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1.
2.
The present paper studies the possibly different feeding strategies of Diplodus sargus to crustaceans, molluscs, worms, and small fish. The buccal jaws are built strongly and bound together by numerous ligaments. The dentition is heterodont: incisors in front and molars in the middle and hind parts. The principal originality of the musculature of this species is the forward insertion of the adductores mandibulae. These are very thick and insert on both the upper and lower jaws, so that contraction of any individual muscle acts on the buccal pieces as a whole, which thus constitute a remarkable crushing device. The pharyngeal jaws are frail as in primitive perciforms: the lower ones are well separated, being bound only anteriorly, while the upper ones consist of the second and third pharyngobranchials and a posterior toothed plate. When feeding on crabs, Diplodus sargus always sucks in the prey and seizes it with the buccal jaws. Mouth opening is accompanied by extensive protrusion of the mouth, with or without neurocranial elevation. Mouth sucking and seizing movements vary little. Once seized, the prey is usually moved to the molars and crushed. The crushing movements may be fast and ample or slow. In the latter case, deformation of the prey is observable. Crushing usually results in the crab being broken into pieces. The pharyngeal jaws grip one part of the prey and shift it to the oesophagus, then seize the second part. Diplodus sargus adapts its feeding behaviour to the type of prey. A snail, for instance, is crushed by the buccal or pharyngeal teeth, the pieces of shell are ejected, and the soft parts conveyed with difficulty to the oesophagus by the pharyngeal jaws. A fish on the other hand, is sucked tail first into the mouth cavity and quickly shifted to the digestive tract by the pharyngeal bones. Behaviour toward different prey differs by the presence or absence of parts of the sequence of feeding movements (for example crushing) or by the fact that certain movements or parts of the sequence are repeated. The variability of any movement in the sequence is the same whatever the sort of prey. Crushing occurs between the buccal incisors and molars and was observed twice between the pharyngeal teeth. Usually, it seems, the latter are involved in transport only. In transport, the left and right pharyngeal jaws may perform different functions: their movements, unlike the symmetrical movements of the buccal jaws, sometimes differ.  相似文献   

3.
The relation between the conservation of active site residues and the molecular mechanism of aminoacylation reaction is an unexplored problem. In the present paper, the influences of the conserved active site residues on the reaction mechanism as well as the electrostatic potential near the reaction center are analyzed for Histidyl tRNA synthetase from Escherichia coli, Thermus thermophilus and Staphylococcus aureus. While the primary structures show both convergence as well as divergence, the secondary level structures of the active sites of the three species show considerable conservation in the respective structural organizations. The conserved active site residues near the reaction center, which have a major role in the reaction mechanism and catalysis, retain their specific position and orientation relative to the substrate in the three species. In order to understand the influence of different conserved and nonconserved residues near the reaction center, two different models are considered. First, a large model of active site with the substrates, Mg2+ ions and water is constructed in which the first shell residues (including both conserved as well as nonconserved) near the reaction center are studied. From the large model, a smaller model is constructed for reaction path modeling individually for three species. Validation of the smaller model is carried out by comparing the energy surfaces of large and small models as a function of reaction coordinates. Further, the electrostatic potential near the reaction center for the large and small model are compared. The transition state structures of the activation step of aminoacylation reaction for E. coli, T. thermophilus and S. aureus are calculated using the combined ab-initio/semi-empirical calculation. The similarity of the energy profiles as a function of the relevant reaction coordinate and the orientation of the catalytic residue, Arg259, indicate that the reaction mechanisms are identical which are guided by the strikingly similar structural pattern formed by conserved residues for three species. The energy surfaces have close resemblance in three species and present a clear perspective that how the reaction proceeds with the aid of different conserved residues. The study of electrostatic potential confirms this view. The present study provides an understanding of the relationship between the conservation of residues and the efficient reaction mechanism of aminoacylation reaction.  相似文献   

