Docking and small angle X-ray scattering studies of purine nucleoside phosphorylase

Docking simulations have been used to assess protein complexes with some success. Small angle X-ray scattering (SAXS) is a well-established technique to investigate protein spatial configuration. This work describes the integration of geometric docking with SAXS to investigate the quaternary structure of recombinant human purine nucleoside phosphorylase (PNP). This enzyme catalyzes the reversible phosphorolysis of N-ribosidic bonds of purine nucleosides and deoxynucleosides. A genetic deficiency due to mutations in the gene encoding for PNP causes gradual decrease in T-cell immunity. Inappropriate activation of T-cells has been implicated in several clinically relevant human conditions such as transplant rejection, rheumatoid arthritis, lupus, and T-cell lymphomas. PNP is therefore a target for inhibitor development aiming at T-cell immune response modulation and has been submitted to extensive structure-based drug design. The present analysis confirms the trimeric structure observed in the crystal. The potential application of the present procedure to other systems is discussed.     

Scanning electron microscopy and intraspecific variation of Chordodes festae Camerano, 1897 and C. peraccae (Camerano, 1894) (Nematomorpha: Gordioidea)

The nematomorph species Chordodes festae Camerano, 1897 and C. peraccae (Camerano, 1894) are redescribed by using scanning electron microscopy (SEM). C. festae has a cuticle with four different areolar types, the crown areoles being the most noticeable with long spiniform processes. The terminal end in the male specimen has two short lobe-like structures and a ventral groove. C. peraccae has three areolar types in which, as in C. festae, some areoles form groups surrounding the crown areoles. Intraspecific variations were found in body length and body colour in both species and, in C. peraccae, also in the cuticle.     

Rubritepida flocculans gen. nov., sp. nov., a new slightly thermophilic member of the alpha-1 subclass of the Proteobacteria

A bacterial isolate, with an optimum growth temperature of about 50 degrees C, was recovered from the hot spring at Egerszalók in Hungary. Phylogenetic analyses using the 16S rRNA gene sequence of strain H-8T indicated that the new organism represented a new genus and species of alpha-1 subclass of the Proteobacteria. The major fatty acids of strain H-8T are 16:0, 18:1 omega7c; the rare fatty acid 19:0 20H cyclo 11,12 is also present. Ubiquinone 9 is the major respiratory quinone, the polar lipids are phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol in addition to two unidentified aminolipids. The new isolate forms red-colored colonies, flocculates in liquid media, is heterotrophic and strictly aerobic. Thiosulfate is oxidized to sulfate, but an increase in biomass could not be measured because of the flocculating behavior. Bacteriochloropyll a was detected by direct spectrophotometric analysis when the organism was grown at 30 degrees C, but could not be detected after growth at 50 degrees C. pufL and pufM genes were present. Heterotrophic growth of strain H-8T occurs on a few carbohydrates, amino acids and organic acids. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we propose that strain H-8T represents a new genus and a new species most closely related to Roseococcus thiosulfatophilus for which we propose the name Rubritepida flocculans.     

Identification of residues important for NAD+ binding by the Thermotoga maritima alpha-glucosidase AglA,a member of glycoside hydrolase family 4

The NAD+-requiring enzymes of glycoside hydrolase family 4 (GHF4) contain a region with a conserved Gly-XXX-Gly-Ser (GXGS) motif near their N-termini that is reminiscent of the fingerprint region of the Rossmann fold, a conserved structural motif of classical nicotinamide nucleotide-binding proteins. The function of this putative NAD+-binding motif in the alpha-glucosidase AglA of Thermotoga maritima was probed by directed mutagenesis. The K(d) for NAD+ of the AglA mutants G10A, G12A and S13A was increased by about 300-, 5-, and 9-fold, respectively, while their K(m) for p-nitrophenyl-alpha-glucopyranoside was not seriously affected. The results indicate that the GXGS motif is indeed important for NAD+ binding by the glycosidases of GHF4.     

Target-derived GFRalpha1 as an attractive guidance signal for developing sensory and sympathetic axons via activation of Cdk5

Immobilized and diffusible molecular cues regulate axon guidance during development. GFRalpha1, a GPI-anchored receptor for GDNF, is expressed as both membrane bound and secreted forms by accessory nerve cells and peripheral targets of developing sensory and sympathetic neurons during the period of target innervation. A relative deficit of GFRalpha1 in developing axons allows exogenous GFRalpha1 to capture GDNF and present it for recognition by axonal c-Ret receptors. Exogenous GFRalpha1 potentiates neurite outgrowth and acts as a long-range directional cue by creating positional information for c-Ret-expressing axons in the presence of a uniform concentration of GDNF. Soluble GFRalpha1 prolongs GDNF-mediated activation of cyclin-dependent kinase 5 (Cdk5), an event required for GFRalpha1-induced neurite outgrowth and axon guidance. Together with GDNF, target-derived GFRalpha1 can function in a non-cell-autonomous fashion as a chemoattractant cue with outgrowth promoting activity for peripheral neurons.     

