High activity of human butyrylcholinesterase at low pH in the presence of excess butyrylthiocholine.

Butyrylcholinesterase is a serine esterase, closely related to acetylcholinesterase. Both enzymes employ a catalytic triad mechanism for catalysis, similar to that used by serine proteases such as alpha-chymotrypsin. Enzymes of this type are generally considered to be inactive at pH values below 5, because the histidine member of the catalytic triad becomes protonated. We have found that butyrylcholinesterase retains activity at pH 相似文献   

HIV-1(Lai) genomic RNA: combined used of NMR and molecular dynamics simulation for studying the structure and internal dynamics of a mutated SL1 hairpin

The genome of all retroviruses consists of two identical copies of an RNA sequence associated in a non-covalent dimer. A region upstream from the splice donor (SL1) comprising a self-complementary sequence is responsible for the initiation of the dimerization. This region is able to dimerize in two conformations: a loop-loop complex or an extended duplex. Here, we solve by 2D NMR techniques the solution structure of a 23-nucleotide sequence corresponding to HIV-1 SL1(Lai) in which the mutation G12-->A12 is included to prevent dimerization. It is shown that this monomer adopts a stem-loop conformation with a seven base pairs stem and a nine nucleotide loop containing the G10 C11 A12 C13 G14 C15 sequence. The stem is well structured in an A-form duplex, while the loop is more flexible even though elements of structure are evident. We show that the structure adopted by the stem can be appreciably different from its relaxed structure when the adenines A8, A9 and A16 in the loop are mechanically constrained. This point could be important for the efficiency of the dimerization. This experimental study is complemented with a 10 ns molecular dynamics simulation in the presence of counterions and explicit water molecules. This simulation brings about information on the flexibility of the loop, such as a hinge motion between the stem and the loop and a labile lattice of hydrogen bonds in the loop. The bases of the nucleotides G10 to C15 were found outside of the loop during a part of the trajectory, which is certainly necessary to initiate the dimerization process of the genuine SL1(Lai) sequence.     

Bactericidal activity of colicin V is mediated by an inner membrane protein, SdaC, of Escherichia coli

Colicin V (ColV) is a peptide antibiotic that kills sensitive cells by disrupting their membrane potential once it gains access to the inner membrane from the periplasmic face. Recently, we constructed a translocation suicide probe, RR-ColV, that is translocated into the periplasm via the TAT pathway and thus kills the host cells. In this study, we obtained an RR-ColV-resistant mutant by using random Tn10 transposition mutagenesis. Sequencing analysis revealed that the mutant carried a Tn10 insertion in the sdaC (also called dcrA) gene, which is involved in serine uptake and is required for C1 phage adsorption. ColV activity was detected both in the cytoplasm and in the periplasm of this mutant, indicating that RR-ColV was translocated into the periplasm but failed to interact with the inner membrane. The sdaC::Tn10 mutant was resistant only to ColV and remained sensitive to colicins Ia, E3, and A. Most importantly, the sdaC::Tn10 mutant was killed when ColV was anchored to the periplasmic face of the inner membrane by fusion to EtpM, a type II integral membrane protein. Taken together, these results suggest that the SdaC/DcrA protein serves as a specific inner membrane receptor for ColV.     

Biochemical and Structural Study of the Atypical Acyltransferase Domain from the Mycobacterial Polyketide Synthase Pks13

Pks13 is a type I polyketide synthase involved in the final biosynthesis step of mycolic acids, virulence factors, and essential components of the Mycobacterium tuberculosis envelope. Here, we report the biochemical and structural characterization of a 52-kDa fragment containing the acyltransferase domain of Pks13. This fragment retains the ability to load atypical extender units, unusually long chain acyl-CoA with a predilection for carboxylated substrates. High resolution crystal structures were determined for the apo, palmitoylated, and carboxypalmitoylated forms. Structural conservation with type I polyketide synthases and related fatty-acid synthases also extends to the interdomain connections. Subtle changes could be identified both in the active site and in the upstream and downstream linkers in line with the organization displayed by this singular polyketide synthase. More importantly, the crystallographic analysis illustrated for the first time how a long saturated chain can fit in the core structure of an acyltransferase domain through a dedicated channel. The structures also revealed the unexpected binding of a 12-mer peptide that might provide insight into domain-domain interaction.     

