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1.
Equilibrium phase diagrams of the ι-carrageenan/maltodextrin/water system have been established at potassium chloride (KCl) concentrations of 0.1, 0.2, and 0.3 M and 80, 85 and 90°C. All pseudo-binary phase diagrams of ι-carrageenan/maltodextrin mixtures suggested classic segregative phase separation. The binodal was heavily skewed toward the maltodextrin axis. The high asymmetry of the ι-carrageenan/maltodextrin/water phase diagram determined by the phase-volume-ratio method was consistent with the compositional analysis of phase-separated ι-carrageenan/maltodextrin samples and can be explained in terms of the Flory–Huggins interaction parameter, reflecting a higher water-binding ability of the charged ι-carrageenan than neutral maltodextrin. Increasing the concentration of ι-carrageenan-gel-promoting KCl from 0.1 to 0.3 M at 80°C enlarged the two-phase domain, whereas increasing temperature from 80 to 90°C at 0.3 M KCl enhanced biopolymer compatibility. The effects of salt concentration and temperature have been related to the differences in the Flory–Huggins interaction parameters of the two biopolymers with water as well as the helix formation of ι-carrageenan in the presence of KCl through the changes in the slopes of tie lines of phase-separated samples.
Gregory R. Ziegler (Corresponding author)Email:
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It has been a decade since the discovery of human DNA polymerase ι (polι). Since that time, the enzyme has been characterized extensively at the biochemical level, but the cellular function of polι remains enigmatic. Recent studies on polι have, however, provided much needed insights into its biological role(s) and suggest that the enzyme plays important functions in protecting humans from the deleterious consequences of exposure to both oxidative- and ultraviolet light-induced DNA damage.  相似文献   

4.
Cells have evolved mutagenic bypass mechanisms that prevent stalling of the replication machinery at DNA lesions. This process, translesion DNA synthesis (TLS), involves switching from high-fidelity DNA polymerases to specialized DNA polymerases that replicate through a variety of DNA lesions. In eukaryotes, polymerase switching during TLS is regulated by the DNA damage-triggered monoubiquitylation of PCNA. How the switch operates is unknown, but all TLS polymerases of the so-called Y-family possess PCNA and ubiquitin-binding domains that are important for their function. To gain insight into the structural mechanisms underlying the regulation of TLS by ubiquitylation, we have probed the interaction of ubiquitin with a conserved ubiquitin-binding motif (UBM2) of Y-family polymerase Polι. Using NMR spectroscopy, we have determined the structure of a complex of human Polι UBM2 and ubiquitin, revealing a novel ubiquitin recognition fold consisting of two α-helices separated by a central trans-proline residue conserved in all UBMs. We show that, different from the majority of ubiquitin complexes characterized to date, ubiquitin residue Ile44 only plays a modest role in the association of ubiquitin with Polι UBM2. Instead, binding of UBM2 is centered on the recognition of Leu8 in ubiquitin, which is essential for the interaction.  相似文献   

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The cDNA encoding human DNA polymerase ι (POLI) was cloned in 1999. At that time, it was believed that the POLI gene encoded a protein of 715 amino acids. Advances in DNA sequencing technologies led to the realization that there is an upstream, in-frame initiation codon that would encode a DNA polymerase ι (polι) protein of 740 amino acids. The extra 25 amino acid region is rich in acidic residues (11/25) and is reasonably conserved in eukaryotes ranging from fish to humans. As a consequence, the curated Reference Sequence (RefSeq) database identified polι as a 740 amino acid protein. However, the existence of the 740 amino acid polι has never been shown experimentally. Using highly specific antibodies to the 25 N-terminal amino acids of polι, we were unable to detect the longer 740 amino acid (ι-long) isoform in western blots. However, trace amounts of the ι-long isoform were detected after enrichment by immunoprecipitation. One might argue that the longer isoform may have a distinct biological function, if it exhibits significant differences in its enzymatic properties from the shorter, well-characterized 715 amino acid polι. We therefore purified and characterized recombinant full-length (740 amino acid) polι-long and compared it to full-length (715 amino acid) polι-short in vitro. The metal ion requirements for optimal catalytic activity differ slightly between ι-long and ι-short, but under optimal conditions, both isoforms exhibit indistinguishable enzymatic properties in vitro. We also report that like ι-short, the ι-long isoform can be monoubiquitinated and polyubiuquitinated in vivo, as well as form damage induced foci in vivo. We conclude that the predominant isoform of DNA polι in human cells is the shorter 715 amino acid protein and that if, or when, expressed, the longer 740 amino acid isoform has identical properties to the considerably more abundant shorter isoform.  相似文献   

