Role of a Repeated Hexapeptide Motif GIHFAP Near C-terminus in Assembly, Stability, and Activity of “HCH Dehydrochlorinase LinA”

Enzyme “hexachlorocyclohexane (HCH) dehydrochlorinase LinA” mediates first step of aerobic microbial degradation of a chlorinated insecticide γ-HCH. The archetypal LinA-type1 consists of 156 amino acids that include a directly repeated hexapeptide motif GIHFAP at positions 141–146 and 148–153. Analysis of a series of LinA mutants, containing none, one, two, or three units of this repeated motif revealed that two units, as present in wild-type LinA, are required for its optimal activity and stability. Moreover, the presence of a bend in its secondary structure due to a proline residue that precedes the distal repeated unit contributes to enhanced LinA activity.     

Determination of lincomycin and tylosin residues in honey using solid-phase extraction and liquid chromatography-atmospheric pressure chemical ionization mass spectrometry

An analytical method for the determination of residues of the antibiotic drugs lincomycin and tylosin in honey was developed. The procedure employed a solid-phase extraction for the isolation of lincomycin and tylosin from diluted honey samples. The antibiotic residues were subsequently analyzed by reversed-phase HPLC with atmospheric pressure chemical ionization mass spectrometric detection. Average analyte recoveries for lincomycin and tylosin ranged from 84 to 107% in replicate sets of honey samples fortified with drug concentrations of 0.01, 0.5, and 10 microg/g. The method detection limits were determined to be 0.007 and 0.01 microg/g for lincomycin and tylosin, respectively.     

Nucleotidylation of unsaturated carbasugar in validamycin biosynthesis

Validamycin A is a member of microbial-derived C(7)N-aminocyclitol family of natural products that is widely used as crop protectant and the precursor of the antidiabetic drug voglibose. Its biosynthetic gene clusters have been identified in several Streptomyces hygroscopicus strains, and a number of genes within the clusters have been functionally analyzed. Of these genes, valB, which encodes a sugar nucleotidyltransferase, was found through inactivation study to be essential for validamycin biosynthesis, but its role was unclear. To characterize the role of ValB in validamycin biosynthesis, four carbasugar phosphate analogues were synthesized and tested as substrate for ValB. The results showed that ValB efficiently catalyzes the conversion of valienol 1-phosphate to its nucleotidyl diphosphate derivatives, whereas other unsaturated carbasugar phosphates were found to be not the preferred substrate. ValB requires Mg(2+), Mn(2+), or Co(2+) for its optimal activity and uses the purine-based nucleotidyltriphosphates (ATP and GTP) more efficiently than the pyrimidine-based NTPs (CTP, dTTP, and UTP) as nucleotidyl donor. ValB represents the first member of unsaturated carbasugar nucleotidyltransferases involved in natural products biosynthesis. Its characterization not only expands our understanding of aminocyclitol-derived natural products biosynthesis, but may also facilitate the development of new tools for chemoenzymatic synthesis of carbohydrate mimetics.     

Isolation and identification of two unknown impurities from the raw material of clindamycin hydrochloride

Clindamycin hydrochloride belongs to the antibiotic family of lincomycin. It has the same antibacterial spectrum as lincomycin, but the antibacterial activity is four to eight times stronger than that of lincomycin. There have been some adverse reactions in clinical use of clindamycin hydrochloride and its finished drug products. The impurities in drugs are directly related to their safety. In this study, two unknown impurities were isolated from the raw material of clindamycin hydrochloride through various chromatographic methods. Their structures were identified as clindamycin isomer (impurity 1) and dehydroclindamycin (impurity 2) by mass spectrometry and NMR spectroscopy. Both of them were found for the first time. The two impurities exhibit a similar but lower antibacterial activity compared with clindamycin hydrochloride.     

