Density functional study of closed-shell attraction on X(ML)<Subscript>3</Subscript><Superscript>+</Superscript>(<Emphasis Type="Italic">X</Emphasis> = O,S, Se; <Emphasis Type="Italic">M</Emphasis> = Au,Ag, Cu) systems

With the help of quantum mechanical calculations, we have examined the series of central system X(ML)₃ ⁺(X = O, S, Se; M = Au, Ag, Cu). Using a scalar–relativistic density functional approach, we studied the geometry structures, Mulliken populations and charges of the systems. Structure parameters of the experimental systems are reproduced well with Xα method. The metallophilic interaction energy is analyzed and decomposed. For the systems with different central atoms and different metal atoms, the nature of the metallophilic attraction interaction is analyzed.     

Possible dynamic anchor points in a benzoxazinone derivative–human oxytocin receptor system — a molecular docking and dynamics calculation

In this study, we performed a molecular docking and dynamics simulation for a benzoxazinone–human oxytocin receptor system to determine the possible hydrophobic and electrostatic interaction points in the dynamic complex. After the homology modeling, the ligand was docked into the putative active using AutoDock 3.05. After the application of energetic and structural filters, the complexes obtained were further refined with a simulated annealing protocol (AMBER8) to remove steric clashes. Three complexes were selected for subjection to the molecular dynamics simulation (5 ns), and the results on the occurrence of average anchor points showed a stable complex between the benzoxazinone derivative and the receptor. The complex could be used as a good starting point for further analysis with site-directed mutagenesis, or further computational research. Figure The location of the ligands (complex B – blue; complex E – red; and complex F – green) in the transmembrane regions (TM1 – red; TM2 – blue; TM3 – yellow; TM4 – purple; TM5 – orange; TM6 – cyan; TM7 – pink) of the hOTR. For clarity, the EC and IC loops are not shown Electronic Supplementary Material Supplementary material is available at     

Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model

Understanding the mechanism of the protein stability change is one of the most challenging tasks. Recently, the prediction of protein stability change affected by single point mutations has become an interesting topic in molecular biology. However, it is desirable to further acquire knowledge from large databases to provide new insights into the nature of them. This paper presents an interpretable prediction tree method (named iPTREE-2) that can accurately predict changes of protein stability upon mutations from sequence based information and analyze sequence characteristics from the viewpoint of composition and order. Therefore, iPTREE-2 based on a regression tree algorithm exhibits the ability of finding important factors and developing rules for the purpose of data mining. On a dataset of 1859 different single point mutations from thermodynamic database, ProTherm, iPTREE-2 yields a correlation coefficient of 0.70 between predicted and experimental values. In the task of data mining, detailed analysis of sequences reveals the possibility of the compositional specificity of residues in different ranges of stability change and implies the existence of certain patterns. As building rules, we found that the mutation residues in wild type and in mutant protein play an important role. The present study demonstrates that iPTREE-2 can serve the purpose of predicting protein stability change, especially when one requires more understandable knowledge.     

Long-time molecular dynamics simulations of botulinum biotoxin type-A at different pH values and temperatures

Botulinum neurotoxins type A (BoNT/A) are highly potent toxins, but are also useful in the treatment of illnesses. We studied the properties of BoNT/A at various temperatures and pH values in order to understand its toxicity and structure variations. The pH values of the environment of BoNT/A are obtained by changing the protonation states of certain titratable residue groups. Our results show that certain parts of the protein are active at acidic pH environments or at high temperatures. The protein is more stable in neutral environments at normal human body temperature, whereas, at high temperature, the protein is more stable in acidic environments. Also, the three domains of the protein tend to have relative motion rather than within individual domains.     

New data from Oman indicate benthic high biomass productivity coupled with low taxonomic diversity in the aftermath of the Permian–Triassic Boundary mass extinction

A new Early Triassic marine fauna is described from an exotic block (olistolith) from the Ad Daffah conglomerate in eastern Oman (Batain), which provides new insights into the ecology and diversity during the early aftermath of the Permian–Triassic Boundary mass extinction. Based on conodont quantitative biochronology, we assign a middle Griesbachian age to the upper part of this boulder. It was derived from an offshore seamount and yielded both nektonic and benthic faunas, including conodonts, ammonoids, gastropods and crinoid ossicles in mass abundance. This demonstrates that despite the stratigraphically near extinction at the Permian–Triassic Boundary, Crinoidea produced enough biomass to form crinoidal limestone as early as middle Griesbachian time. Baudicrinus, previously placed in Dadocrinidae, is now placed in Holocrinidae; therefore, Dadocrinidae are absent in the Early Triassic, and Holocrinidae remains the most basal crown‐group articulates, originating during the middle Griesbachian in the Tethyan Realm. Abundant gastropods assigned to Naticopsis reached a shell size larger than 20 mm and provide another example against any generalized Lilliput effect during the Griesbachian. Whereas the benthic biomass was as high as to allow the resumption of small carbonate factories, the taxonomic diversity of the benthos remained low compared to post‐Early Triassic times. This slow benthic taxonomic recovery is here attributed to low competition within impoverished post‐extinction faunas.     