4.
Characterization of 5 to 25 pmol of purified proteins by tryptic peptide mapping has been accomplished using the Bolton-Hunter reagent (125I-3-[4-hydroxyphenyl]propionic acid N-hydroxysuccinimide ester). Radioacylation is followed by reaction with unlabeled ester and reductive methylation to ensure resistance of lysyl residues to trypsinization. Reduced and alkylated proteins are analzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, trypsinized from individual gel slices, and mapped two-dimensionally on thin layers. The method permits peptide mapping of proteins with specific activities of 1 to 2 × 104 cpm/ng, results in more spots (and often more structural information) than direct iodination procedures, and can be used for characterization of proteins that could not be biosynthetically labeled.  相似文献   

5.
Bacterial periplasmic binding proteins (PBPs) and eukaryotic PBP-like domains (also called as Venus flytrap modules) of G-protein-coupled receptors are involved in extracellular GABA perception. We investigated the structural and functional basis of ligand specificity of the PBP Atu2422, which is implicated in virulence and transport of GABA in the plant pathogen Agrobacterium tumefaciens. Five high-resolution x-ray structures of Atu2422 liganded to GABA, Pro, Ala, and Val and of point mutant Atu2422-F77A liganded to Leu were determined. Structural analysis of the ligand-binding site revealed two essential residues, Phe77 and Tyr275, the implication of which in GABA signaling and virulence was confirmed using A. tumefaciens cells expressing corresponding Atu2422 mutants. Phe77 restricts ligand specificity to α-amino acids with a short lateral chain, which act as antagonists of GABA signaling in A. tumefaciens. Tyr275 specifically interacts with the GABA γ-amino group. Conservation of these two key residues in proteins phylogenetically related to Atu2422 brought to light a subfamily of PBPs in which all members could bind GABA and short α-amino acids. This work led to the identification of a fingerprint sequence and structural features for defining PBPs that bind GABA and its competitors and revealed their occurrence among host-interacting proteobacteria.  相似文献   

6.
The YdjC-family protein is widely distributed, from human to bacteria, but so far no three-dimensional structure and functional analysis of this family of proteins has been reported. We determined the three-dimensional structure of the YdjC homolog TTHB029 at a resolution of 2.9 Å. The overall structure of the monomer consists of (βα)-barrel fold forming a homodimer. Asp21, His60, and His127 residues coordinate to Mg2+ as a possible active site. TTHB029 shows structural similarity to the peptidoglycan N-acetylglucosamine deacetylase from Streptococcus pneumoniae (SpPgdA). The active site groove of SpPgdA includes the Zn2+ coordinated to Asp276, His326, and His330. Despite the low sequence identity, metal-binding residues of Asp-His-His were conserved among the two enzymes. There were definitive differences, however, in that one of the histidines of the metal-binding site was substituted for the other histidine located on the other loop. Moreover, these important metal-binding residues and the residues of the presumed active site are fully conserved in YdjC-family protein.  相似文献   

7.
The faunas living in the vast deep sea regions around the Antarctic are very poorly known. This is especially true for the biodiversity of polychaetes inhabiting these remote areas. Therefore, we report new morphological data of Glyceriformia from the ANDEEP cruises to the South Atlantic Ocean and the Southern Ocean. Based on benthos samples from three expeditions aboard R/V POLARSTERN, two species of Glyceridae (Glycera capitata, G. diva) and four species of Goniadidae (Bathyglycinde sibogana, B. stepaniantsae, Goniada maculata, Progoniada regularis) were studied. Furthermore, new morphological details (especially for the previously unknown tail) for the rarely found taxon B. stepaniantsae are given. The distribution patterns of the different taxa demonstrated that some species have a high dispersal capability and show an extended level of eurybathy, whereas other species are restricted to the deep sea.  相似文献   

