The trajectory of a stiff rod in a curved potential energy trough

The equilibrium trajectory of the axis of a rod subject to an externally imposed curved potential energy trough tends to conform to the shape of the curved trough, but also tends to be straight because of elastic resistance to bending. The actual path of the axis is a balance between the two extremes. We consider a potential energy trough centered along a circular arc of radiusR. For a rod of small length compared toR, we show that the axis at equilibrium forms an arc of a circle of radius greater thanR. The value of the radius of the axial path depends on the relative values of the Hooke’s Law bending constant for the rod and the depth and width of the trough. Motivation for the calculation is provided by nucleosomal DNA, which conforms to the surface of a roughtly cylindrical histone core at physiological ionic strength, but is observed to unwind into a partially extended conformation at very low ionic strength. We suggest that the rigidity to bending of short DNA segments becomes sufficiently great at low ionic strength to overcome attractive interactions with the histone surface. Alternately, of course, if during the cell cycle mutually attractive forces between DNA and histone core are weakened at constant ionic strength, the same type of unfolding would be expected to occur as the strength of the DNA-histone contacts drops below the level required to overcome elastic resistance to bending of the DNA rod.     

Appearance of a State 1 – State 2 transition during chloroplast development in the wheat leaf: Energetic and structural considerations

The ability of developing chloroplasts to dynamically regulate the distribution of excitation energy between photosystem 1 and photosystem 2, and thus perform a State 1 – State 2 transition, was examined from analyses of chlorophyll fluorescence kinetics in 4- and 8-day-old Triticum aestivum L. cv. Maris Dove leaves grown under a diurnal light regime. Chloroplasts at all stages of development in the two leaf systems could undergo a State 1 – State 2 transition, except those found in the basal 0.5 cm of the 4-day-old leaf. The ability to physiologically modify the excitation energy distribution between the chlorophyll matrices of the two photosystems developed after the development of mature, fully photochemically competent photosystem 2 units and the appearance of excitation energy transfer between photosystem 2 and photosystem 1. Also, changes in the degree of energetic interaction between the two photosystems, in vivo rates of electron transport and the chlorophyll a/b ratio could not be correlated with the appearance of a State 1 – State 2 transition. Ultrastructural studies demonstrated a 32% increase in the degree of thylakoid appression in chloroplasts at the base of the 8-day-old leaf compared to the situation in the basal 0.5 cm of the 4-day-old leaf. This difference in thylakoid stacking can account for the differing abilities of these two tissues to perform a State 1 – State 2 transition when considered in the context of the distribution of the two photosystems within appressed and non-appressed regions of thylakoid membranes.     

The semiquinone cycle. A hypothesis of electron transfer and proton translocation in cytochromebc-type complexes

The Q cycle and theb cycle are the main current models of action of the cytochromebc-type complexes of mitochondria, bacteria, and chloroplasts. Both are based on the concept, proposed in 1972, of two sequential one-electron oxidations of (ubi)quinol along two discrete pathways which operate at different redox potentials, and with bound semiubiquinone as an intermediate. The models differ in two respects, viz. in the pathway of electron transfer and the principle of linkage of electron transfer to proton translocation. In this article we outline a new model, called the semiquinone or, simply, SQ cycle, which is based on the electron transfer principles of theb cycle but which incorporates the Q cycle concept of direct coupling between electron transfer and proton translocation through action of ubiquinone.This paper is dedicated to the memory of Bob Casey, who died in Helsinki on the 2nd of August 1985.     

Thermodynamic stability of proteins in salt solutions: A comparison of the effectiveness of protein stabilizers

The denaturation of proteins by guanidine hydrochloride was studied in the presence of different concentrations of stabilizing salts, namely potassium phosphate, ammonium sulfate, and potassium acetate. The denaturation transition was followed by observing changes in the peptide circular dichroism atpH 7.0 and 25°C. From these results the free energy of stabilization for the process native denatured was determined. It was found that the stabilizing power of the anions increased in the order acetate < sulfate < phosphate, in agreement with the anionic lyotropic series. Ribonuclease A, which is known to have a site that can bind either a phosphate or a sulfate ion, showed a larger stabilization by these anions than that for lysozyme, pepsinogen, and myoglobin.     