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Purpose of work

The purpose of this study is to report a ι-carrageenase which degrades ι-carrageenan yielding neo-ι-carratetraose as the main product in the absence of NaCl. The gene for a new ι-carrageenase, CgiB_Ce, from Cellulophaga sp. QY3 was cloned and sequenced. It comprised an ORF of 1,386 bp encoding for a protein of 461 amino acid residues. From its sequence analysis, CgiB_Ce is a new member of GH family 82 and shared the highest identity of 32 % in amino acids with ι-carrageenase CgiA2 from Zobellia galactanovorans indicating that it is a hitherto uncharacterized protein. The recombinant CgiB_Ce had maximum specific activity (1,870 U/mg) at 45 °C and pH 6.5. It was stable between pH 6.0–9.6 and below 40 °C. Although its activity was enhanced by NaCl, the enzyme was active in the absence of NaCl. CgiB_Ce is an endo-type ι-carrageenase that hydrolyzes β-1,4-linkages of ι-carrageenan, yielding neo-ι-carratetraose as the main product (more than 80 % of the total product).  相似文献   

10.
The objective of this work is to investigate the water and aroma barrier properties of films obtained from ι-carrageenan containing glycerol and lipids mixtures of oleic acid (OA) and beeswax (BW) used for encapsulation of active compounds. Water vapor permeability (WVP) is greatly influenced by lipid composition, encapsulated aroma compound and also relative humidity. WVP decreases when films contain encapsulated aroma compound but increases when the moisture content in the films increases. When oleic acid was the main compound of lipid phase, the plasticizing effect of water revealed through water permeability is less marked. The results of ethyl acetate, ethyl butyrate, ethyl hexanoate, 2-hexanone, 1-hexanol and cis-3-hexenol permeabilities reveal that physicochemical interactions between aroma compounds-hydrocolloid and aroma compound-lipid induce structural changes and modify their permeability. This work gives evidence of the ability of ι-carrageenan–OA–BW films to protect encapsulated aroma compound and its influence in barrier properties.  相似文献   