8.
The Na+/H+ exchanger isoform 1 is a ubiquitously expressed integral membrane protein. It resides on the plasma membrane of cells and regulates intracellular pH in mammals by extruding an intracellular H+ in exchange for one extracellular Na+. We characterized structural and functional aspects of the transmembrane segment (TM) VI (residues 227–249) by using cysteine scanning mutagenesis and high resolution NMR. Each residue of TM VI was mutated to cysteine in the background of the cysteineless NHE1 protein, and the sensitivity to water-soluble sulfhydryl-reactive compounds (2-(trimethylammonium)ethyl)methanethiosulfonate (MTSET) and (2-sulfonatoethyl)methanethiosulfonate (MTSES) was determined for those residues with significant activity remaining. Three residues were essentially inactive when mutated to Cys: Asp238, Pro239, and Glu247. Of the remaining residues, proteins with the mutations N227C, I233C, and L243C were strongly inhibited by MTSET, whereas amino acids Phe230, Gly231, Ala236, Val237, Ala244, Val245, and Glu248 were partially inhibited by MTSET. MTSES did not affect the activity of the mutant NHE1 proteins. The structure of a peptide representing TM VI was determined using high resolution NMR spectroscopy in dodecylphosphocholine micelles. TM VI contains two helical regions oriented at an approximate right angle to each other (residues 229–236 and 239–250) surrounding a central unwound region. This structure bears a resemblance to TM IV of the Escherichia coli protein NhaA. The results demonstrate that TM VI of NHE1 is a discontinuous pore-lining helix with residues Asn227, Ile233, and Leu243 lining the translocation pore.  相似文献   

9.
Two species of jaw bearing Ampharetidae (Adercodon pleijeli (Mackie 1994) and Ampharete sp. B) were investigated in order to describe the microanatomy of the mouth parts and especially jaws of these enigmatic polychaetes. The animals of both studied species have 14–18 mouth tentacles that are about 30 µm in diameter each. In both species, the ventral pharyngeal organ is well developed and situated on the ventral side of the buccal cavity. It is composed of a ventral muscle bulb and investing muscles. The bulb consists of posterior and anterior parts separated by a deep median transversal groove. In both species, the triangular teeth or denticles are arranged in a single transversal row on the surface of the posterior part of the ventral bulb just in front of its posterior edge. There are 36 denticles in Adercodon pleijeli and 50 in Ampharete sp. B. The height of the denticles (6–12 µm) is similar in both species. Each tooth is composed of two main layers. The outer one (dental) is the electron‐dense sclerotized layer that covers the tooth. The inner one consists of long microvilli with a collagen matrix between them. The thickness of the dental layer ranges from 0.95 to 0.6 µm. The jaws of the studied worms may play a certain role in scraping off microfouling. The fine structure of the jaws in Ampharetidae is very similar to that of the mandibles of Dorvilleidae, the mandibles and the maxillae of Lumbrineridae, Eunicidae and Onuphidae, and the jaws of other Aciculata. This type of jaw is characterized by unlimited growth and the absence of replacement. The occurrence of jaws in a few smaller Ampharetidae is considered as an apomorphic state.  相似文献   

10.
Prokaryotic and eukaryotic Na+/Ca2+ exchangers (NCX) control Ca2+ homeostasis. NCX orthologs exhibit up to 104-fold differences in their turnover rates (kcat), whereas the ratios between the cytosolic (cyt) and extracellular (ext) Km values (Kint = KmCyt/KmExt) are highly asymmetric and alike (Kint ≤ 0.1) among NCXs. The structural determinants controlling a huge divergence in kcat at comparable Kint remain unclear, although 11 (out of 12) ion-coordinating residues are highly conserved among NCXs. The crystal structure of the archaeal NCX (NCX_Mj) was explored for testing the mutational effects of pore-allied and loop residues on kcat and Kint. Among 55 tested residues, 26 mutations affect either kcat or Kint, where two major groups can be distinguished. The first group of mutations (14 residues) affect kcat rather than Kint. The majority of these residues (10 out of 14) are located within the extracellular vestibule near the pore center. The second group of mutations (12 residues) affect Kint rather than kcat, whereas the majority of residues (9 out 12) are randomly dispersed within the extracellular vestibule. In conjunction with computational modeling-simulations and hydrogen-deuterium exchange mass-spectrometry (HDX-MS), the present mutational analysis highlights structural elements that differentially govern the intrinsic asymmetry and transport rates. The key residues, located at specific segments, can affect the characteristic features of local backbone dynamics and thus, the conformational flexibility of ion-transporting helices contributing to critical conformational transitions. The underlying mechanisms might have a physiological relevance for matching the response modes of NCX variants to cell-specific Ca2+ and Na+ signaling.  相似文献   