Multi-method for the determination of antibiotics of different substance groups in milk and validation in accordance with Commission Decision 2002/657/EC

The presented method is able to analyse 47 substances of the antibiotic groups tetracyclines, quinolones, macrolides, sulfonamides, diamino-pyrimidine derivatives and lincosamides simultaneously in a single analytical run. Applying an in-house validation concept, the validation of the multi-method was successfully accomplished with a low number of experiments. Each substance was validated at least at the concentrations 0.5, 1.0 and 1.5 MRL (maximum residue limit), or respectively, at concentrations as low as possible for substances without MRL. The calculated relevant validation parameters, e.g. the decision limit CCα, the detection capability CCβ, the repeatability, the within-laboratory reproducibility and the recovery, are in an acceptable range and in compliance with the requirements of Commission Decision 2002/657/EC. A proficiency test and the implementation of the method by other laboratories were performed successfully.     

细胞色素b5突变体V45H NMR初步研究

通过分析在H2O和D2O中采集,DQF-COSY,TOCSY和NOESY等二维核磁共振波谱鉴定了细胞色素b5定点突变体V45H(残基Val^45突变为His^45)的大多数氨基酸残基的质子自旋系统,通过解析NOESY谱中的dNN(i,i+1),dαN(i,i+1),dαN(i,i+2),dαN(i,i+3),dαβ(i,i+3)和dβN(i,i+1)等NOE相关,完成了其序列特异性归属以及主链和侧链质子共振信号的全归属。突变体V45H的二级结构分析表明残基Val^45突变为His^45对分子的整体折叠影响不大。但是,与野生型细胞色素b5相比较,突变体V45H主链酰胺质子的化学位移指数提示突变使其血红素疏水腔的微环境受到扰动。以上实验结果为进一步测定V45H的溶液结构和分析残基Val^45在蛋白质中的作用提供了基础。     

高效液相色谱-电喷雾串联质谱法测定蜂蜜中的林可胺类抗生素残留

建立了蜂蜜中林可胺类抗生素林可霉素和氯林可霉素的高效液相色谱-电喷雾串联质谱(HPLC/ESI-MS/MS)检测方法。样品经固相萃取提取净化、反相液相色谱分离后进行质谱分析,在选择反应监测模式(SRM) 下进行特征母-子离子对信号采集。根据保留时间、母离子和两个特征子离子信息进行定性分析,以共同的基峰离子m/z 126进行定量。两种抗生素的检测限(S/N=3) 为 0.1 μg/kg,定量限为 0.5 μg/kg,在1.0～200 μg/L时峰强度与质量浓度的线性关系良好(r2>0.996)。在1.0,5.0,20.0 μg/kg 3个添加水平,两种抗生素的平均回收率范围为80%～110%,日内测定结果的相对标准偏差小于8%,日间测定结果的相对标准偏差小于15%。结果表明,该法简单、灵敏,特异性强,适用于蜂蜜中林可胺类抗生素残留的分析确证。     

One site fits both: A model for the ternary complex of folate + NADPH in R67 dihydrofolate reductase, a D2 symmetric enzyme

R67 dihydrofolate reductase (DHFR) is a novel enzyme that confers resistance to the antibiotic trimethoprim. The crystal structure of R67 DHFR displays a toroidal structure with a central active-site pore. This homotetrameric protein exhibits 222 symmetry, with only a few residues from each chain contributing to the active site, so related sites must be used to bind both substrate (dihydrofolate) and cofactor (NADPH) in the productive R67 DHFR?NADPH?dihydrofolate complex. Whereas the site of folate binding has been partially resolved crystallographically, an interesting question remains: how can the highly symmetrical active site also bind and orient NADPH for catalysis? To model this ternary complex, we employed DOCK and SLIDE, two methods for docking flexible ligands into proteins using quite different algorithms. The bound pteridine ring of folate (Fol I) from the crystal structure of R67 DHFR was used as the basis for docking the nicotinamide-ribose-P_i (NMN) moiety of NADPH. NMN was positioned by both DOCK and SLIDE on the opposite side of the pore from Fol I, where it interacts with Fol I at the pore's center. Numerous residues serve dual roles in binding. For example, Gln 67 from both the B and D subunits has several contacts with the pteridine ring, while the same residue from the A and C subunits has several contacts with the nicotinamide ring. The residues involved in dual roles are generally amphipathic, allowing them to make both hydrophobic and hydrophilic contacts with the ligands. The result is a `hot spot' binding surface allowing the same residues to co-optimize the binding of two ligands, and orient them for catalysis.     