生态系统与耗散结构

1977年,比利时著名科学家伊·普里高津成功地提出耗散结构理论,荣获了诺贝尔奖。普里高津的理论告诉我们:“一个远离平衡态的复杂系统,各元素的作用具有非线性特点,正是这种非线性的相关机制,导致了大量离子的协同动作,突变而产生有序结构。”普里高津的耗散结构理论,研究系统怎样从混沌无序的动态向稳定有序的结构组织演化及其规律,故也称为非平衡系统自组织理论。这一系统理论的奇葩,对于生态系统的深入研究将起到不可估量的作用。同时,这一理论使我们对生态     

Structural basis of hierarchical multiple substates of a protein. II: Monte Carlo simulation of native thermal fluctuations and energy minimization

Conformational fluctuations in a globular protein, bovine pancreatic trypsin inhibitor, in the time range between picoseconds and nanoseconds are studied by a Monte Carlo simulation method. Multiple energy minima are derived from sampled conformations by minimizing their energy. They are distributed in clusters in the conformational space. A hierarchical structure is observed in the simulated dynamics. In the time range between 10(-14) and 10(-10) seconds dynamics is well represented by a superposition of vibrational motions within an energy well with transitions among minima within each cluster. Transitions among clusters take place in the time range of nanoseconds or longer.     

Use of restrained molecular dynamics in water to determine three-dimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II

Refinement of distance geometry (DG) structures of EETI-II (Heitz et al.: Biochemistry 28:2392-2398, 1989), a member of the squash family trypsin inhibitor, have been carried out by restrained molecular dynamics (RMD) in water. The resulting models show better side chain apolar/polar surface ratio and estimated solvation free energy than structures refined "in vacuo." The consistent lower values of residual NMR constraint violations, apolar/polar surface ratio, and solvation free energy for one of these refined structures allowed prediction of the 3D folding and disulfide connectivity of EETI-II. Except for the few first residues for which no NMR constraints were available, this computer model fully agreed with X-ray structures of CMTI-I (Bode et al.: FEBS Lett. 242:285-292, 1989) and EETI-II complexed with trypsin that appeared after the RMD simulation was completed. Restrained molecular dynamics in water is thus proved to be highly valuable for refinement of DG structures. Also, the successful use of apolar/polar surface ratio and of solvation free energy reinforce the analysis of Novotny et al. (Proteins 4:19-30, 1988) and shows that these criteria are useful indicators of correct versus misfolded models.     

Differences in low pH tolerance among closely related sunfish of the genus Enneacanthus

Synopsis Three closely related sunfish in the genus Enneacanthus were examined to determine if differences existed in their tolerance to low pH that could explain their contrasting distributions. Na fluxes of E. obesus, E. gloriosus, and E. chaetodon were measured during 12 h exposure to pH 4.0 and 3.5 (all species), and 3.25 (former 2 species only). All experienced ionic disturbances upon acid exposure resulting from inhibition of active Na influx and stimulation of passive Na efflux, but E. gloriosus and E. chaetodon experienced greater disturbances than E. obesus at all pH's tested. Body and plasma Na concentrations of E. gloriosus were measured after one week of exposure to a range of pH's for comparison with previously published data from E. obesus. Exposure to pH 4.0 and below caused a depression in body and plasma Na concentration of E. gloriosus, and only two of 10 fish survived the one week test period at pH 3.5; none survived at pH 3.25. In contrast, exposure to pH 4.0 for five weeks had no effect on body Na concentration of E. obesus, all 10 fish survived exposure to pH 3.5 for two weeks. Growth of E. gloriosus and E. obesus were measured separately during 12 weeks of exposure to a range of pH's. E. gloriosus exposed to pH 4.25 and 4.0 grew at a lower rate than those at higher pH's (4.5, 5.0, and 5.8), and body Na concentrations of fish at pH's 4.25 and 4.0 were significantly less than the others. With declining pH E. obesus did not exhibit reduced growth until pH 3.75 was reached; no depression in body Na concentration occurred at this pH. These results show that there are marked differences in low pH tolerance among closely related species of Enneacanthus which could affect their distributions and competitive interactions.     

Milling energy requirement of the aneuploid stocks of common wheat,including alien addition lines

Summary Aneuploid stocks, which included Triticum aestivum/alien, disomic, chromosome addition lines, wheat/alien, ditelosomic, chromosome addition lines, and the available aneuploids of Chinese Spring wheat, were used to locate genes that influence milling energy requirement (ME). Genes that affected ME were found on all seven homoeologous chromosome groups. The addition of complete wheat chromosomes 1B, 1D, 2A, 2D, 5B, 6B, 7B and 7D increased ME. Positive effects were also found in specific chromosome arms: 1BS, 2DS, 5AS, 5BS and 6BL. Wheat chromosome 3B conditioned low ME and the gene(s) responsible was located on the short arm. Other negative effects were attributed to wheat chromosome arms 4BL, 4DL, 5DS and 6DS. Alien chromosome additions that conferred high ME included 2H, 5H, 6H and 7H of barley, Hordeum vulgare and 2R, 2R, 4R, 4RL, 6R, 6RL and 7RL of rye, Secale cereale. Those that conferred a low ME included 1H ^ch of H. chilense, and 6u and 7u of Aegilops umbellulata, 5R and 5RS of S. cereale and 5R ^m and 5R ^mS of S. montanum. Although the control of ME is polygenic, there is a major effect of genes located on the short arms of homoeologous group 5 chromosomes.