11.
The present study summarizes observations on the skin plates (“retention plates”) and taste buds (TBs) in the oropharyngeal cavity (OC) of 15 species of surgeonfishes (Acanthuridae), all of which are predominantly herbivorous. Two phenomena mark the OC of these fishes: the presence of skin-plates rich in collagen bundles at the apex of the jaws, and cornified papillae on the surface. It is suggested that these plates help in retaining the sections of algae perforated at their base by the fishe’s denticulate teeth. The TBs, especially type I, are distributed across the buccal valves, palate and floor of the OC, forming species–specific groupings along ridges established by the network of sensory nerves. The number of TBs in the OC increases with growth of the fish up to a certain standard length, especially at the posterior part of the OC, and differs among the various species: e.g., Zebrasoma veliferum possesses 1420 TBs and Parcanthurus hepatus 3410. Species of Naso show a higher number of TBs than most species of Acanthurus, possibly connected with their more diversified diet. The pharyngeal region of these fishes is expanded through lowering the base of the gill-arches, and together with the occurrence of high numbers of TBs in this region, indicates the importance of the posterior region of the OC in herbivorous fishes for identification of the engulfed food particles prior to swallowing. The discussed observations shed light on the micro-evolutionary developments of the OC within the family Acanthuridae and contribute to the taxonomic characterization of the various species.  相似文献   

12.
Many bacteria produce and respond to the quorum sensing signal autoinducer-2 (AI-2). Escherichia coli and Salmonella typhimurium are among the species with the lsr operon, an operon containing AI-2 transport and processing genes that are up regulated in response to AI-2. One of the Lsr proteins, LsrF, has been implicated in processing the phosphorylated form of AI-2. Here, we present the structure of LsrF, unliganded and in complex with two phospho-AI-2 analogues, ribose-5-phosphate and ribulose-5-phosphate. The crystal structure shows that LsrF is a decamer of (αβ)8-barrels that exhibit a previously unseen N-terminal domain swap and have high structural homology with aldolases that process phosphorylated sugars. Ligand binding sites and key catalytic residues are structurally conserved, strongly implicating LsrF as a class I aldolase.  相似文献   

13.
The energy-coupling factor (ECF) transporters are multi-subunit protein complexes that mediate uptake of transition-metal ions and vitamins in about 50% of the prokaryotes, including bacteria and archaea. Biological and structural studies have been focused on ECF transporters for vitamins, but the molecular mechanism by which ECF systems transport metal ions from the environment remains unknown. Here we report the first crystal structure of a NikM, TtNikM2, the substrate-binding component (S component) of an ECF-type nickel transporter from Thermoanaerobacter tengcongensis. In contrast to the structures of the vitamin-specific S proteins with six transmembrane segments (TSs), TtNikM2 possesses an additional TS at its N-terminal region, resulting in an extracellular N-terminus. The highly conserved N-terminal loop inserts into the center of TtNikM2 and occludes a region corresponding to the substrate-binding sites of the vitamin-specific S components. Nickel binds to NikM via its coordination to four nitrogen atoms, which are derived from Met1, His2 and His67 residues. These nitrogen atoms form an approximately square-planar geometry, similar to that of the metal ion-binding sites in the amino-terminal Cu2+- and Ni2+-binding (ATCUN) motif. Replacements of residues in NikM contributing to nickel coordination compromised the Ni-transport activity. Furthermore, systematic quantum chemical investigation indicated that this geometry enables NikM to also selectively recognize Co2+. Indeed, the structure of TtNikM2 containing a bound Co2+ ion has almost no conformational change compared to the structure that contains a nickel ion. Together, our data reveal an evolutionarily conserved mechanism underlying the metal selectivity of EcfS proteins, and provide insights into the ion-translocation process mediated by ECF transporters.  相似文献   

