A world of cytochrome P450s

The world we live in is a biosphere influenced by all organisms who inhabit it. It is also an ecology of genes, with some having rather startling effects. The premise put forth in this issue is cytochrome P450 is a significant player in the world around us. Life and the Earth itself would be visibly different and diminished without cytochrome P450s. The contributions to this issue range from evolution on the billion year scale to the colour of roses, from Darwin to Rachel Carson; all as seen through the lens of cytochrome P450.     

Structure-wise discrimination of adenine and guanine by proteins on the basis of their nonbonded interactions

We have analyzed the nonbonded interactions of the structurally similar moieties, adenine and guanine forming complexes with proteins. The results comprise (a) the amino acid–ligand atom preferences, (b) solvent accessibility of ligand atoms before and after complex formation with proteins, and (c) preferred amino acid residue atoms involved in the interactions. We have observed that the amino acid preferences involved in the hydrogen bonding interactions vary for adenine and guanine. The structural variation between the purine atoms is clearly reflected by their burial tendency in the solvent environment. Correlation of the mean amino acid preference values show the variation that exists between adenine and guanine preferences of all the amino acid residues. All our observations provide evidence for the discriminating nature of the proteins in recognizing adenine and guanine.     

Population Changes of Heterodera glycines and Soybean Yields Resulting from Soil Treatment with Alachlor,Fenamiphos, and Ethoprop

The population dynamics of Heterodera glycines as influenced by alachlor, fenamiphos, and ethoprop alone and in herbicide-nematicide combinations were studied in the field. Numbers of H. glycines juveniles and eggs were higher at midseason and harvest where nematicides were applied. Fenamiphos alone or in combination with alachlor provided better control of H. glycines and greater seed yields than treatments with ethoprop. Numbers of H. glycines eggs at harvest in 1980 were positively correlated with numbers of juveniles at planting in 1981 and negatively related to seed yield in 1981.     

Self-association of glutamic acid-rich fusion peptide analogs of influenza hemagglutinin in the membrane-mimic environments: Effects of positional difference of glutamic acids on side chain ionization constant and intra- and inter-peptide interactions deduced from NMR and gel electrophoresis measurements

Two glutamic acid-rich fusion peptide analogs of influenza hemagglutinin were synthesized to study the organization of the charged peptides in the membranous media. Fluorescence and gel electrophoresis experiments suggested a loose association between the monomers in the vesicles. A model was built which showed that a positional difference of 3, 7 and 4, 8 results in the exposure of Glu3 and Glu7 side chains to the apolar lipidic core. Supportive results include: first, pK_a values of two pH units higher than reference value in aqueous medium for Glu3 and Glu7 CγH, whereas the deviation of pK_a from the reference value for Glu4 and Glu8 CγH is substantially smaller; second, Hill coefficients of titration shift of these protons indicate anti-cooperativity for Glu3 and Glu7 side chain protons but less so for Glu4 and Glu8, implying a strong electrostatic interaction between Glu3 and Glu7 possibly resulting from their localization in an apolar environment; third, positive and larger titration shift for NH of Glu3 is observed compared to that of Glu4, suggesting stronger hydrogen bond between the NH and the carboxylic group of Glu3 than that of Glu4, consistent with higher degree of exposure to hydrophobic medium for the side chain of Glu3.     

Interaction of almond cystatin with pesticides: Structural and functional analysis

Pesticides are chemical substances that eliminate or control a variety of agricultural pests that damage crops and livestock. They not only affect the targeted pests but also affect the nontargeted systems, raising more concerns for their effect on both plant and animal systems. Cystatins (cysteine protease inhibitor) are ubiquitously present in all living cells and show a variety of important physiological functions. The present study shows the effect of different pesticides (pendimethalin, methoxyfenozide, and Cu^II hydroxide) on purified almond cystatin. Almond cystatin showed concentration‐dependent loss in papain inhibitory activity on interaction with the pesticides, showing maximum loss in the presence of Cu(II) hydroxide and minimum in the case of methoxyfenozide. Native polyacrylamide gel electrophoresis showed maximum degradation of purified cystatin in the presence of Cu(II) hydroxide with insignificant effect in the presence of methoxyfenozide. Structural alterations were significant in the case of Cu(II) hydroxide and less in the case of methoxyfenozide as revealed by UV and fluorescence spectral studies. Secondary structural alterations were further conformed by circular dichroism and Fourier transform infrared spectroscopy. The α‐helix content of almond cystatin decreases from 35.64% (native) to 34.83%, 30.79%, and 29.62% for methoxyfenozide‐, pendimethalin‐, and Cu(II) hydroxide–treated cystatin, respectively. A Fourier transform infrared study shows an amide I band shift for almond cystatin from 1649.15 ± 0.5 to 1646.48 ± 0.6, 1640.44 ± 0.6, and 1635.11 ± 0.3 cm⁻¹ for methoxyfenozide, pendimethalin, and Cu(II) hydroxide, respectively. Values obtained for different thermodynamic parameters (ΔH ⁰, ΔG ⁰, N , and ΔS ⁰) by isothermal titration calorimetric experiments reveal maximum binding of almond cystatin with Cu(II) hydroxide followed by pendimethalin and little interaction with methoxyfenozide.     

