A QM/MM study of the reaction mechanism of (R)‐hydroxynitrile lyases from Arabidopsis thaliana (AtHNL)

Hydroxynitrile lyases (HNLs) catalyze the conversion of chiral cyanohydrins to hydrocyanic acid (HCN) and aldehyde or ketone. Hydroxynitrile lyase from Arabidopsis thaliana (AtHNL) is the first R‐selective HNL enzyme containing an α/β‐hydrolases fold. In this article, the catalytic mechanism of AtHNL was theoretically studied by using QM/MM approach based on the recently obtained crystal structure in 2012. Two computational models were constructed, and two possible reaction pathways were considered. In Path A, the calculation results indicate that the proton transfer from the hydroxyl group of cyanohydrin occurs firstly, and then the cleavage of C1‐C2 bond and the rotation of the generated cyanide ion (CN^?) follow, afterwards, CN^? abstracts a proton from His236 via Ser81. The C1‐C2 bond cleavage and the protonation of CN^? correspond to comparable free energy barriers (12.1 vs. 12.2 kcal mol^?1), suggesting that both of the two processes contribute a lot to rate‐limiting. In Path B, the deprotonation of the hydroxyl group of cyanohydrin and the cleavage of C1‐C2 bond take place in a concerted manner, which corresponds to the highest free energy barrier of 13.2 kcal mol^?1. The free energy barriers of Path A and B are very similar and basically agree well with the experimental value of HbHNL, a similar enzyme of AtHNL. Therefore, both of the two pathways are possible. In the reaction, the catalytic triad (His236, Ser81, and Asp208) acts as the general acid/base, and the generated CN^? is stabilized by the hydroxyl group of Ser81 and the main‐chain NH‐groups of Ala13 and Phe82. Proteins 2015; 83:66–77. © 2014 Wiley Periodicals, Inc.     

Coupling between overall rotational diffusion and domain motions in proteins and its effect on dielectric spectra

In this work, we formulate a closed‐form solution of the model of a semirigid molecule for the case of fluctuating and reorienting molecular electric dipole moment. We illustrate with numeric calculations the impact of protein domain motions on dielectric spectra using the example of the 128 kDa protein dimer of Enzyme I. We demonstrate that the most drastic effect occurs for situations when the characteristic time of protein domain dynamics is comparable to the time of overall molecular rotational diffusion. We suggest that protein domain motions could be a possible explanation for the high‐frequency contribution that accompanies the major relaxation dispersion peak in the dielectric spectra of protein aqueous solutions. We propose that the presented computational methodology could be used for the simultaneous analysis of dielectric spectroscopy and nuclear magnetic resonance data. Proteins 2015; 83:1571–1581. © 2015 Wiley Periodicals, Inc.     

Systemic lupus erythematosus: molecular cloning and analysis of 22 individual recombinant monoclonal kappa light chains specifically hydrolyzing human myelin basic protein

Antibodies hydrolyzing myelin basic protein (MBP) can play an important role in the pathogenesis of multiple sclerosis (MS) and systemic lupus erythematosus (SLE). An immunoglobulin light chain phagemid library derived from peripheral blood lymphocytes of patients with SLE was used. Small pools of phage particles displaying light chains with different affinities for MBP were isolated by affinity chromatography on MBP‐Sepharose, and the fraction eluted with 0.5 M NaCl was used for preparation of individual monoclonal light chains (MLChs, 26–27 kDa). Seventy‐two of 440 individual colonies were randomly chosen, expressed in Escherichia coli in a soluble form, and MLChs were purified by metal chelating chromatography. Twenty‐two of 72 MLChs have high affinity and efficiently hydrolyze only MBP (not other control proteins) demonstrating various pH optima in a 5.7–9.0 range and different substrate specificity in the hydrolysis of four different MBP oligopeptides. Four MLChs demonstrated serine protease‐like and three thiol protease‐like activities, while 11 MLChs were metalloproteases. The activity of three MLChs was inhibited by both phenylmethylsulfonyl fluoride (PMSF) and Ethylenediaminetetraacetic acid (EDTA), two other by EDTA and iodoacetamide, and one by PMSF, EDTA, and iodoacetamide. The ratio of relative activity in the presence of Ca²⁺, Mg²⁺_, Mn²⁺, Ni²⁺, Zn²⁺, Cu²⁺, and Co²⁺ was individual for each of 22 MLCh preparations. It is the first examples of human MLChs, which probably can possess two or even three different proteolytic activities. These observations suggest an extreme diversity of anti‐MBP abzymes in SLE patients. The immune systems of individual SLE patients can generate a variety of anti‐MBP abzymes, which can attack MBP of myelin‐proteolipid sheath of axons and play an important role in MS and SLE pathogenesis. Copyright © 2015 John Wiley & Sons, Ltd.     

