Computer prediction of biological activity spectra for low-molecular peptides and peptidomimetics

The wide variety of the biological effects of peptides and their high activity are the main reasons for the search for new basic drug structures among them. The most promising compounds can be selected using the PASS computer system (Prediction of Activity Spectra for Substances). This system was originally developed to predict the activities of low-molecular “drug-like” organic compounds. Its predictive capacity is described here by the example of 134 peptides and peptidomimetics with nine known biological activities. Its average predictive power is shown to be approximately 97%. Such an accuracy demonstrates that computer prediction can be applied both to the evaluation of effects and mechanisms of action of endogenous and synthetic peptides and to the screening of new therapeutic agents among the most promising basic structures.     

The we Gene is a Modifier of the walGene in Mice

Interaction of gene wellhaarig (we) with genes waved alopecia(wal) and hairless (hr) was studied in mice. The mutant gene weis responsible for the development of a specific waved coat in homozygotes. Homozygous mice carrying mutant gene walalso have a wavy coat, though a partial alopecia develops with time in these animals. In homozygotes for thehr gene, hair loss is observed beginning from the age of ten days. A series of crosses we/weand wal/wal yielded animals with we/+wal/wal and we/we wal/wal genotypes. In micewe/+wal/wal carrying gene we at a single dose, alopecia is accelerated significantly as compared to the single-dose homozygotes +/+wal/wal. In we/we wal/wal mice, alopecia starts earlier than in we/+wal/wal mice; by the age of one month, the double homozygotes are almost hairless except for small body areas covered with a sparse coat. In addition, curliness of the first-generation hair in mice we/we wal/wal is much more expressed than in +/+wal/wal and we/we+/+ mice. The obtained evidence suggests that the wegene is a modifier of the wal gene because the former enhances the effects of the walgene, which is confirmed by the earlier onset of alopecia and progression of the latter in mice having the we/+wal/wal genotype and especially in we/we wal/wal animals. The we/we hr/+ mice do not differ in coat from we/we+/+ mice; in both cases, the coat is wavy. The coat of double homozygotes we/we hr/hr, is similar to that of we/we+/+ mice until ten days of age, when the signs of alopecia appear. By the age of 21 days, mice we/we hr/hr have lost their coat completely like mice +/+ hr/hr. Hence, the we gene is a modifier of the walgene though it does not interact with hrgene during the coat formation.     

Model-based biotechnological potential analysis of <Emphasis Type="Italic">Kluyveromyces marxianus</Emphasis> central metabolism

The non-conventional yeast Kluyveromyces marxianus is an emerging industrial producer for many biotechnological processes. Here, we show the application of a biomass-linked stoichiometric model of central metabolism that is experimentally validated, and mass and charge balanced for assessing the carbon conversion efficiency of wild type and modified K. marxianus. Pairs of substrates (lactose, glucose, inulin, xylose) and products (ethanol, acetate, lactate, glycerol, ethyl acetate, succinate, glutamate, phenylethanol and phenylalanine) are examined by various modelling and optimisation methods. Our model reveals the organism’s potential for industrial application and metabolic engineering. Modelling results imply that the aeration regime can be used as a tool to optimise product yield and flux distribution in K. marxianus. Also rebalancing NADH and NADPH utilisation can be used to improve the efficiency of substrate conversion. Xylose is identified as a biotechnologically promising substrate for K. marxianus.     

Isolation and Characterization of Fragments of the ATP-Dependent Protease Lon from Escherichia coli Obtained by Limited Proteolysis

Conditions of limited proteolysis of the protease Lon from Escherichia coli that provided the formation of fragments approximately corresponding to the enzyme domains were found for studying the domain functioning. A method of isolation of the domains was developed, and their functional characteristics were compared. The isolated proteolytic domain (LonP fragment) of the enzyme was shown to exhibit both peptidase and proteolytic activities; however, it cleaved large protein substrates at a significantly lower rate than the full-size protease Lon. On the other hand, the LonAP fragment, containing both the ATPase and the proteolytic domains, retained almost all of the enzymatic properties of the full-size protein. Both LonP and LonAP predominantly form dimers unlike the native protease Lon functioning as a tetramer. These results suggest that the N-terminal domain of protease Lon may play a considerable role in the process of the enzyme oligomerization.     

Early incorporation of obscurin into nascent sarcomeres: implication for myofibril assembly during cardiac myogenesis