Overexpression of the Vacuolar Sugar Carrier AtSWEET16 Modifies Germination,Growth, and Stress Tolerance in Arabidopsis

Here, we report that SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTER (SWEET16) from Arabidopsis (Arabidopsis thaliana) is a vacuole-located carrier, transporting glucose (Glc), fructose (Fru), and sucrose (Suc) after heterologous expression in Xenopus laevis oocytes. The SWEET16 gene, similar to the homologs gene SWEET17, is mainly expressed in vascular parenchyma cells. Application of Glc, Fru, or Suc, as well as cold, osmotic stress, or low nitrogen, provoke the down-regulation of SWEET16 messenger RNA accumulation. SWEET16 overexpressors (35S_Pro:SWEET16) showed a number of peculiarities related to differences in sugar accumulation, such as less Glc, Fru, and Suc at the end of the night. Under cold stress, 35S_Pro:SWEET16 plants are unable to accumulate Fru, while under nitrogen starvation, both Glc and Fru, but not Suc, were less abundant. These changes of individual sugars indicate that the consequences of an increased SWEET16 activity are dependent upon the type of external stimulus. Remarkably, 35S_Pro:SWEET16 lines showed improved germination and increased freezing tolerance. The latter observation, in combination with the modified sugar levels, points to a superior function of Glc and Suc for frost tolerance. 35S_Pro:SWEET16 plants exhibited increased growth efficiency when cultivated on soil and showed improved nitrogen use efficiency when nitrate was sufficiently available, while under conditions of limiting nitrogen, wild-type biomasses were higher than those of 35S_Pro:SWEET16 plants. Our results identify SWEET16 as a vacuolar sugar facilitator, demonstrate the substantial impact of SWEET16 overexpression on various critical plant traits, and imply that SWEET16 activity must be tightly regulated to allow optimal Arabidopsis development under nonfavorable conditions.Sugars are of enormous importance for plant properties and the agronomic values of most crop species (John, 1992). In plants, they serve as energy reserves, as building blocks for carbohydrate polymers like starch or cellulose, as precursors for amino and carboxylic acids, and as osmolytes required for the molecular antifreezing program initiated after exposure to cold temperatures (Nägele et al., 2010).Sugars in leaves are synthesized either during the day via photosynthesis or in the night as a product of starch degradation. The major sugar synthesized in most plants during the day is Suc, which, after the export of triose phosphates from the chloroplast, is synthesized in the cytosol. During nocturnal starch degradation, maltose leaves the chloroplast and serves as a substrate for the cytosolic synthesis of heteroglycans (Fettke et al., 2005). Subsequent to this, heteroglycans are degraded by phosphorylases (Fettke et al., 2005) and act as a carbon source to synthesize Suc, which can be hydrolyzed by cytosolic or vacuolar invertases to monosaccharides (Roitsch and González, 2004). These processes, in sum, enable leaf mesophyll cells to synthesize Glc and Fru, in addition to Suc, during the day and at night.Besides these metabolic processes, sugars are transported between different intracellular compartments and between different cells in order to serve as a long-distance carbon supply for sink organs. Due to their large size and hydrate shell, the movement of neutral sugars like Suc, Glc, or Fru across membranes requires the presence of membrane-bound carriers. For example, in the plant plasma membrane, a wide number of monosaccharide- and Suc-specific carriers were identified and have been analyzed with biochemical and molecular approaches. The Arabidopsis (Arabidopsis thaliana) genome harbors more than 50 isoforms of putative monosaccharide carriers, most of which belong to the sugar transport protein subfamily (Büttner and Sauer, 2000), while about 20 putative disaccharide carriers sucrose transporters (named SUT and SUC) are present in this plant species (Lalonde et al., 2004). Most of the sugar transport protein, SUT, or SUC carriers analyzed so far reside in the plasma membrane and import, as proton-coupled transporters, apoplastic sugars against a concentration gradient (Lalonde et al., 2004). This proton-driven sugar import allows a substantial accumulation of Suc in phloem sieve elements, building the driving force for interorgan long-distance sugar transport (Turgeon and Wolf, 2009). All monosaccharide and disaccharide carriers mentioned above exhibit 12 predicted transmembrane domains and group into the large major facilitator superfamily of carriers (Marger and Saier, 1993).In both photosynthetic active mesophyll cells as well as storage tissues, the large central vacuole represents the internal storage compartment for sugars (Martinoia et al., 2007, 2012), leading, in sugar beet (Beta vulgaris) or sugarcane (Saccharum officinarum), up to even 20% sugars per fresh biomass (John, 1992). Suc import into the vacuole occurs either via facilitated diffusion (Kaiser and Heber, 