Protein-protein interactions as a target for drugs in proteomics

Protein-protein interactions play a central role in numerous processes in the cell and are one of the main fields of functional proteomics. This review highlights the methods of bioinformatics and functional proteomics of protein-protein interaction investigation. The structures and properties of contact surfaces, forces involved in protein-protein interactions, kinetic and thermodynamic parameters of these reactions were considered. The properties of protein contact surfaces depend on their functions. The contact surfaces of permanent complexes resemble domain contacts or the protein core and it is reasonable to consider such complex formation as a continuation of protein folding. Characteristics of contact surfaces of temporary protein complexes share some similarities with active sites of enzymes. The contact surfaces of the temporary protein complexes have unique structure and properties and they are more conservative in comparison with active site of enzymes. So they represent prospective targets for a new generation of drugs. During the last decade, numerous investigations were undertaken to find or design small molecules that block protein dimerization or protein(peptide)-receptor interaction, or, on the contrary, to induce protein dimerization.     

Plant mitochondria actively import DNA via the permeability transition pore complex

Plant mitochondria are remarkable with respect to their content in foreign, alien and plasmid-like DNA, raising the question of the transfer of this information into the organelles. We demonstrate the existence of an active, transmembrane potential-dependent mechanism of DNA uptake into plant mitochondria. The process is restricted to double-strand DNA, but has no obvious sequence specificity. It is most efficient with linear fragments up to a few kilobase pairs. When containing appropriate information, imported sequences are transcribed within the organelles. The uptake likely involves the voltage-dependent anion channel and the adenine nucleotide translocator, i.e. the core components of the mitochondrial permeability transition pore complex in animal cells, but it does not rely on known mitochondrial membrane permeabilization processes. We conclude that DNA import into plant mitochondria might represent a physiological phenomenon with some functional relevance.     

Purification and properties of a carbonyl reductase involved in stereoselective reduction of ethyl 4-chloro-3-oxobutanoate from Cylindrocarpon sclerotigenum IFO 31855

A NADPH-dependent carbonyl reductase (CSCR1) was purified to homogeneity from Cylindrocarpon sclerotigenum IFO 31855. The enzyme catalyzed the stereoselective reduction of ethyl 4-chloro-3-oxobutanoate to the corresponding (S)-alcohol with a >99% enantiomer excess. The relative molecular mass of the enzyme was estimated to be 68,000 by gel filtration chromatography and 24,800 on SDS polyacrylamide gel electrophoresis. The enzyme had an extremely narrow substrate specificity and it highly reduced conjugated diketone, 2,3-butanedion, in addition to ethyl 4-chloro-3-oxobutanoate. The enzyme activity was inhibited by HgCl(2) (100%), 5,5'-dithiobis(2-nitrobenzoic acid) (56%), dicoumarol (42%), and CuSO(4) (46%). The N-terminal amino acid sequence of the enzyme (P-Q-G-I-P-T-A-S-R-L) showed no apparent similarity with those of other oxidoreductases.     

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)

Background  

Standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. We used the database of Clusters of Orthologous Groups of proteins (COGs) to reannotate the genomes of two archaea, Aeropyrum pernix, the first member of the Crenarchaea to be sequenced, and Pyrococcus abyssi.     

Structural organization of nicotinic acetylcholine receptors

Nicotinic acetylcholine receptor of the electric ray Torpedo is the most comprehensively characterized neurotransmitter receptor. It consists of five subunits (alpha2beta gammadelta) amino acid sequences of which were determined by cDNA cloning and sequencing. The shape and size of the receptor were determined by electron cryomicroscopy. It has two agonist/competitive antagonist binding sites which are located between subunits near the membrane surface. The receptor ion channel is formed by five transmembrane helices (M2) of all five subunits. The position of the binding site for noncompetitive ion channel blockers was found by photoaffinity labelling and site-directed mutagenesis. The intrinsic feature of the receptor structure is the position of the agonist/competitive antagonist binding sites in close vicinity to the ion channel spanning the bilayer membrane. This peculiarity may substantially enhance allosteric transitions transforming the ligand binding into the channel opening and physiological response. Muscle nicotinic acetylcholine receptors from birds and mammals are also pentaoligomers consisting of four different subunits (alpha2beta gammadelta or alpha2beta epsilondelta) with high homology to the Torpedo receptor. Apparently, the pentaoligomeric structure is the main feature of all nicotinic, both muscle and neuronal, receptors. However, the neuronal receptors are formed only by two subunit types (alpha and beta) or are even pentahomomers (alpha7 neuronal receptors). All nicotinic receptors are ligand-gated ion channel, the properties of the channels being essentially determined by amino acid residues forming M2 transmembrane fragments.     

