Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.

We present an approach which can be used to identify native-like folds in a data base of protein conformations in the absence of any sequence homology to proteins in the data base. The method is based on a knowledge-based force field derived from a set of known protein conformations. A given sequence is mounted on all conformations in the data base and the associated energies are calculated. Using several conformations and sequences from the globin family we show that the native conformation is identified correctly. In fact the resolution of the force field is high enough to discriminate between a native fold and several closely related conformations. We then apply the procedure to several globins of known sequence but unknown three dimensional structure. The homology of these sequences to globins of known structures in the data base ranges from 49 to 17%. With one exception we find that for all globin sequences one of the known globin folds is identified as the most favorable conformation. These results are obtained using a force field derived from a data base devoid of globins of known structure. We briefly discuss useful applications in protein structural research and future development of our approach.     

Application of a directed conformational search for generating 3-D coordinates for protein structures from alpha-carbon coordinates.

A directed conformational search algorithm using the program CONGEN (ref. 3), which samples backbone conformers, is described. The search technique uses information from the partially built structures to direct the search process and is tested on the problem of generating a full set of backbone Cartesian coordinates given only alpha-carbon coordinates. The method has been tested on six proteins of known structure, varying in size and classification, and was able to generate the original backbone coordinates with RMSs ranging from 0.30-0.87A for the alpha-carbons and 0.5-0.99A RMSs for the backbone atoms. Cis peptide linkages were also correctly identified. The procedure was also applied to two proteins available with only alpha-carbon coordinates in the Brookhaven Protein Data Bank; thioredoxin (SRX) and triacylglycerol acylhydrolase (TGL). All-atom models are proposed for the backbone of both these proteins. In addition, the technique was applied to randomized coordinates of flavodoxin to assess the effects of irregularities in the data on the final RMS. This study represents the first time a deterministic conformational search was used on such a large scale.     

Phosphorus efficiency of plants

Föhse et al. (1988) have shown that P influx per unit root length in seven plant species growing in a low-P soil varied from 0.6×10^-14 to 4.8×10^-14 mol cm^-1s^-1. The objective of this work was to investigate the reasons for these differences. No correlation was found between P influx and root radius, root hairs, cation-anion balance and Ca uptake. However, when root hairs were included in mathematical model calculations, the differences of P influx could be accounted for. These calculations have shown that in soils low in available P, contribution to P uptake by root hairs was up to 90% of total uptake. The large contribution of root hairs to P uptake was partly due to their surface area, which was similar to that of the root cylinder. However, the main reason for the high P uptake efficiency of root hairs was their small radius (approx. 5×10^-4 cm) and their perpendicular growth into the soil from the root axis. Because of the small radius compared to root axes, P concentration at root hair surfaces decreased at a slower pace and therefore P influx remained higher. Under these conditions higher I_max (maximum influx) or smaller K_m values (Michaelis constant) increased P influx. The main reasons for differences found in P influx among species were the size of I_max and the number and length of root hairs. In a soil low in available P, plant species having more root hairs were able to satisfy a higher proportion of their P demand required for maximum growth.     

Theory of chaperonin action: inertial model for enhancement of prokaryotic Rubisco assembly.

We have performed a computational simulation of the aggregation and chaperonin-dependent reconstitution of dimeric prokaryotic ribulose bisphosphate carboxylase/oxygenase (Rubisco), based on the data of P. Goloubinoff et al. (1989, Nature 342, 884-889) and P. V. Viitanen et al. (1990, Biochemistry 29, 5665-5671). The aggregation is simulated by a set of 12 differential equations representing the aggregation of the Rubisco folding intermediate, Rubisco-I, with itself and with aggregates of Rubisco-I, leading up to dodecamers. Four rate constants, applying to forward or reverse steps in the aggregation process, were included. Optimal values for these constants were determined using the ellipsoid algorithm as implemented by one of us (Ecker, J.G. & Kupferschmid, M., 1988, Introduction to Operations Research, Wiley, New York, pp. 315-322). Intensive exploration of simpler aggregation models did not identify an alternative that could simulate the data as well as this one. The activity of the chaperonin in this system was simulated by using this aggregation model, combined with a model similar to that proposed by Goloubinoff et al. (1989). The model assumes that the chaperonin can bind the folding intermediate rapidly, and that the chaperonin complex releases the Rubisco molecule slowly, permitting time for its spontaneous folding while interacting with the chaperonin. This is followed by self-association of the folded Rubisco monomer to yield the active dimeric Rubisco. A modification of the model that simulates temperature effects was also constructed. The most important results we obtained indicate that the chaperonin-dependent reconstitution of Rubisco can be simulated adequately without invoking any catalysis of folding by the chaperonin. In addition, the simulations predict values for the association rate constant of Rubisco-I with the chaperonin, and other variables, that are subject to experimental verification.     

