Interaction of two tumor suppressors: Phosphatase CTDSPL and Rb protein

Earlier we established that CTDSPL gene encoding small carboxy-terminal domain serine phosphatase can be considered a classical tumor suppressor gene. Besides, transfection of tumor cell line MCF-7 with CTDSPL led to the content decrease of inactive phosphorylated form of another tumor suppressor, retinoblastoma protein (Rb), and subsequently to cell cycle arrest at the G1/S boundary. This result implied that small phosphatase CTDSPL is able to specifically dephosphorylate and activate Rb protein. In order to add some fuel to this hypothesis, in the present work we studied the interaction of two tumor suppressors CTDSPL and Rb in vitro. GST pool-down assay revealed that CTDSPL is able to precipitate Rb protein from MCF-7 cell extracts, while surface plasmon resonance technique showed that interaction of the two proteins is direct. Results of this study reassert that phosphatase CTDSPL and Rb could be involved in the common mechanism of cell cycle regulation.     

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields

Calcium ions (Ca²⁺) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca²⁺ models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca²⁺ models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA–DNA interactions. In the simulations performed using the two standard models, Ca²⁺ ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc₂ and CaCl₂ solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca²⁺ ions in the simulations of Ca²⁺‐mediated DNA–DNA interactions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter‐DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca²⁺ to DNA phosphate is strong enough to affect the direction of the electric field‐driven translocation of DNA through a solid‐state nanopore. To address these shortcomings of the standard Ca²⁺ model, we introduce a custom model of a hydrated Ca²⁺ ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca²⁺ can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 752–763, 2016.     

De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation

The DNA origami method has brought nanometer-precision fabrication to molecular biology labs, offering myriads of potential applications in the fields of synthetic biology, medicine, molecular computation, etc. Advancing the method further requires controlling self-assembly down to the atomic scale. Here we demonstrate a computational method that allows the equilibrium structure of a large, complex DNA origami object to be determined to atomic resolution. Through direct comparison with the results of cryo-electron microscopy, we demonstrate de novo reconstruction of a 4.7 megadalton pointer structure by means of fully atomistic molecular dynamics simulations. Furthermore, we show that elastic network-guided simulations performed without solvent can yield similar accuracy at a fraction of the computational cost, making this method an attractive approach for prototyping and validation of self-assembled DNA nanostructures.     

Status,number, and monitoring of the common eider (<Emphasis Type="Italic">Somateria mollissima</Emphasis>) population in the barents sea and the White Sea

The breeding, molting, and wintering ranges of the common eider (Somateria mollissima) were mapped and described in the southern part of the Barents Sea region, including the White Sea population in the western White Sea and the Murmansk population in the northwestern White Sea and the southeastern Barents Sea. The present-day abundance was determined for both populations: since the 1950s, it was the highest in the 2000s for the entire period of ornithological monitoring in the region. Aerial survey from a helicopter is considered to be the only reliable method for estimation of the total population number. The best season for surveying the White Sea population is March–early April (wintering); the most favorable period for surveying the Murmansk population is August (postbreeding/molting). The population status of the common eider in the northern and eastern parts of the Barents Sea has not yet been evaluated. On Franz-Josef Land, the common eider is distributed sporadically, and its number was assessed using expert estimates. The current abundance of the common eider on Novaya Zemlya is unknown. Helicopter-based aerial survey performed in late summer during the postbreeding season is the only relevant method to obtain reliable estimates for the population of the common eider inhabiting Franz-Josef Land and Novaya Zemlya.     

The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study

LacI is commonly used as a model to study the protein-DNA interaction and gene regulation. The headpiece of the lac-repressor (LacI) protein is an ideal system for investigation of nonspecific binding of the whole LacI protein to DNA. The hinge region of the headpiece has been known to play a key role in the specific binding of LacI to DNA, whereas its role in nonspecific binding process has not been elucidated. Here, we report the results of explicit solvent molecular dynamics simulation and continuum electrostatic calculations suggesting that the hinge region strengthens the nonspecific interaction, accounting for up to 50% of the micro-dissociation free energy of LacI from DNA. Consequently, the rate of microscopic dissociation of LacI from DNA is reduced by 2~3 orders of magnitude in the absence of the hinge region. We find the hinge region makes an important contribution to the electrostatic energy, the salt dependence of electrostatic energy, and the number of salt ions excluded from binding of the LacI-DNA complex.     