嗜热蛋白酶PH1704别构中心量子化学计算与突变体动力学简

通过量子化学计算,确定嗜热菌Pyrococcus horikoshii OT3的PH1704蛋白酶别构位点的关键残基为Arg113,Tyr120和Asn129. 其中,Arg113及Asn129与别构抑制剂结合,参与别构调控. Tyr120残基位于亚基交界面附近,并与亲核残基Cys100之间以氢键相连,可通过影响亚基聚合来影响酶的亲核催化. DJ-1超家族的4种构建蛋白的结构显示,120位点位于亚基交界面处,影响亚基的聚合,进而影响蛋白酶的活力,并间接参与别构调控. 分子生物学实验显示,突变体R113T/Y120P/N129D的kcat/km(L·μmol-1·min-1)值是野生型kcat/km值的6倍,h系数由野生型的0.86转变为1.3,负协同效应消失. 113和129位点处阴离子别构剂脱离,从而破坏113,120和129位点间的封闭环结构,使AC交界面α7螺旋(124~129,524~529)间聚合度增强;120位点残基由Tyr转变为Pro,与Cys100间氢键断裂,亲核进攻的阻力减小,从而使酶活力提高,别构负调控消失.     

嗜热蛋白酶PH1704别构中心量子化学计算与突变体动力学

通过量子化学计算, 确定嗜热菌Pyrococcus horikoshii OT3的PH1704蛋白酶别构位点的关键残基为Arg113, Tyr120和Asn129. 其中, Arg113及Asn129与别构抑制剂结合, 参与别构调控. Tyr120残基位于亚基交界面附近, 并与亲核残基Cys100之间以氢键相连, 可通过影响亚基聚合来影响酶的亲核催化. DJ-1超家族的4种构建蛋白的结构显示, 120位点位于亚基交界面处, 影响亚基的聚合, 进而影响蛋白酶的活力, 并间接参与别构调控. 分子生物学实验显示, 突变体R113T/Y120P/N129D的k_cat/k_m(L·μmol^-1·min^-1)值是野生型k_cat/k_m值的6倍, h系数由野生型的0.86转变为1.3, 负协同效应消失. 113和129位点处阴离子别构剂脱离, 从而破坏113, 120和129位点间的封闭环结构, 使AC交界面α7螺旋(124~129, 524~529)间聚合度增强; 120位点残基由Tyr转变为Pro, 与Cys100间氢键断裂, 亲核进攻的阻力减小, 从而使酶活力提高, 别构负调控消失.     

Validation of a multi-residue method for the determination of several antibiotic groups in honey by LC-MS/MS

The presented multi-method was developed for the confirmation of 37 antibiotic substances from the six antibiotic groups: macrolides, lincosamides, quinolones, tetracyclines, pleuromutilines and diamino-pyrimidine derivatives. All substances were analysed simultaneously in a single analytical run with the same procedure, including an extraction with buffer, a clean-up by solid-phase extraction, and the measurement by liquid chromatography tandem mass spectrometry in ESI+ mode. The method was validated on the basis of an in-house validation concept with factorial design by combination of seven factors to check the robustness in a concentration range of 5-50 μg kg(-1). The honeys used were of different types with regard to colour and origin. The values calculated for the validation parameters-decision limit CCα (range, 7.5-12.9 μg kg(-1)), detection capability CCβ (range, 9.4-19.9 μg kg(-1)), within-laboratory reproducibility RSD(wR) (<20% except for tulathromycin with 23.5% and tylvalosin with 21.4 %), repeatability RSD(r) (<20% except for tylvalosin with 21.1%), and recovery (range, 92-106%)-were acceptable and in agreement with the criteria of Commission Decision 2002/657/EC. The validation results showed that the method was applicable for the residue analysis of antibiotics in honey to substances with and without recommended concentrations, although some changes had been tested during validation to determine the robustness of the method.     

