Phosphorylation of Phospholipase C‐δ1 Regulates its Enzymatic Activity

Phosphorylation of phospholipase C‐δ₁ (PLC‐δ₁) in vitro and in vivo was investigated. Of the serine/threonine kinases tested, protein kinase C (PKC) phosphorylated the serine residue(s) of bacterially expressed PLC‐δ₁ most potently. It was also demonstrated that PLC‐δ₁ directly bound PKC‐α via its pleckstrin homology (PH) domain. Using deletion mutants of PLC‐δ₁ and synthetic peptides, Ser35 in the PH domain was defined as the PKC mediated in vitro phosphorylation site of PLC‐δ₁. In vitro phosphorylation of PLC‐δ₁ by PKC stimulated [³H]PtdIns(4,5)P₂ hydrolyzing activity and [³H]Ins(1,4,5)P₃‐binding of the PLC‐δ₁. On the other hand, endogenous PLC‐δ₁ was constitutively phosphorylated and phosphoamino acid analysis revealed that major phosphorylation sites were threonine residues in quiescent cells. The phosphorylation level and the species of phosphoamino acid were not changed by various stimuli such as PMA, EGF, NGF, and forskolin. Using matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry, we determined that Thr209 of PLC‐δ₁ is one of the constitutively phosphorylated sites in quiescent cells. The PLC activity was potentiated when constitutively phosphorylated PLC‐δ₁ was dephosphorylated by endogenous phosphatase(s) in vitro. Additionally, coexpression with PKC‐α reduced serine phosphorylation of PLC‐δ₁ detected by an anti‐phosphoserine antibody and PLC‐δ₁‐dependent basal production of inositol phosphates in NIH‐3T3 cells, suggesting PKC‐α activates phosphatase or inactivates another kinase involved in PLC‐δ₁ serine phosphorylation to modulate the PLC‐δ₁ activity in vivo. Taken together, these results suggest that PLC‐δ₁ has multiple phosphorylation sites and phosphorylation status of PLC‐δ₁ regulates its activity positively or negatively depends on the phosphorylation sites. J. Cell. Biochem. 108: 638–650, 2009. © 2009 Wiley‐Liss, Inc.     

Structural studies on KijD1, a sugar C‐3′‐methyltransferase

Kijanimicin is an antitumor antibiotic isolated from Actinomadura kijaniata. It is composed of three distinct moieties: a pentacyclic core, a monosaccharide referred to as d ‐kijanose, and a tetrasaccharide chain composed of l ‐digitoxose units. d ‐Kijanose is a highly unusual nitro‐containing tetradeoxysugar, which requires at least ten enzymes for its production. Here we describe a structural analysis of one of these enzymes, namely KijD1, which functions as a C‐3′‐methyltransferase using S‐adenosylmethionine as its cofactor. For this investigation, two ternary complexes of KijD1, determined in the presence of S‐adenosylhomocysteine (SAH) and dTDP or SAH and dTDP‐3‐amino‐2,3,6‐trideoxy‐4‐keto‐3‐methyl‐d ‐glucose, were solved to 1.7 or 1.6 Å resolution, respectively. Unexpectedly, these structures, as well as additional biochemical analyses, demonstrated that the quaternary structure of KijD1 is a dimer. Indeed, this is in sharp contrast to that previously observed for the sugar C‐3′‐methyltransferase isolated from Micromonospora chalcea. By the judicious use of site‐directed mutagenesis, it was possible to convert the dimeric form of KijD1 into a monomeric version. The quaternary structure of KijD1 could not have been deduced based solely on bioinformatics approaches, and thus this investigation highlights the continuing need for experimental validation.     

