Kinetics of the dimerization of retroviral proteases: the "fireman's grip" and dimerization

All retroviral proteases belong to the family of aspartic proteases. They are active as homodimers, each unit contributing one catalytic aspartate to the active site dyad. An important feature of all aspartic proteases is a conserved complex scaffold of hydrogen bonds supporting the active site, called the "fireman's grip," which involves the hydroxyl groups of two threonine (serine) residues in the active site Asp-Thr(Ser)-Gly triplets. It was shown previously that the fireman's grip is indispensable for the dimer stability of HIV protease. The retroviral proteases harboring Ser in their active site triplet are less active and, under natural conditions, are expressed in higher enzyme/substrate ratio than those having Asp-Thr-Gly triplet. To analyze whether this observation can be attributed to the different influence of Thr or Ser on dimerization, we prepared two pairs of the wild-type and mutant proteases from HIV and myeloblastosis-associated virus harboring either Ser or Thr in their Asp-Thr(Ser)-Gly triplet. The equilibrium dimerization constants differed by an order of magnitude within the relevant pairs. The proteases with Thr in their active site triplets were found to be approximately 10 times more thermodynamically stable. The dimer association contributes to this difference more than does the dissociation. We propose that the fireman's grip might be important in the initial phases of dimer formation to help properly orientate the two subunits of a retroviral protease. The methyl group of threonine might contribute significantly to fixing such an intermediate conformation.     

A new water-soluble N-protecting group, 2-(phenyl(methyl)sulfonio)ethyloxycarbonyl tetrafluoroborate, and its application to solid phase peptide synthesis in water.

A new water-soluble N-protecting group, 2-[phenyl(methyl)sulfoniolethyloxycarbonyl tetrafluoroborate, has been prepared and its application to solid phase peptide synthesis in water has been studied. Leu-enkephalin amide was successfully synthesized in water by the solid phase method using this protecting group.     

Interactive effects of elevated CO2, N deposition and climate change on extracellular enzyme activity and soil density fractionation in a California annual grassland

Elevated CO₂, N deposition and climate change can alter ecosystem‐level nutrient cycling both directly and indirectly. We explored the interactive effects of these environmental changes on extracellular enzyme activity and organic matter fractionation in soils of a California annual grassland. The activities of hydrolases (polysaccharide‐degrading enzymes and phosphatase) increased significantly in response to nitrate addition, which coincided with an increase in soluble C concentrations under ambient CO₂. Water addition and elevated CO₂ had negative but nonadditive effects on the activities of these enzymes. In contrast, water addition resulted in an increase in the activities of lignin‐degrading enzymes (phenol oxidase and peroxidase), and a decrease in the free light fraction (FLF) of soil organic matter. Independent of treatment effects, lignin content in the FLF was negatively correlated with the quantity of FLF across all samples. Lignin concentrations were lower in the aggregate‐occluded light fraction (OLF) than the FLF, and there was no correlation between percent lignin and OLF quantity, which was consistent with the protection of soil organic matter in aggregates. Elevated CO₂ decreased the quantity of OLF and increased the OLF lignin concentration, however, which is consistent with increased degradation resulting from increased turnover of soil aggregates. Overall, these results suggest that the effects of N addition on hydrolase activity are offset by the interactive effects of water addition and elevated CO₂, whereas water and elevated CO₂ may cause an increase in the breakdown of soil organic matter as a result of their effects on lignin‐degrading enzymes and soil aggregation, respectively.     

Metal-mediated and metal-catalyzed hydrolysis of nitriles

The essential goals of this review are the following: (i) to verify various factors which affect the metal-mediated hydrolysis of organonitriles; (ii) to draw attention to unusual conversions of RCN species, yet underdeveloped and non-systematic, which involve hydrolysis and lead to compounds of synthetic and/or pharmacological significance. The metal-mediated and/or metal-catalyzed reactions of RCN species are surveyed and the experimental material on metal-mediated hydration of RCN species at diverse metal centers along the Periodic Table is summarized in a tabular form.     

Quantitative structure–activity relationship study of new potent and selective antagonists at the 5-HT1A and adrenergic α1d receptors: Derivatives of spiroethyl phenyl(substituted)piperazine

The antagonistic activities of derivatives of spiroethyl phenyl(substituted)piperazine at the 5-HT_1A and adrenergic α_1d receptors is quantitatively analyzed employing physicochemical and structural parameters. The derived correlation equation revealed that a substituent, other than 2-CH₃ in the phenyl ring, having higher molar refraction, MR, and a substituent producing higher positive field effect at the 3-position are beneficial in increasing the binding affinity at the 5-HT_1A receptor. In addition, a less hydrophobic substituent at the 4-position is also helpful in augmenting the binding affinity. The 5-R substituents which have higher MR values, however, elicit a detrimental effect. Two disubstituted compounds which are not present in the original data-set and have higher theoretical binding affinities are designed from the correlation equation. These compounds consisting of 2-OCH(CH₃)₂, 3-Cl and 2-C₃H₇, 3-Cl in the phenyl ring, have theoretical pK_i values 10.57 and 10.12 respectively. For the adrenergic α_1d receptor, a less bulky group at the 3-position with 5-Cl (or simply a 3-Cl) is advantageous in increasing the binding affinity. Likewise, a substituent exhibiting a less negative resonance effect at the 4-position and the substituent with low polarizability and showing more a negative resonance effect at the 5-position are suitable for enhancement of the binding affinity. The analysis provides the grounds for rationalizing substituent selection in designing better potency antagonists in the series.     