Discovery and structural characterization of an allosteric inhibitor of bacterial cis‐prenyltransferase

Undecaprenyl pyrophosphate synthase (UPPs) is an essential enzyme in a key bacterial cell wall synthesis pathway. It catalyzes the consecutive condensations of isopentenyl pyrophosphate (IPP) groups on to a trans-farnesyl pyrophosphate (FPP) to produce a C55 isoprenoid, undecaprenyl pyrophosphate (UPP). Here we report the discovery and co-crystal structures of a drug-like UPPs inhibitor in complex with Streptococcus pneumoniae UPPs, with and without substrate FPP, at resolutions of 2.2 and 2.1 Å, respectively. The UPPs inhibitor has a low molecular weight (355 Da), but displays potent inhibition of UPP synthesis in vitro (IC₅₀ 50 nM) that translates into excellent whole cell antimicrobial activity against pathogenic strains of Streptococcal species (MIC₉₀ 0.4 µg mL⁻¹). Interestingly, the inhibitor does not compete with the substrates but rather binds at a site adjacent to the FPP binding site and interacts with the tail of the substrate. Based on the structures, an allosteric inhibition mechanism of UPPs is proposed for this inhibitor. This inhibition mechanism is supported by biochemical and biophysical experiments, and provides a basis for the development of novel antibiotics targeting Streptococcus pneumoniae.     

Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase

Enzyme active site residues are often highly conserved, indicating a significant role in function. In this study we quantitate the functional contribution for all conserved molecular interactions occurring within a Michaelis complex for mannitol 2-dehydrogenase derived from Pseudomonas fluorescens (pfMDH). Through systematic mutagenesis of active site residues, we reveal that the molecular interactions in pfMDH mediated by highly conserved residues not directly involved in reaction chemistry can be as important to catalysis as those directly involved in the reaction chemistry. This quantitative analysis of the molecular interactions within the pfMDH active site provides direct insight into the functional role of each molecular interaction, several of which were unexpected based on canonical sequence conservation and structural analyses.     

外源H_2S对NO_3~-胁迫下番茄幼苗生理生化特性的影响

采用营养液水培方法,通过外源施加H2S供体NaHS(100μmol/L),研究了信号分子H2S对100mmol/L NO3-胁迫下番茄幼苗生理生化特性的影响。结果表明:(1)NO3-胁迫下,随着处理时间的延长,番茄幼苗的株高、根长、鲜重和干重显著降低,叶绿素(a、b)含量、净光合速率、气孔导度、蒸腾速率均显著降低,而胞间CO2浓度以及丙二醛(MDA)、H2O2含量增加,超氧化物歧化酶(SOD)、过氧化物酶(POD)、过氧化氢酶(CAT)和抗坏血酸过氧化物酶(APX)活性显著降低,抗坏血酸(AsA)和还原性谷胱甘肽(GSH)含量显著降低。(2)与NO3-胁迫处理相比,外源NaHS处理1、3、5d后,番茄幼苗的株高、根长、鲜重和干重显著增加,叶绿素(a、b)含量、净光合速率、气孔导度、蒸腾速率均显著升高,而胞间CO2浓度显著降低;MDA和H2O2含量降低,SOD、POD、CAT和APX活性显著增强,AsA和GSH含量显著增加,而且幼苗的硝酸还原酶、谷氨酰胺合成酶、谷氨酸合酶的活性显著增强;L-半胱氨酸脱巯基酶活性和内源H2S含量增加。研究认为,外源H2S可能通过提高抗氧化物酶的活性和增加抗氧化物质含量来缓解NO3-对番茄幼苗造成的伤害,从而增强其对NO3-胁迫耐性。     

