Stabilization of T4 polynucleotide kinase by macromolecular crowding.

T4 polynucleotide kinase rapidly loses activity during its reaction on duplex DNA termini. Addition of high concentrations of nonspecific polymers reverses or prevents this inactivation. In contrast, additions of related materials of lower molecular weight are relatively ineffective in stabilizing the kinase. Such a pattern suggests that the stabilizing effects of polymers on kinase activity are due to macromolecular crowding. An effect of crowding on the known tendency of the kinase to undergo oligomerization reactions is consistent with our observations.     

Aggregation in the lime aphid (Eucallipterus tiliae L.)

Summary Lime aphids feed on the contents of sieve tubes in the leaf veins. Aphids on the undersides of large leaves tend to select the smallest veins, while those on small leaves tend to select the larger veins. This tendency increases with the size of the aphid. Since only 4% of the total leaf area is covered by the larger veins, crowding is imposed on those aphids feeding from them. In spring, when the leaves are young and small, close spacing of the aphids results due to their tendency to select large veins. In summer, when the leaves are mature and large, wider spacing between aphids occurs due to their tendency to occupy more of the leaf surface.     

Excluded volume effects on the refolding and assembly of an oligomeric protein. GroEL, a case study

We have studied the effect of macromolecular crowding reagents, such as polysaccharides and bovine serum albumin, on the refolding of tetradecameric GroEL from urea-denatured protein monomers. The results show that productive refolding and assembly strongly depends on the presence of nucleotides (ATP or ADP) and background macromolecules. Nucleotides are required to generate an assembly-competent monomeric conformation, suggesting that proper folding of the equatorial domain of the protein subunits into a native-like structure is essential for productive assembly. Crowding modulates GroEL oligomerization in two different ways. First, it increases the tendency of refolded, monomeric GroEL to undergo self-association at equilibrium. Second, crowding can modify the relative rates of the two competing self-association reactions, namely, productive assembly into a native tetradecameric structure and unproductive aggregation. This kinetic effect is most likely exerted by modifications of the diffusion coefficient of the refolded monomers, which in turn determine the conformational properties of the interacting subunits. If they are allowed to become assembly-competent before self-association, productive oligomerization occurs; otherwise, unproductive aggregation takes place. Our data demonstrate that the spontaneous refolding and assembly of homo-oligomeric proteins, such as GroEL, can occur efficiently (70%) under crowding conditions similar to those expected in vivo.     

Does the crowded cell-like environment reduce the chaperone-like activity of α-crystallin?

The effect of crowding on the chaperone-like activity of α-crystallin has been studied using aggregation of UV-irradiated glycogen phosphorylase b (Phb) from rabbit skeletal muscle as an aggregation test system. The merit of this test system is the possibility of testing agents that directly affect the stage of aggregation of the protein molecules. It was shown that the solution of Phb denatured by UV contained aggregates with a hydrodynamic radius of 10.4 nm. These aggregates are relatively stable at 20 °C; however, they reveal a tendency to stick further in the presence of crowding agents. The study of the effect of α-crystallin on the aggregation of UV-irradiated Phb in the presence of the crowding agents by dynamic light scattering at 37 °C showed that under crowding conditions the antiaggregation ability of α-crystallin was weakened. On the basis of the analytical ultracentrifugation, size-exclusion chromatography, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis data, the scheme of interaction of UV-irradiated Phb and α-crystallin has been proposed. It is assumed that chaperone-target protein complexes of two types are formed, namely, the complexes of dissociated forms of α-crystallin with a protein substrate and high-mass α-crystallin-denatured protein complexes. The complexes of the first type reveal a weak propensity to aggregate even under crowding conditions. The complexes of the second type are characterized by the lower rate of aggregation in comparison with that of original UV-irradiated Phb. However, crowding stimulates the rate of aggregation of these complexes, resulting in the above-mentioned decrease in the chaperone-like activity of α-crystallin.     