Age-dependent decreases of phosphorus and magnesium in human achilles’ tendons

To elucidate changes of human tendons with aging, the authors studied age-related changes of elements in human Achilles’ tendons by inductively coupled plasma-atomic emission spectrometry. The subjects consisted of seven men and seven women, ranging in age from 61 to 97 yr. It was found that the content of calcium increased progressively with aging in the Achilles’ tendons, whereas the contents of phosphorus and magnesium decreased gradually with aging. The previous investigations demonstrated that the content of calcium and phosphorus increased progressively with aging in most, but not all, human tissues, except for the bones. In ligaments, such as the anterior cruciate ligament and the ligament of the head of the femur, which are histologically similar to the Achilles’ tendon, it was previously found that both the contents of calcium and phosphorus increased with aging in the ligaments. It should be noted that the content of phosphorus in the Achilles’ tendons decreased during the aging process. In addition, it was found that there was a very high direct correlation between phosphorus and magnesium contents in the tendons, but not between calcium and phosphorus contents.     

TESTING HYPOTHESES OF NEURAL EVOLUTION IN GYMNOTIFORM ELECTRIC FISHES USING PHYLOGENETIC CHARACTER DATA

In this paper, we propose a method to test alternative hypotheses of phenotypic evolution. The method compares patterns observed in phylogenetic character data with patterns expected by explicit models of evolutionary process. Observed patterns of character-state diversity are assessed from four properties of character-state change derived from a phylogenetic analysis: the sequence and correlation of transformations on a cladogram and the spatial and functional localization of these transformations to parts of an organism. Patterns expressed in terms of the localization of transformations are compared with the expectations of null models that the number of transformations is proportional to measures of size or complexity. Deviations from the values expected by the null models are then compared with qualitative expectations of the models. The method is applied to characters in the nervous system of gymnotiform electric fishes. Patterns in the diversity of 63 reconstructed character-state changes are compared with the expectations of 10 published models of neural evolution. A total of 63 expectations are reviewed, of which 33 (52%) are found to be consistent with the gymnotiform neural data. In general, the models reviewed are not successful at making global predictions, in part because they have been cast in excessively general terms. The data support the conclusion that evolution in the nervous system of gymnotiforms has involved a mosaic of processes, each operating differentially on functional and developmental systems and at different spatial and temporal scales. The results also indicate that more refined models are required, each making more explicit predictions.     

Alkylcobalt chelates with Schiff bases derived from a β-diketone bearing both alkyl and aryl groups

Organocobalt(III) complexes with Schiff bases derived from a β-diketone bearing both an alkyl and an aryl group have been prepared. The template syntheses using benzoylacetone and ethylenediamine as complexing agents provide a route to alkylcobalt chelates with the corresponding tri- and tetradentate Schiff bases. However, if a β-diketone with two aryl groups, e.g. dibenzoylmethane, was employed as the starting ketoenol component, no organometallic products were detected; a new mixed-ligand ‘inorganic’ chelate of cobalt(II), [Co{O=C(Ph)CH=C(Ph)O}₂(en)], was isolated instead. Its structure as well as that of one of the alkylcobalt complexes with a tridentate Schiff base composed of benzoylacetone and ethylenediamine have been established by X-ray techniques. The current scope of the template synthesis of alkylcobalt complexes with Schiff bases is summarized.