Integrin expression patterns during early limb muscle development in the mouse

Cell-extracellular matrix interactions play crucial roles in limb muscle development but practically nothing is known on what integrins are involved before the differentiation of muscle precursor cells (MPCs) in the limb muscle masses. In this study we determine the expression patterns of integrins during early forelimb muscle development in the mouse. alpha6beta1 integrin is downregulated in the lateral dermomyotome when delamination of MPCs occurs. In late E9.5 embryos, alpha1beta1 and alpha5beta1 are expressed in a pattern very similar to pax3, which marks MPCs migrating to the limb bud. After myf5 upregulation in the limb bud, alpha1beta1 and alpha5beta1 expression is maintained and the alpha4beta1 integrin starts being expressed.     

Cercaria sevillana n sp,a new cercaria (Digenea: Microphallidae) from Nassarius reticulatus (L) (Mollusca: Prosobranchia) in Portugal

Cercaria sevillana n. sp. (Digenea: Microphallidae) was discovered infecting the gonads and digestive gland of the prosobranch Nassarius reticulatus (L.) (Nassariidae) collected from the Ria de Aveiro, Portugal. Cercariae were obtained by natural emission and were studied under a differential interference contrast microscope and scanning electron microscope (SEM). C. sevillana n. sp. is identical to the cercaria found by Dolgikh (1965) in the same mollusc host from the Black Sea, but erroneously named C. misenensis Palombi, 1940, which is a parasite of Cerithium rupestre Risso, 1826 (Cerithiidae). Cercaria sevillana n. sp. can be distinguished from C. misenensis by its tail being shorter than the cercarial body, as well as by differences in the pattern of penetration glands the size and shape of the stylet and excretory vesicle, and its behavioural pattern. An unusual structure of the tail of this new cercaria was observed by SEM; it is characterised by the presence of annular folded membranes arranged as overlapping flounces around its central axis. This resembles the traditional skirts of the women of Seville. Such a morphological feature of the tail has not been previously observed, but may be a feature of many microphallid cercariae.     

U0ltrastructural description of the musculature,the intraepidermal nervous system,and their interrelation in Pseudochordodes bedriagae (Nematomorpha)

The ultrastructure of the body wall muscles and the intraepidermal nervous system of the Gordiida Pseudochordodes bedriagae are described. The body wall muscles are of the circomyarian type, since the sarcomeres constitute a system of continuous peripheral helices. The organisation of the sarcomeres follows a pattern that resembles that of the striated muscles. The muscle fibres are separated into areas by invaginations formed exclusively by the plasma membrane (T component), while the sarcoplasmic reticulum lies at the sides of the Z granules forming subsarcolemmal cisternae, and in the zone near the nucleus, like flattened vesicles, contributing with the T component to the formation of dyads and triads. The muscle fibres present two types of adaptations for their innervation: (1) cytoplasmic projections towards the epidermis, and (2) invaginations of the plasmalemma. The motor peripheral nervous system is conformed by the nerve fibres that run within the epidermis and their projections towards the basal membrane in order to contact the adaptations of the muscle fibres in a basi-epidermal synapsis. The presence of an intraepithelial peripheral nervous system in Gordiida confirms a structural pattern common to other taxa of Nemathelminthes.     

Expression of constructs of the neuronal isoform of myosin-Va interferes with the distribution of melanosomes and other vesicles in melanoma cells

Myosin-Va has been implicated in melanosome translocation, but the exact molecular mechanisms underlying this function are not known. In the dilute, S91 melanoma cells, melanosomes move to the cell periphery but do not accumulate in the tips of dendrites as occurs in wild-type B16 melanocytes; rather, they return and accumulate primarily at the pericentrosomal region in a microtubule-dependent manner. Expression of the full-length neuronal isoform of myosin-Va in S91 cells causes melanosomes to disperse, occupying a cellular area approximately twice that observed in non-transfected cells, suggesting a partial rescue of the dilute phenotype. Overexpression of the full tail domain in S91 cells is not sufficient to induce melanosome dispersion, rather it causes melanosomal clumping. Overexpression of the head and head-neck domains of myosin-Va in B16 cells does not alter the melanosome distribution. However, overexpression of the full tail domain in these cells induces melanosome aggregation and the appearance of tail-associated, aggregated particles or vesicular structures that exhibit variable degrees of staining for melanosomal and Golgi beta-COP markers, as well as colocalization with the endogenous myosin-Va. Altogether, the present data suggest that myosin-Va plays a role in regulating the direction of microtubule-dependent melanosome translocation, in addition to promoting the capture of melanosomes at the cell periphery as suggested by previous studies. These studies also reinforce the notion that myosin-V has a broader function in melanocytes by acting on vesicular targeting or intracellular protein trafficking.     

Molecular modeling and dynamics of the sodium channel inactivation gate

The intracellular linker L(III-IV) of voltage-gated sodium channels is known to be involved in their mechanism of inactivation. Its primary sequence is well conserved in sodium channels from different tissues and species. However, the role of charged residues in this region, first thought to play an important role in inactivation, has not been well identified, whereas the IFM triad (I1488-M1490) has been characterized as the crucial element for inactivation. In this work, we constructed theoretical models and performed molecular dynamics simulations, exploring the role of L(III-IV)-charged residues in the presence of a polar/nonpolar planar interface represented by a dielectric discontinuity. From structural predictions, two alpha-helical segments are proposed. Moreover, from dynamics simulations, a time-conserved motif is detected and shown to play a relevant role in guiding the inactivation particle toward its receptor site.