Molecular Anchor Research Articles

Structural and Functional Insights into (S)-Ureidoglycine Aminohydrolase, Key Enzyme of Purine Catabolism in Arabidopsis thaliana

The ureide pathway has recently been identified as the metabolic route of purine catabolism in plants and some bacteria. In this pathway, uric acid, which is a major product of the early stage of purine catabolism, is degraded into glyoxylate and ammonia via stepwise reactions of seven different enzymes. Therefore, the pathway has a possible physiological role in mobilization of purine ring nitrogen for further assimilation. (S)-Ureidoglycine aminohydrolase enzyme converts (S)-ureidoglycine into (S)-ureidoglycolate and ammonia, providing the final substrate to the pathway. Here, we report a structural and functional analysis of this enzyme from Arabidopsis thaliana (AtUGlyAH). The crystal structure of AtUGlyAH in the ligand-free form shows a monomer structure in the bicupin fold of the β-barrel and an octameric functional unit as well as a Mn(2+) ion binding site. The structure of AtUGlyAH in complex with (S)-ureidoglycine revealed that the Mn(2+) ion acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction. Further kinetic analysis characterized the functional roles of the active site residues, including the Mn(2+) ion binding site and residues in the vicinity of (S)-ureidoglycine. These analyses provide molecular insights into the structure of the enzyme and its possible catalytic mechanism.

Localisation of novel forms of glutamate transporters and the cystine-glutamate antiporter in the choroid plexus: Implications for CSF glutamate homeostasis

The choroid plexus is a structure within each ventricle of the brain that is composed of fenestrated vessels surrounded by secretory epithelial cells. The epithelial cells are linked by tight junctions to create a permeability barrier. The epithelial cells are derived from neuroectoderm, and are thus defined by some authors as a subtype of macroglia. Glutamate is a tightly regulated substance in the CSF, as it is in the rest of the brain. In the brain macroglia express multiple sodium dependent and independent glutamate transporters and are the main regulators of extracellular glutamate. However, the identities of the transporters in the choroid plexus and their localisations have remained poorly defined. In this study we examined the expression and distribution of multiple splice variants of classical sodium-dependent glutamate transporters, as well as the cystine-glutamate antiporter, and the PDZ protein NHERF1, (which acts as a molecular anchor for proteins such as the glutamate transporter GLAST). We identified three forms of sodium-dependent transporters (GLAST1a, GLAST1c and GLT1b) that are expressed at the apical surface of the epithelial cells, a location that matches the distribution of NHERF1 and the cystine-glutamate antiporter. We propose that this coincident localisation of GLAST1a/GLAST1c/GLT1b and the cystine-glutamate antiporter would permit the cyclical trafficking of glutamate and thus optimise the accumulation of cystine for the formation of glutathione in the choroid plexus.

Molecular Anchor Restricts Protein Movement

Molecular Anchor Restricts Protein Movement

Design of Dye Acceptors for Photovoltaics from First-Principles Calculations

We investigate a set of donor-π-acceptor (D-π-A) dyes with new acceptor groups for dye-sensitized solar cells, using time-dependent density-functional-theory calculations of the electronic structure and optical absorption. We considered three types of modifications on existing dye structures: (i) replacement of the side cyano group (CN) on the molecular anchor, (ii) insertion and alteration of the intermediate spacer groups, and (iii) modification of the number and positions of cyano CN groups on a phenyl-ring spacer. We find that with these modifications, the dye electronic levels and corresponding optical absorption properties can be gradually tuned, rendering possible the identification of dyes with desirable structural, electronic, and optical properties. For example, dyes with phenyl and CN-substituted phenyl groups are promising candidates for red light absorption and high molar extinction coefficients.

