Solution structure, mutagenesis, and NH exchange studies of the MutT enzyme–Mg-8-oxo-dGMP complex

The MutT pyrophosphohydrolase from E. coli (129 residues) catalyzes the hydrolysis of nucleoside triphosphates (NTP), including 8-oxo-dGTP, by substitution at Pβ, to yield NMP and pyrophosphate. The product, 8-oxo-dGMP is an unusually tight binding, slowly exchanging inhibitor with a K_D=52 nM, (ΔG°=−9.8 kcal/mol) which is 6.1 kcal/mol tighter than the binding of dGMP (ΔG°=−3.7 kcal/mol). The higher affinity for 8-oxo-dGMP results from a more favorable ΔH_binding (−32 kcal/mol) despite an unfavorable −TΔS°_binding (+22 kcal/mol). The solution structure of the MutT–Mg²⁺-8-oxo-dGMP complex shows a narrowed, hydrophobic nucleotide-binding cleft with Asn-119 and Arg-78 among the few polar residues. The N119A, N119D, R78K and R78A single mutations, and the R78K+N119A double mutant all showed largely intact active sites, on the basis of small changes in the kinetic parameters of dGTP hydrolysis and in ¹H–¹⁵N HSQC spectra. However, the N119A mutation profoundly weakened the active site binding of 8-oxo-dGMP by 4.3 kcal/mol (1650-fold). The N119D mutation also weakened 8-oxo-dGMP binding but only by 2.1 kcal/mol (37-fold), suggesting that Asn-119 functioned both as a hydrogen bond donor to C8=O, and a hydrogen bond acceptor from N7H of 8-oxo-dGMP, while aspartate at position −119 functioned as an acceptor of a single hydrogen bond. Much smaller weakening effects (0.3–0.4 kcal/mol) on the binding of dGMP and dAMP were found, indicating specific hydrogen bonding of Asn-119 to 8-oxo-dGMP. While formation of the wild type MutT–Mg²⁺-8-oxo-dGMP complex slowed the backbone NH exchange rates of 45 residues distributed throughout the protein, the same complex of the N119A mutant slowed the exchange rates of only 11 residues at or near the active site, indicating an increase in conformational flexibility of the N119A mutant. The R78K and R78A mutations weakened the binding of 8-oxo-dGMP by 1.7 and 1.1 kcal/mol, respectively, indicating a lesser role of Arg-78 than of Asn-119 in the selective binding of 8-oxo-dGMP, likely donating a single hydrogen bond to its C6=O. The R78K+N119A double mutant weakened the binding of 8-oxo-dGMP (K_I^slope=3.1 mM) by 6.5±0.2 kcal/mol which overlaps, within error with the sum of the effects of the two single mutants (6.0±0.3 kcal/mol). Such additive effects of the two single mutants in the double mutant are most simply explained by the independent functioning of Asn-119 and Arg-78 in the binding of 8-oxo-dGMP. Independent functioning of these two residues in nucleotide binding is consistent with their locations in the MutT–Mg²⁺-8-oxo-dGMP complex, on opposite sides of the active site cleft, with a distance of 8.4±0.5 Å between their side chain nitrogens.     

过氧化物模拟酶在介体型生物传感器方面应用初探

meso-四(4-磺基苯)卟啉锰(Ⅲ)作为过氧化物模拟酶可催化H_2O_2与K_4Fe(CN)_6反应。电流响应与H_2O_2浓度在3.0×10~(-4)～1.0×10~(-3)mol/L范围内呈线性关系。重现性和回收率良好。抗坏血酸和DL-半胱氨酸干扰严重。     

Self-assembled peptide tubelets with 7 A pores

Here we report the preparation and structural characteristics of self-assembling peptide tubelets composed of 32-membered rings formed of alternating alpha-amino acids and cis-3-aminocyclohexanecarboxylic acids. The tubelets possess a partial hydrophobic core environment, provided by the projection of the cyclohexane C2 methylene moiety into the lumen, and a Van der Waals pore diameter of about 7 A.     

DEUSS: a perdeuterated poly(oxyethylene)-based resin for improving HRMAS NMR studies of solid-supported molecules

A novel resin called DEUSS (perdeuterated poly(oxyethylene)-based solid support) has been prepared by anionic polymerization of deuterated [D4]ethylene oxide, followed by cross-linking with deuterated epichlorohydrin. DEUSS can be suspended in a wide range of solvents including organic and aqueous solutions, in which it displays a high swelling capacity. As measured by proton HRMAS of the swollen polymer, the signal intensity of the oxyethylene protons is reduced by a factor of 110 relative to the corresponding nondeuterated poly(oxyethylene)poly(oxypropylene) (POEPOP) resin, thus facilitating detailed HRMAS NMR studies of covalently linked molecules. This 1H NMR invisible matrix was used for the solid-phase synthesis of peptides, oligoureas, and a series of amides as well as their characterization by HRMAS NMR spectroscopy. On-bead NMR spectra of high quality and with resolution comparable to that of liquid samples were obtained and readily interpreted. The complete absence of the parasite resin signals will be of great advantage, for example, for the optimization of multistep solid-phase stereoselective reactions, and for the conformational study of resin-bound molecules in a large variety of solvents.     

A Large Conformational Change of a Bridged β-Cyclodextrin Dimer in Aqueous Solution

A novel bridged β-CD dimer in which two β-cyclodextrins were linked by a naphthalene at positions 2 and 7 has been synthesized. 1H and 13CNMR measurements showed that a large change in the conformation of the dimer occurred in aqueous solution. The dimer interacted with methyl and ethyl orange to form stable inclusion complexes via "induced fit" mechanism.     

