Opening and closing of the hydrophobic cavity of LolA coupled to lipoprotein binding and release

Outer membrane-specific lipoproteins of Escherichia coli are released from the inner membrane through the action of Lol-CDE, which leads to the formation of a complex between the lipoprotein and LolA, a periplasmic chaperone. LolA then transfers lipoproteins to LolB, a receptor in the outer membrane. The structures of LolA and LolB are very similar, having an incomplete beta-barrel covered with an alpha-helical lid forming a hydrophobic cavity inside. The cavity of LolA, but not that of LolB, is closed and thus inaccessible to the bulk solvent. Previous studies suggested that Arg at position 43 of LolA is critical for maintaining this closed structure. We show here, through a crystallographic study, that the cavity of the LolA(R43L) mutant, in which Leu replaces Arg-43, is indeed open to the external milieu. We then found that the binding of a fluorescence probe distinguishes the open/close state of the cavity. Furthermore, it was revealed that the hydrophobic cavity of LolA opens upon the binding of lipoproteins. Such a liganded LolA was found to be inactive in the release of lipoproteins from the inner membrane. On the other hand, the liganded LolA became fully functional when lipoproteins were removed from LolA by detergent treatment or transferred to LolB. Free LolA thus formed was inaccessible to a fluorescence probe. These results, taken together, reveal the LolA cycle, in which the hydrophobic cavity undergoes opening and closing upon the binding and release of lipoproteins, respectively.     

Critical contribution of aromatic rings to specific recognition of polyether rings. The case of ciguatoxin CTX3C-ABC and its specific antibody 1C49

To address how proteins recognize polyether toxin compounds, we focused on the interaction between the ABC ring compound of ciguatoxin 3C and its specific antibody, 1C49. Surface plasmon resonance analyses indicated that Escherichia coli-expressed variable domain fragments (Fv) of 1C49 had the high affinity constants and slow dissociation constants typical of antigen-antibody interactions. Linear van't Hoff analyses suggested that the interaction is enthalpy-driven. We resolved the crystal structure of 1C49 Fv bound to ABC ring compound of ciguatoxin 3C at a resolution of 1.7A. The binding pocket of the antibody had many aromatic rings and bound the antigen by shape complementarity typical of hapten-antibody interactions. Three hydrogen bonds and many van der Waals interactions were present. We mutated several residues of the antibody to Ala, and we used surface plasmon resonance to analyze the interactions between the mutated antibodies and the antigen. This analysis identified Tyr-91 and Trp-96 in the light chain as hot spots for the interaction, and other residues made incremental contributions by conferring enthalpic advantages and reducing the dissociation rate constant. Systematic mutation of Tyr-91 indicated that CH-pi and pi-pi interactions between the aromatic ring at this site and the antigen made substantial contributions to the association, and van der Waals interactions inhibited dissociation, suggesting that aromaticity and bulkiness are critical for the specific recognition of polyether compounds by proteins.     

Stromal fibroblasts activated by tumor cells promote angiogenesis in mouse gastric cancer

Myofibroblasts, also known as activated fibroblasts, constitute an important niche for tumor development through the promotion of angiogenesis. However, the mechanism of stromal fibroblast activation in tumor tissues has not been fully understood. A gastric cancer mouse model (Gan mice) was recently constructed by simultaneous activation of prostaglandin (PG) E2 and Wnt signaling in the gastric mucosa. Because both the PGE2 and Wnt pathways play a role in human gastric tumorigenesis, the Gan mouse model therefore recapitulates the molecular etiology of human gastric cancer. Microvessel density increased significantly in Gan mouse tumors. Moreover, the expression of vascular endothelial growth factor A (VEGFA) was predominantly induced in the stromal cells of gastric tumors. Immunohistochemistry suggested that VEGFA-expressing cells in the stroma were alpha-smooth muscle actin-positive myofibroblasts. Bone marrow transplantation experiments indicated that a subset of gastric myofibroblasts is derived from bone marrow. Importantly, the alpha-smooth muscle actin index in cultured fibroblasts increased significantly when stimulated with the conditioned medium of Gan mouse tumor cells, indicating that gastric tumor cells activate stromal fibroblasts. Furthermore, conditioned medium of Gan mouse tumor cells induced VEGFA expression both in embryonic and gastric fibroblasts, which further accelerated the tube formation of human umbilical vein endothelial cells in vitro. Notably, stimulation of fibroblasts with PGE2 and/or Wnt1 did not induce VEGFA expression, thus suggesting that factors secondarily induced by PGE2 and Wnt signaling in the tumor cells are responsible for activation of stromal fibroblasts. Such tumor cell-derived factors may therefore be an effective target for chemoprevention against gastric cancer.     