14.
15.
Apple snail perivitellins are emerging as ecologically important reproductive proteins. To elucidate if the protective functions of the egg proteins of Pomacea canaliculata (Caenogastropoda, Ampullariidae), involved in embryo defenses, are present in other Pomacea species we studied scalarin (PsSC), the major perivitellin of Pomacea scalaris. Using small angle X-ray scattering, fluorescence and absorption spectroscopy and biochemical methods, we analyzed PsSC structural stability, agglutinating activity, sugar specificity and protease resistance. PsSC aggluttinated rabbit, and, to a lesser extent, human B and A erythrocytes independently of divalent metals Ca2+ and Mg2+ were strongly inhibited by galactosamine and glucosamine. The protein was structurally stable between pH 2.0 to 10.0, though agglutination occurred only between pH 4.0 to 8.0 (maximum activity at pH 7.0). The agglutinating activity was conserved up to 60°C and completely lost above 80°C, in agreement with the structural thermal stability of the protein (up to 60°C). PsSC was able to withstand in vitro gastrointestinal digestion, and showed no trypsin inhibition activity. The presence of lectin activity has been reported in eggs of other Pomacea snails, but here we link for the first time, this activity to an apple snail multifunctional perivitellin. This novel role for a snail egg storage protein is different from closely related P.canaliculata defensive proteins.  相似文献   

16.
Phosphatidyl-myo-inositol mannosides (PIMs) are unique glycolipids found in abundant quantities in the inner and outer membranes of the cell envelope of all Mycobacterium species. They are based on a phosphatidyl-myo-inositol lipid anchor carrying one to six mannose residues and up to four acyl chains. PIMs are considered not only essential structural components of the cell envelope but also the structural basis of the lipoglycans (lipomannan and lipoarabinomannan), all important molecules implicated in host-pathogen interactions in the course of tuberculosis and leprosy. Although the chemical structure of PIMs is now well established, knowledge of the enzymes and sequential events leading to their biosynthesis and regulation is still incomplete. Recent advances in the identification of key proteins involved in PIM biogenesis and the determination of the three-dimensional structures of the essential phosphatidyl-myo-inositol mannosyltransferase PimA and the lipoprotein LpqW have led to important insights into the molecular basis of this pathway.  相似文献   

17.
Aromatic amino acids play an important role in ultraviolet (UV)-induced photochemical reactions in proteins. In this work, we aim at gaining insight into the photochemical reactions induced by near-UV light excitation of aromatic residues that lead to breakage of disulfide bridges in our model enzyme, Fusarium solani pisi cutinase, a lipolytic enzyme. With this purpose, we acquired transient absorption data of cutinase, with supplemental experimental data on tryptophan (Trp) and lysozyme as reference molecules. We here report formation kinetics and lifetimes of transient chemical species created upon UV excitation of aromatic residues in proteins. Two proteins, lysozyme and cutinase, as well as the free amino acid Trp, were studied under acidic, neutral, and alkaline conditions. The shortest-lived species is assigned to solvated electrons (lifetimes of a few microseconds to nanoseconds), whereas the longer-lived species are assigned to aromatic neutral and ionic radicals, Trp triplet states, and radical ionic disulphide bridges. The pH-dependent lifetimes of each species are reported. Solvated electrons ejected from the side chain of free Trp residues and aromatic residues in proteins were observed 12 ns after excitation, reaching a maximum yield after ∼40 ns. It is interesting to note that the formation kinetics of solvated electrons is not pH-dependent and is similar in the different samples. On the other hand, a clear increase of the solvated electron lifetime is observed with increasing pH. This observation is correlated with H3O+ being an electron scavenger. Prolonged UV illumination of cutinase leads to a larger concentration of solvated electrons and to greater absorption at 410 nm (assigned to disulphide electron adduct RSSR •−), with concomitant faster decay kinetics and near disappearance of the Trp radical peak at 330 nm, indicating possible additional formation of TyrO formed upon reaction of Trp with Tyr residues. Prolonged UV illumination of cutinase also leads to a larger concentration of free thiol groups, known to originate from the dissociation of RSSR •−. Additional mechanisms that may lead to the near disappearance of Trp are discussed. Our study provides insight into one key UV-light-induced reaction in cutinase, i.e., light-induced disruption of disulphide bridges mediated by the excitation of aromatic residues. Knowledge about the nature of the formed species and their lifetimes is important for the understanding of UV-induced reactions in humans that lead to light-induced diseases, e.g., skin cancer and cataract formation.  相似文献   