11.
Carrageenans are sulfated galactans found in the cell walls of numerous red seaweeds (Rhodophyta). They are classified according to the number and the position of sulfate ester groups and the occurrence of 3,6-anhydro-galactose. Although the carrageenan biosynthesis pathway is not fully understood, it is usually accepted that the last step consists of the formation of a 3,6-anhydro ring found in κ- and ι-carrageenans through the enzymatic conversion of d-galactose-6-sulfate or d-galactose-2,6-disulfate occurring in μ- and ν-carrageenan, respectively. We purified two enzymes, sulfurylase I (65 kD) and sulfurylase II (32 kD), that are able to catalyze the conversion of ν- into ι-carrageenan. We compared their sulfate release rates (i.e. arising from the formation of the anhydro ring) with the viscosity of the solution and demonstrated two distinct modes of action. In addition, we found that some mixtures of sulfurylase I and II lead to the formation of carrageenan solutions with unexpectedly low viscosities. We discuss the implication of these findings for the assembly of a densely aggregated matrix in red algal cell walls.Agars and carrageenans are the most abundant components of the cell walls in numerous red algae (Rhodophyta) and can represent up to 50% of algal dry weight. These sulfated galactans are densely packed in the cell wall in a three-dimensional solid network of pseudocrystalline fibers, which assemble during the deposition of cell wall macromolecules (Craigie, 1990). Sulfated galactans constitute a large family of hydrocolloids that are made up of linear chains of Gal with alternating α(1→3) and β(1→4) linkages. In agarose, the α-linked Gal units are in the l configuration (l unit), while in carrageenans, they are in the d configuration (d unit; Rees, 1969). Agarose refers to an unmodified neutral backbone of agarobioses (LA-G) of which up to 20% may carry methyl groups or sulfate ester groups (Fig. 1). Carrageenans are classified according to the number and position of sulfated esters (S) and by the occurrence of a 3,6-anhydro ring in the α-linked residues (DA unit) found in gelling κ-carrageenan (DA-G4S) and ι-carrageenan (DA2S-G4S; Rees, 1969; Knutsen et al., 1994; Usov, 1998). However, carrageenans have very heterogeneous chemical structures, depending on algal source, life stage, and extraction procedure (Craigie, 1990; Usov, 1998). This structural complexity is attributed to the occurrence of a mixture of carrageenans in extracts as well as to the presence of hybrid or copolymer chains that arise when ideal carrabiose motifs co-occur in purified carrageenans (Greer and Yaphe, 1984; Craigie, 1990; Bixler, 1996; Guibet et al., 2008). The most well-known carrageenan copolymers are those found in native or unprocessed κ- and ι-carrageenan chains. They usually contain fractions of their biosynthetic precursors named μ-carrageenan (D6S-G4S) and ν-carrageenan (D2S6S-G4S), respectively (Fig. 1; Bellion et al., 1983; van de Velde et al., 2002b).Open in a separate windowFigure 1.Formation of agarose, κ-, and ι-carrageenan repeating disaccharide moieties generated enzymatically from their respective biosynthetic precursors, porphyran, μ-, and ν-carrageenan.The biosynthetic pathways of agars and carrageenans are currently only hypothetical. However, based on the structures of agarobiose and carrabiose moieties that co-occur in polysaccharide chains, the proposed sequences of catalytic events accounting for the chemical structures of agars and carrageenans usually assume that three classes of enzymes are involved: galactosyl transferases, sulfotransferases, and Gal-6-sulfurylases (in agarose; Rees, 1961a, 1961b), referred to as “sulfohydrolases” in carrageenans (Wong and Craigie, 1978). The α- and β-galactosyl transferases catalyze the polymerization of the Gal backbone. Sulfotransferases decorate the neutral Gal chain with sulfate side groups. These reactions have been shown to take place in the Golgi apparatus, but none of these enzymes have been isolated in vitro (Tveter-Gallagher et al., 1984; Gretz et al., 1990). Only the final step of agarose biosynthesis has been unambiguously demonstrated with the characterization of the enzymatic activity of Gal-6-sulfurylases, which catalyze the formation of the 3,6-anhydro rings in agarose (Rees, 1961a, 1961b). This reaction was also shown to occur in vivo (Hemmingson et al., 1996a, 1996b). The formation of the κ- and ι-carrageenan anhydro rings was also observed after incubation of μ- and ν-carrageenans, respectively, with red algal protein extracts that have been named sulfohydrolases (Wong and Craigie, 1978; Zinoun et al., 1997). These observations confirm that the formation of anhydro rings is catalyzed at the final step of biosynthesis.The anhydro ring is a chemical structure widely used in carbohydrate chemistry to selectively modify sugar residues (Varma et al., 2004; Hou and Lowary, 2009; Tanaka et al., 2009). In contrast to synthetic moieties, there are very few examples of sugar residues with an anhydro ring in vivo. To our knowledge, in addition to the 3,6-anhydro-Gal residues encountered in agars and carrageenans, the only other documented natural anhydro ring is the 1,6-anhydro N-acetyl-muramic acid located at the glucan chain end of a peptidoglycan (murein; Hölfte et al., 1975; Heidrich and Wollmer, 2002). This 1,6-anhydro ring is an intraresidue glycosidic bond and occurs when a glycosidic bond is cleaved via a transglycosylation mechanism. The enzymatic mechanism leading to the 3,6-anhydro ring in agars and carrageenans is, to date, unknown. Nevertheless, the anhydro ring is probably the result of a nucleophilic substitution where the ester sulfate located at position 6 is replaced with the hydroxyl group at position 3, similar to the reaction that occurs when carrageenans are treated with alkalis (Cianca et al., 1997; Viana et al., 2004). The conversion of the α-d-Gal-6-sulfate (μ-carrabiose) and 2,6-disulfate (ν-carrabiose) into their corresponding 3,6-anhydro derivatives greatly reduces the hydrophilic nature of the Gal residues, inverts the chair conformation of the pyranose rings from 1C4 to 4C1, and, as a consequence, allows the carrageenans to adopt a helical conformation required for sol/gel transition (Lawson and Rees, 1970; van de Velde et al., 2002b).The Gal-6-sulfurylases found in agarophytes and the analogous sulfohydrolase activities extracted from carrageenophytes represent a novel class of enzymes owing to the chemical reactions they catalyze as well as to their involvement in building the matrix of the cell wall. In addition, these enzymes have only been found in the red algal lineage. As a consequence, they represent one of the evolutionary innovations associated with the emergence of red seaweeds. In this context, we purified and biochemically characterized the enzymes that catalyze the formation of anhydro rings in carrageenans. We found that at least two enzymes convert ν- into ι-carrageenan in Chondrus crispus gametophytes and that these enzymes differ in their Mr and in their mode of action. In addition, we prepared a viscous carrageenan solution whose properties were directly related to the mode of action of these enzymes. The implications of our findings are discussed in the context of cell wall biosynthesis. More specifically, given that carrageenans are reputed to give high-strength gels at low concentrations, we suggest that sulfurylases allow carrageenans to be densely packed in algal cell walls.  相似文献   