Complexation of Some Amino Acids and Peptides by p-Sulfonatocalix[4]arene and Hexasodium p-Sulfonatocalix[6]arene in Aqueous Solution

The stability constants (log K), the reaction enthalpy( H) and entropy ( S) of the complexesformed between some amino acids (glycine, L-alanine,L-valine, L-leucine, L-phenylalanine, L-tryptophan,L-threonine, and L-lysine) and peptides (glycyl-glycine,glycyl-L-alanine, glycyl-L-leucine, glycyl-L-phenylalanine,L-leucyl-glycine, L-leucyl-L-alanine, glycyl-L-valine,L-leucyl-glycyl-glycine, and glycyl-glycyl-glycine) withp-sulfonatocalix[4]arene and hexasodiump-sulfonatocalix[6]arene in aqueous solutions by meansof calorimetric titration have been investigated. The reportedresults demonstrate that the amino acids and peptides under studyform complexes with both p-sulfonatocalix[4]areneand hexasodium p-sulfonatocalix[6]arene. In the case of theamino acids and peptides the complexation with water-solublecalixarenes in aqueous solution is favored by enthalpiccontributions and disfavored by entropic contributions. However,no influence of the ring size of the calixarenes upon thecomplexation is observed. By comparison with the reaction ofthe sodium salt of phenol-4-sulfonic acid with amino acids amacrocyclic effect in case of the calixarenes is possible.     

Aluminium(III) as a promoter of cellular oxidation

Aluminium has been known as a neurotoxic agent to experimental animals since the last century (Arch. Exp. Pharmacol. 40 (1897) 98). However, great interest arose in it bioinorganic chemistry as well biology when it was demonstrated to be the causative agent in pathologies related to the long-term dialysis treatment of uremic subjects with renal failure (Life Chem. 11 (1994) 197), and as a potential etiopathogenic cofactor for several neurodegenerative diseases. The inorganic biochemistry of aluminium is still largely to be discovered. In this review the pro-oxidative property of aluminium toward biological membrane will be presented and its implications in involvement in human pathology will be discussed in an interdisciplinary frame from the bioinorganic point of view.     

Kinetics of thermochemical pretreatment of lignocellulosic materials

The results of an experimental study of the acid hydrolysis of hardwood are presented in the form of values for the three parameters, activation energy, power on the acid concentration, and pre-exponen-tial factor, of the first order kinetic constants for each of the following reaction participants: xylan remaining, glucan remaining, xylose formed, and xylose decomposed. These are used as a base for a quantitative theory to predict the temperature, time, and acid concentrations needed for effective pretreatment of the substrate for subsequent enzymatic hydrolysis of the glucan. This theory is based on the assumption that successful pretreatment requires >90% removal of the xylan, <10% removal of the glucan, and >80% xylose yield. This theory is compared with selected published data.     

对甲苯磺酸铜的电化学表征

合成了对甲苯磺酸铜,用X光单晶衍射确定了其结构.实验结果表明,该盐容易脱除全部结晶水,在空气中不潮解.分别测定了对甲苯磺酸铜(Cu(p-OTs)2)在H2O、CH3OH和DMF中的电化学参数.实验结果表明Cu(p-OTs)2在不同溶剂中的反应机理各异. Cu(II)的电化学还原在H2O中是分两步进行,而在CH3OH和DMF中的电化学还原是一步两电子过程.对实验结果进行了分析讨论.     

Metabolomic-based investigation of Yinlan alleviating hyperlipidemia by inhibiting blood stasis and phlegm turbidity through the PXR-CYP3A4-ABCB1-FXR pathway

Yinlan lipid regulatory capsule (YL) is a composite traditional Chinese medicine (TCM) new drug to alleviate hyperlipidemia, while its therapeutic mechanism in vivo was not clarified with nontargeted metabolomics investigation. An animal model was established in rats fed a high-fat diet, and their body weights, body mass index (BMI) and blood cholesterol levels were measured. Serum, liver and kidney tissue samples were also extracted for PXR-CYP3A4-ABCB1-FXR signaling pathway research using PCR and UHPLC–MS. The obtained plasma samples were analyzed by UHPLC-Q-TOF-MS metabolomic investigation, which revealed PXR-CYP3A4-related metabolites and changes induced by YL. Finally, the key metabolites were chosen as index components, and their levels in the serum, liver, small intestine and bile were used for simultaneous UHPLC–MS-MS determination. The results indicated that YL was effective in rebalancing blood TG and TC levels (compared to controls). With respect to the PXR-CYP3A4-ABCB1 pathway, as a result of YL’s effect, gene expression or activity of the two targets decreased significantly in both the liver and kidney. The same trend was observed in the serum samples mentioned above. Metabolomics screening and data revealed that 44 metabolites can be regarded as biomarkers related to hyperlipidemia, fatty acids synthesis, and body energy consumption, as well as synthesis, transportation and exertion of cholesterol. YL’s treatment focused on 26 of them, primarily bile acids, indicating that the antihyperlipidemic effect of this drug lies in its inhibitory activity of cholesterol metabolism. Subsequent analysis of those in vivo components revealed that significant increases (compared to the model group) occurred in the blood, liver, small intestine and bile in groups that received medium and high doses of YL (while the low dose was relatively unchanged). Those target components exhibit a close relationship with PXR and/or CYP3A4. The use of YL repressed PXR expression and subsequently decreased CYP3A4 activity. As a result, synthesis of related bile acids increased, while cholesterol levels decreased, consequently leading to the attenuation of hyperlipidemia. This study comprehensively investigated the antihyperlipidemia mechanism of YL based on its repression of PXR-CYP3A4 activity and related metabolite yield, establishing an accurate method for evaluating the therapeutic effect of YL.