Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling

Reverse gyrase is an ATP-dependent topoisomerase that is unique to hyperthermophilic archaea and eubacteria. The only reverse gyrase structure determined to date has revealed the arrangement of the N-terminal helicase domain and the C-terminal topoisomerase domain that intimately cooperate to generate the unique function of positive DNA supercoiling. Although the structure has elicited hypotheses as to how supercoiling may be achieved, it lacks structural elements important for supercoiling and the molecular mechanism of positive supercoiling is still not clear. We present five structures of authentic Thermotoga maritima reverse gyrase that reveal a first view of two interacting zinc fingers that are crucial for positive DNA supercoiling. The so-called latch domain, which connects the helicase and the topoisomerase domains is required for their functional cooperation and presents a novel fold. Structural comparison defines mobile regions in parts of the helicase domain, including a helical insert and the latch that are likely important for DNA binding during catalysis. We show that the latch, the helical insert and the zinc fingers contribute to the binding of DNA to reverse gyrase and are uniquely placed within the reverse gyrase structure to bind and guide DNA during strand passage. A possible mechanism for positive supercoiling by reverse gyrases is presented.     

Polyamine levels in normal human serum. Comparison of analytical methods

A comparison of levels of the polyamines, putrescine, spermidine and spermine, in individual and pooled normal human serum, as determined by three independent methods, high pressure cation-exchange chromatography (HPCC), radioimmunoassay (RIA) and gas chromatography-mass spectrometry (GC-MS), has been made. Generally good correlations were found for values derived by the three different methods.     

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JOCB BULLETIN

Welcome to the JOCB Bulletin     

Comparative effect of amidated pectin and psyllium on cholesterol homeostasis in rats

The effects of amidated pectin and psyllium on serum, hepatic and faecal cholesterol concentration were compared in female rats fed diets supplemented with palm fat and cholesterol at 50 and 10 g/kg, respectively. Control rats were fed a diet supplemented with cellulose at 60 g/kg. In treated rats, cellulose was replaced with either amidated pectin or psyllium. Amidated pectin and psyllium intake significantly decreased serum cholesterol from 3.41 μmol/ml (control) to 1.68 and 2.04 μmol/ml, respectively, and hepatic cholesterol from 31.9 μmol/g (control) to 7.2 and 9.0 μmol/g, respectively. Histology with lipid-staining Sudan Black B revealed that liver tissue from control rats was infiltrated with lipids, but staining was absent in livers of treated rats. No hepatic pathophysiology was apparent in treated rats. Amidated pectin and psyllium intake significantly increased faecal fat content. Faecal cholesterol content was significantly increased in rats that were fed amidated pectin, and non-significantly increased in rats that were fed psyllium. Body weight and food intake did not differ among treatment groups. In conclusion, amidated pectin, a novel sequestrant of sterols, demonstrated a similar effect on rat serum and hepatic cholesterol concentration to psyllium, which is a well-established hypocholesterolaemic agent.     

Misfolding of the amyloid beta-protein: a molecular dynamics study

Amyloid beta-proteins spontaneously aggregate and build plaques in the brains of Alzheimer's disease patients. The polypeptide has been the subject of extensive in vitro and computational research. Still, the pathway to aggregational forms and their exact conformations remain largely unclear. Here we present an extensive molecular dynamics approach simulating the protein in various temperatures, pH conditions, and with different charge states of the N- and C-termini, thus exploring the conformational space of the protein at large. Our results show that the protein is able to sample different conformations, many of which are rich in beta structure content, and all characterized by a rapid loss of helix 1 that converts into a pi-helix, while helix 2 samples random and beta-rich structures. Moreover, a hydrophobic cluster is observed involving Val18, Phe19, Ala21, and Gly25. The results are carefully compared with recent NMR and spectroscopic data, and are in global agreement with the experimental findings.     

The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica

The aminopeptidase from Aeromonas proteolytica (AAP) contains two zinc ions in the active site and catalyzes the degradation of peptides. Herein we report the crystal structures of AAP at 0.95-Å resolution at neutral pH and at 1.24-Å resolution at low pH. The combination of these structures allowed the precise modeling of atomic positions, the identification of the metal bridging oxygen species, and insight into the physical properties of the metal ions. On the basis of these structures, a new putative catalytic mechanism is proposed for AAP that is likely relevant to all binuclear metalloproteases.The coordinates for the 0.95-Å resolution structure and the 1.24-Å structure at pH 4.7 were deposited in the RCSB Protein Data Bank and have PDB ID numbers of 1RTQ and 2DEA, respectively.