Spatial features of proteins related to their phosphorylation and associated structural changes

Protein phosphorylation is widely used in biological regulatory processes. The study of spatial features related to phosphorylation sites is necessary to increase the efficacy of recognition of phosphorylation patterns in protein sequences. Using the data on phosphosites found in amino acid sequences, we mapped these sites onto 3D structures and studied the structural variability of the same sites in different PDB entries related to the same proteins. Solvent accessibility was calculated for the residues known to be phosphorylated. A significant change in accessibility was shown for many sites, but several ones were determined as buried in all the structures considered. Most phosphosites were found in coil regions. However, a significant portion was located in the structurally stable ordered regions. Comparison of structures with the same sites in modified and unmodified states showed that the region surrounding a site could be significantly shifted due to phosphorylation. Comparison between non‐modified structures (as well as between the modified ones) suggested that phosphorylation stabilizes one of the possible conformations. The local structure around the site could be changed due to phosphorylation, but often the initial conformation of the site surrounding is not altered within bounds of a rather large substructure. In this case, we can observe an extensive displacement within a protein domain. Phosphorylation without structural alteration seems to provide the interface for domain‐domain or protein‐protein interactions. Accounting for structural features is important for revealing more specific patterns of phosphorylation. It is also necessary for explaining structural changes as a basis for regulatory processes.     

NADPH-dependent electron transport chain in microsomes and lipid peroxidation catalyzed by metal ions.

Like iron ions copper ions are also able to stimulate the NADPH-dependent lipid peroxidation in rat liver microsomes. This effect is strongly dependent on the concentration of Cu2+ added. Initial concentrations of Cu2+ above 50 microM completely inhibit the formation of malonaldehyde. The activator and inhibitor functions may be interpreted by a simultaneous participation of Cu+ ions formed in the chain branching and termination reaction of the free radical lipid peroxidation process. Inhibition studies with pCMB and the His-reagent diethyl pyrocarbonate indicate an essential role of cysteine and histidine residues in the Cu+-NADPH-dependent lipid peroxidation process.     

Potential for Microscale Bacterial Fe Redox Cycling at the Aerobic-Anaerobic Interface

Recent studies of bacterial Fe(II) oxidation at circumneutral pH by a newly-isolated lithotrophic β-Proteobacterium (strain TW2) are reviewed in relation to a conceptual model that accounts for the influence of biogenic Fe(III)-binding ligands on patterns of Fe(II) oxidation and Fe(III) oxide deposition in opposing gradients of Fe(II) and O₂. The conceptual model envisions complexation of Fe(III) by biogenic ligands as mechanism which alters the locus of Fe(III) oxide deposition relative to Fe(II) oxidation so as to delay/retard cell encrustation with Fe(III) oxides. Experiments examining the potential for bacterial Fe redox cycling in microcosms containing ferrihydrite-coated sand and a coculture of a lithotrophic Fe(II)-oxidizing bacterium (strain TW2) and a dissimilatory Fe(III)-reducing bacterium (Shewanella algae strain BrY) are described and interpreted in relation to an extended version of the conceptual model in which Fe(III)-binding ligands promote rapid microscale Fe redox cycling. The coculture systems showed minimal Fe(III) oxide accumulation at the sand-water interface, despite intensive O₂ input from the atmosphere and measurable dissolved O₂ to a depth of 2 mm below the sand-water interface. In contrast, a distinct layer of oxide precipitates formed in systems containing Fe(III)-reducing bacteria alone. Voltammetric microelectrode measurements revealed much lower concentrations of dissolved Fe(II) in the coculture systems. Examination of materials from the cocultures by fluorescence in situ hybridization indicated close physical juxtapositioning of Fe(II)-oxidizing and Fe(III)reducing bacteria in the upper few mm of sand. Together these results indicate that Fe(II)-oxidizing bacteria have the potential to enhance the coupling of Fe(II) oxidation and Fe(III) reduction at redox interfaces, thereby promoting rapid microscale cycling of Fe.     

A new look at reactions with participation of metal-porphyrines

Reactions ofnucleophilic substitution and enzymatic processes with participation of metal-porphyrins (MP) are considered from the point of view of Zn-tetraphenylporphin (Zn-TPhP) coordination with corresponding ligand/nucleophyl/substrate/base. Linear correlations perform between kinetic parameters of process of coordination of Zn-TPhP in chloroform (constants of stability) and reactions of nucleophilic substitution both in aqueous and organic solvents with participation ofpyridines, N-oxides ofpyridines, anilines, primary amines and oxidation of anilines by horseradish peroxidase in aqueous solutions (rate constants). Thermodynamic parameters of complexation and nucleophilic substitution mutually correlate linearly in the case of pyridines, anilines and primary amines.     

