Exocyclic carbons adjacent to the N6 of adenine are targets for oxidation by the Escherichia coli adaptive response protein AlkB

The DNA and RNA repair protein AlkB removes alkyl groups from nucleic acids by a unique iron- and α-ketoglutarate-dependent oxidation strategy. When alkylated adenines are used as AlkB targets, earlier work suggests that the initial target of oxidation can be the alkyl carbon adjacent to N1. Such may be the case with ethano-adenine (EA), a DNA adduct formed by an important anticancer drug, BCNU, whereby an initial oxidation would occur at the carbon adjacent to N1. In a previous study, several intermediates were observed suggesting a pathway involving adduct restructuring to a form that would not hinder replication, which would match biological data showing that AlkB almost completely reverses EA toxicity in vivo. The present study uses more sensitive spectroscopic methodology to reveal the complete conversion of EA to adenine; the nature of observed additional putative intermediates indicates that AlkB conducts a second oxidation event in order to release the two-carbon unit completely. The second oxidation event occurs at the exocyclic carbon adjacent to the N(6) atom of adenine. The observation of oxidation of a carbon at N(6) in EA prompted us to evaluate N(6)-methyladenine (m6A), an important epigenetic signal for DNA replication and many other cellular processes, as an AlkB substrate in DNA. Here we show that m6A is indeed a substrate for AlkB and that it is converted to adenine via its 6-hydroxymethyl derivative. The observation that AlkB can demethylate m6A in vitro suggests a role for AlkB in regulation of important cellular functions in vivo.     

AlkB recognition of a bulky DNA base adduct stabilized by chemical cross-linking

E.coli AlkB is a direct DNA/RNA repair protein that oxidatively reverses N1 alkylated purines and N3 alkylated pyrimidines to regular bases.Previous crystal structures have revealed N1-methyl adenine(1-meA) recognition by AlkB and a unique base flipping mechanism,but how the AlkB active site can accommodate bulky base adducts is largely unknown.Employing a previously developed chemical cross-linking technique,we crystallized AlkB with a duplex DNA containing a caged thymine base(cagedT).The structure reveal...     

Preparation and characterization of the native iron(II)-containing DNA repair AlkB protein directly from Escherichia coli

The Escherichia coli AlkB protein was recently found to repair cytotoxic DNA lesions 1-methyladenine and 3-methylcytosine by using a novel iron-catalyzed oxidative demethylation mechanism. This protein belongs to a family of 2-ketoglutarate-Fe(II)-dependent dioxygenase proteins that utilize iron and 2-ketoglutarate to activate dioxygen for oxidation reactions. We report here the overexpression and isolation of the native Fe(II)-AlkB with a bound cofactor, 2-ketoglutarate, directly from E. coli. UV-vis measurements showed an absorption peak at 560 nm, which is characteristic of a bidentate 2-ketoglutarate bound to an iron(II) ion. Addition of excess amounts of single-stranded DNA to this isolated Fe(II)-AlkB protein caused a 9 nm shift of the 560 nm band to a higher energy, indicating a DNA-binding-induced geometry change of the active site. X-ray absorption spectra of the active site iron(II) in AlkB suggest a five-coordinate iron(II) center in the protein itself and a centrosymmetric six-coordinate iron(II) site upon addition of single-stranded DNA. This geometry change may play important roles in the DNA damage-searching and damage-repair functions of AlkB. These results provide direct evidence for DNA binding to AlkB which modulates the active site iron(II) geometry. The isolation of the native Fe(II)-AlkB also allows for further investigation of the iron(II) center and detailed mechanistic studies of the dioxygen-activation and damage-repair reactions performed by AlkB.     

Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active‐Site Residues

The AlkB family demethylases AlkB, FTO, and ALKBH5 recognize differentially methylated RNA/DNA substrates, which results in their distinct biological roles. Here we identify key active‐site residues that contribute to their substrate specificity. Swapping such active‐site residues between the demethylases leads to partially switched demethylation activities. Combined evidence from X‐ray structures and enzyme kinetics suggests a role of the active‐site residues in substrate recognition. Such a divergent active‐site sequence may aid the design of selective inhibitors that can discriminate these homologue RNA/DNA demethylases.     

