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

На граматичних вершинах

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

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

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

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

A Fascinating Polynomial Sequence arising from an Electrostatics Problem on the Sphere

A positive unit point charge approaching from infinity a perfectly spherical isolated conductor carrying a total charge of +1 will eventually cause a negatively charged spherical cap to appear. The determination of the smallest distance $\rho(d)$ ($d$ is the dimension of the unit sphere) from the point charge to the sphere where still all of the sphere is positively charged is known as Gonchar's problem. Using classical potential theory for the harmonic case, we show that $1+\rho(d)$ is equal to the largest positive zero of a certain sequence of monic polynomials of degree $2d-1$ with integer coefficients which we call Gonchar polynomials. Rather surprisingly, $\rho(2)$ is the Golden ratio and $\rho(4)$ the lesser known Plastic number. But Gonchar polynomials have other interesting properties. We discuss their factorizations, investigate their zeros and present some challenging conjectures.Comment: 12 pages, 6 figures, 1 tabl

A general linear relaxometry model of R1 using imaging data.

PURPOSE: The longitudinal relaxation rate (R1 ) measured in vivo depends on the local microstructural properties of the tissue, such as macromolecular, iron, and water content. Here, we use whole brain multiparametric in vivo data and a general linear relaxometry model to describe the dependence of R1 on these components. We explore a) the validity of having a single fixed set of model coefficients for the whole brain and b) the stability of the model coefficients in a large cohort. METHODS: Maps of magnetization transfer (MT) and effective transverse relaxation rate (R2 *) were used as surrogates for macromolecular and iron content, respectively. Spatial variations in these parameters reflected variations in underlying tissue microstructure. A linear model was applied to the whole brain, including gray/white matter and deep brain structures, to determine the global model coefficients. Synthetic R1 values were then calculated using these coefficients and compared with the measured R1 maps. RESULTS: The model's validity was demonstrated by correspondence between the synthetic and measured R1 values and by high stability of the model coefficients across a large cohort. CONCLUSION: A single set of global coefficients can be used to relate R1 , MT, and R2 * across the whole brain. Our population study demonstrates the robustness and stability of the model. Magn Reson Med, 2014. © 2014 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. Magn Reson Med 73:1309-1314, 2015. © 2014 Wiley Periodicals, Inc

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