How do kinetochores CLASP dynamic microtubules?

Maintenance of genetic stability during cell division requires binding of chromosomes to the mitotic spindle, a process that involves attachment of spindle microtubules to kinetochores. This enables chromosomes to move to the metaphase plate, to satisfy the spindle checkpoint and finally to segregate during anaphase. Recent studies on the function MAST in Drosophila and its human homologue CLASP1, have revealed that these microtubule-associated proteins play an essential role for the kinetochore-microtubule interaction. CLASP1 localizes to the plus ends of growing microtubules and to the most external kinetochore domain. Depletion of CLASP1 causes abnormal chromosome congression, collapse of the mitotic spindle and attachment of kinetochores to very short microtubules that do not show dynamic behavior. These results suggest that CLASP1 is required at kinetochores to regulate the dynamic behavior of attached microtubules.     

Proteomics and the dynamic plasma membrane: Quo Vadis?

Quo Vadis: where are you going? Advances in MS-based proteomics have enabled research to move from obtaining the basic protein inventory of cells and organelles to the ability of monitoring their dynamics, including changes in abundance, location and various PTMs. In this respect, the cellular plasma membrane is of particular interest, by not only serving as a barrier between the "cell interior" and the external environment, but moreover by organizing and clustering essential components to enable dynamic responses to internal and external stimuli. Defining and characterizing the dynamic plasma membrane proteome is crucial for understanding fundamental biological processes, disease mechanisms and for finding drug targets. Protein identification, characterization of dynamic PTMs and protein-ligand interactions, and determination of transient changes in protein expression and composition are among the challenges in functional proteomic studies of the plasma membrane. We review the recent progress in MS-based plasma membrane proteomics by presenting key examples from eukaryotic systems, including mammals, yeast and plants. We highlight the importance of enrichment and quantification technologies required for detailed functional and comparative analysis of the dynamic plasma membrane proteome.     

Is allostery an intrinsic property of all dynamic proteins?

Allostery involves coupling of conformational changes between two widely separated binding sites. The common view holds that allosteric proteins are symmetric oligomers, with each subunit existing in "at least" two conformational states with a different affinity for ligands. Recent observations such as the allosteric behavior of myoglobin, a classical example of a nonallosteric protein, call into question the existing allosteric dogma. Here we argue that all (nonfibrous) proteins are potentially allosteric. Allostery is a consequence of re-distributions of protein conformational ensembles. In a nonallosteric protein, the binding site shape may not show a concerted second-site change and enzyme kinetics may not reflect an allosteric transition. Nevertheless, appropriate ligands, point mutations, or external conditions may facilitate a population shift, leading a presumably nonallosteric protein to behave allosterically. In principle, practically any potential drug binding to the protein surface can alter the conformational redistribution. The question is its effectiveness in the redistribution of the ensemble, affecting the protein binding sites and its function. Here, we review experimental observations validating this view of protein allostery.     

Scaling up population dynamic processes in a ladybird–aphid system

Here, we study how scaling up to the metapopulation level affects predictions of a population dynamics model motivated by an aphidophagous predator–aphid system. The model incorporates optimization of egg distribution in predatory females, cannibalism among their offspring, and self-regulation of the prey population. These factors determine the within-year dynamics of the system and translate the numbers of prey and predator individuals at the beginning of the season into their numbers at the end of the season at the level of one patch—one suitable host plant or a group of these. At the end of each season, all populations of prey and all populations of predators are mixed (this simulates aphid host-alternation and ladybird migration to hibernation sites), and then redistributed at the beginning of the next season. Prey individuals are distributed at random among the patches as a “prey rain”, while adult predators that survived from the previous season optimize the distribution of their offspring, in that they prefer patches with sufficient amount of prey and absence of other predators. This redistribution followed by within-season dynamics is then iterated over many seasons. We look at whether small-scale trends in population dynamics predicted by this model are consistent with large-scale outcomes. Specifically, we show that even on the metapopulation scale, the impact of predators on prey metapopulation is relatively low. We further show how the dates of predator arrival to and departure from the system affect the qualitative behaviour of the model predictions.     