12.
We examined the conformational preferences of the 2-O-sulfated-3,6-α-D-anhydrogalactose (compound I) and two 1,3 linked disaccharides constituting-κ or ι-carrageenans using density functional and ab initio methods in gas phase and aqueous solution. Systematic modifications of two torsion angles leading to 324 and 144 starting geometries for the compound I and each disaccharide were used to generate adiabatic maps using B3LYP/6-31G(d). The lower energy conformers were then fully optimized using B3LYP, B3PW91 and MP2 with several basis sets. Overall, we discuss the impact of full relaxation on the energy and structure of the dominant conformations, present the performance comparison with previous molecular mechanics calculations if available, and determine whether our results are impacted, when polarization and diffuse functions are added to the 6-31G(d) basis set, or when the MP2 level of theory is used.  相似文献   

13.
A gene of unknown function from the genome of the agar-degrading deep-sea bacterium Microbulbifer thermotolerans JAMB-A94T was functionally identified as a ι-carrageenase gene. This gene, designated as cgiA, is located together with two β-agarase genes, agaA and agaO in a cluster. The cgiA gene product is 569 amino acids and shares 29% identity over 185 amino acids with the ι-carrageenase from Zobellia galactanivorans Dsij DSM 12802. Recombinant, cgiA-encoded ι-carrageenase (55 kDa) was hyper-produced in Bacillus subtilis. The recombinant enzyme shows maximal activity at 50°C, the highest reported optimal temperature for a carrageenase. It cleaved β-1,4 linkages in ι-carrageenan to produce a high ratio of ι-carrageenan tetramer, more than 75% of the total product, and did not cleave the β-1,4 linkages in κ- or λ-carrageenan. Therefore, this enzyme may be useful for industrial production of ι-carrageenan oligosaccharides, which have demonstrated antiviral potential against diverse viruses. Furthermore, we performed site-directed mutagenesis on the gene to identify the catalytic amino acid residues. We demonstrated that a conserved Glu351 was essential for catalysis; however, this enzyme lacked a catalytic Asp residue, which is generally critical for the catalytic activity of most glycoside hydrolases.  相似文献   