Homo‐C‐nucleoside analogs IV. Synthesis of 4‐(2,5‐anhydro‐D‐altro‐pentitol‐1‐yl)‐2‐phenyl‐2H‐1,2,3‐triazole homo‐C‐nucleoside. CD assignment of the absolute configuration of the carbon bridge

Dehydrative cyclization of 4‐(D‐altro ‐pentitol‐1‐yl)2‐phenyl‐2H ‐1,2,3‐triazole in basic medium with one moler equivalent of p‐toluene sulfonyl chloride in pyridine solution gave the homo‐C‐ nucleoside 4‐(2,5‐anhydro‐D‐altro ‐1‐yl)‐2‐phenyl‐2H ‐1,2,3‐triazole. The structure and anomeric configuration was determined by acylation, nuclear magnetic resonance (NMR), and mass spectroscopy. The stereochemistry at the carbon bridge of homo‐C‐ nucleoside 2‐phenyl‐2H ‐1,2,3‐triazoles was determined by circular dichroism (CD) spectroscopy.     

An Approach to Incorporate Multi‐Enzyme Digestion into C‐TAILS for C‐Terminomics Studies

Protein C‐termini study is still a challenging task and far behind its counterpart, N‐termini study. MS based C‐terminomics study is often hampered by the low ionization efficiency of C‐terminal peptides and the lack of efficient enrichment methods. We previously optimized the C‐terminal amine‐based isotope labeling of substrates (C‐TAILS) method and identified 369 genuine protein C‐termini in Escherichia coli. A key limitation of C‐TAILS is that the prior protection of amines and carboxylic groups at protein level makes Arg‐C as the only specific enzyme in practice. Herein, we report an approach combining multi‐enzyme digestion and C‐TAILS, which significantly increases the identification rate of C‐terminal peptides and consequently improves the applicability of C‐TAILS in biological studies. We carry out a systematic study and confirm that the omission of the prior amine protection at protein level has a negligible influence and allows the application of multi‐enzyme digestion. We successfully apply five different enzyme digestions to C‐TAILS, including trypsin, Arg‐C, Lys‐C, Lys‐N, and Lysarginase. As a result, we identify a total of 722 protein C‐termini in E. coli, which is at least 66% more than the results using any single enzyme. Moreover, the favored enzyme and enzyme combination are discovered. Data are available via ProteomeXchange with identifier PXD004275.     

Smad3 gene C‐terminal phosphorylation site mutation aggravates CCl4‐induced inflammation in mice

The expression of C‐terminal phosphorylated Smad3 (pSmad3C) is down‐regulated with the progression of liver disease. Thus, we hypothesized that pSmad3C expression may be negatively related to liver disease. To develop novel therapeutic strategies, a suitable animal model is required that will allow researchers to study the effect of Smad3 domain‐specific phosphorylation on liver disease progression. The current study aimed to construct a new mouse model with the Smad3 C‐terminal phosphorylation site mutation and to explore the effects of this mutation on CCl₄‐induced inflammation. Smad3 C‐terminal phosphorylation site mutant mice were generated using TetraOne? gene fixed‐point knock‐in technology and embryonic stem cell microinjection. Resulting mice were identified by genotyping, and the effects on inflammation were explored in the presence or absence of CCl₄. No homozygous mice were born, indicating that the mutation is embryonic lethal. There was no significant difference in liver phenotype and growth between the wild‐type (WT) and heterozygous (HT) mice in the absence of reagent stimulation. After CCl₄‐induced acute and chronic liver damage, liver pathology, serum transaminase (ALT/AST) expression and levels of inflammatory factors (IL‐6/TNF‐α) were more severely altered in HT mice than in WT mice. Furthermore, pSmad3C protein levels were lower in liver tissue from HT mice. These results suggest that Smad3 C‐terminal phosphorylation may have a protective effect during the early stages of liver injury. In summary, we have generated a new animal model that will be a novel tool for future research on the effects of Smad3 domain‐specific phosphorylation on liver disease progression.     

