Resilience of the iron environment in heme proteins

Conformational flexibility is essential to the functional behavior of proteins. We use an effective force constant introduced by Zaccai, the resilience, to quantify this flexibility. Site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. The vibrational density of states of the heme Fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the Fe environment, which we compare quantitatively with values derived from the temperature dependence of atomic mean-squared displacements in molecular dynamics simulations. Vibrational normal modes in the THz frequency range dominate the resilience. Both experimental and computational methods find a higher resilience for cytochrome c than for myoglobin, which we attribute to the increased number of covalent links to the peptide in the former protein. For myoglobin, the resilience of the iron environment is larger than the average resilience previously determined for hydrogen sites using neutron scattering. Experimental results suggest a slightly reduced resilience for cytochrome c upon oxidation, although the change is smaller than reported in previous Mössbauer investigations on a bacterial cytochrome c, and is not reproduced by the simulations. Oxidation state also has no significant influence on the compressibility calculated for cyt c, although a slightly larger compressibility is predicted for myoglobin.     

Identification of Electric-Field-Dependent Steps in the Na,K-Pump Cycle

The charge-transporting activity of the Na⁺,K⁺-ATPase depends on its surrounding electric field. To isolate which steps of the enzyme’s reaction cycle involve charge movement, we have investigated the response of the voltage-sensitive fluorescent probe RH421 to interaction of the protein with BTEA (benzyltriethylammonium), which binds from the extracellular medium to the Na⁺,K⁺-ATPase’s transport sites in competition with Na⁺ and K⁺, but is not occluded within the protein. We find that only the occludable ions Na⁺, K⁺, Rb⁺, and Cs⁺ cause a drop in RH421 fluorescence. We conclude that RH421 detects intramembrane electric field strength changes arising from charge transport associated with conformational changes occluding the transported ions within the protein, not the electric fields of the bound ions themselves. This appears at first to conflict with electrophysiological studies suggesting extracellular Na⁺ or K⁺ binding in a high field access channel is a major electrogenic reaction of the Na⁺,K⁺-ATPase. All results can be explained consistently if ion occlusion involves local deformations in the lipid membrane surrounding the protein occurring simultaneously with conformational changes necessary for ion occlusion. The most likely origin of the RH421 fluorescence response is a change in membrane dipole potential caused by membrane deformation.     

Lack of demographic equilibrium indicates natural,large‐scale forest dynamics,not a problematic forest conservation policy – a reply to Brzeziecki et al.

Brzeziecki et al. 2016 (Journal of Vegetation Science 27: 460–467.) describe a decrease in population densities and proportion of younger individuals for several tree species in permanent research plots in the core zone of the Bia?owie?a National Park. They attribute insufficient tree recruitment inter alia to the strict protection. Although the authors performed a thorough analysis of tree population dynamics, the scales of the study mean that their far‐reaching conclusions on the causes and consequences of the lack of demographic equilibrium cannot be supported by the data. The inadequate spatial and temporal scales of the study did not allow for the observation of representative population dynamics. Furthermore, they did not compare the results obtained in the strictly protected area with known demographic dynamics of trees in surrounding managed forests or under other forms of nature conservation. Looking from the wider ecosystem perspective, it is clear that strict protection is not a cause for concern and, instead, that such a near‐natural forest manifests population dynamics at rather larger scales.     

Effect of bacterial infection on the lipid composition of carp blood lymphocytes

The initial stage of bacterial infection is characterized by an increase in the level of total lipids and polyenoic fatty acids in membrane phospholipids of blood lymphocytes of carp (Cyprinus carpio L.). In the fish infected with aeromonads, changes in the ratios of fatty acids in phospholipids are similar for either lymphocytes, liver, or whole blood. The extent to which these changes are pronounced depends on the original physiological status of the fish.     

Synthesis of 4-Deoxy-4-C-hydroxymethyl-α-L-Lyxo-Pyranosyl Thymine

Abstract

The synthesis of 1-[4-deoxy-4-C-hydroxymethyl-α-L-lyxopyranosyl]thymine has been accomplished by two synthetic routes both starting from methyl 2, 3-O-isopropylidene-β-D-ribopyranoside. The first route makes use of a ring opening, ring closure reaction sequence to increase the proportion of the desired L-isomers. The second route utilizes the soft nucleophilic character of malonyl anions and ozonolytic cleavage of enol ether to introduce the branched chain. The newly obtained pyranosyl nucleoside obtains a ⁴C₁ conformation with an equatorially oriented thymine moiety.     