14.
Abasic (apurinic/apyrimidinic, AP) sites are the most common DNA lesions formed in cells, induce severe blocks to DNA replication, and are highly mutagenic. Human Y-family translesion DNA polymerases (pols) such as pols η, ι, κ, and REV1 have been suggested to play roles in replicative bypass across many DNA lesions where B-family replicative pols stall, but their individual catalytic functions in AP site bypass are not well understood. In this study, oligonucleotides containing a synthetic abasic lesion (tetrahydrofuran analogue) were compared for catalytic efficiency and base selectivity with human Y-family pols η, ι, κ, and REV1 and B-family pols α and δ. Pol η and pol δ/proliferating cell nuclear antigen (PCNA) copied past AP sites quite effectively and generated products ranging from one-base to full-length extension. Pol ι and REV1 readily incorporated one base opposite AP sites but then stopped. Pols κ and α were severely blocked at AP sites. Pol η preferentially inserted T and A; pol ι inserted T, G, and A; pol κ inserted C and A; REV1 preferentially inserted C opposite AP sites. The B-family pols α and δ/PCNA preferentially inserted A (85% and 58%, respectively) consonant with the A-rule hypothesis. Pols η and δ/PCNA were much more efficient in next-base extension, preferably from A positioned opposite an AP site, than pol κ. These results suggest that AP sites might be bypassed with moderate efficiency by single B- and Y-family pols or combinations, possibly by REV1 and pols ι, η, and δ/PCNA at the insertion step opposite the lesion and by pols η and δ/PCNA at the subsequent extension step. The patterns of the base preferences of human B-family and Y-family pols in both insertion and extension are pertinent to some of the mutagenesis events induced by AP lesions in human cells.  相似文献   

15.
Pol ζ, Pol η, Pol ι, Pol κ and Rev1 are specialized DNA polymerases that are able to synthesize DNA across a damaged template. DNA synthesis by such translesion polymerases can be mutagenic due to the miscoding nature of most damaged nucleotides. In fact, many mutational and hypermutational processes in systems ranging from yeast to mammals have been traced to the activity of such polymerases. We show however, that the translesion polymerases are dispensable for repeat-induced point mutation (RIP) inNeurospora crassa. Additionally, we demonstrate that theupr-1 gene, which encodes the catalytic subunit of Pol ζ, is a highly polymorphic locus in Neurospora. Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession Nos DQ 231523, DQ 231524, DQ 235021, DQ 235525-DQ 235541, DQ 240287, DQ 240288, DQ 354228, DQ 354235-DQ 354237, DQ 386416-DQ 386422, DQ 387872, DQ494492-DQ494503 and DQ417211-DQ417220.  相似文献   

16.
Human DNA polymerase ι is a lesion bypass polymerase of the Y family, capable of incorporating nucleotides opposite a variety of lesions in both near error-free and error-prone bypass. With undamaged templating purines polymerase ι normally favors Hoogsteen base pairing. Polymerase ι can incorporate nucleotides opposite a benzo[a]pyrene-derived adenine lesion (dA*); while mainly error-free, the identity of misincorporated bases is influenced by local sequence context. We performed molecular modeling and molecular dynamics simulations to elucidate the structural basis for lesion bypass. Our results suggest that hydrogen bonds between the benzo[a]pyrenyl moiety and nearby bases limit the movement of the templating base to maintain the anti glycosidic bond conformation in the binary complex in a 5′-CAGA*TT-3′ sequence. This facilitates correct incorporation of dT via a Watson−Crick pair. In a 5′-TTTA*GA-3′ sequence the lesion does not form these hydrogen bonds, permitting dA* to rotate around the glycosidic bond to syn and incorporate dT via a Hoogsteen pair. With syn dA*, there is also an opportunity for increased misincorporation of dGTP. These results expand our understanding of the versatility and flexibility of polymerase ι and its lesion bypass functions in humans.  相似文献   