大分子拥挤对DNA结构的影响

大分子拥挤(macromolecular crowding effect)代表了细胞内高度拥挤状态,其源于非特异性容积排斥效应,是细胞内与pH、离子强度等同等重要的生理因素。生物大分子介导的拥挤环境对于DNA-DNA、DNA-蛋白质的相互作用以及DNA高级结构、细胞核或核区结构的稳定具有重要作用。在拥挤环境中,大分子总浓度的增加将增强溶质的浓缩倾向,从而降低溶液的自由能。拥挤效应是胞内大分子环境的总体反映,具有高度的缓冲性,保证了胞内反应的稳定进行及细胞功能的正常行使。     

Three-dimensional stochastic off-lattice model of binding chemistry in crowded environments

Molecular crowding is one of the characteristic features of the intracellular environment, defined by a dense mixture of varying kinds of proteins and other molecules. Interaction with these molecules significantly alters the rates and equilibria of chemical reactions in the crowded environment. Numerous fundamental activities of a living cell are strongly influenced by the crowding effect, such as protein folding, protein assembly and disassembly, enzyme activity, and signal transduction. Quantitatively predicting how crowding will affect any particular process is, however, a very challenging problem because many physical and chemical parameters act synergistically in ways that defy easy analysis. To build a more realistic model for this problem, we extend a prior stochastic off-lattice model from two-dimensional (2D) to three-dimensional (3D) space and examine how the 3D results compare to those found in 2D. We show that both models exhibit qualitatively similar crowding effects and similar parameter dependence, particularly with respect to a set of parameters previously shown to act linearly on total reaction equilibrium. There are quantitative differences between 2D and 3D models, although with a generally gradual nonlinear interpolation as a system is extended from 2D to 3D. However, the additional freedom of movement allowed to particles as thickness of the simulation box increases can produce significant quantitative change as a system moves from 2D to 3D. Simulation results over broader parameter ranges further show that the impact of molecular crowding is highly dependent on the specific reaction system examined.     

Variability in migratory tendency within and among natural populations of the pea aphid,Acyrthosiphon pisum

Summary The migratory tendencies of pea aphids were measured by determining the numbers of winged and non-winged offspring produced by parthenogenetic wingless females after a crowding test. Sources of variability in this measure were investigated. The migratory tendency of an individual clone was found to be stable. Spatial and temporal patterns in migratory tendency were found among nine natural populations. These patterns probably reflect differences in the frequencies of a large number of genetically distinct clones. Hypotheses based on the relative fitness of immigrant and resident clones and the heritability of migratory tendency are offered to account for these results. High migration rates may be required to account for genetic differentiation within and among some parthenogenetic populations of the pea aphid.     

The contrasting effect of macromolecular crowding on amyloid fibril formation

Background

Amyloid fibrils associated with neurodegenerative diseases can be considered biologically relevant failures of cellular quality control mechanisms. It is known that in vivo human Tau protein, human prion protein, and human copper, zinc superoxide dismutase (SOD1) have the tendency to form fibril deposits in a variety of tissues and they are associated with different neurodegenerative diseases, while rabbit prion protein and hen egg white lysozyme do not readily form fibrils and are unlikely to cause neurodegenerative diseases. In this study, we have investigated the contrasting effect of macromolecular crowding on fibril formation of different proteins.

Methodology/Principal Findings

As revealed by assays based on thioflavin T binding and turbidity, human Tau fragments, when phosphorylated by glycogen synthase kinase-3β, do not form filaments in the absence of a crowding agent but do form fibrils in the presence of a crowding agent, and the presence of a strong crowding agent dramatically promotes amyloid fibril formation of human prion protein and its two pathogenic mutants E196K and D178N. Such an enhancing effect of macromolecular crowding on fibril formation is also observed for a pathological human SOD1 mutant A4V. On the other hand, rabbit prion protein and hen lysozyme do not form amyloid fibrils when a crowding agent at 300 g/l is used but do form fibrils in the absence of a crowding agent. Furthermore, aggregation of these two proteins is remarkably inhibited by Ficoll 70 and dextran 70 at 200 g/l.

Conclusions/Significance

We suggest that proteins associated with neurodegenerative diseases are more likely to form amyloid fibrils under crowded conditions than in dilute solutions. By contrast, some of the proteins that are not neurodegenerative disease-associated are unlikely to misfold in crowded physiological environments. A possible explanation for the contrasting effect of macromolecular crowding on these two sets of proteins (amyloidogenic proteins and non-amyloidogenic proteins) has been proposed.     