Comparing Denitrification Estimates for a Texas Estuary by Using Acetylene Inhibition and Membrane Inlet Mass Spectrometry

Characterizing denitrification rates in aquatic ecosystems is essential to understanding how systems may respond to increased nutrient loading. Thus, it is important to ensure the precision and accuracy of the methods employed for measuring denitrification rates. The acetylene (C₂H₂) inhibition method is a simple technique for estimating denitrification. However, potential problems, such as inhibition of nitrification and incomplete inhibition of nitrous oxide reduction, may influence rate estimates. Recently, membrane inlet mass spectrometry (MIMS) has been used to measure denitrification in aquatic systems. Comparable results were obtained with MIMS and C₂H₂ inhibition methods when chloramphenicol was added to C₂H₂ inhibition assay mixtures to inhibit new synthesis of denitrifying enzymes. Dissolved-oxygen profiles indicated that surface layers of sediment cores subjected to the MIMS flowthrough incubation remained oxic whereas cores incubated using the C₂H₂ inhibition methods did not. Analysis of the microbial assemblages before and after incubations indicated significant changes in the sediment surface populations during the long flowthrough incubation for MIMS analysis but not during the shorter incubation used for the C₂H₂ inhibition method. However, bacterial community changes were also small in MIMS cores at the oxygen transition zone where denitrification occurs. The C₂H₂ inhibition method with chloramphenicol addition, conducted over short incubation intervals, provides a cost-effective method for estimating denitrification, and rate estimates are comparable to those obtained by the MIMS method.     

Changes in the ratio of cyclic nucleotide phosphodiesterase forms in the thymocytes of irradiated mice

An increase in the activity of cyclic nucleotide phosphodiesterase was noted during the first hour following irradiation of mice with a dose of 11 Gy and after in vitro irradiation of the thymocyte suspension. Using the methods of gel-filtration and sedimentation and in studying the kinetic characteristics it was shown that the effect of radiation changed the degree of the enzyme aggregation, i. e. the share of the dissociated forms, which possessed a higher catalytic activity, increased.     

Cupryphans,metal‐binding,redox‐active,redesigned conopeptides

Contryphans are bioactive peptides, isolated from the venom of marine snails of the genus Conus, which are characterized by the short length of the polypeptide chain and the high degree of unusual post‐translational modifications. The cyclization of the polypeptide chain through a single disulphide bond, the presence of two conserved Pro residues, and the epimerization of a Trp/Leu residue confer to Contryphans a stable and well‐defined structure in solution, conserved in all members of the family, and tolerant to multiple substitutions. The potential of Contryphans as scaffolds for the design of redox‐active (macro)molecules was tested by engineering a copper‐binding site on two different variants of the natural peptide Contryphan‐Vn. The binding site was designed by computational modeling, and the redesigned peptides were synthesized and characterized by optical, fluorescence, electron spin resonance, and nuclear magnetic resonance spectroscopy. The novel peptides, named Cupryphan and Arg–Cupryphan, bind Cu²⁺ ions with a 1:1 stoichiometry and a K_d in the 100 nM range. Other divalent metals (e.g., Zn²⁺ and Mg²⁺) are bound with much lower affinity. In addition, Cupryphans catalyze the dismutation of superoxide anions with an activity comparable to other nonpeptidic superoxide dismutase mimics. We conclude that the Contryphan motif represents a natural robust scaffold which can be engineered to perform different functions, providing additional means for the design of catalytically active mini metalloproteins.     

Targeted Intracellular Site-Specific Drug Delivery: Photosensitizer Targeting to Melanoma Cell Nuclei

A number of drugs are regarded as possessing local activity because their effects take place at an extremely short distance from their location site in the cell. The response of different cellular compartments to these effects is different. Such substances as photosensitizers (PSs), which are used in photodynamic cancer therapy, should be targeted to the cell compartments where their effect is the most pronounced. This study describes the construction and properties of the chimeric modular recombinant transporters (MRTs) expressed in Escherichia coli and used for PS targeting. These constructs include (1) the -melanocyte-stimulating hormone as a ligand module, which is internalized by the target cells (mouse melanoma); (2) the optimized SV40 large T-antigen nuclear localization signal; (3) the hemoglobin-like protein from E. coli as a carrier module; (4) the endosomolytic module, the translocation domain of the diphtheria toxin. These MRTs were used for PS targeting to the mouse melanoma cell nuclei, the most PS-damaged intracellular compartment, which resulted in a PS photocytotoxic effect increase of several orders of magnitude. In our opinion, MRTs, which target locally active drugs into the desired cell compartment and thereby enhance the drug response, represent a new generation of the pharmacological agents.