Determination of the Absolute Configuration of Two Pairs of C‐8 − C‐9′ Linked Neolignan Enantiomers

Two pairs of new neolignan enantiomers, (±)‐torreyayunan A ( 1a / 1b ) and (±)‐torreyayunan B ( 2a / 2b ), featuring a rare C‐8 ? C‐9′ linked skeleton, were isolated from leaves and twigs of Torreya yunnanensis. Their absolute configuration involving two chiral centers was determined by combined spectral and Density Functional Theory (DFT) calculation. This is the first report of the absolute configuration of this group of neolignans. Chirality 26:825–828, 2014. © 2014 Wiley Periodicals, Inc.     

Structural transition from dimeric to tetrameric i‐motif,caused by the presence of TAA at the 3′‐end of human telomeric C‐rich sequence

Widely dispersed in genomic DNA, the tandem C‐rich repetitive stretches may fold below physiological pH, into i‐motif structures, stabilized by C·C⁺ pairing. Herein, structural status of a 9‐mer stretch d(CCCTAACCC), [the truncated double repeat of human telomeric sequence], and its extended version, comprising of additional ? TAA segment at the 3′‐end, representing the complete double repeat d(CCCTAACCCTAA), has been investigated. The pH dependent monophasic UV‐melting, Gel and CD data suggested that while the truncated version adopts a bimolecular i‐motif structure, its complete double repeat (12‐mer) sequence exists in two (bimolecular and tetramolecular) forms. A model is proposed for the tetramolecular i‐motif with conventional C · C⁺ base pairs, additionally stabilized by asymmetric A · A base pairs at the ?3′ TAA flanking ends and Watson–Crick A · T hydrogen bonding between intervening bases on antiparallel strands. Expanding the known topologies of DNA i‐motifs, such atypical geometries of i‐motifs may have implications in their recognition by proteins. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 150–160, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Tuning the binding of coumarin 6 with DNA by molecular encapsulators: effect of β‐cyclodextrin and C‐hexylpyrogallol[4]arene

We report in this paper that the binding of coumarin 6 (C6) to DNA can be tuned by complexing it with host structures, viz. β‐cyclodextrin (β‐CD) and C‐hexylpyrogallol‐4‐arene (C‐HPA). Because host molecules are used as carriers of small molecules onto target sites, the exposed part of the guest molecule needs to be found out, and the relationship between the host : guest ratio and the mode of binding with the target macromolecule, that is, the DNA needs to be analyzed, in order to comprehend the preferred binding moiety and tune the binding. In this paper, the formation of the inclusion complex of C6 with β‐CD and with C‐HPA is studied by UV‐visible, fluorescence, 2D rotating‐frame nuclear Overhauser effect correlation spectroscopy and diffusion‐ordered spectroscopy nuclear magnetic resonance spectra and molecular modeling. C6 forms a 1:1 complex with β‐CD and a 1:2 complex with C‐HPA. The studies on the protonation of C6 in the presence and the absence of the host molecules suggest that the chromone part of C6 is outside the β‐CD molecule, whereas it is fully covered by C‐HPA. The binding of C6 with calf thymus DNA (ctDNA) occurs through intercalation and hydrogen bonding, and the host–guest structures remain intact on binding with ctDNA. The oxygens of the C6 molecules are exposed when inside the host molecules and aid in the hydrogen bonding with DNA. Copyright © 2014 John Wiley & Sons, Ltd.     

Hepatitis C virus NS3‐4A inhibits the peroxisomal MAVS‐dependent antiviral signalling response