神农架金丝猴的生态学观察

金丝猴(Rhinopithecus roxellanae)仅产于我国,属国家Ⅰ级保护动物,自然分布于四川、陕西、甘肃的部分地区和湖北省神农架自然保护区。1983年以来,笔者对神农架金丝猴生存环境生态习性等作了长期观察研究,结果报道如下。     

多鳞铲颌鱼的生态适应性及地理分布成因的探讨

本文根据对多鳞铲颔鱼的分布、生物学特性及栖居河段的生态环境等所做的调查和研究,探讨了多鳞铲颌鱼的生态适应性及分布成因等问题。做为对北方寒冷气候的适应,多鳞铲颌鱼有蛰伏泉穴越冬的习性,越冬期近6个月;推测多鳞铲颌鱼是由原始鲃类演化来的,形成于更新世早期;现代分布状况可能是受第四纪冰期的影响而造成的。     

天南星科的生态地理和起源

本文将天南星科105个属的分布区归纳为12个分布类型和29个亚型,对每一类型的属进行生态地理分析。本科计有88个热带属,占全科的83.8％,是一个热带科。全科有两大分化中心:热带亚洲为属的多样化中心,热带美洲是种的分化中心。根据天南星科各属的生态地理研究,结合到科的系统发育程序,作者得出结论说:天南星科的原始类群在晚白垩纪时起源于亚洲大陆南缘,即欧亚古陆的亚洲南缘地带的水域生态环境。     

Root development and configuration in intensively managed radiata pine plantations

Summary In south-east Australia, where radiata pine (Pinus radiata D. Don) is grown on sandy soils low in nutrients and short of water, early establishment, and rapid growth to canopy closure lead to increased productivity. At this stage demands for nutrients and water are high, and trees respond vigorously to silvicultural inputs.For several months after transplanting in winter roots are confined within a narrow planting wedge, low temperature restricts new root growth and slows recovery from water stress in plants. From spring, depending upon the configuration and vigour of the roots transplanted, lateral roots extend radially throughout the soil.Although there were small decreases in concentration of roots radially from the stems of very young trees, such spatial differences disappeared between ages 2 and 3, so that rooting density was independent of distance from the stem. The pattern of vertical distribution of lateral roots was not influenced by age and 80–90% of the lateral roots were within the top 30 cm soil. Roots developed rapidly as the trees grew towards canopy closure, but in general the rooting densities of these pines are among the lowest reported for plants. In rapidly growing trees approaching canopy closure, the secondary thickening of the lateral roots was sufficient to double the weight of roots without altering root length.Knowledge about root growth and root configuration during the early phase of plantation development will assist management decisions where intensive silviculture is practiced, and hence ensure the most efficient use of nutrients and water.     

The habitat diversity and fish reproductive function of floodplain ecosystems

Synopsis Fish reproduction in floodplain ecosystems, based on relative abundance and total biomass of 0+ juveniles, was studied using the synchronic approach to typological analysis in conjunction with Point Abundance Sampling by modified electrofishing. In 3 different flood plains of the Upper Rhône River, 1015 point samples yielding 4573 juveniles (0+) from 21 species were collected from 48 ecosystems of various geomorphological origin. The results demonstrate the lotic-to-lentic succession of floodplain ecosystems to be a series of non-sequential reproductive zones, with spawning conditions being reflected by the specific composition and guild structure of the YOY fish assemblages. The habitat diversity and the fish reproductive potential of floodplain ecosystems are strongly influenced by geomorphological origin and by past and present hydrological conditions. The YOY assemblages of autogenically driven ecosystems (usually of anastomose or meander origin) tend to differ both in composition and in quantity from those found in allogenically driven ecosystems (generally of braided origin). Ecosystems of intermediate character, and fish reproduction thereof, occur as the result of either ecosystem rejuvenation or senescence: autogenically driven ecosystems by allogenic mechanisms, or allogenically driven ecosystems by anthropic and/or autogenic mechanisms, respectively. Because of co-occurrence of ecosystems at similar and at different successional status, the flood plain as an entity is seen as stable with respect to fish reproduction.     

南京地区繁缕和小繁缕群体的研究

繁缕(Stellaria media)和小繁缕(S.apetala)是两个形态相似的近缘种,有人把后者作为前者的亚种或变种来处理。本文通过对南京地区不同生境的三个自然群体和三个人工控制栽培群体的取样,以群体为单位,分别测算了叶、萼片、雄蕊、花瓣、果实和种子的8个数量性状的变异,绘制了多角形图;对花粉粒和种子进行了扫描;还通过花蕾套袋试验对种子活力作了检查。结果发现繁缕和小繁缕都是近亲繁殖植物,在形态上区别明显,对生态环境的要求基本相同,但小繁缕似更能耐受人为的践踏和刈割。