A dilemma about whether thionitroxide radical (RSNHO) or S-nitrosothiol (RSNO) is observed in protein S-nitrosylation has arisen recently. To illustrate the effect of chemical environment on these structures, this paper presents quantum mechanical molecular dynamics of thionitroxide, and cis-and trans-S-nitrosothiols in the gas phase, methanol, and water. By using Car-Parrinello molecular dynamics (CPMD), we have observed that there is free rotation about the S-N bond at 300 K in thionitroxide, but no such rotation is observed for S-nitrosothiol. The C-S-N-O torsion angle distribution in thionitroxide is s-ignificantly dependent upon the surrounding environment, leading to either gauche-, cis-, or trans-conformation. In the case of S-nitrosothiol the C-S-N-O plane is twisted slightly by 5°-15° in the cis-isomer, while the periplanar structure is well-retained in the trans-isomer. The calculated results are in agreement with the X-ray crystallographic data of small molecular RSNO species. Interestingly, for both compounds, the CPMD simulations show that solvation can cause a decrease in the S-N bond length. Moreover, the oxygen atom of thionitroxide is found to be a good hydrogen-bond acceptor, forming an oxyanion-hole-like hydrogen bonding network.
Mobile genomic islands (GIs) can be excised from the chromosome,then form a circular intermediate and be reintegrated into the chromosome by the GI internal integrase.Some mobile GIs can also be transferred into a new receptor cell by transformation,conjugation,or transduction.The action sites of the integrase are usually flanked direct repeats (DRs) of the GIs.Accurate localization of the flanking sequences is a precondition for determining the mobility of the GI.Mobile GIs are generally associated with transfer RNAs (tRNAs).Based on the correlation between flanking sequences and tRNA sequences,the flanking sequences of 11 putative mobile GIs in Pseudomonas aeruginosa PAO1,P.aeruginosa PA14,P.fluorescens Pf-5 and P.fluorescens Pf0-1 were identified.Among the 11 GIs,Pf0-1GI-1 is responsible for benzoate degradation.PAO1GI-1,Pf5GI-2,Pf5GI-3,and Pf5GI-4 were confirmed experimentally to be excised from a chromosome to form a circular intermediate.The action sites of the integrases are these GIs direct repeats.Due to distinct DRs,cutting sites for the internal integrase of PAO1GI-1,Pf5GI-2,Pf5GI-3 and Pf5GI-4 were determined outside the T-loop of the tRNA Gly gene,outside the anticodon loop of the tRNA Ser gene and tRNALys gene,and at the asymmetric 3'-end of the tRNA Leu gene,respectively.PAO1GI-1 and other mobile GIs may be transferred into many different strains that belong to different phyla because of the clear flanking sequences.This study describes basic information about the action sites of the integrases,assesses the mobility of GIs,and can help design and transfer mobile GIs to candidate strains.
In this paper, we describe the synthesis of a novel copper ion hapten using the copper mercaptide of penicillenic acid (CMPA) derived from penicillin. Results from tests with immune rabbits indicate that: (i) A new antigen synthesized with CMPA has good stability and is safe for immunizing animals with no toxic phenomena being found in animal experiments; (ii) the immunogenic antigen (CMPA-BSA) can stimulate the immune system to produce specific antibodies with high titrations, up to 150000; and (iii) antibodies in antisera showed higher affinity to OVA-GSH-CuCl than OVA-GSH, which indicates that the antibodies have specific affinity towards copper ions. These results confirm that the novel hapten and relevant antigen for copper ion have been successfully synthesized, giving progress towards an immunoassay for copper ions in environmental and food samples.
tmRNA,a combination of a tRNA-related fragment and a small mRNA fragment,was confirmed as the integration site of genomic islands(GIs).Using sequence alignment and comparative genomics,68 GIs associated with tmRNA genes were identified among 13 genera of Enterobacteriaceae.Among them,53 GIs were found in Escherichia coli and Salmonella enterica.Among these 53 GIs,tandem GIs were verified in eight S.enterica and two E.coli chromosomes.The downstream regions of the tmRNA genes in most of the E.coli and S.enterica chromosomes include one GI or tandem GIs region and a remnant variable region distal to the tmRNA.The chronology of integration of tandem GIs into the genome indicated that GIs farther from the tmRNA were incorporated into the genome earlier than those nearer from the tmRNA.The integrases of the tmRNA gene-associated GIs can be further categorized into three subtypes:HP1 integrases,PhiCTX integrases,and P4 integrases,which are the most predominant.The GIs were first integrated into the chromosome by the P4 integrase,subsequently by the PhiCTX integrase,and finally by the HP1 integrase.Thus,the tmRNA gene is an important site for investigating the genetics and evolution of tandem GIs.