Hepatitis C virus (HCV) is the cause of one of the most prevalent viral infections worldwide. Upon infection, the HCV genome activates the RIG‐I‐MAVS signalling pathway leading to the production of direct antiviral effectors which prevent important steps in viral propagation. MAVS localizes at peroxisomes and mitochondria and coordinate the activation of an effective antiviral response: peroxisomal MAVS is responsible for a rapid but short‐termed antiviral response, while the mitochondrial MAVS is associated with the activation of a stable response with delayed kinetics. The HCV NS3‐4A protease was shown to specifically cleave the mitochondrial MAVS, inhibiting the downstream response. In this study, we have analysed whether HCV NS3‐4A is also able to cleave the peroxisomal MAVS and whether this would have any effect on the cellular antiviral response. We show that NS3‐4A is indeed able to specifically cleave this protein and release it into the cytosol, a mechanism that seems to occur at a similar kinetic rate as the cleavage of the mitochondrial MAVS. Under these conditions, RIG‐I‐like receptor (RLR) signalling from peroxisomes is blocked and antiviral gene expression is inhibited. Our results also show that NS3‐4A is able to localize at peroxisomes in the absence of MAVS. However, mutation studies have shown that this localization pattern is preferred in the presence of a fully cleavable MAVS. These findings present evidence of a viral evasion strategy that disrupts RLR signalling on peroxisomes and provide an excellent example of how a single viral evasion strategy can block innate immune signalling from different organelles.     

Synthesis,conformational study,and spectroscopic characterization of the cyclic Cα,α‐disubstituted glycine 9‐amino‐9‐fluorenecarboxylic acid

A series of terminally blocked peptides (to the pentamer level) from l ‐Ala and the cyclic C^α,α‐disubstituted Gly residue Afc and one Gly/Afc dipeptide have been synthesized by solution method and fully characterized. The molecular structure of the amino acid derivative Boc‐Afc‐OMe and the dipeptide Boc‐Afc‐Gly‐OMe were determined in the crystal state by X‐ray diffraction. In addition, the preferred conformation of all of the model peptides was assessed in deuterochloroform solution by FT‐IR absorption and ¹H‐NMR. The experimental data favour the conclusion that the Afc residue tends to adopt either the fully‐extended (C₅) or a folded/helical structure. In particular, the former conformation is highly populated in solution and is also that found in the crystal state in the two compounds investigated. A comparison with the structural propensities of the strictly related C^α,α‐disubstituted Gly residues Ac₅c and Dϕg is made and the implications for the use of the Afc residue in conformationally constrained analogues of bioactive peptides are briefly examined. A spectroscopic (UV absorption, fluorescence, CD) characterization of this novel aromatic C^α,α‐disubstituted Gly residue is also reported. Copyright © 1999 European Peptide Society and John Wiley & Sons, Ltd.     

Swiprosin‐1 is expressed in mast cells and up‐regulated through the protein kinase CβI/η pathway

Swiprosin‐1 exhibits the highest expression in CD8⁺ T cells and immature B cells and has been thought to play a role in lymphocyte physiology. Here we report that swiprosin‐1 is also expressed in mast cells and up‐regulated in both in vitro cultured mast cells by phorbol ester and in vivo model tissues of passive cutaneous anaphylaxis and atopic dermatitis. Targeted inhibition of the specific protein kinase C (PKC) isotypes by siRNA revealed that PKC‐βI/η are involved in the expression of swiprosin‐1 in the human mast cell line HMC‐1. In contrast, down‐regulation of swiprosin‐1 by A23187 or ionomycin suggests that calcium‐signaling plays a negative role. The ectopic expression of swiprosin‐1 augmented PMA/A23187‐induced NF‐κB promoter activity, and resulted in increased expression of cytokines. Moreover, knock‐down of swiprosin‐1 attenuated PMA/A23187‐induced cytokine expression. Collectively, these results suggest that swiprosin‐1 is a PKC‐βI/η‐inducible gene and it modulates mast cell activation through NF‐κB‐dependent pathway. J. Cell. Biochem. 108: 705–715, 2009. © 2009 Wiley‐Liss, Inc.     