响应面法优化热带假丝酵母104菌株产羰基还原酶发酵培养基

通过菌种优选得到产高选择性羰基还原酶的热带假丝酵母(Candida tropicalis)104菌株,可不对称还原1-(3,5-二三氟甲基)苯基乙酮生成(S)-1-(3,5-二三氟甲基)苯基乙醇,对映体过量值>99.9%。采用部分因子实验设计考察发酵培养基中各组分对产酶的影响,结果表明,酵母粉、葡萄糖和NH4Cl浓度对产酶影响显著。继而采用最陡爬坡路径逼近最大响应区域,并结合中心组合实验和响应面对3个显著性因素进行分析,得到优化的发酵培养基组成:葡萄糖47.14g/L,酵母粉13.25g/L,NH4Cl2.71g/L,MgSO4·7H2O0.4g/L,KH2PO41g/L和K2HPO41g/L。采用该优化培养基,供试菌株的羰基还原酶活力达851.13U/L,较优化前提高了65.2%。     

Interaction of the amyloid imaging tracer FDDNP with hallmark Alzheimer's disease pathologies

The distinctive cortical uptake of the tracer ¹⁸F-FDDNP (2-(1-{6-[(2-fluoroethyl(methyl)amino]-2-naphthyl}ethylidene)malononitrile) in Alzheimer's disease (AD) is believed to be because of its binding to both neurofibrillary tangles (NFTs) and highly fibrillar senile plaques. We therefore investigated the binding of a tracer concentration of ³H-FDDNP to brain sections containing AD hallmark pathologies. Semi-adjacent sections were labelled with ³H-PIB (Pittsburgh compound-B, 2-[4'-(methylamino)phenyl]-6-hydroxybenzothiazole) and ¹⁴C-SB13 (4- N -methylamino-4'-hydroxystilbene) for comparison. Neocortical sections containing widespread senile plaques and cerebrovascular amyloid angiopathy, produced a sparse and weak labelling following incubation with ³H-FDDNP. Furthermore, in sections containing NFTs, there was no overt labelling of the pathology by ³H-FDDNP. In contrast, sections labelled with ³H-PIB displayed extensive labelling of diffuse plaques, classical plaques, cerebrovascular amyloid angiopathy and NFTs. ¹⁴C-SB13 produced a broadly similar binding pattern to PIB. Radioligand binding assays employing in vitro generated amyloid-β peptide fibrils demonstrated a ∼10-fold reduced affinity for ³H-FDDNP (85.0 ± 2.0 nM) compared with ³H-PIB (8.5 ± 1.3 nM). These data provide an alternative mechanistic explanation for the observed low cortical uptake of ¹⁸F-FDDNP in AD; in that the ligand is only weakly retained by the hallmark neuropathology because of its low affinity for amyloid structures.     

Three members of the human pyruvate dehydrogenase kinase gene family are direct targets of the peroxisome proliferator-activated receptor beta/delta

The nuclear receptors peroxisome proliferator-activated receptors (PPARs) are known for their critical role in the metabolic syndrome. Here, we show that they are direct regulators of the family of pyruvate dehydrogenase kinase (PDK) genes, whose products act as metabolic homeostats in sensing hunger and satiety levels in key metabolic tissues by modulating the activity of the pyruvate dehydrogenase complex. Mis-regulation of this tightly controlled network may lead to hyperglycemia. In human embryonal kidney cells we found the mRNA expression of PDK2, PDK3 and PDK4 to be under direct primary control of PPAR ligands, and in normal mouse kidney tissue Pdk2 and Pdk4 are PPAR targets. Both, treatment of HEK cells with PPARbeta/delta-specific siRNA and the genetic disruption of the Pparbeta/delta gene in mouse fibroblasts resulted in reduced expression of Pdk genes and abolition of induction by PPARbeta/delta ligands. These findings suggest that PPARbeta/delta is a key regulator of PDK genes, in particular the PDK4/Pdk4 gene. In silico analysis of the human PDK genes revealed two candidate PPAR response elements in the PDK2 gene, five in the PDK3 gene and two in the PDK4 gene, but none in the PDK1 gene. For seven of these sites we could demonstrate both PPARbeta/delta ligand responsiveness in context of their chromatin region and simultaneous association of PPARbeta/delta with its functional partner proteins, such as retinoidXreceptor, co-activator and mediator proteins and phosphorylated RNA polymerase II. In conclusion, PDK2, PDK3 and PDK4 are primary PPARbeta/delta target genes in humans underlining the importance of the receptor in the control of metabolism.     

Tricks of the trade used to accelerate high-resolution structure determination of membrane proteins

The rate at which X-ray structures of membrane proteins are solved is on a par with that of soluble proteins in the late 1970s. There are still many obstacles facing the membrane protein structural community. Recently, there have been several technical achievements in the field that have started to dramatically accelerate structural studies. Here, we summarize these so-called ‘tricks-of-the-trade’ and include case studies of several mammalian transporters.     

Modulation of Fas-FasL related apoptosis by PBN in the early phases of choline deficient diet-mediated hepatocarcinogenesis in rats

This study focused on the detection of apoptosis related events in very early phases of choline-deficient (CD)-induced hepatocarcinogenesis (at 2-5 weeks). Flow cytometry of isolated intact primary hepatocytes from CD diet fed rats indicated increased expression of the apoptosis-associated protein Fas. Increased apoptosis in CD-treated livers was confirmed by Western blot analyses of caspases and cytochrome c. This study was also able to detect differences in apoptotic events following phenyl butyl nitrone (PBN) treatment. Fas expression was inhibited by PBN, indicating that PBN is anti-apoptotic. It is speculated that in the early stages of CD-induced hepatotoxicity, PBN is involved in inhibiting pro-inflammatory factor-driven apoptosis of normal hepatocytes, which protects against the initiation of carcinogenesis. The CD diet model is also considered as a model for non-alcoholic steatohepatitis (NASH) in humans and early expression of Fas could also be a good index of the progression of NASH.