Identification of galacto-N-biose phosphorylase from Clostridium perfringens ATCC13124

Lacto-N-biose phosphorylase (LNBP) from bifidobacteria is involved in the metabolism of lacto-N-biose I (Galβ1→3GlcNAc, LNB) and galacto-N-biose (Galβ1→3GalNAc, GNB). A homologous gene of LNBP (CPF0553 protein) was identified in the genome of Clostridium perfringens ATCC13124, which is a gram-positive anaerobic intestinal bacterium. In the present study, we cloned the gene and compared the substrate specificity of the CPF0553 protein with LNBP from Bifidobacterium longum JCM1217 (LNBP_Bl). In the presence of α-galactose 1-phosphate (Gal 1-P) as a donor, the CPF0553 protein acted only on GlcNAc and GalNAc, and GalNAc was a more effective acceptor than GlcNAc. The reaction product from GlcNAc/GalNAc and Gal 1-P was identified as LNB or GNB. The CPF0553 protein also phosphorolyzed GNB much faster than LNB, which suggests that the protein should be named galacto-N-biose phosphorylase (GNBP). GNBP showed a k _cat/K _m value for GNB that was approximately 50 times higher than that for LNB, whereas LNBP_Bl showed similar k _cat/K _m values for both GNB and LNB. Because C. perfringens possesses a gene coding endo-α-N-acetylgalactosaminidase, GNBP may play a role in the intestinal residence by metabolizing GNB that is available as a mucin core sugar.     

Effects of Aluminum on the Growth of Tea Plant and Activation of Antioxidant System

The origin and distribution of carbonic anhydrase (CA), which could accelerate karst processes, are explored in this paper. The soil samples used in the study were collected from four different kinds of karst ecosystems of Southwest China. The results indicate that CA activity could be detected in surface layer soils, and that CA activity varied obviously among the soils in different karst ecosystems. Of the four kinds of karst site, the mean CA activity of the surface soil in Misuga, Liupanshui, which had the lowest vegetation cover, was the lowest with 0.02 U g ^–1 dry soil. Nongla and Jinfu mountain, where there is abundant vegetable species diversity and dense vegetation, had higher mean CA activity in the surface soil with 3.83 U g ^–1 dry soil and 3.13 U g ^–1 dry soil, respectively. Moreover, there was certain difference in CA activities of soils among different kinds of karst landscape in the same kind of karst ecosystem. On the other hand, the higher CA activity could be detected in the soils in the vicinity of the plant roots, and CA activity in soil exhibited both obvious seasonal and vertical changes. These facts implied that plant roots and soil microorganisms might serve as important sources of CA. Besides, the results indicate that CA activity is found in bacteria, actinomycetes and fungi. Actinomycetes had higher intracellular CA activity, while fungi had higher extracellular CA activity. This study shows that higher microbial CA activities are found in Jinfu Mountain, while lower microbial CA activities are found in Misuga, Liupanshui.     

Pleuromutilin derivatives having a purine ring. Part 1: new compounds with promising antibacterial activity against resistant Gram-positive pathogens

In the course of our research aimed at the discovery of metabolic stable pleuromutilin derivatives with more potent antibacterial activity against Gram-positive pathogens than previous analogues, a series of compounds bearing a purine ring were prepared and evaluated. From SAR studies, we identified two promising compounds 85 and 87, which have excellent in vitro activity against a number of Gram-positive pathogens, including existing drug-resistant strains, and potent in vivo efficacy.     

Critical contribution of VH-VL interaction to reshaping of an antibody: the case of humanization of anti-lysozyme antibody, HyHEL-10

To clarify the effects of humanizing a murine antibody on its specificity and affinity for its target, we examined the interaction between hen egg white lysozyme (HEL) and its antibody, HyHEL-10 variable domain fragment (Fv). We selected a human antibody framework sequence with high homology, grafted sequences of six complementarity-determining regions of murine HyHEL-10 onto the framework, and investigated the interactions between the mutant Fvs and HEL. Isothermal titration calorimetry indicated that the humanization led to 10-fold reduced affinity of the antibody for its target, due to an unfavorable entropy change. Two mutations together into the interface of the variable domains, however, led to complete recovery of antibody affinity and specificity for the target, due to reduction of the unfavorable entropy change. X-ray crystallography of the complex of humanized antibodies, including two mutants, with HEL demonstrated that the complexes had almost identical structures and also paratope and epitope residues were almost conserved, except for complementary association of variable domains. We conclude that adjustment of the interfacial structures of variable domains can contribute to the reversal of losses of affinity or specificity caused by humanization of murine antibodies, suggesting that appropriate association of variable domains is critical for humanization of murine antibodies without loss of function.