1984) or electrogenically via antiport against protons (Willenbrink and Doll, 1979). The latter process is driven by the significant proton-motive force across the vacuolar membrane (Schumacher and Krebs, 2010) and allows a substantial Suc accumulation in storage organs of high-sugar species (Getz, 1987; Getz and Klein, 1995). However, no Suc importer at the vacuolar membrane (tonoplast) has been identified on the molecular level yet, while tonoplast-located Suc exporters have been identified. This vacuolar Suc export is mediated by members of the SUT4-type clade of carriers, in cereals named SUT2 (Endler et al., 2006; Eom et al., 2011), procuring a proton-driven Suc export into the cytosol (Schulz et al., 2011). Loss of function of this type of carrier in Arabidopsis, poplar (Populus spp.), or rice (Oryza sativa) leads to an accumulation of Suc in leaves (Eom et al., 2011; Payyavula et al., 2011; Schneider et al., 2012), elegantly proving that this type of carrier fulfills an export function under in vivo conditions.In contrast to vacuolar Suc import, the import of monosaccharides into this compartment has been deciphered on the molecular level. In the Arabidopsis tonoplast, two different monosaccharide importers have been identified, namely the vacuolar Glc transporter protein and three isoforms of the tonoplast monosaccharide transporter (TMT; Wormit et al., 2006; Aluri and Büttner, 2007). While vacuolar Glc transporter loss-of-function plants do not show significant changes in monosaccharide levels (Aluri and Büttner, 2007), decreased TMT activity correlates with impaired vacuolar sugar import and low levels of both Glc and Fru in leaves (Wormit et al., 2006). This fact and the observations that (1) TMT1 is a sugar/proton antiporter (Schulz et al., 2011), (2) increased TMT activity provokes improved seed biomass (Wingenter et al., 2010), and (3) TMT activity is highly regulated via protein phosphorylation (Wingenter et al., 2011) clearly underline the superior function of TMT for monosaccharide loading into the plant vacuole.So far, two carriers, ESL1 and ERDL6, have been found to be responsible for Glc export from the plant vacuole (Yamada et al., 2010; Poschet et al., 2011). ESL1 (for early responsive to dehydration6-like1) represents a carrier majorly expressed in pericycle and xylem parenchyma cells and is known to be induced by drought stress (Yamada et al., 2010). Loss-of-function mutants of the ERDL6 (for early responsive to dehydration6-like6) carrier show increased leaf Glc levels and decreased seed weight, indicating that controlled Glc export via this carrier is critical for interorgan movement of sugars in Arabidopsis (Poschet et al., 2011). ESL1 seems to transport Glc in a facilitated diffusion, while in contrast to the plasma membrane-located sugar carriers and to TMT, the transport mode of ERDL6 has not been identified so far.In marked contrast to the carriers mentioned above, the recent identification of the so-called SWEET proteins opened our understanding of how cellular sugar export is achieved. SWEET proteins occur in plants as well as in animals and humans and consist of only seven predicted transmembrane domains (Chen et al., 2010). The observation that the expression of several plant SWEET proteins is strongly induced by various pathogens indicated that they serve as sugar exporters. That hypothesis has been proven for some SWEET isoforms by heterologous expression in Xenopus laevis oocytes (Chen et al., 2010), and detailed analysis revealed that Arabidopsis SWEET11 and SWEET12 catalyze Suc export from source leaves and are critical for interorgan sugar transport (Chen et al., 2012).In a recent quantitative trait locus analysis, we identified SWEET17 as a novel determinant of leaf Fru content, especially under cold conditions and conditions of low nitrogen supply (Chardon et al., 2013). In fact, a detailed molecular-physiological analysis revealed that SWEET17 is the first vacuole-located SWEET protein and that it serves as a Fru-specific exporter, connecting the vacuolar lumen to the cytosol. In contrast to SWEET17, the subcellular localization of its closest homolog, SWEET16, is elusive. Moreover, transport properties of SWEET16 are unknown, and the effect of increased SWEET16 activity (or any other SWEET proteins) on plant properties has not been determined. The latter aspect is of particular interest, since most genes coding for SWEET proteins are only comparably weakly expressed or are only expressed in certain cell types (Chen et al., 2010; Chardon et al., 2013).In this report, we analyzed the intracellular localization of SWEET16 and studied its transport properties in X. laevis oocytes. Moreover, we constructed constitutive SWEET16-overexpressing Arabidopsis lines and report the impact of this overexpression of a vacuolar SWEET protein on plant development and stress tolerance. Our results support the hypothesis that the activity of a SWEET facilitator has to be controlled in planta to cope with altering environmental and developmental conditions.     