Melanogenesis‐Inhibitory Activities of Isomeric C‐seco Limonoids and Deesterified Limonoids

Treatment of eight C‐seco limonoids including six of salannin‐type, 1 – 6 , and two of nimbin‐type, 7 and 8 , with a combination of BF₃ · Et₂O and iodide ion yielded the isomeric C‐seco derivatives, i.e., six isosalannins, 1a – 6a , and two isonimbins, 7a and 8a , respectively. Ohchinin ( 1 ) was further subjected to LiAlH₄ reduction which yielded a deesterified trihydroxy limonoid, nimbidinol ( 9 ). In addition, ten limonoids including seven of azadirone‐type, 10 – 16 , and three of gedunin‐type, 17 – 19 , all of which possess no ester functionality in the molecule, were obtained from the neutral fraction of Azadirachta indica seed extract after alkaline hydrolysis. Among the above, twelve compounds, i.e., 1a – 4a , 6a , 9 , 13 – 16 , 18 , and 19 , were new compounds, and their structures were elucidated on the basis of extensive spectroscopic analysis and comparison with literature data. Upon evaluation of all these limonoids for their inhibitory activities against melanogenesis in B16 melanoma cells induced with α‐melanocyte‐stimulating hormone (α‐MSH), five structurally modified limonoids, 3‐deacetyl‐28‐oxosalannin ( 6a ), 9 , 17‐epi‐17‐hydroxynimbocinol ( 14 ), 17‐epi‐17‐hydroxy‐15‐methoxynimbocinol ( 15 ), and 7‐deacetyl‐17‐epinimolicinol ( 18 ), in addition to a natural limonoid, 1 , exhibited potent inhibitory activities with 26 – 66% reduction of melanin content at 100 μm concentration with almost no or low toxicity to the B16 melanoma cells (70 – 99% cell viability at 100 μm ).     

C‐terminal domain of SARS‐CoV main protease can form a 3D domain‐swapped dimer

SARS coronavirus main protease (M^pro) plays an essential role in the extensive proteolytic processing of the viral polyproteins (pp1a and pp1ab), and it is an important target for anti-SARS drug development. We have reported that both the M^pro C-terminal domain alone (M^pro-C) and the N-finger deletion mutant of M^pro (M^pro-Δ7) exist as a stable dimer and a stable monomer (Zhong et al., J Virol 2008; 82:4227-4234). Here, we report structures of both M^pro-C monomer and dimer. The structure of the M^pro-C monomer is almost identical to that of the C-terminal domain in the crystal structure of M^pro. Interestingly, the M^pro-C dimer structure is characterized by 3D domain-swapping, in which the first helices of the two protomers are interchanged and each is enwrapped by four other helices from the other protomer. Each folding subunit of the M^pro-C domain-swapped dimer still has the same general fold as that of the M^pro-C monomer. This special dimerization elucidates the structural basis for the observation that there is no exchange between monomeric and dimeric forms of M^pro-C and M^pro-Δ7.     

Binding Pockets and Permeation Channels for Dioxygen through Cofactorless 3‐Hydroxy‐2‐methylquinolin‐4‐one 2,4‐Dioxygenase in Association with Its Natural Substrate, 3‐Hydroxy‐2‐methylquinolin‐4(1H)‐one. A Perspective from Molecular Dynamics Simulations

This work describes an investigation of pathways and binging pockets (BPs) for dioxygen (O₂) through the cofactorless oxygenase 3‐hydroxy‐2‐methylquinolin‐4‐one 2,4‐dioxygenase in complex with its natural substrate, 3‐hydroxy‐2‐methylquinolin‐4(1H)‐one, in aqueous solution. The investigation tool was random‐acceleration molecular dynamics (RAMD), whereby a tiny, randomly oriented external force is applied to O₂ in order to accelerate its movements. In doing that, care was taken that the external force only continues, if O₂ moves along a direction for a given period of time, otherwise the force changed direction randomly. Gates for expulsion of O₂ from the protein, which can also be taken as gates for O₂ uptake, were found throughout almost the whole external surface of the protein, alongside a variety of BPs for O₂. The most exploited gates and BPs were not found to correspond to the single gate and BP proposed previously from the examination of the static model from X‐ray diffraction analysis of this system. Therefore, experimental investigations of this system that go beyond the static model are urgently needed.