DNA Gold Nanoparticle Conjugates Incorporating Thiooxonucleosides: 7-Deaza-6-thio-2′-deoxyguanosine as Gold Surface Anchor

A new protocol for the covalent attachment of oligonucleotides to gold nanoparticles was developed. Base-modified nucleosides with thiooxo groups were acting as molecular surface anchor. Compared to already existing conjugation protocols, the new linker strategy simplifies the synthesis of DNA gold nanoparticle conjugates. The phosphoramidite of 7-deaza-6-thio-2'-deoxyguanosine (6) was used in solid-phase synthesis. Incorporation of the sulfur-containing nucleosides can be performed at any position of an oligonucleotide; even multiple incorporations are feasible, which will increase the binding stability of the corresponding oligonucleotides to the gold nanoparticles. Oligonucleotide strands immobilized at the end of a chain were easily accessible during hybridization leading to DNA gold nanoparticle network formation. On the contrary, oligonucleotides immobilized via a central position could not form a DNA-AuNP network. Melting studies of the DNA gold nanoparticle assemblies revealed sharp melting profiles with a very narrow melting transition.

Inv acts as a molecular anchor for Nphp3 and Nek8 in the proximal segment of primary cilia

A primary cilium is an antenna-like structure extending from the surface of most vertebrate cells. It is structurally divided along its vertical axis into sub-compartments that include the ciliary tip, the shaft, the ciliary necklace segment, the transitional zone and the basal body. We recently discovered that the shaft of the primary cilia has a distinct molecular compartment, termed the "Inv compartment", which is characterized by the accumulation of Inv at the base of primary cilia. Inv was discovered as a causative gene in inv mutant mice. It was later found to be responsible for the infantile type of nephronophthisis (NPHP2). Nephronophthisis (NPHP) is an autosomal recessive kidney disease. Nine causative genes have been identified, with all examined products thought to function in cilia, basal body and/or centrioles. However, their exact intra-ciliary localization and relationship have not been clear. Here, we report that products of Nphp3 and Nek8 (the mouse orthologs of the causative genes for NPHP3 and NPHP9, respectively) localize to the Inv compartment. We also show that Inv is essential for the compartmental localization of Nphp3 and Nek8, whereas localization of Inv does not require Nphp3 or Nek8. Nphp1 and Nphp4 also localize at the proximal region of the cilium, but not in Inv compartment. Our results indicate that Inv acts as an anchor for Nphp3 and Nek8 in the Inv compartment, and suggest that Inv compartment is a candidate site for intra-ciliary interaction of Inv, Nphp3 and Nek8.

Csm3, Tof1, and Mrc1 Form a Heterotrimeric Mediator Complex That Associates with DNA Replication Forks

Mrc1 (mediator of replication checkpoint), Tof1 (topoisomerase I interacting factor), and Csm3 (chromosome segregation in meiosis) are checkpoint-mediator proteins that function during DNA replication and activate the effector kinase Rad53. We reported previously that Mrc1 and Tof1 are constituents of the replication machinery and that both proteins are required for the proper arrest and stabilization of replication forks in the presence of hydroxyurea. In our current study, we show that Csm3 is a component of moving replication forks and that both Tof1 and Csm3 are specifically required for the association of Mrc1 with these structures. In contrast, the deletion of mrc1 did not affect the association of Tof1 and Csm3 with the replication fork complex. In agreement with previous observations in yeast cells, the results of a baculovirus coexpression system showed that these three proteins interact directly with each other to form a mediator complex in the absence of replication forks.

A simple approach for the growth of highly ordered ZnO nanotube arrays

A simple two-step approach to produce highly ordered ZnO nanotube arrays is introduced. In the first step, Zn nanotubes were prepared by the electrodeposition of Zn into the pores of anodic alumina membrane (AAM), and then they were oxidized in air and converted into ZnO nanotubes. This approach is very simple, molecular anchor free, and is capable of growing ZnO nanotubes at low temperature. The ZnO nanotubes synthesized by this method exhibit an intense and sharp cathodoluminescence at 378 nm and a weak defect emission at about 500 nm at room temperature, indicating good quality of the prepared samples. Our approach is very general, which provides an alternative method for preparing highly ordered metal oxide nanotube arrays with good quality at relatively low temperatures.

