The crystal structure of a binary complex of two pseudopilins: EpsI and EpsJ from the type 2 secretion system of Vibrio vulnificus

Type II secretion systems (T2SS) translocate virulence factors from the periplasmic space of many pathogenic bacteria into the extracellular environment. The T2SS of Vibrio cholerae and related species is called the extracellular protein secretion (Eps) system that consists of a core of multiple copies of 11 different proteins. The pseudopilins, EpsG, EpsH, EpsI, EpsJ and EpsK, are five T2SS proteins that are thought to assemble into a pseudopilus, which is assumed to interact with the outer membrane pore, and may actively participate in the export of proteins. We report here biochemical evidence that the minor pseudopilins EpsI and EpsJ from Vibrio species interact directly with one another. Moreover, the 2.3 Å resolution crystal structure of a complex of EspI and EpsJ from Vibrio vulnificus represents the first atomic resolution structure of a complex of two different pseudopilin components from the T2SS. Both EpsI and EpsJ appear to be structural extremes within the family of type 4a pilin structures solved to date, with EpsI having the smallest, and EpsJ the largest, “variable pilin segment” seen thus far. A high degree of sequence conservation in the EpsI:EpsJ interface indicates that this heterodimer occurs in the T2SS of a large number of bacteria. The arrangement of EpsI and EpsJ in the heterodimer would correspond to a right-handed helical character of proteins assembled into a pseudopilus.     

The Informational Concept of Searching for Periodicity in Symbol Sequences

A method of informational decomposition has been developed, allowing one to reveal hidden periodicity in any symbol sequence. The informational decomposition is calculated without conversion of a symbol sequence into a numerical one, which facilitates finding periodicities in a symbol sequence. The method permits introducing an analog of the autocorrelation function of a symbol sequence. The method developed by us has been applied to reveal hidden periodicities in nucleotide and amino acid sequences, as well as in different poetical texts. Hidden periodicity has been detected in various genes, testifying to their quantum structure. The functional and structural role of hidden periodicity is discussed.     

The study of the bioenergetic characteristics of the red blood cells of Black Sea fish: the common stingray (<Emphasis Type="Italic">Dasyatis pastinaca</Emphasis> L.) and black scorpionfish (<Emphasis Type="Italic">Scorpaena porcus</Emphasis> L.)

The oxygen consumption rate in red blood cell suspensions of two Black Sea fish species, a cartilaginous fish, the common stingray (Dasyatis pastinaca L.) and the teleost black scorpionfish (Scorpaena porcus L.) has been studied. The proposed stimulants of activators and inhibitors of the mitochondria electron transport chain had very predictable responses, indicating that mitochondria in fish erythrocytes have a classical set of respiratory enzymes. Despite the fact that the basic respiratory activity of common stingray erythrocytes was greater than those of the scorpionfish, the responses of common stingray red blood cells to the exposure during investigation of the respiratory activity of the mitochondria have an inverse relationship. The oxygen consumption rates in suspensions of scorpionfish erythrocytes in response to the stimulant were higher according to both the amplitude and the duration of the response. Investigations have shown the high energy potential of the red blood cell mitochondria of the scorpionfish and stingray. This may be the energy basis for maintaining the high intracellular concentrations of ATP required not only to keep an adequate level of intracellular metabolism, but also to provide a special mode of blood flow through the capillary beds.     

Gangliosides GM1 and GD1a normalize respiratory rates of rat brain mitochondria reduced by <Emphasis Type="Italic">tert</Emphasis>-butyl hydroperoxide

The rate of oxygen consumption by glutamate- and malate-energized rat brain mitochondria, which was stimulated by an uncoupler 2,4-dinitrophenol (DNP), declined in the presence of a prooxidant tert-butyl hydroperoxide. Preincubation with gangliosides GM1 or GD1a at micromolar (but not nanomolar) concentrations significantly slowed down this decline in the mitochondrial respiration, as shown by measuring absolute respiratory rates and ratios of the mitochondrial respiratory rate in the presence of DNP to the basal respiratory rate (V _DNP/V ₀). Gangliosides GM1 and GD1a also slowed down a decline in the DNP-stimulated mitochondrial respiration induced by long-term incubation (“aging”) of mitochondria on ice. The data obtained are likely to reflect a prooxidant-induced reduction in the activity of enzymes of the mitochondrial respiratory chain as well as a GM1- and GD1a-induced decrease in the degree of their inactivation. Interestingly, in the presence of the Trk receptor tyrosine kinase inhibitor (K252a) this effect of gangliosides was not manifested in any way. Our data suggest that the direct impact of gangliosides on mitochondrial signaling pathways, specifically on the Trk receptor tyrosine kinase, plays a certain role in the mechanism of their protective effect on cerebral neurons and, probably, neuroglia.     

