Analyzing the normal mode dynamics of macromolecules by the component synthesis method: Residue clustering and multiple-component approach

A study of the component synthesis method (CSM) for analyzing the normal mode dynamics of macromolecules is reported. The procedure involves a reduction of the dimensions of the normal mode problems for large molecular systems and the accurate extraction of the low-frequency modes. A macromolecule is divided into small components based on a hierarchical clustering of the residues in the structure. Interactions between coupled components are treated by the method of static correlation. The normal modes of the components are obtained first, and a fraction of the low-frequency normal modes of the components under mutual correlations are then used as a reduced basis for solving for the normal modes of the whole molecule. Multiple components are introduced for large macromolecules so that the dimensions of the eigenvalue problems at the component level are small. The method is applied to the protein crambin. In test calculations in which the dimensions of the eigenvalue equations are reduced to 1/6 of their natural size, the errors in the normal mode frequencies calculated by the CSM procedure are only about 1–2% when compared with the exact values. The rms fluctuations of all atoms in crambin calculated by the CSM procedure are basically identical to the exact results. The CSM procedure is shown to be accurate for calculating the normal modes of large macromolecules with a significant reduction of the size of the problem. © 1994 John Wiley & Sons, Inc.     

Developmental changes of glucocorticoid receptors in the rat pancreas

Glucocorticoids are known to play a role in the maturation of the exocrine pancreas. The exact mechanism of glucocorticoid action in pancreatic ontogeny is, however, not clear. The present study characterized and quantitated the binding of [3H]dexamethasone to cytosol fractions from pancreata of rats at various ages. Trunk blood samples from these rats were also checked for levels of free and bound corticosterone. Specific and saturable bindings for dexamethasone were found in pancreatic cytosol fractions from newborn suckling and adult rats. Competition studies showed a preference for steroids with glucocorticoid activity. Specific binding was relatively low in pancreatic cytosol from newly born and 1-day old pups. A significant rise was seen after day 15. Cytosolic binding capacities were greatest from pancreata obtained from pups at weaning (3rd to 5th weeks). Values then declined toward the adult level. Scatchard analysis revealed a single class of binding sites with a dissociation constant (Kd) of 7.3 (+/- 1.1) X 10(-8) M and number of binding sites equalled to 1.29 (+/- 0.18) X 10(-13) mole/mg of cytosolic protein in adult rat pancreas. Pancreata from 25- and 15-day old rats had Kds of 3.4 (+/- 0.8) X 10(-8) M and 2.7 (+/- 0.7) X 10(-8) M with the number of binding sites equal to 1.77 (+/- 0.21) X 10(-13) mole/mg protein and 1.31 (+/- 0.16) X 10(-13) mole/mg protein respectively. Total plasma corticosterone concentration was low before day 10. It rose significantly by day 15, peaked at day 25, and then declined after weaning. About 5-15% of corticosterone during weaning and about 20-30% before and after weaning were in the free form. The peak level of dexamethasone binding corresponded to an increase in the plasma corticosterone level during weaning. This suggests a close relationship between plasma corticosterone levels and pancreatic glucocorticoid receptors. Both may, therefore, play a role in pancreatic development in the rat.     

Chromosome aberration and ploidy equilibrium of Vicia faba in tissue culture

Summary Different phytohormone concentrations induced different fequencies of various chromosome aberrations in calli of Vicia faba. NAA 10 ppm plus KT 2.5 ppm produced more haploids and NAA 30 ppm plus NAA 7.5 ppm produced more tetraploids and breakage. The relationship among the aberrations was analyzed. The hypothesis of ploidy equilibrium was established. The chromosome doubling rate and reduction rate of each treated group were calculated in relation to the observed data and the hypothesis. The frequency of tetraploids and breakage are correlated with each other. The frequency of total aberrations is linearly correlated with that of micronucleus formation. The regression equation is x=31.92+ 10.67 y.     

Influence of GATC sequences on Escherichia coli DNA mismatch repair in vitro.

The effect of the number and position of DNA adenine methylation (dam) sites, i.e., d(GATC) sequences, on mismatch repair in Escherichia coli was investigated. The efficiency of repair was measured in an in vitro assay which used an f1 heteroduplex containing a G/T mismatch within the single EcoRI site. Both an increase in the number of dam sites and a shortened distance between dam site and mismatched site increased the efficiency of mismatch repair. The sequences adjacent to d(GATC) also affected the efficiency of methylation-directed mismatch repair. Furthermore, heteroduplexes with one extra dam site located close to either the 5' or 3' end of the excised base increased the repair efficiency to about the same extent. The findings suggest that the mismatch repair pathway has no preferred polarity.     

冬小麦春化过程中可溶性蛋白质组成的变化与形态发生的关系

冬小麦“农大139”经40天左右的春化处理才能迅速而整齐地抽穗,但经14—21天低温处理,已经具有在夏季抽穗的可能性,虽然抽穗推迟且极不整齐;再将春化时间延长,则抽穗百分比增加,且从播种到抽穗的时间缩短。这表明,春化过程中低温对发育的作用有两种效应:前期低温是诱发生理状态的转变,后期低温则只具有加速发育的作用,两个时期的转变是在春化的中期。蛋白质合成抑制剂乙基硫氨酸和对-氟苯丙氨酸能抑制冬小麦的春化,抑制时期也是在春化过程的中期。不同时间低温处理后冬小麦幼芽中可溶性蛋白质含量及组成发生了变化,春化过程中期(低温处理14天之后)不仅含量比对照增加了一倍,而且有新的蛋白质谱带出现。春麦中无类似现象,未经低温处理的春麦已含有冬麦中新出现的谱带。说明冬小麦春化过程的第14—21天左右是与春化过程有关的蛋白质合成的关键时期,该时期新合成的蛋白质与植株的发育状态之间存在着密切的相关关系。     

白兰瓜果实输入~(14)C-葡萄糖的转化与蔗糖合成

~(14)C 追踪试验结果表明,白兰瓜幼果中输入的~(14)C-葡萄糖,50%以上转化为稀酸水解和稀酸不水解的结构物质;果实发育后期,输入后48小时,在果肉和种子中分别只有18%和32%的~(14)C 参入结构物质。根据醇溶性糖的纸层析鉴定,幼果薄片渗入的~(14)C-葡萄糖仅转化为果糖,而发育后期果实则更多转化为蔗糖。显然,幼果的代谢模式是使物质和能量导向结构物质的形成;而后期果实生长已基本停止,物质代谢的方向又转向蔗糖合成的轨道上来。蔗糖合成底物试验结果表明,供给幼果不同底物都只有很低的蔗糖合成活性;发育后期果实供给UDPG+F-6-P 底物时可测出较高的蔗糖合成活性,初步推测白兰瓜中蔗糖合成主要是通过蔗糖磷酸酯合成酶来实现的。