The S2 subsites of cathepsins K and L and their contribution to collagen degradation

The exchange of residues 67 and 205 of the S2 pocket of human cysteine cathepsins K and L induces a permutation of their substrate specificity toward fluorogenic peptide substrates. While the cathepsin L-like cathepsin K (Tyr67Leu/Leu205Ala) mutant has a marked preference for Phe, the Leu67Tyr/Ala205Leu cathepsin L variant shows an effective cathepsin K-like preference for Leu and Pro. A similar turnaround of inhibition was observed by using specific inhibitors of cathepsin K [1-(N-Benzyloxycarbonyl-leucyl)-5-(N-Boc-phenylalanyl-leucyl)carbohydrazide] and cathepsin L [N-(4-biphenylacetyl)-S-methylcysteine-(D)-Arg-Phe-beta-phenethylamide]. Molecular modeling studies indicated that mutations alter the character of both S2 and S3 subsites, while docking calculations were consistent with kinetics data. The cathepsin K-like cathepsin L was unable to mimic the collagen-degrading activity of cathepsin K against collagens I and II, DQ-collagens I and IV, and elastin-Congo Red. In summary, double mutations of the S2 pocket of cathepsins K (Y67L/L205A) and L (L67Y/A205L) induce a switch of their enzymatic specificity toward small selective inhibitors and peptidyl substrates, confirming the key role of residues 67 and 205. However, mutations in the S2 subsite pocket of cathepsin L alone without engineering of binding sites to chondroitin sulfate are not sufficient to generate a cathepsin K-like collagenase, emphasizing the pivotal role of the complex formation between glycosaminoglycans and cathepsin K for its unique collagenolytic activity.     

Structural basis for the antagonistic roles of RNP-8 and GLD-3 in GLD-2 poly(A)-polymerase activity

Cytoplasmic polyadenylation drives the translational activation of specific mRNAs in early metazoan development and is performed by distinct complexes that share the same catalytic poly(A)-polymerase subunit, GLD-2. The activity and specificity of GLD-2 depend on its binding partners. In Caenorhabditis elegans, GLD-2 promotes spermatogenesis when bound to GLD-3 and oogenesis when bound to RNP-8. GLD-3 and RNP-8 antagonize each other and compete for GLD-2 binding. Following up on our previous mechanistic studies of GLD-2–GLD-3, we report here the 2.5 Å resolution structure and biochemical characterization of a GLD-2–RNP-8 core complex. In the structure, RNP-8 embraces the poly(A)-polymerase, docking onto several conserved hydrophobic hotspots present on the GLD-2 surface. RNP-8 stabilizes GLD-2 and indirectly stimulates polyadenylation. RNP-8 has a different amino-acid sequence and structure as compared to GLD-3. Yet, it binds the same surfaces of GLD-2 by forming alternative interactions, rationalizing the remarkable versatility of GLD-2 complexes.     

The thylakoid proton gradient promotes an advanced stage of signal peptide binding deep within the Tat pathway receptor complex

Tat (twin arginine translocation) systems transport folded proteins across the thylakoid membrane of chloroplasts and the plasma membrane of most bacteria. Tat precursors are targeted by hydrophobic cleavable signal peptides with twin arginine (RR) motifs. Bacterial precursors possess an extended consensus, (S/T)RRXFLK, of which the two arginines and the phenylalanine are essential for efficient transport. Thylakoid Tat precursors possess twin arginines but lack the consensus phenylalanine. Here, we have characterized two stages of precursor binding to the thylakoid Tat signal peptide receptor, the 700-kDa cpTatC-Hcf106 complex. The OE17 precursor tOE17 binds to the receptor by RR-dependant electrostatic interactions and partially dissociates during blue native gel electrophoresis. In addition, the signal peptide of thylakoid-bound tOE17 is highly exposed to the membrane surface, as judged by accessibility to factor Xa of cleavage sites engineered into signal peptide flanking regions. By contrast, tOE17 containing a consensus phenylalanine in place of Val(-20) (V - 20F) binds the receptor more strongly and is completely stable during blue native gel electrophoresis. Thylakoid bound V - 20F is also completely protected from factor Xa at the identical sites. This suggests that the signal peptide is buried deeply in the cpTatC-Hcf106 binding site. We further provide evidence that the proton gradient, which is required for translocation, induces a tighter interaction between tOE17 and the cpTat machinery, similar to that exhibited by V - 20F. This implies that translocation involves a very intimate association of the signal peptide with the receptor complex binding site.