Analysis of adhesion proteins from neural eye tissues of eight-day-old chick embryos

Two groups of proteins were isolated from the retina and pigment epithelium of eight-day-old chick embryos. Experiments with suspension cultures of retinal cells demonstrated that only the retinal extracts and the fraction of its acidic proteins can stimulate cell aggregation in vitro. Analysis by the method of high-performance liquid chromatography showed that fractions of acidic and basic retinal proteins, which markedly differ in their electric charge and biological activity, have similar composition. To study the effect of these proteins on the morphological and functional state of pigment epitheliumin vitro, a new experimental model is proposed, with the posterior segment of the newt (Pleurodeles waltl) eye used as a test tissue. The fraction of basic proteins isolated from the chick embryonic pigment epithelium stabilized cell differentiation in the newt pigment epithelium. The analyzed proteins proved to be biologically active at extremely low doses, corresponding to 10⁻¹² M solutions.     

Macromolecular assembly-driven processing of the 2/3 cleavage site in the alphavirus replicase polyprotein

Semliki Forest virus (SFV) is a member of the Alphavirus genus, which produces its replicase proteins in the form of a nonstructural (ns) polyprotein precursor P1234. The maturation of the replicase occurs in a temporally controlled manner by protease activity of nsP2. The template preference and enzymatic capabilities of the alphaviral replication complex have a very important connection with its composition, which is irreversibly altered by proteolysis. The final cleavage of the 2/3 site in the ns polyprotein apparently leads to significant rearrangements within the replication complex and thus denotes the "point of no return" for viral replication progression. Numerous studies have devised rules for when and how ns protease acts, but how the alphaviral 2/3 site is recognized remained largely unexplained. In contrast to the other two cleavage sites within the ns polyprotein, the 2/3 site evidently lacks primary sequence elements in the vicinity of the scissile bond sufficient for specific protease recognition. In this study, we sought to investigate the molecular details of the regulation of the 2/3 site processing in the SFV ns polyprotein. We present evidence that correct macromolecular assembly, presumably strengthened by exosite interactions rather than the functionality of the individual nsP2 protease, is the driving force for specific substrate targeting. We conclude that structural elements within the macrodomain of nsP3 are used for precise positioning of a substrate recognition sequence at the catalytic center of the protease and that this process is coordinated by the exact N-terminal end of nsP2, thus representing a unique regulation mechanism used by alphaviruses.     

Within and between species competition in a seabird community: statistical exploration and modeling of time-series data

In a changing environment, the maintenance of communities is subject to many constraints (phenology, resources, climate, etc.). One such constraint is the relationship between conspecifics and competitors. In mixed colonies, seabirds may have to cope with interspecific and intraspecific competition for both space and food resources. We applied competitive interaction models to data on three seabird breeding populations: black-legged kittiwake (Rissa tridactyla), common guillemot (Uria aalge) and Brünnich's guillemot (Uria lomvia) collected over 27-years at Kharlov Island in the Barents Sea. We found a competitive effect only for the kittiwake breeding population size on the common guillemot breeding population size when kittiwakes were abundant. The timing of kittiwake breeding negatively affected the number of breeding Brünnich's guillemots. The timing of breeding was negatively correlated to biomass of the main pelagic fish in the Barents Sea, the capelin (Mallotus villosus), which suggests an indirect action. The community matrix shows that the community was not stable. The kittiwake population did not decrease as seen in north Norwegian populations. Likewise, the common guillemot population, after a crash in 1985, was recovering at Kharlov while Norwegian populations were decreasing. Only the Brünnich's guillemot showed a decrease at Kharlov until 1999. We suggest that the stability of the kittiwake and common guillemot populations at Kharlov is due to better feeding conditions than in colonies of the Norwegian coast, linked to a possible eastward shift of the capelin population with the temperature increase of the Barents Sea.     

Effect of salinity change on cardiac activity in Hiatella arctica and Modiolus modiolus, in the White Sea

A great majority of salinity studies have dealt with intertidal species. Little is known about the way subtidal animals respond to salinity fluctuations. Even less details are available on invertebrates from the White Sea, which salinity is ca. 25. The heart rate of two subtidal Bivalvia—Hiatella arctica and Modiolus modiolus—exposed to different salinities was recorded. Changes in cardiac activity were monitored for 9 days of the animals’ acclimation to salinities of 15, 20, 30 and 35, and for 4 days of reacclimation (return to the initial salinity of 25). The initial response to salinity change was a significant heart rate reduction. On the other hand, cardiac activity in M. modiolus intensified at salinities of 30 and 35. Reacclimation induced different HR responses: from a decrease to a rise, depending on the species and the salinity applied in the experiment. The differences in responses to salinity are discussed with respect to the morphological and ecological characteristics of the species.