固相萃取-液相色谱-质谱/质谱法同时测定蜂蜜中的多类药物残留

建立了采用固相萃取-液相色谱-质谱/质谱(SPE-LC-MS/MS)对蜂蜜中磺胺类、硝基咪唑类、喹诺酮类、大环内酯类、林可酰胺类和吡喹酮共计6大类54种药物残留同时测定的方法。蜂蜜经磷酸盐缓冲溶液(pH 8)稀释,Oasis HLB固相萃取柱净化后,通过液相色谱-质谱联用技术进行检测(正离子方式,多反应监测模式)。采用同位素稀释内标法或外标法进行定量,线性关系良好,相关系数大于0.992。方法的定量限(LOQ,以信噪比(S/N)大于10计)分别为磺胺类和硝基咪唑类药物1.0 μg/kg,喹诺酮类和林可酰胺类药物2.0 μg/kg,大环内酯类药物3.0 μg/kg,吡喹酮0.3 μg/kg。总体回收率为32.6%～114%,相对标准偏差为1.3%～28.9%。该方法的定量限满足目前国内外药物的最大残留限量要求,可作为蜂蜜中相关药物残留量的筛选检测方法。     

Polycationic gramicidin s analogues with both high antibiotic activity and very low hemolytic activity

The substitution of each constituent amino acid residue of gramicidin S (GS), cyclo(-Val(1,1')-Orn(2,2')-Leu(3,3')-D-Phe(4,4')-Pro(5,5')-)(2) with Lys residue indicated that each side chain structure of the constituent amino acid residues affect largely the antibiotic activity and hemolytic activity of GS. Further, the substitution of D-Phe(4,4') and Pro(5,5') residues with basic amino acid residues as a Lys residue results the high antibiotic activity and the very low hemolytic activity. Thus, we have found novel positions on the scaffold of GS at D-Phe(4,4') and Pro(5,5') residues whose modification will significantly increase the therapeutic index.     

Are antibiotic screening approaches sufficiently adequate? A proficiency test

A proficiency test including the screening analysis of antibiotics in beef using cryogenicly minced materials was organized by RIKILT in 2009. The test included blank beef samples and beef samples spiked with either flumequine or a combination of lincomycin and spectinomycin around the maximum residue limits [1]. The suitability of the materials was demonstrated with a homogeneity and a stability study. This study showed that cryogenically minced spiked muscle material is suited for proficiency tests aiming at the screening and the confirmatory analysis.Of the 26 participants, 23 carried out their in-house screening approach involving microbial, biochemical or instrumental methods, or a combination of these to cover the broad range of antibiotic groups. The false negative rate was 73% for microbial methods, 50% for biochemical and 22% for instrumental methods. These results indicate that substantial effort is needed to improve screening approaches and that more regular proficiency tests are needed to reveal the shortcomings in the currently applied screening methods.     

Structure effects of the protonated lincomycin molecule on the mechanism of its complexation with organic compounds

The mechanism of complexation of the protonated lincomycin molecule with para-substituted nitrobenzenes in the gas phase is analyzed by quantum chemical methods. The regioselectivity of lincomycin protonation is treated in a B3LYP/6-31G(d′, p) approximation; the geometrical structure and conformation of the molecule are analyzed. The lincomycin molecule is protonated at the nitrogen atom of the pyrrolidine cycle. In stable conformers, a pseudovoid is formed and stabilized by intramolecular hydrogen bonding. The cross section of the pseudovoid (1.77–2.62 Å) is too small for the protonated lincomycin molecule to participate in host guest complexation with organic compounds. According to B3LYP/6-31G(d′, p) calculations, complexation of the protonated lincomycin molecule with nitrobenzenes occurs through hydrogen bonding.     