18.
The apoflavodoxin protein from Azotobacter vinelandii harboring three tryptophan (Trp) residues, was biosynthetically labeled with 5-fluorotryptophan (5-FTrp). 5-FTrp has the advantage that chemical differences in its microenvironment can be sensitively visualized via 19F NMR. Moreover, it shows simpler fluorescence decay kinetics. The occurrence of FRET was earlier observed via the fluorescence anisotropy decay of WT apoflavodoxin and the anisotropy decay parameters are in excellent agreement with distances between and relative orientations of all Trp residues. The anisotropy decay in 5-FTrp apoflavodoxin demonstrates that the distances and orientations are identical for this protein. This work demonstrates the added value of replacing Trp by 5-FTrp to study structural features of proteins via 19F NMR and fluorescence spectroscopy.  相似文献   

19.
Du QS  Meng JZ  Wang CH  Long SY  Huang RB 《PloS one》2011,6(12):e28206

Background

The proteins in a family, which perform the similar biological functions, may have very different amino acid composition, but they must share the similar 3D structures, and keep a stable central region. In the conservative structure region similar biological functions are performed by two or three catalytic residues with the collaboration of several functional residues at key positions. Communication signals are conducted in a position network, adjusting the biological functions in the protein family.

Methodology

A computational approach, namely structural position correlation analysis (SPCA), is developed to analyze the correlation relationship between structural segments (or positions). The basic hypothesis of SPCA is that in a protein family the structural conservation is more important than the sequence conservation, and the local structural changes may contain information of biology functional evolution. A standard protein P(0) is defined in a protein family, which consists of the most-frequent amino acids and takes the average structure of the protein family. The foundational variables of SPCA is the structural position displacements between the standard protein P(0) and individual proteins Pi of the family. The structural positions are organized as segments, which are the stable units in structural displacements of the protein family. The biological function differences of protein members are determined by the position structural displacements of individual protein Pi to the standard protein P(0). Correlation analysis is used to analyze the communication network among segments.

Conclusions

The structural position correlation analysis (SPCA) is able to find the correlation relationship among the structural segments (or positions) in a protein family, which cannot be detected by the amino acid sequence and frequency-based methods. The functional communication network among the structural segments (or positions) in protein family, revealed by SPCA approach, well illustrate the distantly allosteric interactions, and contains valuable information for protein engineering study.  相似文献   

20.
The Synechocystis Slr0642 protein and its plastidial Arabidopsis (Arabidopsis thaliana) ortholog At2g32040 belong to the folate-biopterin transporter (FBT) family within the major facilitator superfamily. Both proteins transport folates when expressed in Escherichia coli. Because the structural requirements for transport activity are not known for any FBT protein, we applied mutational analysis to identify residues that are critical to transport and interpreted the results using a comparative structural model based on E. coli lactose permease. Folate transport was assessed via the growth of an E. coli pabA abgT strain, which cannot synthesize or take up folates or p-aminobenzoylglutamate. In total, 47 residues were replaced with Cys or Ala. Mutations at 22 positions abolished folate uptake without affecting Slr0642 expression in membranes, whereas other mutations had no effect. Residues important for function mostly line the predicted central cavity and are concentrated in the core α-helices H1, H4, H7, and H10. The essential residue locations are consistent with a folate-binding site lying roughly equidistant from both faces of the transporter. Arabidopsis has eight FBT proteins besides At2g32040, often lacking conserved critical residues. When six of these proteins were expressed in E. coli or in Leishmania folate or pterin transporter mutants, none showed evidence of folate or pterin transport activity, and only At2g32040 was isolated by functional screening of Arabidopsis cDNA libraries in E. coli. Such negative data could reflect roles in transport of other substrates. These studies provide the first insights into the native structure and catalytic mechanism of FBT family carriers.  相似文献   

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