Anti-stress activity of Propionibacterium freudenreichii: identification of a reactivative protein

Propionibacterium freudenreichii subsp. shermanii is known to prevent mutations caused by various agents such as N-methyl-N'-nitro-N-nitrosoguanidine, 9-aminoacridine, 4-nitro-quinoline-1-oxide and by UV radiation in both prokaryotic and eukaryotic cells. It was also shown to prevent or repair damage caused by H(2)O(2) or UV radiation in Salmonella typhimurium and Escherichia coli, a characteristic previously designated as reactivative effect. In order to characterise this effect at the molecular level, we have purified the active component from a P. freudenreichii cell-free extract using a combination of ammonium sulfate precipitation, anion-exchange and size-exclusion chromatography. The isolated 35 kDa protein was then identified using both N-terminal and internal peptide sequencing as a cysteine synthase. The latter was localised in the P. freudenreichii proteomic map. It is constitutively expressed but also clearly induced during adaptation to detergent and heat, but not acid, stresses. The biological meaning of cysteine synthase in the context of adaptation to oxidative and non-oxidative stresses is discussed.     

Mitochondria structural reorganization during mouse embryonic stem cell derivation

Mouse embryonic stem (ES) cells are widely used in developmental biology and transgenic research. Despite numerous studies, ultrastructural reorganization of inner cell mass (ICM) cells during in vitro culture has not yet been described in detail. Here, we for the first time performed comparative morphological and morphometric analyses of three ES cell lines during their derivation in vitro. We compared morphological characteristics of blastocyst ICM cells at 3.5 and 4.5 days post coitum on feeder cells (day 6, passage 0) with those of ES cells at different passages (day 19, passage 2; day 25, passage 4; and passage 15). At passage 0, there were 23–36% of ES-like cells with various values of the medium cross-sectional area and nucleocytoplasmic parameters, 55% of fibroblast-like (probably trophoblast derivatives), and ~?19% of dying cells. ES-like cells at passage 0 contained autolysosomes and enlarged mitochondria with reduced numerical density per cell. There were three types of mitochondria that differed in matrix density and cristae width. For the first time, we revealed cells that had two and sometimes three morphologically distinct mitochondria types in the cytoplasm. At passage 2, there were mostly ES cells with a high nucleocytoplasmic ratio and a cytoplasm depleted of organelles. At passage 4, ES cell morphology and morphometric parameters were mostly stable with little heterogeneity. According to our data, cellular structures of ICM cells undergo destabilization during derivation of an ES cell line with subsequent reorganization into the structures typical for ES cells. On the basis of ultrastructural analysis of mitochondria, we believe that the functional activity of these organelles changes during early stages of ES cell formation from the ICM.     

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.     

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.     

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.     

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.     

Dinuclear versus mononuclear ruthenium(II) and osmium(II) complexes as potent mediators of glucose oxidase; crystal structure of [OsCl(4,4′-bpy)(bpy)<Subscript>2</Subscript>]BF<Subscript>4</Subscript>

New and known homo- and heterodinuclear Ru^II and Os^II complexes with 4,4-bipyridine (4,4-bpy), pyrazine, and 4-pyCH=CHpy-4 as bridging ligands (LL) of the type [Cl(bpy)₂M(LL)MCl(bpy)₂]X₂ (bpy=2,2-bipyridine; X=PF₆ or BF₄) have been studied in their capacity to exchange electrons with a reduced active site of glucose oxidase (GO) from Aspergillus niger. Cyclic voltammograms (CVs) of the dimers in the aqueous buffered solution, when compared with CVs of the parent monomeric species [MCl(LL)(bpy)₂]BF₄ and [MCl₂(bpy)₂] which could be generated at pH7, if the dimers undergo monomerization, indicate that the dimers are the dominating species under such conditions. All electrochemically oxidized dinuclear complexes studied show high rates of oxidation of GO reduced by d-glucose and the corresponding observed second-order rate constants are in the range (5–64)×10⁵ M^–1 s^–1 at 25 °C. However, these values are lower than that for the mononuclear complex [OsCl(4,4-bpy)(bpy)₂]BF₄ (1.1×10⁷ M^–1 s^–1), suggesting that potentially two-electron dimeric mediators have no advantage compared with corresponding monomeric complexes of Ru^II and Os^II. The structure of [OsCl(4,4-bpy)(bpy)₂]BF₄ was confirmed by X-ray crystallography. The monodentate 4,4-bpy ligand is coordinated cis to the chloride. Its higher reactivity toward reduced GO is accounted for in terms of the antenna effect of the monodentate 4,4-bpy ligand. The antenna length equals 9.2 Å and matches the depth of the enzyme active site pocket of ca. 10 Å. The mechanism of the antenna effect is discussed     

Genetic differentiation in a captive population of the endangered Siberian crane (Grus leucogeranus Pall.)

DNA fingerprinting, followed by multivariate analysis of data, was used to characterize genetic heterogeneity in captive populations of the endangered Siberian and sandhill cranes. The genetic structure revealed reflected the natural population and species distributions. The relevant groups differed not only from each other, but also from interspecies and inter-population hybrids bred in captivity. In this study we have tested an approach to the analysis of population structure based on individual genotypes. Interpretation of fingerprinting data by means of the analytical system applied here is a useful and reliable procedure for the estimation of genetic relationships between individuals.     

Impaired synapse function during postnatal development in the absence of CALEB, an EGF-like protein processed by neuronal activity

In an attempt to characterize the molecular components by which electric activity influences the development of synapses, we searched for cell surface proteins modulated by calcium influx and glutamate receptor activity. Here, we report that neuronal depolarization facilitates the conversion of CALEB, which results in a truncated transmembrane form with an exposed EGF domain. To characterize the role of CALEB in synapse development, synaptic features were investigated in slices of the colliculus superior from CALEB-deficient mice. In the absence of CALEB, the number of synapses and their morphological characteristics remained unchanged. However, in CALEB-deficient mice, synapses displayed higher paired-pulse ratios, less depression during prolonged repetitive activation, a lower rate of spontaneous postsynaptic currents, and a lower release probability at early but not mature postnatal stages. Our findings indicate that CALEB provides a molecular basis for maintaining normal release probability at early developmental stages.