低温胁迫下枇杷幼果种子膜脂过氧化、保护酶活性及显微结构的变化

枇杷(Eriobotrya japonica)开花结果正值冬季低温期,易受低温影响,因此寒害成为抑制枇杷健康生长、发育的重要因素之一。种子作为产生多种内源激素的中心,其健康程度与枇杷果实正常发育息息相关。该研究以四川省成都市龙泉驿区柏合镇的‘早钟六号’枇杷幼果种子为材料,经不同低温(6、3、0、-3℃)胁迫不同时间(12、24、36、48 h)后,对其相对电导率、丙二醛(MDA)、超氧化物歧化酶(SOD)、过氧化氢酶(CAT)和过氧化物酶(POD)的变化进行测定以及细胞解剖结构分析,旨在探究枇杷幼果种子抗寒机制,为提高四川地区枇杷抗寒栽培新技术提供理论和实践依据。结果表明:低温胁迫下,枇杷幼果种子相对电导率及MDA含量随着处理温度的降低整体呈上升趋势;保护酶SOD、CAT活性在低温胁迫前期不同程度升高,至某个低温后呈下降趋势;而POD活性总体呈升-降-升趋势;相对电导率、MDA含量、SOD活性、CAT活性、POD活性的变化临界温度均为6℃,胁迫临界时间分别为12、24、48、36 h,而MDA含量变化临界温度为3℃,胁迫临界时间为36 h;显微结构表明枇杷幼果种子6℃低温开始受冻,最先受冻部位为种皮,其次为种胚真叶原始体或真叶,最后到细胞破裂,说明枇杷幼果种子随着处理温度降低,细胞结构受损越严重。综上,枇杷幼果种子受冻临界温度为6℃,受冻临界时间为12 h。     

水稻种衣剂对秧苗生理生化及叶绿素荧光参数的影响

以‘深两优5814’水稻种子为试验材料,用2.5%吡·咪、3%恶·咪、锐胜和适乐时分别包衣种子,测定水稻幼苗抗氧化酶活性、MDA含量、GSH含量、叶绿素含量和叶绿素荧光参数,探讨种衣剂对幼苗的胁迫机理,为种衣剂的安全高效应用提供理论依据。结果表明:(1)种衣剂能提高水稻幼苗的抗氧化酶活性,播种后14d,2.5%吡·咪和锐胜处理组叶片的SOD活性上升,3%恶·咪处理组叶片的POD活性上升;播种后22d,2.5%吡·咪和3%恶·咪处理组叶片的CAT活性上升;播种后26d,锐胜和适乐时处理组叶片的CAT活性上升;2.5%吡·咪和3%恶·咪显著提高了播种后22d叶片的MDA含量。4种种衣剂均能提升幼苗叶片GSH含量,并以3%恶·咪的提升效果最为明显。(2)4种种衣剂均能降低叶绿素含量,但随培养时间的延长叶片内叶绿素含量逐渐恢复到正常水平。(3)4种种衣剂对水稻叶片最大光化学效率φPo无显著影响,吸光性能指数PIABS值也未呈下降趋势,比活性参数ABS/CSM值随培养时间的延长出现下降趋势,其中以3%恶·咪处理组下降最为明显;同时,3%恶·咪处理组叶片的热耗散DIo/CSM值也显著高于对照。研究认为,各种衣剂对水稻幼苗生长造成了一定的胁迫,但水稻自身防御体系能有效缓解农药胁迫作用,种衣剂的使用处于安全水平,但3%恶·咪的胁迫较严重,使用效果较差。     