The oncogenic T cell LIM-protein Lmo2 forms part of a DNA-binding complex specifically in immature T cells.

The LIM-only protein LMO2 is expressed aberrantly in acute T-cell leukaemias as a result of the chromosomal translocations t(11;14) (p13;q11) or t(7;11) (q35;p13). In a transgenic model of tumorigenesis by Lmo2, T-cell acute leukaemias arise after an asymptomatic phase in which an accumulation of immature CD4(-) CD8(-) double negative thymocytes occurs. Possible molecular mechanisms underlying these effects have been investigated in T cells from Lmo2 transgenic mice. Isolation of DNA-binding sites by CASTing and band shift assays demonstrates the presence of an oligomeric complex involving Lmo2 which can bind to a bipartite DNA motif comprising two E-box sequences approximately 10 bp apart, which is distinct from that found in erythroid cells. This complex occurs in T-cell tumours and it is restricted to the immature CD4(- )CD8(-) thymocyte subset in asymptomatic transgenic mice. Thus, ectopic expression of Lmo2 by transgenesis, or by chromosomal translocations in humans, may result in the aberrant protein interactions causing abnormal regulation of gene expression, resulting in a blockage of T-cell differentiation and providing precursor cells for overt tumour formation.     

Expression of <Emphasis Type="Italic">Ruminococcus albus</Emphasis> Xylanase Gene (<Emphasis Type="Italic">xyn</Emphasis>A) in <Emphasis Type="Italic">Streptococcus bovis</Emphasis> 12-U-1

The objective of this study was to ligate the xylanase gene A (xynA) isolated from Ruminococcus albus 7 into the promoter and signal-peptide region of the lichenase [β-(1,3-1,4)-glucanase] gene of Streptococcus bovis JB1. This fusion gene was inserted into the pSBE11 vector, and the resulting recombinant, plasmid pXA, was used to transform S. bovis 12-U-1 cells. The transformant, S. bovis 12UXA, secreted the xylanase, which was stable against freeze-thaw treatment and long-time incubation at 37°C. The introduction of pXA and production of xylanase did not affect cell growth, and the xylanase produced degraded xylan from oat-spelt and birchwood. Received: 24 June 2002 / Accepted: 7 October 2002     

Toxicity of <Emphasis Type="Italic">Bacillus sphaericus</Emphasis> LP1-G Against Susceptible and Resistant <Emphasis Type="Italic">Culex quinquefasciatus</Emphasis> and the Cloning of the Mosquitocidal Toxin Gene

Bacillus sphaericus LP1-G, belonging to flagellar serotype H3, has been found to have moderate toxicity against two resistant Culex quinquefasciatus colonies (RLCq1 and RLCq2) and the susceptible contrast (SLCq). With an aim of screening mosquitocidal acting factor, a partial genome library was prepared from a partial HindIII digest of the total DNA from Bacillus sphaericus LP1-G. Two thousand twenty Escherichia coli clones were screened for toxicity against susceptible SLCq, and a toxic clone, designated E-UL68, was chosen for further study. The recombinant E-UL68 performed toxicity against both susceptible and two resistant colonies, having the same level of toxicity as that of wide-type strain LP1-G. Sequence analysis revealed that the inserted fragment was composed of 3876 nucleotides and contained a complete gene, whose sequence was identical to that of the mtx gene from B. sphaericus SSII-1. Because the binary toxin produced during sporulation of strain LP1-G has no activity against the target mosquitoes, this indicates that the Mtx toxin or other active factors might perhaps be responsible for the toxicity of LP1-G against different colonies of mosquito larvae.Received: 7 October 2002 / Accepted: 4 November 2002     

Mycorrhizal perennials of the "matorral xerófilo" and the "selva baja caducifolia" communities in the semiarid Tehuacán-Cuicatlán Valley,Mexico

We investigated the mycorrhizal status of perennial xeric plant species occurring in the "matorral xerófilo" (arid tropical scrub) and the ecotone of the "selva baja caducifolia" (tropical deciduous forest) communities in the semiarid valley of Tehuacán-Cuicatlán, south-central Mexico. The perennial species examined are dominant/codominant elements within the "matorral xerófilo" and the "selva baja caducifolia", both endangered communities in the Biosphere Reserve Tehuacán-Cuicatlán Valley. Of the 50 sampled species, 45 were mycorrhizal. To our knowledge, we report arbuscular mycorrhizae (AM) for the first time in 37 species, of which 21 are endemic to Mexico and nine are endemic to the Valley. We also report AM for the first time in three genera, Buddleja, Hechtia and Zornia, and in one plant family, Buddlejaceae. Beaucarnea gracilis, a threatened species, and Mimosa purpusii, a potentially rare species, are both mycorrhizal. This is the first study of the mycorrhizal status of plant species within the Valley.