Dynamics of protein-protein encounter: a Langevin equation approach with reaction patches

We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric and thermal forces. As three model systems with distinctly different properties we consider the pairs barnase:barstar, cytochrome c:cytochrome c peroxidase and p53:MDM2. In each case, proteins are modeled either as spherical particles, as dipolar spheres or as collection of several small beads with one dipole. Spherical reaction patches are placed on the model proteins according to the known experimental structures of the protein complexes. In the computer simulations, concentration is varied by changing box size. Encounter is defined as overlap of the reaction patches and the corresponding first passage times are recorded together with the number of unsuccessful contacts before encounter. We find that encounter frequency scales linearly with protein concentration, thus proving that our microscopic model results in a well-defined macroscopic encounter rate. The number of unsuccessful contacts before encounter decreases with increasing encounter rate and ranges from 20-9000. For all three models, encounter rates are obtained within one order of magnitude of the experimentally measured association rates. Electrostatic steering enhances association up to 50-fold. If diffusional encounter is dominant (p53:MDM2) or similarly important as electrostatic steering (barnase:barstar), then encounter rate decreases with decreasing patch radius. More detailed modeling of protein shapes decreases encounter rates by 5-95 percent. Our study shows how generic principles of protein-protein association are modulated by molecular features of the systems under consideration. Moreover it allows us to assess different coarse-graining strategies for the future modelling of the dynamics of large protein complexes

Apparent facilitation of an invasive mealybug by an invasive ant

Summary: In the southeast United States, the invasive ant Solenopsis invicta is known to derive important carbohydrate (honeydew) resources from mealybugs utilizing grasses. Most important appears to be an invasive mealybug, Antonina graminis. We studied whether this mealybug and a similar native species also benefit from association with S. invicta. We found that mealybug occurrence increases significantly with increasing proximity to S. invicta mounds, suggesting that mealybugs benefit as well. Mutual benefits derived by S. invicta and A. graminis are consistent with a hypothesis proposing that associations among invasive species can be important in their success at introduced location

Reverse Khas'minskii condition

The aim of this paper is to present and discuss some equivalent characterizations of p-parabolicity in terms of existence of special exhaustion functions. In particular, Khas'minskii in [K] proved that if there exists a 2-superharmonic function k defined outside a compact set such that $\lim_{x\to \infty} k(x)=\infty$, then R is 2-parabolic, and Sario and Nakai in [SN] were able to improve this result by showing that R is 2-parabolic if and only if there exists an Evans potential, i.e. a 2-harmonic function $E:R\setminus K \to \R^+$ with \lim_{x\to \infty} \E(x)=\infty. In this paper, we will prove a reverse Khas'minskii condition valid for any p>1 and discuss the existence of Evans potentials in the nonlinear case.Comment: final version of the article available at http://www.springer.co

На граматичних вершинах

On the Ivan Vykhovanets’life and career the famous Ukrainian linguist and founder of Ukrainian school grammarians

Exploring barriers in expertise seeking : why don\u27t they ask an expert?

This paper reports findings from a research project that explores reasons why some employees prefer to seek expertise to resolve work-related problems from direct colleagues rather than designated internal experts. Several studies suggest that while an expert generally provides a higher quality solution in a shorter time, workers tend to ask friendly or proximate colleagues to help with knowledge-based problems at work. Prior research provides only fragmented insights into understanding the barriers to asking a designated internal expert for help at work. To address this gap, we asked post-graduate students enrolled in a knowledge management subject at a large Australian university to share their perspectives in an online discussion forum. Content analysis of the collected perspectives enabled identification of twenty-one factors that may limit the seeking of expertise from a designated internal expert. The factors are grouped in four categories: environment, accessibility, communication and personality. In addition one context variable is described, determining the extent to which the barriers are influential in a specific situation. By synthesising the results, we have proposed two models of expertise-seeking barriers. A literature review helps validate the barriers identified by the study. Key theoretical and practical implications are also discussed.<br /

Modeling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behavior across species

A quantitative understanding of organism-level behavior requires predictive models that can capture the richness of behavioral phenotypes, yet are simple enough to connect with underlying mechanistic processes. Here we investigate the motile behavior of nematodes at the level of their translational motion on surfaces driven by undulatory propulsion. We broadly sample the nematode behavioral repertoire by measuring motile trajectories of the canonical lab strain $C. elegans$ N2 as well as wild strains and distant species. We focus on trajectory dynamics over timescales spanning the transition from ballistic (straight) to diffusive (random) movement and find that salient features of the motility statistics are captured by a random walk model with independent dynamics in the speed, bearing and reversal events. We show that the model parameters vary among species in a correlated, low-dimensional manner suggestive of a common mode of behavioral control and a trade-off between exploration and exploitation. The distribution of phenotypes along this primary mode of variation reveals that not only the mean but also the variance varies considerably across strains, suggesting that these nematode lineages employ contrasting ``bet-hedging'' strategies for foraging.Comment: 46 pages, 18 figures, 6 table

Differentiation of multipotent vascular stem cells contributes to vascular diseases.

It is generally accepted that the de-differentiation of smooth muscle cells, from the contractile to the proliferative/synthetic phenotype, has an important role during vascular remodelling and diseases. Here we provide evidence that challenges this theory. We identify a new type of stem cell in the blood vessel wall, named multipotent vascular stem cells. Multipotent vascular stem cells express markers, including Sox17, Sox10 and S100β, are cloneable, have telomerase activity, and can differentiate into neural cells and mesenchymal stem cell-like cells that subsequently differentiate into smooth muscle cells. On the other hand, we perform lineage tracing with smooth muscle myosin heavy chain as a marker and find that multipotent vascular stem cells and proliferative or synthetic smooth muscle cells do not arise from the de-differentiation of mature smooth muscle cells. In response to vascular injuries, multipotent vascular stem cells, instead of smooth muscle cells, become proliferative, and differentiate into smooth muscle cells and chondrogenic cells, thus contributing to vascular remodelling and neointimal hyperplasia. These findings support a new hypothesis that the differentiation of multipotent vascular stem cells, rather than the de-differentiation of smooth muscle cells, contributes to vascular remodelling and diseases

Response of selected microorganisms to experimental planetary environments

The anaerobic utilization of phosphite or phosphine and the significance of this conversion to potential contamination of Jupiter were investigated. A sporeforming organism was isolated from Cape Canaveral soil which anaerobically converts hypophosphite to phosphate. This conversion coincides with an increase in turbidity of the culture and with phosphate accumulation in the medium. Investigations of omnitherms (organisms which grow over a broad temperature range, i.e. 3 -55 C were also conducted. The cellular morphology of 28 of these isolates was investigated, and all were demonstrated to be sporeformers. Biochemical characterizations are also presented. Procedures for replicate plating were evaluated, and those results are also presented. The procedures for different replicate-plating techniques are presented, and these are evaluated on the basis of reproducibility, percentage of viable transfer, and ease of use. Standardized procedures for the enumeration of microbial populations from ocean-dredge samples from Cape Canaveral are also presented