Transmembrane auxin carrier systems – dynamic regulators of polar auxin transport

Recent investigations of the biochemistry, physiology and molecular genetics of polar auxin transport have greatly advanced our understanding of the process and of the part it plays in the regulation of development and in the responses of cells, tissues and organs to internal and external stimuli. The molecular and physiological characterization of mutants which exhibit lesions in polar auxin transport has led to the isolation and sequencing of genes which encode putative components of auxin carrier systems, or proteins which directly or indirectly regulate these systems. This work has revealed that specific auxin uptake and efflux carriers are coded not by single genes, but by whole families of genes, the expression of which is tissue or stimulus specific. Furthermore, evidence is accumulating rapidly that at least the auxin efflux carrier is a multi-component system consisting of both catalytic and regulatory subunits, including a separate phytotropin-binding protein. Other genes have been tentatively identified which code proteins that regulate the expression of genes coding auxin carrier components, or which regulate the intracellular traffic or activity of auxin carriers. Investigations of the turn-over and Golgi-mediated trafficking of auxin carrier proteins have revealed that essential components of at least the efflux carrier have a very short half-life in the plasma membrane and are replaced without the need for concurrent protein synthesis, leading to speculation that they might cycle between internal stores and the plasma membrane. The way is now clear for the development of specific molecular probes with which to investigate the intracellular transport and targeting of auxin carrier proteins.     

Investigation of flap flexibility of β-secretase using molecular dynamic simulations

Flap motif and its dynamics were extensively reported in aspartate proteases, e.g. HIV proteases and plasmepsins. Herein, we report the first account of flap dynamics amongst different conformations of β-secretase using molecular dynamics simulation. Various parameters were proposed and a selected few were picked which could appropriately describe the flap motion. Three systems were studied, namely Free (BACE_Free) and two ligand-bound conformations, which belonged to space groups P6₁22 (BACE_Bound1) and C222₁ (BACE_Bound2), respectively and four parameters (distance between the flaps tip residue, Thr72 and Ser325, d₁; dihedral angle, ? (Thr72-Asp32-Asp228-Ser325); TriCα angles, θ₁ (Thr72-Asp32-Ser325), and θ₂ (Thr72-Asp228-Ser325)) were proposed to understand the change in dynamics of flap domain and the extent of flap opening and closing. Analysis of, θ₂, d₁, θ₁ and ? confirmed that the BACE_Free adopted semi-open, open and closed conformations with slight twisting during flap opening. However, BACE_Bound1 (P6122) showed an adaptation to open conformation due to lack of hydrogen bond interaction between the ligand and flap tip residue. A slight flap twisting, ? (lateral twisting) was observed for BACE_Bound1 during flap opening which correlates with the opening of BACE_Free. Contradictory to the BACE_Bound1, the BACE_Bound2 locked the flap in a closed conformation throughout the simulation due to formation of a stable hydrogen bond interaction between the flap tip residue and ligand. Analyses of all three systems highlight that d₁, θ₂ and ? can be precisely used to describe the extent of flap opening and closing concurrently with snapshots along the molecular dynamics trajectory across several conformations of β-secretase.     

Planning versus online control: dynamic illusion effects in grasping?

The planning/control model of action assumes that grasping is sensitive to the context of an object only in early stages of the movement (planning), but not in later stages (control). In consequence, the effects of context-induced illusions (such as the Ebbinghaus/Titchener illusion) should decrease during a grasping movement. Here, we tested this claim by reanalysing a large data set (N = 26) on grasping in the Ebbinghaus illusion. Contrary to the predictions of the planning/control model, we found that the effects of the illusion did not decrease over time. Instead, the illusion effects stayed remarkably constant.     

“Wasting disease” and other dynamic phenomena in Zostera beds

The greatest decline of seagrass beds that is known is certainly the almost simultaneous breakdown of the North Atlantic populations of Zostera marina L., due to the “wasting disease”. Several explanations have been presented for this ecological disaster; however, none of those is satisfactory. It appears that for several localities a local explanation can be given.Apart from this general decline, it appears that, at least in Western Europe, there is a great variation in the temporal and spatial development cycles of the intertidal Zostera-beds. These variations can be ascribed to a number of factors, such as winter temperature (frost or no frost), grazing by birds (grazing or no grazing) and the balance between sedimentation (including sanding) and erosion. The combination “frost-grazing” leads to an annual cycle of the biomass, and a homogeneous bed structure. The combination “no frost-no grazing” causes raising of the seagrass bed, due to sedimentation up to a level where the environmental conditions become less favourable to seagrass; then breakdown sets in. These beds are heterogeneous and show a pluriannual developmental cycle.     

Shifting dynamic forces in fish stock fluctuations triggered by age truncation?