Obscurin is a recently identified giant multidomain muscle protein whose functions remain poorly understood. The goal of this study was to investigate the process of assembly of obscurin into nascent sarcomeres during the transition from non-striated myofibril precursors to striated structure of differentiating myofibrils in cell cultures of neonatal rat cardiac myocytes. Double immunofluorescent labeling and high resolution confocal microscopy demonstrated intense incorporation of obscurin in the areas of transition from non-striated to striated regions on the tips of developing myofibrils and at the sites of lateral fusion of nascent sarcomere bundles. We found that obscurin rapidly and precisely accumulated in the middle of the A-band regions of the terminal newly assembled half-sarcomeres in the zones of transition from the continuous, non-striated pattern of sarcomeric α-actinin distribution to cross-striated structure of laterally expanding nascent Z-discs. The striated pattern of obscurin typically ended at these points. This occurred before the assembly of morphologically differentiated terminal Z-discs of the assembling sarcomeres on the tips of growing myofibrils. The presence of obscurin in the areas of the terminal Z-discs of each new sarcomere was detected at the same time or shortly after complete assembly of sarcomeric structure. Many non-striated fibers with very low concentration of obscurin were already immunopositive for sarcomeric actin and myosin. This suggests that obscurin may serve for organization and alignment of myofilaments into the striated pattern. The comparison of obscurin and titin localization in these areas showed that obscurin assembly into the A-bands occurred soon after or concomitantly with incorporation of titin. Electron microscopy of growing myofibrils demonstrated intense formation and integration of myosin filaments into the “open” half-assembled sarcomeres in the areas of the terminal Z–I structures and at the lateral surfaces of newly formed, terminally located nascent sarcomeres. This process progressed before the assembly of the second-formed, terminal Z-discs of new sarcomeres and before the development of ultrastructurally detectable mature M-lines that define the completion of myofibril assembly, which supports the data of immunocytochemical study. Abundant non-aligned sarcomeres in immature myofibrils located on the growing tips were spatially separated and underwent the transition to the registered, aligned pattern. The sarcoplasmic reticulum, the organelle known to interact with obscurin, assembled around each new sarcomere. These results suggest that obscurin is directly involved in the proper positioning and alignment of myofilaments within nascent sarcomeres and in the establishment of the registered pattern of newly assembled myofibrils and the sarcoplasmic reticulum at advanced stages of myofibrillogenesis. This paper is dedicated to the memory of Professor Pavel P. Rumyantsev (1927–1988), a pioneer in studies of cardiac muscle differentiation, who is a lasting inspiration to all who worked with him.     

Localization of substance P- and FMRFamide-like immunoreactivity in the atrium of the snail Achatina fulica

By immunohistochemical and immunocytochemical methods localization of Substanse P (SP) and FMRFamide in the atrium of the snail Achatina fulica was investigated. Nerve fibers innervating the snail atrium contact tightly with the granular cells (GC) situated between muscle and endocardial cells, forming neuroendocrine units. Both neuromediators were found in the cells of the neuroendocrine units. By immunohistochemistry SP- and FMRFamide-immunoreactive material was revealed in the granules of the atrial GC. Elecrtonmicroscopical immunocytochemistry has confirmed the presence of SP- and FMRFamide-immunoreactive material in the granules of the GC and shown their presence in the neurosecretory granules of the nerve endings contacting both the atrial GC and cardiomyocytes.     

Regulation of caspase activity in apoptosis

Intracellular cysteine aspartate-specific proteases (caspases) play both signaling and effector roles in realizing the program of cell death. Caspases function as proteolytic cascades unique for each cell type and signal triggering apoptosis. All parts of the proteolytic cascades are duplicated and controlled by feedback signals. Amplification cycles between pairs of caspases (the third and the sixth, the ninth and the third, the twelfth and the sixth, and others) help multiply the initial apoptotic signal. The presence of physiological inhibitors of apoptosis that directly interact with caspases creates a multilevel regulatory network of apoptosis in cell. The caspase proteolytic cascades are also regulated by sphingolipid secondary messengers, among them ceramide, sphingosine, and their phosphates. Moreover, an association of the caspase signaling with ubiquitin-dependent proteolysis is shown in cells. In particular, the use of extracellular activators and inhibitors of caspases allows irreversible activation of apoptosis in tumor cells or the prevention of neuron death in neurodegenerative diseases.     

Characterization of cis-regulatory elements of the homeobox gene Xanf-1

Investigation of molecular mechanisms underlying early patterning of the nervous system is an important task of modern developmental biology. Previously, we identified a novel homeobox gene, Anf, that is expressed in the most anterior zone at the beginning of neuroectoderm specification. The expression pattern of Anf corresponds to primordia of the telencephalon and the rostral part of the diencephalon. In the present work, we investigated cis-regulation of expression of the Xenopus laevis Anf, Xanf-1. Two elements, highly conserved in Xenopus, chick and human, were identified within the Xanf-1 promoter region. The first element, located near position -500, is necessary for overall enhancement of the Xanf-1 expression. The second element, near position -200, is crucial for maintenance of the Xanf-1 expression at moderate levels and also for specific localization of the expression in the anterior neuroectoderm. Thus, the distal part of this element is responsible for suppression of Xanf-1 posterior to the normal expression domain of this gene. The data obtained corroborate with the Nieuwkoop two-signal model of neural induction. This model states that at the first step of induction, all neuroectoderm acquires potencies to develop toward forebrain structures, but later these potencies are suppressed in posterior regions.     

Effect of water soluble non-membrane proteins on the phospholipid structure

The interaction of water-soluble nonmembraneous proteins (trypsin and the basic pancreatic trypsin inhibitor (BPTI)) with soybean phospholipids was studied using multilamellar vesicles. Multilamellar vesicles were obtained from soybean lipid extracts and mixtures of individual phospholipids based on phosphatidylcholine. These mixtures contain different phospholipids: "bilayer", "nonbilayer", and negatively charged. It was shown that the content of both proteins in the complex depends on pH and the presence of negatively charged components. On the basis of this finding, the conclusion about the electrostatic nature of lipid-protein interaction was made. The structural organization of soybean phospholipids in multilamellar vesicles was studied in the presence and absence of the proteins using broad-line 31P-NMR spectroscopy. It was found that, in mixtures of phospholipids of complex composition, different types of phases coexist, and phospholipids of different classes can compensate the effects of each other. Trypsin and BPTI affect the structure of phospholipids in a similar way, inducing considerable structural changes in multilamellar vesicles of preparations containing negatively charged components in whose structure there coexisted primordially the bilayer and isotropic phases.