17.
目的甲型H1N1流感病毒A/California/7/2009与A/California/4/2009病毒序列比较同源性在99%以上,本实验旨在比较两株病毒感染BALB/c小鼠研究感染力强弱。方法分别将A/California/7/2009(CA7)与A/California/4/2009(CA4)两株病毒分别连续10倍稀释后,对4~6周龄雌性BALB/c小鼠经乙醚麻醉后进行滴鼻攻毒,每个稀释度接种10只实验小鼠,测定CA7 MLD50为101.24/0.05 mL,检测小鼠感染、致病的多项指标,观察期为14 d。结果相同TCID50的CA7和CA4病毒感染小鼠,CA4感染小鼠后14 d内死亡率为20%,而CA7感染小鼠后8 d内死亡率为100%。CA7 106TCID50感染的小鼠病理表现为重度弥漫性间质性肺炎,CA4 106TCID50感染的小鼠病理表现为中度-重度间质性肺炎。结论在相同条件下,CA7感染力明显强于CA4。  相似文献   

18.
Copoly(α-amino acid)s consisting of γ-benzyl-l-glutamate and N5-β-d-glucopyranosyl-l-glutamine were prepared by the reaction of copoly(l-glutamate) containing succinimide ester, which served as active site for the coupling reaction with β-d-glucopyranosylamine. The α-helical conformation of these copolymers became unstable in DMF as the content of glutamine derivative increased. A dry film made from this copolymer could take a full α-helical conformation even at such a high content as 80% of the glutamine derivative, but in a wet film this ordered structure was partially disrupted by hydration. The hydraulic permeability of this copoly(α-amino acid) was clearly dependent on the molar content of glucopyranosyl groups. The attachment of fibroblast cells to these hydrated copolymer films was effectively depressed in the presence of a serum-free medium. The cells attached to the substrate were spherical in shape.  相似文献   

19.
This isomer of PGF is relatively resistant to metabolic degradation in the Cynomolgus monkey. Thus, 16–20 per cent of the amount injected was excreted unchanged in the urine. Five metabolites with 20, 18, 16 and 14 carbon atoms in the skeleton were identified. The data are similar to those earlier seen in the rat and further support the idea that this analogue of PGF could have a long half-life time in the mammalian body and thus a long duration of its pharmacological actions.  相似文献   

20.
Poly(N-δ-trimethyl-l-ornithine), (Me3Orn)n, is usually not able to attain the α-helical conformation in aqueous solution independent of its pH value; however, it becomes α-helical at low concentrations of sodium perchlorate over a wide pH range according to the circular dichorism (c.d.) spectra. Cl?, SO42? and H2PO4? do not induce α-helix formation. One can conclude that a distinct topology of the anions bound by the side chains is responsible for the α-helix-inducing effect of some water-structure-breaking anions such as perchlorate. This means that the anions are inserted between the ?N+ of the side groups shielding the positive charges repelling one another. The insertion of the anions requires that the water molecules surrounding the ions can be stripped off, which is easily possible if they are water-structure-breaking ones. At higher perchlorate concentrations, the c.d. spectrum changes. It is characterized by a negative shoulder near 208 nm and a pronounced minimum at ≈ 226 nm. With increasing temperature, the c.d. spectrum of the α-helix occurs. Finally the α-helix undergoes a conformational change to the random coil. The apparent transition enthalpy ΔHvH is remarkably lower than that of the homologue (Me3Lys)n, obviously due to a lower cooperativity of the transition. In contrast to poly(l-ornithine), (Orn)n, the c.d. spectrum of (Me3Orn)n remains almost unchanged after adding anionic surfactants such as sodium octyl sulphate (SOS) or sodium dodecyl sulphate (SDS). In organic solvents like methanol or isopropanol, in contrast to (Orn)a and (Lys)n, no α-helix formation occurs. However, in mixtures of these alcohols or dioxane with water, α-helix formation is induced by perchlorate, as in pure water. The thermal stability of the α-helix in these systems is increased.  相似文献   

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