Accumulating evidence shows that environmental fluctuations and exploitation jointly affect marine fish populations, and understanding their interaction is a key issue for fisheries ecology. In particular, it has been proposed that age truncation induced by fisheries exploitation may increase the population's sensitivity to climate. In this study, we use unique long‐term abundance data for the Northeast Arctic stock of cod (Gadus morhua) and the Norwegian Spring‐Spawning stock of herring (Clupea harengus), which we analyze using techniques based on age‐structured population matrices. After identifying time periods with different age distributions in the spawning stock, we use linear models to quantify the relative effect of exploitation and temperature on the population growth rates. For the two populations, age truncation was found to be associated with an increasing importance of temperature and a relatively decreasing importance of exploitation, while the population growth rate became increasingly sensitive to recruitment variations. The results suggested that the removal of older age classes reduced the buffering capacity of the population, thereby making the population growth rate more dependent on recruitment than adult survival and increasing the effect of environmental fluctuations. Age structure appeared as a key characteristic that can affect the response of fish stocks to climate variations and its consequences may be of key importance for conservation and management.     

A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–DNA glycosylase

In contrast to proteins recognizing small-molecule ligands, DNA-dependent enzymes cannot rely solely on interactions in the substrate-binding centre to achieve their exquisite specificity. It is widely believed that substrate recognition by such enzymes involves a series of conformational changes in the enzyme–DNA complex with sequential gates favoring cognate DNA and rejecting nonsubstrates. However, direct evidence for such mechanism is limited to a few systems. We report that discrimination between the oxidative DNA lesion, 8-oxoguanine (oxoG) and its normal counterpart, guanine, by the repair enzyme, formamidopyrimidine-DNA glycosylase (Fpg), likely involves multiple gates. Fpg uses an aromatic wedge to open the Watson–Crick base pair and everts the lesion into its active site. We used molecular dynamics simulations to explore the eversion free energy landscapes of oxoG and G by Fpg, focusing on structural and energetic details of oxoG recognition. The resulting energy profiles, supported by biochemical analysis of site-directed mutants disturbing the interactions along the proposed path, show that Fpg selectively facilitates eversion of oxoG by stabilizing several intermediate states, helping the rapidly sliding enzyme avoid full extrusion of every encountered base for interrogation. Lesion recognition through multiple gating intermediates may be a common theme in DNA repair enzymes.     

When should males lek? Insights from a dynamic state variable model

A central focus in the study of lek evolution is to understandthe clustering of male mating territories. Lekking males typicallydefend small clumped territories and experience intense competitionassociated with dense aggregations. We used dynamic state variablemodeling to evaluate three alternative selective pressures proposedto explain the evolution of lekking. These are female matingbias for large clusters, reduction in predation risk in largeclusters, and male harassment of estrous females. We modeledmale mating decisions during a single breeding season usinga lekking ungulate as a model system. Males could choose fromeight alternative tactics that included a nonreproductive tactic,territorial tactics ranging from low to high clustering, andthe option to join a mixed-sex herd. The model predicted a state-and time-dependent strategy that maximizes mating success overthe course of the season. We then simulated a population of100 males that used the optimal strategy and calculated theproportion of the population that adopted each tactic. Our modelgenerated unique predictions for the three selective pressureswe considered. Female mating bias, when nonlinearly relatedto cluster size, had the greatest potential to generate largeclusters of territorial males, whereas predation risk and harassmentof females typically did not promote male clustering. More generally,our model highlights the conditions that will favor lekking.Lek-like clustering was consistently produced when the benefitsin clustering increased in specific nonlinear ways. Our modelthus emphasizes clarifying the shapes of relationships betweenpotential selective factors and the size of territory clusters.     

Low-dimensional dynamic self-organization in δ-sleep: effect of partial sleep deprivation

Studies on extended data including 37 electroencephalographic (EEG) records of -sleep, each 10³ s long (six subjects; up to seven nights per subject, comprising normal sleep, partial deprivation and recovery), confirmed earlier conclusions that rare episodes of low-dimensional dynamic self-organization, with lifetimes between 10 and 20 s, are present in stage 4 sleep. Particular care was taken of the Theiler correction which, in some -sleep signals, required the deletion of trajectory points covering nearly one pseudo-period. The percentage of segments showing an episode, i.e. the attractor probability, decreased with a change in sleep conditions — either deprivation or recovery prior to the next deprivation. Repetition of deprivation over three nights resulted in an adaptation process, manifested by an increase in attractor probability. After the sharp decrease in probability observed when recovery was established prior to the next deprivation, and on return to normal conditions of sleep at 2200 hours, the probability was immediately close to that observed in normal baseline sleep conditions free of any interference. The observation of a definite effect of sleep deprivation and recovery upon the number of stage 4 attractors observed provides a line of approach to the physiological significance of the probability of such attractors.