Kinetics of Antibiotic Sorption by Monocarboxyl Cellulose

Kinetics of the sorption of lincomycin and gentamicin from aqueous solutions of their salts and bases, as well as a cephalosporin group antibiotic cephalexin having the zwitterionic nature, by monocarboxyl cellulose is studied. It is disclosed that the sorption of the studied antibiotics is characterized by a combined diffusion type of kinetics. Effective diffusion coefficients (D _eff) are determined, and it is shown that they correspond to the times (t _1/2) of half-equilibrium establishment and increase with passing from lincomycin to gentamicin and, further, to cephalexin. The D _eff and t _1/2 values are found to depend on solution pH and the degree of cellulose sorbent swelling.     

Complete Switch of Reaction Specificity of an Aldolase by Directed Evolution In Vitro: Synthesis of Generic Aliphatic Aldol Products

A structure‐guided engineering of fructose‐6‐phosphate aldolase was performed to expand its substrate promiscuity toward aliphatic nucleophiles, that is, unsubstituted alkanones and alkanals. A “smart” combinatorial library was created targeting residues D6, T26, and N28, which form a binding pocket around the nucleophilic carbon atom. Double‐selectivity screening was executed by high‐performance TLC that allowed simultaneous determination of total activity as well as a preference for acetone versus propanal as competing nucleophiles. D6 turned out to be the key residue that enabled activity with non‐hydroxylated nucleophiles. Altogether 25 single‐ and double‐site variants (D6X and D6X/T26X) were discovered that show useful synthetic activity and a varying preference for ketone or aldehyde as the aldol nucleophiles. Remarkably, all of the novel variants had completely lost their native activity for cleavage of fructose 6‐phosphate.     

Synthesis of a Resorcylic Acid Lactone (RAL) Library Using Fluorous‐Mixture Synthesis and Profile of its Selectivity Against a Panel of Kinases

A library of resorcylic acid lactones (RAL) containing a cis‐enone moiety targeting kinases bearing a cysteine residue within the ATP‐binding pocket was prepared using a fluorous‐mixture synthesis and evaluated against a panel of 19 kinases thus providing important structure–activity trends. Two new analogues were then profiled for their selectivity against a panel of 402 kinases providing the broadest evaluation of this pharmacophores’ selectivity.     

基于分子动力学模拟的VmoLac非特异性底物催化活性的理论研究

采用分子动力学模拟方法研究了VmoLac的非特异性底物催化活性, 模拟了VmoLac/3-oxo-C10-AHL, VmoLac/3-oxo-C6-AHL, VmoLac/γ-nonalacton和VmoLac/ethyl-paraoxon 4个复合物. 分析了分子动力学模拟过 程中不同底物结合引起VmoLac构象变化的主要原因. 结果表明, 3-oxo-C10-AHL和γ-nonalacton的结合会使VmoLac活性口袋附近的Loop8结构域运动明显, 利于底物结合在Loop8疏水通道外侧进而引起催化反应; VmoLac活性口袋周围的门控残基W264和Y230之间距离的变化会影响底物的结合; Y98与长链内酯、 壬内酯的羰基碳之间形成的进攻距离较小, 而与短链内酯的羰基碳以及对氧磷的磷原子之间形成的进攻距离较大, 短的距离更有利于发生亲核进攻反应; D257是引发VmoLac催化反应的关键残基; 当VmoLac催化3-oxo-C10-AHL和γ-nonalacton时, D257与极化水以及底物形成更多的氢键, 使底物与酶更容易结合. 从理论催化机制角度解释了VmoLac催化长链内酯(3-oxo-C10-AHL)比短链内酯(3-oxo-C6-AHL)的能力强, 催化壬内酯(γ-nonalacton)比对氧磷(ethyl-paraoxon)能力强的原因, 为实验结果提供了理论证明.