Density-dependent natural selection in Drosophila: Adaptation to adult crowding

The effects of adult crowding on two components of fitness were studied in three sets of Drosophila melanogaster populations, subjected to life-stage-specific, density-dependent natural selection in the laboratory for over 50 generations. Three days of crowding, early in adult life, were observed to increase mortality significantly during the episode of crowding, as well as decrease subsequent fecundity. Populations selected for adaptation to high adult densities suffered significantly lower mortality during episodes of adult crowding, as compared to populations selected specifically for adaptation to larval crowding, as well as control populations typically maintained at low larval and adult densities. Moreover, populations adapted to larval crowding seemed to be adversely affected by adult crowding to a greater extent than the controls, raising the possibility of trade-offs between adaptations to larval and adult crowding, respectively. Preliminary evidence suggests that the populations adapted to adult crowding may have evolved a propensity to stay away from the food medium, which is where most deaths occur when adults are crowded in culture vials. This revised version was published online in July 2006 with corrections to the Cover Date.     

Effects of nutrient level on thinning and non-thinning crowding in even-aged populations of subterranean clover

Populations of subterranean clover were used to examine the effect of lowering nutrient supply on crowding in even-aged monospecific populations. Two hypotheses were being tested. Under one, termed ‘altered-speed’, reducing the nutrient supply to populations merely slows down the crowding process. Under the other, called ‘altered-form’, reducing the nutrient supply intensifies the crowding process (Morris & Myerscough 1984). The populations were grown at eight densities of sowing and three levels of nutrient supply. Non-thinning yield-density curves and self-thinning lines were fitted to the data. For the thinning populations, reducing the nutrient supply led to altered-form crowding, with thinning lines of reduced slope and intercept for total and shoot weight being observed in populations grown at lower levels of nutrient supply. For the non-thinning yield-density curves, lowering the nutrient supply did alter crowding effects, but not to the extent necessary to give full altered-form crowding. Rather, crowding effects intermediate between altered-speed and altered-form were observed. No altered-speed crowding was observed in this experiment. Comparison was made between the altered-speed crowding observed in other data (Hozumi & Ueno 1954: White & Harper 1970) with the altered-form crowding observed here and elsewhere (Hozumi & Ueno 1954). In these data, altered-form crowding was consistently associated with an increase in the proportion of root in the plants' growth as nutrient level was reduced, while in altered-speed crowding there was a complete lack of any such nutrient effect on root-shoot proportion. This was taken as evidence that under altered-speed crowding, variations in the level of nutrient supply did not lead to major change in the way that plants interfered with each other. For altered-form crowding, major change in the way plants interfered with each other's growth did occur as nutrient level fell.     

Self-association of polynucleosome chains by macromolecular crowding

The crowding of macromolecules in the cell nucleus, where their concentration is in the range of 100 mg/ml, is predicted to result in strong entropic forces between them. Here the effects of crowding on polynucleosome chains in vitro were studied to evaluate if these forces could contribute to the packing of chromatin in the nucleus in vivo. Soluble polynucleosomes approximately 20 nucleosomes in length formed fast-sedimenting complexes in the presence of inert, volume-occupying agents poly(ethylene glycol) (PEG) or dextran. This self-association was reversible and consistent with the effect of macromolecular crowding. In the presence of these crowding agents, polynucleosomes formed large assemblies as seen by fluorescence microscopy after labelling DNA with the fluorescent stain DAPI, and formed rods and sheets at a higher concentration of crowding agent. Self-association caused by crowding does not require exogenous cations. Single, approximately 800 nucleosome-long chains prepared in 100 muM Hepes buffer with no added cations, labelled with the fluorescent DNA stain YOYO-1, and spread on a polylysine-coated surface formed compact 3-D clusters in the presence of PEG or dextran. This reversible packing of polynucleosome chains by crowding may help to understand their compact conformations in the nucleus. These results, together with the known collapse of linear polymers in crowded milieux, suggest that entropic forces due to crowding, which have not been considered previously, may be an important factor in the packing of nucleosome chains in the nucleus.     

Capitula in the Asteridae: A widespread and varied phenomenon

The presence of capitula, the head-type of inflorescences, is widespread in the Asterideae. Several families, predominantly terminal in the clade, display the tendency of maximizing reproductive output by condensing indeterminate inflorescences to the point of capitulum formation. This is accomplished by the process of halting or suppressing development of the internodes, an example of paedomorphosis of the progenesis type. This tendency is either infrequent or absent in the basal members of the Asteridae. When inflorescence condensation is present, closely related taxa often demonstrate the progression of the paedomorphosis. More examples of capitulum formation are found in the more advanced families, culminating with the Asteraceae, almost all of which display fully condensed capitula of some sort. Other phenomena are also apparent besides the basic inflorescence condensation. Edge effects are often seen, ranging from a mere crowding of the outermost flowers to the formation of additional flower types. In some taxa, inflorescence condensation continues beyond the basic capitulum form, yielding even more condensed inflorescences that then become determinate. More highly condensed inflorescences have independently evolved several times in the Asteraceae, and some tertiarily condensed inflorescences have evolved as well.     