Profiling mechanisms of alkane hydroxylase activity in vivo using the diagnostic substrate norcarane

Mechanistically informative chemical probes are used to characterize the activity of functional alkane hydroxylases in whole cells. Norcarane is a substrate used to reveal the lifetime of radical intermediates formed during alkane oxidation. Results from oxidations of this probe with organisms that contain the two most prevalent medium-chain-length alkane-oxidizing metalloenzymes, alkane omega-monooxygenase (AlkB) and cytochrome P450 (CYP), are reported. The results--radical lifetimes of 1-7 ns for AlkB and less than 100 ps for CYP--indicate that these two classes of enzymes are mechanistically distinguishable and that whole-cell mechanistic assays can identify the active hydroxylase. The oxidation of norcarane by several recently isolated strains (Hydrocarboniphaga effusa AP103, rJ4, and rJ5, whose alkane-oxidizing enzymes have not yet been identified) is also reported. Radical lifetimes of 1-3 ns are observed, consistent with these organisms containing an AlkB-like enzyme and inconsistent with their employing a CYP-like enzyme for growth on hydrocarbons.     

Probing the structure and function of the Escherichia coli DNA alkylation repair AlkB protein through chemical cross-linking

Engineering chemical cross-linking groups at the protein/DNA interface provide a powerful method for probing the putative active site and a damage searching mechanism of the Escherichia coli alkylation DNA repair protein AlkB.     

Selective Enzymatic Demethylation of N2,N2‐Dimethylguanosine in RNA and Its Application in High‐Throughput tRNA Sequencing

The abundant Watson–Crick face methylations in biological RNAs such as N¹‐methyladenosine (m¹A), N¹‐methylguanosine (m¹G), N³‐methylcytosine (m³C), and N²,N²‐dimethylguanosine (m²₂G) cause significant obstacles for high‐throughput RNA sequencing by impairing cDNA synthesis. One strategy to overcome this obstacle is to remove the methyl group on these modified bases prior to cDNA synthesis using enzymes. The wild‐type E. coli AlkB and its D135S mutant can remove most of m¹A, m¹G, m³C modifications in transfer RNA (tRNA), but they work poorly on m²₂G. Here we report the design and evaluation of a series of AlkB mutants against m²₂G‐containing model RNA substrates that we synthesize using an improved synthetic method. We show that the AlkB D135S/L118V mutant efficiently and selectively converts m²₂G modification to N²‐methylguanosine (m²G). We also show that this new enzyme improves the efficiency of tRNA sequencing.     

Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N¹‐methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate‐determining hydrogen‐atom abstraction on competitive σ‐ and π‐pathways on a quintet spin‐state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen‐bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.     

Direct repair of the exocyclic DNA adduct 1,N6-ethenoadenine by the DNA repair AlkB proteins

The exocyclic DNA base adduct 1,N6-ethenoadenine (epsilonA) is directly repaired by the AlkB proteins in vitro.     

Modelling of ORL1 receptor-ligand interactions

An opioid receptor like (ORL1) receptor is one of a family of G-protein-coupled receptors (GPCR); it represents a new pharmaceutical target with extensive therapeutic potential for the regulation of important biological functions such as nociception, mood disorders, drug abuse, learning or cardiovascular control. Although the crystal structure of the inactive form of the ORL1 receptor has been determined, little is known about its activation. By using X-ray structures of the β2-adrenegic receptor in its inactive (2RH1) and active (3P0G) states as templates, inactive and active homology models of the ORL1 receptor were constructed. Structurally diverse sets of strongly binding antagonists and agonists were docked with both ORL1 receptor forms. The major receptor-ligand interactions responsible for antagonist and agonist binding were identified. Although both sets of ligands, agonists and antagonists, bind to the same region of the receptor, they occupy partially different binding pockets. Agonists bind to the inactive receptor in a slightly different manner than antagonists. This difference is more pronounced in binding to the active ORL1 receptor model and points to the amino acids at the extracellular end of TM6, suggesting that this region is important for receptor-activation.     