Development of an ultrasensitive immunoassay using affinity maturated antibodies for the measurement of rodent insulin

The measurement of plasma insulin is important for clinical diagnosis of diabetes and for preclinical research of metabolic diseases, especially in rodent models used in drug discovery research for type 2 diabetes. Fasting immunoreactive insulin (F-IRI) concentrations are used to calculate the homeostasis model assessment ratio (HOMA-R), an index of insulin sensitivity. However, even the most sensitive commercially available enzyme-linked immunosorbent assay (ELISA) kits cannot measure the very low F-IRI concentrations in normal rats and mice. Therefore, we sought to develop a new rodent insulin ELISA with greater sensitivity for low F-IRI concentrations. Despite repeated efforts, high-affinity antibodies could not be generated by immunizing mice with mouse insulin (self-antigen). Therefore, we generated two weak monoclonal antibodies (13G4 and 26B2) that were affinity maturated and used to develop a highly sensitive ELISA. The measurement range of the sandwich ELISA with the affinity maturated antibodies (13G4m1 and 26B2m1) was 1.5 to 30,000 pg/ml, and its detection limit was at least 10 times lower than those of commercially available kits. In conclusion, we describe the development of a new ultrasensitive ELISA suitable for measuring very low plasma insulin concentrations in rodents. This ELISA might be very useful in drug discovery research in diabetes.     

Towards soil management with Zn and Mn: estimates of fertilisation efficacy of Citrus trees

Nutrient management recommendations for fruit crops lack the understanding of the efficiency of soil fertilisation with manganese (Mn) and zinc (Zn), which could substitute, in part, the traditional foliar applications. Fruit yield of trees in response to Zn and Mn supply via soil may be limited either by sorption reactions with soil colloids or low solubility of fertilisers. We investigated the effects of fertiliser sources and rates of Mn and Zn applied to soils with different sorption capacities on nutrient uptake, biochemical responses and biomass of Citrus. Two experiments were carried out with 2‐year‐old sweet orange trees that received applications of Mn or Zn. The first experiment evaluated the application of Mn fertilisers (MnCO₃ and MnSO₄) at three levels of the nutrient (0, 0.7 and 3.5 g plant^?1 of Mn) in two types of soil (18.1% and 64.4% of clay, referred to as sandy loam and clay soils, respectively). The second experiment, likewise, evaluated Zn fertilisers (ZnO and ZnSO₄) and nutrient levels (0, 1.0 and 5.0 g plant^?1 of Zn). Application of Mn and Zn increased nutrient availability in the soils as well as leaf nutrient concentrations in the trees. The lowest rates, 0.7 g plant^?1 of Mn and 1.0 g plant^?1 of Zn, both as sulphate, were sufficient to supply these micronutrients to sufficient levels in leaves, flowers and fruits. Metal toxicity to plants occurred with higher doses of both nutrients and to a large extent in the sandy soil. In this case, protein bands lower than 25 kDa were observed as well a decrease on leaf chlorophyll content. In the clay soil, despite increased micronutrient concentrations in the plant, responses were less pronounced because of higher adsorption of metals in the soil. Superoxide dismutase (SOD, EC 1.15.1.1) isoenzyme activity was determined by non‐denaturing polyacrylamide gel electrophoresis (PAGE). The Cu/Zn‐SOD isoenzymes increased with increased Zn rates, but in contrast, when Mn was applied at the highest rate, the activity of Cu/Zn‐SODs decreased. The SOD activity pattern observed indicated increased production of superoxide and consequently an oxidative stress condition at the highest rates of Zn and Mn applied. The results demonstrated that the soil application of Mn and Zn can supply nutrient demands of orange trees, however the low solubility of fertilisers and the high sorption capacity of soils limit fertilisation efficiency. On the contrary, application of sulphate source in sandy soils may cause excess uptake of Mn and Zn and oxidative stress, which impairs the photosynthetic apparatus and consequently tree growth.