Molecular anchor Cu–S formed on a thiophene mediated Si(111)-(7×7) surface

Thiophene molecule selectively binds to the adjacent adatom-rest atom pair on the Si(111)-(7x7) surface through its alpha-carbon atoms, leading to the covalent attachment of a C-S-C linkage and remaining C=C (beta-carbon) bond onto the surface. Photoemission studies show that Cu atom readily adsorbs onto the S atom of the functional group to form the Cu-S molecular anchor in two forms: one points away from the thiophene C=C group; the other points toward the C=C group.

Novel Strategy for Diameter-Selective Separation and Functionalization of Single-Wall Carbon Nanotubes

The problem of separating single-wall carbon nanotubes (CNTs) by diameter and/or chirality is one of the greatest impediments toward the widespread application of these promising materials in nanoelectronics. In this paper, we describe a novel physical-chemical method for diameter-selective CNT separation that is both simple and effective and that allows up-scaling to large volumes at modest cost. Separation is based on size-selective noncovalent matching of an appropriate anchor molecule to the wall of the CNT, enabling suspension of the CNTs in solvents in which they would otherwise not be soluble. We demonstrate size-selective separation in the 1-2 nm diameter range using easily synthesized oligo-acene adducts as a diameter-selective molecular anchor. CNT field effect transistors fabricated from diameter-selected CNTs show markedly improved electrical properties as compared to nonselected CNTs.

One-step fabrication of gold nanoparticles-silica composites with enhanced catalytic activity

A fast and simple one-step method for the fabrication of stable gold nanoparticles-silica composites by using 1,4,7,10,13,16,21,24-octaazabicyclo[8.8.8]hexacosane(azacryptand) as a molecular anchor between nanoparticles and silica as well as reductant and stabilizer in the formation of the nanoparticles is reported. Gold nanoparticles-coated silica materials can be fabricated by mixing HAuCl 4 aqueous solution with the aqueous mixture of azacryptand and silica materials such as submicrometer silica particles and silica gel. The prepared nanoparticles-coated silica gel can effectively catalyze reduction of 4-nitrophenol by sodium borohydride in aqueous solution.

Fabrication and growth mechanism of metal (Zn, Sn) nanotube arrays and metal (Cu, Ag) nanotube/nanowire junction arrays

We report the successful synthesis of metal (Zn, Sn) nanotube arrays and metal (Cu, Ag) nanotube/nanowire junction arrays electrochemically deposited through nanoporous anodic alumina membranes. The metal (Zn, Sn) nanotube arrays were achieved by preferentially plating at circular step edges of the Au nanorings with hydrogen gas generation, critical to the evolution of tube formation. Quite interestingly, if there is no hydrogen gas generation, the metal (Cu, Ag) nanotube/nanowire junction arrays were obtained. This approach is very simple, molecular anchor free, and is generally capable of growing other metal nanotube arrays and nanotube/nanowire junction arrays.

Patterned attachment of carbon nanotubes to silane modified silicon

A monolayer of methyl terminated hexadecyltrichlorosilane was self-assembled onto a p-type silicon (1 0 0) substrate to provide a resist for electrochemical anodisation with an atomic force microscope cantilever. Through precise control of the cantilever’s position on the surface and the applied bias voltage, a variety of different surface architectures have been fabricated on the substrate. Single-walled carbon nanotubes (SWCNT), with high carboxylic acid functionality, have been immobilised to these etched regions using a condensation reaction. Highly selective condensation has been shown to be possible, both directly onto etched silicon regions as well as with the use of amine terminated 3-aminopropyltriethoxysilane as a molecular anchor. This has enabled the controlled attachment of nanotubes on nanoscale features.