Umpolung strategy for the synthesis of 2-deoxy-C-aryl glycosides: a serendipitous,efficient route for C-furanoside analogues

[reaction: see text] 2-Deoxy-C-aryl glycosides are potential synthetic targets as they form a very vital moiety of several biologically active natural products. This paper describes a synthetic route using an umpolung strategy, which has not been explored till date. Our synthetic endeavor led to a versatile intermediate aryl ketone 10, which has paved the way for two important classes of C-glycosides, viz., C-alkyl furanosides 12 and methyl 2-deoxy-C-aryl pyranosides 14.     

Regio-selective hydroxylation of gem-difluorinated octanes by alkane hydroxylase (AlkB)

gem-Difluoromethylene substituted molecules constitute a distinct class of fluorinated compounds. In this study, special chemistry has been developed for their preparation based on the highly selective terminal hydroxylation of these gem-difluorinated octanes by AlkB (alkane hydroxylase) from Pseudomonas putida Gpo1 to form gem-difluorinated octan-1-ols. The hydroxylation reaction is performed by whole-cell catalysis. Identification of the distal- and proximal-hydroxylation products was made by ¹H, ¹³C, and ¹⁹F NMR; GC and GC/MSD; and/or by comparison with authentic standards in GC. To the best of our knowledge, we have obtained the first synthesis of 2,2-, 3,3- and 4,4-difluorooctan-1-ols, from simple and inexpensive starting materials.     

Synthesis of a new complex Chromium (Ⅲ) 2-mercaptonicotinate

Chromium is an essential trace element for mammals[1-3].Diabetes is a chronic disease with major health consequence. Studies show that the occurrence of diabetes have great thing to do with the chromium deficient. Almost 40 years after the first report of glucose tolerance factor(GTF)[4]no conclusive evidence for an isolable ,biologically active form of chromium exited. Three materials have been proposed to be the biologically active form of chromium: "glucose tolerance factor", chromium Picolinate and low-molecular-weight chromium-binding substance (LWMCr)[5]So there is potential for the design of new chromium drugs[6].Chromium compounds have been used in medicine for centuries and there is potential for the design of new chromium drugs.2-Mercaptonicotinic acid(MN) displays the interesting biological activity. Chromium( Ⅲ )2-mercaptonicotinate is a common and effective biologically active form of Chromium. The test of biological activity indicated that may be useful in treating of diabetes. In this paper, we reported the The synthesis route is as follow:The structure of the complex has been characterized by IR, elemental analysis, MS,atomic absorption spectroscopy, X-ray powder diffraction and TG-DTA analysis.They indicate that the structure of Chromium 2-mercaptonicotinate.HPLC is used for determination of the purity. Studies show that the complex has a good biological activity for supplement tiny dietary chromium,lowering blood glucose levels, lowering serum lipid levels and increasing lean body mass.     

Similarity searching using reduced graphs

Reduced graphs provide summary representations of chemical structures. In this work, the effectiveness of reduced graphs for similarity searching is investigated. Different types of reduced graphs are introduced that aim to summarize features of structures that have the potential to form interactions with receptors while retaining the topology between the features. Similarity searches have been carried out across a variety of different activity classes. The effectiveness of the reduced graphs at retrieving compounds with the same activity as known target compounds is compared with searching using Daylight fingerprints. The reduced graphs are shown to be effective for similarity searching and to retrieve more diverse active compounds than those found using Daylight fingerprints; they thus represent a complementary similarity searching tool.     