Density-dependent accumulation of phase characteristics in a natural population of the desert locust Schistocerca gregaria

Abstract. Phase characteristics of locusts from parents that experienced different population densities were investigated under field conditions in Morocco. The density experienced by adults induced a marked phase change in colour, behaviour and morphometry of their offspring. A high-density subpopulation gave rise to a preponderance of black hatchlings that exhibited a high level of aggregation as later stage nymphs and showed gregarious morphometric features as adults, whereas a low-density subpopulation produced a majority of green hatchlings with a lesser tendency to group as final-instar nymphs and more solitarious morphometry as adults. The constrained isolation of insects from the low-density subpopulation, or crowding of insects from the high-density subpopulation, resulted in a behavioural and morphometric change towards even more solitarious characteristics in the former and more pronounced gregarious characteristics in the latter, relative to field-caught insects of the same age. These results from the field are consistent with those in the laboratory and provide more evidence for the dual roles of an individual locust's experience of crowding as well as that of its parents in density-dependent phase change.     

目标和干扰子之间的拓扑性质差异可以削弱拥挤效应

"拥挤效应"被认为是外周视觉物体辨认过程中的一个重要瓶颈.它是指当目标被干扰子包围,在外周视野呈现时,观察者辨认目标的能力被大大削弱,尤其是当目标和干扰子之间存在某种相似性时.许多研究分别试图在不同层次上提出解释这一现象的机制.本文通过三个实验,使用了不同的视觉刺激图形的辨认任务(例如,三角形和箭头的朝向判断、数字和字母的辨认以及S形图形的朝向辨认),测量了目标和干扰子之间中心距离的阈值,结果一致地发现,当目标和干扰子之间存在拓扑性质差异(洞的个数差异)时,拥挤效应会显著降低,并且排除了目标和干扰子之间的主观相似性、形状和面积差异等可能的因素.从知觉组织的角度验证了当目标和干扰子之间存在拓扑性质差异时,拥挤效应会显著降低,这是首次发现的一个影响拥挤效应的新的维度.本文结果不仅为拥挤效应的机制提供了一个新的解释,也为大范围首先拓扑知觉在知觉物体形成中的作用提供了支持性证据.     

Effect of molecular crowding on the enzymes of glycogenolysis

Cell cytoplasm contains high concentrations of macromolecules occupying a significant part of the cell volume (crowding conditions). According to modern concepts, crowding has a pronounced effect on the rate and equilibrium of biochemical reactions and stimulates the formation of more compact structures. This review considers different aspects of the crowding effect in vivo and in vitro, its role in regulation of cell volume, the effect of crowding on various interactions, such as protein-ligand and protein-protein interactions, as well as on protein denaturation, conformation transitions of macromolecules, and supramolecular structure formation. The influence of crowding arising from the presence of high concentrations of osmolytes on the interactions of the enzymes of glycogenolysis has been demonstrated. It has been established that, in accordance with predictions of crowding theory, trimethylamine N-oxide (TMAO) and betaine highly stimulate the association of phosphorylase kinase (PhK) and its interaction with glycogen. However, high concentrations of proline, betaine, and TMAO completely suppress the formation of PhK complex with phosphorylase b (Phb). The protective effect of osmolyte-induced molecular crowding on Phb denaturation by guanidine hydrochloride is shown. The influence of crowding on the interaction of Phb with allosteric inhibitor FAD has been revealed. The results show that, under crowding conditions, the equilibrium of the isomerization of Phb shifts towards a more compact dimeric state with decreased affinity for FAD.     

