and has a half width of 41.3 cm-1. This absorption band is highly polarized, with its maximum intensity occurring when the electric field of the measuring light is parallel to the c axis of ...

Experimental results are reported from measurements of the temperature dependence of the absorption and photoconductivity spectra and the absorption spectra within a magnetic field of high-purity Ge semiconductors into which were introduced quenched-in shallow acceptors. Specifically, the study examined the far-IR absorption properties of the crystals impregnated with B, Al, ...

A series of sequence changes in the spacer region of the FLP recombination target (FRT) site are presented which drastically reduce site function without affecting recognition by the FLP protein. The effects follow a pattern which indicates that two structural features of the FRT site are essential for ...

The full-length retroviral RNA transcript serves as (i) mRNA for the gag and pol gene products, (ii) genomic RNA that is assembled into progeny virions, and (iii) a pre-mRNA for spliced subgenomic mRNAs. Therefore, a balance of spliced and unspliced RNA is required to generate the appropriate levels of protein and RNA products for virion production. We have introduced an insertion mutation near ...

Structure-guided re-design of the acceptor binding site of D-fructose-6-phosphate aldolase from E. coli leads to the construction of FSA A129S/A165G double mutant with an activity between 5- to >900-fold higher than that of wild-type towards N-Cbz-aminoaldehyde derivatives. PMID:21499643

SnO2 is widely used as a transparent conductor and sensor material. Better understanding and control of its conductivity would enhance its performance in existing applications and enable new ones, such as in light emitters. Using density functional theory, we show that the conventional attribution of n-type conductivity to intrinsic point defects is incorrect. Unintentional incorporation of ...

A series of isatin sulfonamide analogs having a Michael acceptor were prepared and their potencies for inhibiting caspase-1, -3, -6, -7, and -8 were evaluated. These compounds have nanomolar potency for inhibiting the executioner caspases, caspase-3 and caspase-7, and have a low potency for inhibiting caspase-1, caspase-6, and caspase-8. The inhibition mechanism was ...

The contribution of donor-acceptor interchain electron-electron scattering to the dc resistivity is calculated for one-dimensional charge-transfer metallic conductors. The interchain electron-electron interaction is due to Coulombic or phonon-exchange interactions. The resistivity arises from U processes when the relative signs of the slopes of the donor and ...

The contribution of donor-acceptor interchain electron-electron scattering to the dc resistivity is calculated for one-dimensional charge-transfer metallic conductors. The interchain electron-electron interaction is due to Coulombic or phonon-exchange interactions. The resistivity arises from U processes when the relative signs of the slopes of the donor and ...

Based on the conservation of nucleotides at splicing sites and the features of base composition and base correlation around these sites we use the method of increment of diversity combined with quadratic discriminant analysis (IDQD) to study the dependence structure of splicing sites and predict the exons/introns and their boundaries ...

... the Coulomb potential) in the quantum well. By diagonalization of the acceptor Hamiltonian in this basis the series of acceptor state energies and ...

... Title : ASSOCIATIVE MEMORY ACCEPTORS. ... This device, called an associative memory acceptor, is then studied under real-time operation. ...

In isolated, intact liver mitochondria from hyperthyroid rats, the L-glycerol-3-phosphate binding site(s) of the L-glycerol-3-phosphate dehydrogenase was (were) found to be influenced by the nature of the electron acceptor, as well as by the pH and the presence of calcium ions. With the hydrophobic electron acceptor menadione a single ...

Sequences governing RNA splicing are difficult to study in situ due to the great difficulty of traditional targeted mutagenesis. Zinc-finger nuclease (ZFN) technology allows for the rapid and efficient introduction of site-specific mutations into mammalian chromosomes. Using a ZFN pair along with a donor plasmid to manipulate the outcomes of DNA repair, we introduced several ...

A site-specific and quantitative approach for label-free monitoring of molecular recognition is presented. Specifically, the binding site of an artificial receptor is probed selectively by UVRR spectroscopy. The ligand binding constant can be determined by non-negative matrix factorization. PMID:20830343

The peptidoglycan glycosyltransferases (PGTs) catalyze the processive polymerization of a C55 lipid-linked disaccharide (Lipid II) to form peptidoglycan, the main component of the bacterial cell wall. Our ability to understand this reaction has been limited due to challenges identifying the appropriate substrate analogues to selectively interrogate the donor (the elongating strand) and ...

The peptidoglycan glycosyltransferases (PGTs) catalyze the processive polymerization of a C55 lipid-linked disaccharide (Lipid II) to form peptidoglycan, the main component of the bacterial cell wall. Our ability to understand this reaction has been limited due to challenges identifying the appropriate substrate analogs to selectively interrogate the donor (the elongating strand) and ...

The influence of chemical modification on the parameters of the binding of cholinergic ligands by the nicotinic acetylcholine receptor of squid optical ganglia was investigated. The presence of two subpopulations of recognition sites, differing in the composition of the groups contained in them, was detected. It was established with high probability that ...

I-cell disease (mucolipidosis II) is presented as a model for endo- and exo-cytosis phenomena in man. A hypothesis is presented for the structure of the carbohydrate recognition site on fibroblast-derived beta-D-N-acetylhexosaminidase that may extend to the other affected hydrolases and that is responsible for specific uptake of the enzyme by fibroblasts. ...

The interaction of oestrogen receptors with their nuclear acceptor sites was studied to ascertain whether these acceptor sites are involved in the regulation of ovalbumin-gene expression in the chick oviduct. As previously described, two distinct oestrogen-receptor species exist, and both are translocated into the ...