Ligand Fishing with Cellular Membrane-Coated Magnetic Beads: A New Method for the Screening of Potentially Active Compounds from Natural Products

Ligand fishing with target biomolecule-immobilized magnetic beads (MBs) has been established and developed for nearly 10 years. Advantages of this technique, such as the ease of operation, associated with a diversity of automated online approaches, make it a valuable tool for affinity studies. However, transmembrane proteins have not been used as the target biomolecules in the assay, since they are usually not available in a purified and bioactive form. In addition, few publications have reported the use of this method for screening active compounds derived from natural products. In this work, for the first time, cellular membrane-coated MBs, which to a large extent maintain the activity of the transmembrane proteins, were used for the fishing assay. We demonstrated application of red blood cell membrane-coated MBs for fishing potential active components from a natural product (Angelica dahurica). The potential active compounds, such as imperatorin, bergapten, and pabulenol, were detected. The result correlated well with cell membrane chromatography (CMC) coupled with HPLC. Comparisons of the developed MBs fishing assay with the CMC method showed the noteworthy advantages of the fishing technique regarding the consumption of cellular membranes, buffers as well as length of operation time.     

Syntheses and fully diastereospecific photochromic reactions of thiophenophan-1-enes with chiral bridges

Thiophenophan-1-enes with chiral polyether bridges were prepared and their diastereospecific photochromic reactions were studied. The coupling reaction of substituted dithienylethenes and various chiral synthons afforded thiophenophan-1-enes, namely, bridged dithienylethenes, as single enantiomers without optical resolution, thus indicating that these reactions occurred diastereoselectively. Upon UV irradiation, each optically active thiophenophan-1-ene isomerized to the corresponding enantiomer of the closed form and returned to the initial enantiomer of the open form upon visible irradiation. Because thiophenophan-1-enes never isomerized to other diastereomers even at a high temperature, they underwent diastereospecific photochromic reactions. Large changes were observed in the measurement of the optical rotations of the solutions of thiophenophan-1-enes at 588?nm according to their photochromic reactions. As there was no absorption at this wavelength for both isomers of each thiophenophan-1-enes, the nondestructive readout of the photochromic reaction could be carried out by using these chiral thiophenophan-1-enes.     

基于超重力技术开展Co-N-CNTs催化剂制备及其氧还原性能的研究

开发高效的非贵金属氧还原(ORR)催化剂是促进燃料电池商业化进程的关键。本研究利用超重力技术制备了一种优良的非贵金属ORR催化剂Co-N-CNTs。物理表征表明,通过超重力技术可以使作为活性位点的金属Co纳米颗粒均匀分布在Co-N-CNTs催化剂表面,X射线光电子能谱(XPS)揭示Co-N-CNTs催化剂中的N元素不仅可以和碳纳米管(CNTs)中的C元素形成吡咯氮和石墨氮,还可以形成具有更高氧还原活性的吡啶氮结构。电化学测试结果表明,通过超重力技术制备的Co-N-CNTs催化剂的起始电位和半波电位与商业Pt/C催化剂相当;而且,Co-N-CNTs催化剂展现出优良的抗甲醇性能。     

Geometric structure determination of N694C lipoxygenase: a comparative near-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure study

The mononuclear nonheme iron active site of N694C soybean lipoxygenase (sLO1) has been investigated in the resting ferrous form using a combination of Fe-K-pre-edge, near-edge (using the minuit X-ray absorption near-edge full multiple-scattering approach), and extended X-ray absorption fine structure (EXAFS) methods. The results indicate that the active site is six-coordinate (6C) with a large perturbation in the first-shell bond distances in comparison to the more ordered octahedral site in wild-type sLO1. Upon mutation of the asparagine to cysteine, the short Fe-O interaction with asparagine is replaced by a weak Fe-(H(2)O), which leads to a distorted 6C site with an effective 5C ligand field. In addition, it is shown that near-edge multiple scattering analysis can give important three-dimensional structural information, which usually cannot be accessed using EXAFS analysis. It is further shown that, relative to EXAFS, near-edge analysis is more sensitive to partial coordination numbers and can be potentially used as a tool for structure determination in a mixture of chemical species.