Genetic variation of density responses in relation to wing polymorphism in the oriental chinch bug,Cavelerius saccharivorus Okajima (Heteroptera: Lygaeidae)

Responses to nymphal density in the determination of wing form were compared between the offspring from brachypter x brachypter crosses and those from macropter x macropter crosses of the oriental chinch bug, Cavelerius saccharivorus. In the offspring from crosses between macropters, there was a strong tendency for macropters to increase to a rather high level with increasing nymphal density in both sexes. In contrast to this, in the offspring from crosses between brachypters, the appearance rate of macropters attained a maximum value in moderately crowded conditions and conversely decreased to a lower level in more crowded conditions in both sexes. Thus density response patterns concerning the determination of wing form were quite different between the offspring from different crosses in the wing form, indicating that there is a genetic basis underlying wing polymorphism in this species. As for the body size of emerged adults, macropters tended to be larger than brachypters in the same crowded condition. Moreover, the rate of decrease of body size with nymphal density was lower in the offspring from crosses between macropters than in the offspring from crosses between brachypters. This indicated that the former offspring are more tolerant of nymphal crowding than the latter. The difference in such a tolerance against nymphal crowding between the offspring from different crosses was considered to be related to the difference in the appearance of macropters in the crowded conditions between them.     

Effect of the acute crowding stress on the rat brown adipose tissue metabolic function

Our previous results have shown that metabolic and thermal stressors influence interscapular brown adipose tissue (IBAT) metabolic activity by increasing oxygen consumption and, consequently, altering the toxic reactive oxygen species (ROS) production and the antioxidative system activity. Since there is not enough evidence about the effect of psychosocial stressors on these processes, we studied the effect of acute crowding stress on the IBAT and hypothalamic monoamine oxidase (MAO) activity as well as IBAT antioxidative enzymes, manganese (MnSOD), copper-zinc superoxide dismutase (CuZnSOD) and catalase (CAT), as the relevant indicators of IBAT metabolic alternations under the stress exposure and the returning of animals to control conditions. The results indicated that acute crowding stress did not change the hypothalamic and IBAT MAO activities, the generation of ROS and, consequently, the IBAT CuZnSOD and CAT activities. However, all three antioxidative enzymes were affected only after the recovery period. It seems that peripheral overheating of rats during acute crowding changes the stress nature, by becoming more thermal than psychosocial and by suppression the hypothalamic efferent pathways involved in the IBAT thermogenesis regulation. However, it seems that returning of the animals to the control conditions after the stress termination causes the reactivation of IBAT thermogenesis with tendency to normalise the body temperature.     

The ecology of sexual selection: Mean crowding of females and resource-defence polygyny

Summary Resource-defence polygyny is a mating system that offers an opportunity for strong sexual selection. I express the degree of aggregation or clustering of females at resources at the time of mating using Lloyd's measures of microspatial aggregation, mean crowding (m ^*) and patchiness (P). Here, I show that Lloyd's two ecological measures of aggregation can be used to quantify the relationship between resource-based polygyny and sexual selection. The advantage of using these measures is that some of the statistical machinery for estimating the degree of mean crowding and testing for density dependence in comparative ecological studies can be applied to estimating the strength of sexual selection and comparing different mating systems. When females vary in their tendency to aggregate with other females and males vary from one another in their ability to guard aggregations of females, a run-away process of sexual selection is possible. The largest aggregations of females have a higher proportion of the females most prone to aggregate or most tolerant of crowding. The males with the highest mating success have daughters more prone to aggregate and sons better at defending aggregated females against other males. As a result, females are selected to over-aggregate with respect to resources. The run-away process halts when single males cannot defend and maintain exclusive reproductive access to clusters of females as evidenced by extraharem copulations and paternity.     

Macromolecular Crowding Modulates Folding Mechanism of α/β Protein Apoflavodoxin

Protein dynamics in cells may be different from those in dilute solutions in vitro, because the environment in cells is highly concentrated with other macromolecules. This volume exclusion because of macromolecular crowding is predicted to affect both equilibrium and kinetic processes involving protein conformational changes. To quantify macromolecular crowding effects on protein folding mechanisms, we investigated the folding energy landscape of an α/β protein, apoflavodoxin, in the presence of inert macromolecular crowding agents, using in silico and in vitro approaches. By means of coarse-grained molecular simulations and topology-based potential interactions, we probed the effects of increased volume fractions of crowding agents (ϕ_c) as well as of crowding agent geometry (sphere or spherocylinder) at high ϕ_c. Parallel kinetic folding experiments with purified Desulfovibro desulfuricans apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and Dextran (spherocylinder) synthetic crowding agents. In conclusion, we identified the in silico crowding conditions that best enhance protein stability, and discovered that upon manipulation of the crowding conditions, folding routes experiencing topological frustrations can be either enhanced or relieved. Our test-tube experiments confirmed that apoflavodoxin''s time-resolved folding path is modulated by crowding agent geometry. Macromolecular crowding effects may be a tool for the manipulation of protein-folding and function in living cells.