Non-target effects of repeated methiocarb slug pellet application on carabid beetle (Coleoptera: Carabidae) activity in winter-sown cereals

The effects of repeated annual application of methiocarb-based slug pellets, broadcast on the soil surface and drilled into the seed bed, on carabid beetle activity were investigated over a four year period on a winter-sown cereal field using pitfall traps in barriered plots. Following applications in late autumn all winter-active carabid populations were severely depressed; total carabid activity falling to less than 5% and 10–15% following broadcast and drilled applications, respectively, compared with untreated plots. Spring and summer-active species, not active at the time of application, were largely unaffected by applications and were responsible for a gradual recovery of total activity from early spring onwards. Activity of all affected winter species remained demonstrably depressed on treated areas for the remainder of their seasonal incidence. However, all except one species, Bembidion obtusum, recovered to normal activity levels in the following season prior to reapplication. Recovery patterns are discussed in terms of the known biology of the species involved. Evidence that a minority of summer-active species were also affected by treatments, sometimes positively and sometimes negatively, were attributed to indirect effects possibly involving prey availability and foraging behaviour. The long-term ecological and short-term agronomic implications of methiocarb effects on carabid populations in winter-sown cereals are discussed.     

色氨酸残基在磷酸烯醇式丙酮酸羧化酶催化功能中的作用

在pH7.5条件下,用NBS对PEP羧化酶中色氨酸残基进行共价修饰表明,PEP羧化酶中48个色氨酸残基均能被NBS修饰。用邹承鲁图解法求得,其中4个残基为酶表现催化活性所必需的。 PEP羧化酶的变构效应剂G6P、Gly及Mal分别与酶预保温后,再经NBS修饰,前两种处理中,同样浓度的NBS所用修饰的色氨酸残基数和处理后的残存酶活与对照相比有很大的差异,而用Mal处理的,两者与对照相差无几。     

Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds.

The local environment of an amino acid in a folded protein determines the acceptability of mutations at that position. In order to characterize and quantify these structural constraints, we have made a comparative analysis of families of homologous proteins. Residues in each structure are classified according to amino acid type, secondary structure, accessibility of the side chain, and existence of hydrogen bonds from the side chains. Analysis of the pattern of observed substitutions as a function of local environment shows that there are distinct patterns, especially for buried polar residues. The substitution data tables are available on diskette with Protein Science. Given the fold of a protein, one is able to predict sequences compatible with the fold (profiles or templates) and potentially to discriminate between a correctly folded and misfolded protein. Conversely, analysis of residue variation across a family of aligned sequences in terms of substitution profiles can allow prediction of secondary structure or tertiary environment.     

长叶车前花叶病毒(HRV_(sh))外壳蛋白赖氨酸残基的修饰

我们曾报道长叶车前花叶病毒上海分离株(简称HRVsh)的外壳蛋白有二个赖氨酸残基,在PH8.5无变性剂存在的条件下,完整病毒颗粒表面的赖氨酸残基可与三硝基苯磺酸(TNPS)起反应,反应后的TNP-HRVsh病毒颗粒的感染力丧失达90％以上。 本文又进行了甲基乙亚胺甲酯(MEI)对HRVsh赖氨酸残基的修饰反应,修饰后的MEI-HRVsh病毒颗粒的感染力也同样丧失90％以上。 从三硝基苯磺酸修饰的病毒颗粒(TNP-HRVsh)中分离得到的RNA能与天然的HRVsh的外壳蛋白重建病毒颗粒,并具有感染力,说明修饰过程中核酸并不受影响。 进一步用同位素~(35)S,~(32)P双标记病毒,再以TNPS修饰标记的病毒,得到(~(35)S,~(32)P)-HRVsh及TNP-(~(35)S,~(32)P)-HRVsh。将两者分别接种于系统寄主青菜(Brassica chinensis)的一片叶片,一天后在非接种叶片上都可测得~(35)S,~(32)P的放射计数。其中,(~(35)S,~(32)P)-HRVsh的~(35)S/~(32)P比值降低了,而TNP-(~(35)S,~(32)P)-HRVsh的~(35)S/~(32)P比值保持不变。说明HRVsh外壳蛋白赖氨酸残基的修饰并不影响病毒颗粒进入寄主细胞,以及在寄主细胞间的转移。同位素双标记的结果表明,其感染力丧失的原因可能是由于上述修饰作用阻止了病毒在感染中所必须的脱壳过程。