The His-Pro-Phe motif of angiotensinogen is a crucial determinant of the substrate specificity of renin

The amino acid sequence His-Pro-Phe as N-terminal residues 6-8 of the natural renin substrate, angiotensinogen, is conserved among species. We investigated whether this His-Pro-Phe motif functions as the determinant of the substrate specificity of renin. Mutant angiotensinogens in which the Ile-His-Pro-Phe-His-Leu sequence at positions 5-10 of wild-type angiotensinogen was replaced by either His-Pro-Phe-His-Leu-Leu or Ala-Ile-His-Pro-Phe-His were cleaved by renin at the C-terminal side of residues 9 and 11, respectively, while wild-type angiotensinogen was cleaved at residue 10. A triple Ala substitution for the His-Pro-Phe motif of angiotensinogen prevented its cleavage by renin. In contrast, triple Ala substitution for residues 9-11, including the natural site of cleavage by renin, allowed cleavage between the two Ala residues at positions 10 and 11. Furthermore, the 33-residue C-terminal peptide of human megsin, which carries a naturally occurring His-Pro-Phe sequence, was cleaved by renin at the C-terminal side of the His-Pro-Phe-Leu-Phe sequence. These results indicate that the His-Pro-Phe motif of angiotensinogen is a crucial determinant of the substrate specificity of renin. By binding to a corresponding pocket on renin, the His-Pro-Phe motif may act as a molecular anchor to recruit the scissile peptide bond to a favorable site for catalysis.

Role of Molecular Anchor Groups in Molecule-to-Semiconductor Electron Transfer

The dynamics of heterogeneous electron transfer (ET) from the polycyclic aromatic chromophore perylene to nanostructured TiO2 anatase was investigated for two different anchor groups with transient absorption spectroscopy in an ultrahigh vacuum. Data from ultraviolet photoelectron spectroscopy and from linear absorption spectroscopy showed that the donor state of the chromophore was located around 900 meV above the lower edge of the conduction band. With the wide band limit fulfilled the rate of the heterogeneous ET reaction was only controlled by the strength of the electronic coupling and not reduced by Franck-Condon factors. Two different time constants for the electron transfer, i.e., 13 and 28 fs, were measured with carboxylic acid and phosphonic acid as the respective anchor groups. The difference in the ET time constants was explained with the different extension of the donor orbital onto the respective anchor group to reach the empty electronic states of the semiconductor. The time constants were extracted by means of a simple rate equation model. The validity of applying this model on this ultrafast time scale was verified by comparing the rate equation model with an optical Bloch equation model.

Fragment-based Screening of the Donor Substrate Specificity of Human Blood Group B Galactosyltransferase Using Saturation Transfer Difference NMR

Saturation transfer difference NMR experiments on human blood group B alpha-(1,3)-galactosyltransferase (GTB) for the first time provide a comprehensive set of binding epitopes of donor substrate analogs in relation to the natural donor UDP-Gal. This study revealed that the enzyme binds several UDP-activated sugars, including UDP-Glc, UDP-GlcNAc, and UDP-GalNAc. In all cases, UDP is the dominant binding epitope. To identify the minimum requirements for specific binding, a detailed analysis utilizing a fragment-based approach was employed. The binding of donor substrate to GTB is essentially controlled by the base as a "molecular anchor." Uracil represents the smallest fragment that is recognized, whereas CDP, AMP, and GDP do not exhibit any significant binding affinity for the enzyme. The ribose and beta-phosphate moieties increase the affinity of the ligands, whereas the pyranose sugar apparently weakens the binding, although this part of the molecule controls the specificity of the enzyme. Accordingly, UDP represents the best binder. The binding affinities of UDP-Gal, UDP-Glc, and UMP are about the same, but lower than that of UDP. Furthermore, we observed that beta-D-galactose and alpha-D-galactose bind weakly to GTB. Whereas beta-D-galactose binds to the acceptor and donor sites, it is suggested that alpha-D-galactose occupies a third hitherto unknown binding pocket. Finally, our experiments revealed that modulation of enzymatic activity by metal ions critically depends on the total enzyme concentration, raising the question as to which of the bivalent metal cations Mg(2+) and Mn(2+) is more relevant under physiological conditions.

Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex

The Drosha-DGCR8 complex initiates microRNA maturation by precise cleavage of the stem loops that are embedded in primary transcripts (pri-miRNAs). Here we propose a model for this process that is based upon evidence from both computational and biochemical analyses. A typical metazoan pri-miRNA consists of a stem of approximately 33 bp, with a terminal loop and flanking segments. The terminal loop is unessential, whereas the flanking ssRNA segments are critical for processing. The cleavage site is determined mainly by the distance (approximately 11 bp) from the stem-ssRNA junction. Purified DGCR8, but not Drosha, interacts with pri-miRNAs both directly and specifically, and the flanking ssRNA segments are vital for this binding to occur. Thus, DGCR8 may function as the molecular anchor that measures the distance from the dsRNA-ssRNA junction. Our current study thus facilitates the prediction of novel microRNAs and will assist in the rational design of small hairpin RNAs for RNA interference.

Efficient and Stable Display of Functional Proteins on Bacterial Magnetic Particles Using Mms13 as a Novel Anchor Molecule

Magnetic particles are increasingly used for various biomedical applications because they are easy to handle and separate from biological samples. In this work, a novel anchor molecule was used for targeted protein display onto magnetic nanoparticles. The magnetic bacterium Magnetospirillum magneticum AMB-1 synthesizes intracellular bacterial magnetic particles (BMPs) covered with a lipid bilayer membrane. In our recent research, an integral BMP membrane protein, Mms13, was isolated and used as an anchor molecule to display functional proteins onto BMPs. The anchoring properties of Mms13 were confirmed by luciferase fusion studies. The C terminus of Mms13 was shown to be expressed on the surface of BMPs, and Mms13 was bound to magnetite directly and tightly permitting stable localization of a large protein, luciferase (61 kDa), on BMPs. Consequently, luminescence intensity obtained from BMPs using Mms13 as an anchor molecule was >400 or 1,000 times higher than Mms16 or MagA, which previously were used as anchor molecules. Furthermore, the immunoglobulin G-binding domain of protein A (ZZ) was displayed uniformly on BMPs using Mms13, and antigen was detected by transmission electron microscopy using antibody-labeled gold nanoparticles on a single BMP displaying the ZZ-antibody complex. The results of this study demonstrated the utility of Mms13 as a molecular anchor, which will facilitate the assembly of other functional proteins onto BMPs in the near feature.

Dissecting independent channel and scaffolding roles of the Drosophila transient receptor potential channel

Drosophila transient receptor potential (TRP) serves dual roles as a cation channel and as a molecular anchor for the PDZ protein, INAD (inactivation no afterpotential D). Null mutations in trp cause impairment of visual transduction, mislocalization of INAD, and retinal degeneration. However, the impact of specifically altering TRP channel function is not known because existing loss-of-function alleles greatly reduce protein expression. In the current study we describe the isolation of a set of new trp alleles, including trp 14 with an amino acid substitution juxtaposed to the TRP domain. The trp 14 flies stably express TRP and display normal molecular anchoring, but defective channel function. Elimination of the anchoring function alone in trp Δ 1272, had minor effects on retinal morphology whereas disruption of channel function caused profound light-induced cell death. This retinal degeneration was greatly suppressed by elimination of the Na+/Ca2+ exchanger, CalX, indicating that the cell death was due primarily to deficient Ca2+ entry rather than disruption of the TRP-anchoring function.

O,N,N‘-Trialkylisoureas as Mild Activating Reagents for N-Acylsulfonamide Anchors

[chemical reaction: see text]. Prior to detachment of compounds synthesized on sulfonamide based safety-catch linkers, the molecular anchor has to be activated. This is achieved by alkylation of the nitrogen atom of the N-acylsulfonamide using different established protocols. As an addition to the existing repertoire of activating reagents, we suggest the use of O,N,N'-trialkylisoureas. Besides the demonstration of the feasibility of these mild alkylating agents for this purpose, custom-tailored novel O,N,N'-trialkylisoureas prepared from electron-deficient alcohols are reported.