Pancreatic endocrine tumors - management guidelines (recommended by the Polish Network of Neuroendocrine Tumors)

Pancreatic endocrine tumors (PETs) are rare neoplasms of this organ. The majority of PETs are tumors without hormonal activity. In this publication, we present the diagnostic and therapeutic guidelines for the management of these tumors proposed by the Polish Network of Neuroendocrine Tumors. These guidelines refer to biochemical and location diagnostics, including scintygraphy of somatostatin receptors, endoscopic ultrasonography and other anatomical and functional imaging methods. High importance is attached to correct histopathological diagnosis which determines further management of patients with PETs. Antitumor therapy requires multidirectional procedure, and therefore the rules of surgical treatment, biotherapy, chemotherapy and peptide receptor radionuclide therapy are discussed.     

Genetic diversity of ornamentalAllium species and cultivars assessed with isozymes

The aim of the study was to verify the similarity of 13 species and 5 cultivars of ornamental alliums and classify them into groups based on morphological and isozyme variation. The work embraced: Allium aflatunense, A. caeruleum, A. christophii, A. giganteum, A. karataviense, A. moly, A. nigrum, A. pyrenaicum, A. rosenbachianum, A. schubertii, A. siculum (syn. Nectaroscordum siculum), A. sphaerocephalon, A. strictum, A. stipitatum 'Album', A. 'Ivory Queen', A. 'Lucy Ball', A. 'Mont Blanc', and A. 'Purple Sensation'. Scape length, inflorescence diameter, and flowering period were recorded. Isozyme marker polymorphism was assessed by starch gel electrophoresis. Eight polymorphic isozyme systems (AAT, GPI, PGM, ALAT, ACP, DIAP, ALDO, PGD) were selected from 16 analysed in the taxa. Besides the differences between the taxa, the isozymes revealed intraspecific polymorphism in 5 systems. A total of 37 markers were obtained and used for dendrogram construction. The most similar taxa were A. karataviense with A. 'Ivory Queen', and A. karataviense with A. christophii (similarity level 0.78). A high similarity of 11 taxa belonging to one group (A. aflatunense, A. christophii, A. giganteum, A. karataviense, A. nigrum, A. schubertii, A. 'Ivory Queen', A. 'Lucy Ball', A. stipitatum 'Album', A. 'Mont Blanc', A. 'Purple Sensation') suggested that this group could be identified with the subgenus Melanocrommyum.     

Protecting groups transfer: unusual method of removal of tr and tbdms groups by transetherification

The triphenylmethyl (Tr) group undergoes a transfer (transetherification or disproportionation) between the molecules of 5'-O-Tr-2'-deoxynucleosides in a process mediated by anhydrous sulfates of Cu(+2), Fe(+2), or Ni(+2) to yield mixtures of 3',5'-bis-O-Tr and 3'-O-Tr products. If phenylmethanol is present in a reaction medium, detritylation results with concomitant formation of phenylmethyl triphenylmethyl ether. The behavior of t-butyldimethylsilyl (TBDMS) group in 5'-O-TBDMS-2'-deoxynucleosides is exactly the same. Such type of transetherifications was not observed before for the O-Tr and O-TBDMS groups.     

Biodegradation of diesel fuel by a microbial consortium in the presence of 1-alkoxymethyl-2-methyl-5-hydroxypyridinium chloride homologues

Fast development of ionic liquids as gaining more and more attention valuable chemicals will undoubtedly lead to environmental pollution. New formulations and application of ionic liquids may result in contamination in the presence of hydrophobic compounds, such as petroleum mixtures. We hypothesize that in the presence of diesel fuel low-water-soluble ionic liquids may become more toxic to hydrocarbon-degrading microorganisms. In this study the influence of 1-alkoxymethyl-2-methyl-5-hydroxypyridinium chloride homologues (side-chain length from C₃ to C₁₈) on biodegradation of diesel fuel by a bacterial consortium was investigated. Whereas test performed for the consortium cultivated on disodium succinate showed that toxicity of the investigated ionic liquids decreased with increase in side-chain length, only higher homologues (C₈–C₁₈) caused a decrease in diesel fuel biodegradation. As a result of exposure to toxic compounds also modification in cell surface hydrophobicity was observed (MATH). Disulphine blue active substances method was employed to determine partitioning index of ionic liquids between water and diesel fuel phase, which varied from 1.1 to 51% for C₃ and C₁₈ homologues, respectively. We conclude that in the presence of hydrocarbons acting as a solvent, the increased bioavailability of hydrophobic homologues is responsible for the decrease in biodegradation efficiency of diesel fuel.