Classification analysis of a latent dinucleotide periodicity of plant genomes

The information decomposition (ID) method has been used for searching dinucleotide periodicities, including latent ones, in plant genomes. In nucleotide sequences of genomes of various plants from the Gen-Bank database, 14 766 sequences with a periodicity of two nucleotides have been found at a high level of statistical significance. Classification of the periodicity matrices of the detected DNA sequences has yielded 141 classes of dinucleotide periodicity. Since ID does not detect periodicities with nucleotide deletions or insertions, modified profile analysis (MPA) has been applied to the obtained classes to reveal DNA sequences with dinucleotide periodicities containing nucleotide deletions and insertions. Combined use of ID and MPA has permitted the detection of 80 396 DNA sequences with dinucleotide periodicities in the genomes of various plants. The biological role of dinucleotide periodicity in the detected sequences is discussed.     

A new native EcHsp31 structure suggests a key role of structural flexibility for chaperone function

Heat shock proteins and proteases play a crucial role in cell survival under conditions of environmental stress. The heat shock protein Hsp31, produced by gene hchA at elevated temperatures in Escherichia coli, is a homodimeric protein consisting of a large A domain and a smaller P domain connected by a linker. Two catalytic triads are present per dimer, with the Cys and His contributed by the A domain and an Asp by the P domain. A new crystal Form II confirms the dimer and catalytic triad arrangement seen in the earlier crystal Form I. In addition, several loops exhibit increased flexibility compared to the previous Hsp31 dimer structure. In particular, loops D2 and D3 are intriguing because their mobility leads to the exposure of a sizable hydrophobic patch made up by surface areas of both subunits near the dimer interface. The residues creating this hydrophobic surface are completely conserved in the Hsp31 family. At the same time, access to the catalytic triad is increased. These observations lead to the hypothesis for the functioning of Hsp31 wherein loops D2 and D3 play a key role: first, at elevated temperatures, by becoming mobile and uncovering a large hydrophobic area that helps in binding to client proteins, and second, by removing the client protein from the hydrophobic patch when the temperature decreases and the loops adopt their low-temperature positions at the Hsp31 surface. The proposed mode of action of flexible loops in the functioning of Hsp31 may be a general principle employed by other chaperones.     

Hsp31, the Escherichia coli yedU gene product,is a molecular chaperone whose activity is inhibited by ATP at high temperatures

The Escherichia coli chromosome contains several uncharacterized heat-inducible loci that may encode novel molecular chaperones or proteases. Here we show that the 31-kDa product of the yedU gene is an efficient homodimeric molecular chaperone that is conserved in a number of pathogenic eubacteria and fungi. Heat shock protein (Hsp) 31 relies on temperature-driven conformational changes to expose structured hydrophobic domains that are likely responsible for substrate binding. Complementing the function of refolding, remodeling, and holding chaperones, Hsp 31 preferentially interacts with early unfolding intermediates and rapidly releases them in an active form after transfer to low temperatures. Although Hsp 31 does not appear to exhibit intrinsic ATPase activity, binding of ATP at high temperatures restricts the size or availability of the substrate binding site, thereby modulating chaperone activity. The possible role of ATP in coordinating the function of the cellular complement of molecular chaperones is discussed.     

The locally optimal method of cyclic alignment to reveal latent periodicities in genetic texts. The NAD-binding protein sites

A program package has been developed to search for hidden tandem repeats of any specified type in the protein sequence databases. The applied algorithm of the locally optimal cyclic alignment is able to find subsequences possessing a certain profile-based periodicity type when no appreciable homology between periods is observed, as well as in the presence of arbitrary insertions/deletions. The profile can be adjusted to search for the periodicity types structurally and functionally important. The Swiss-Prot database has been analyzed to reveal the periodicities undetectable earlier that are caused by the secondary and super-secondary structure regularities of the NAD-binding sites. In particular, a significant periodicity of 24 aa was found to be characteristic of the absolute majority of domains possessing the Rossman (or Rossman-like) fold and displaying the apparent regularity in their secondary structures, not being obvious at the primary structure level.