How DNA Polymerase X Preferentially Accommodates Incoming dATP Opposite 8-Oxoguanine on the Template

The modified base 8-oxo-7,8-dihydro-2′-deoxyguanosine (oxoG) is a common DNA adduct produced by the oxidation of DNA by reactive oxygen species. Kinetic data reveal that DNA polymerase X (pol X) from the African swine fever virus incorporates adenine (dATP) opposite to oxoG with higher efficiency than the non-damaged G:C basepair. To help interpret the kinetic data, we perform molecular dynamics simulations of pol X/DNA complexes, in which the template base opposite to the incoming dNTP (dCTP, dATP, dGTP) is oxoG. Our results suggest that pol X accommodates the oxoG_syn:A mispair by sampling closed active conformations that mirror those observed in traditional Watson-Crick complexes. Moreover, for both the oxoG_syn:A and oxoG:C ternary complexes, conformational sampling of the polymerase follows previously described large subdomain movements, local residue motions, and active site reorganization. Interestingly, the oxoG_syn:A system exhibits superior active site geometry in comparison to the oxoG:C system. Simulations for the other mismatch basepair complexes reveal large protein subdomain movement for all systems, except for oxoG:G, which samples conformations close to the open state. In addition, active site geometry and basepairing of the template base with the incoming nucleotide, reveal distortions and misalignments that range from moderate (i.e., oxoG:A_syn) to extreme (i.e., oxoG_anti/syn:G). These results agree with the available kinetic data for pol X and provide structural insights regarding the mechanism by which this polymerase can accommodate incoming nucleotides opposite oxoG. Our simulations also support the notion that α-helix E is involved both in DNA binding and active site stabilization. Our proposed mechanism by which pol X can preferentially accommodate dATP opposite template oxoG further underscores the role that enzyme dynamics and conformational sampling operate in polymerase fidelity and function.     

The encounter of distinct Morimus asper (Coleoptera: Cerambycidae) phylogeographic lineages on the Balkan Peninsula: conservation implications

Journal of Insect Conservation - The first step in monitoring and management of any taxa includes resolving taxonomic ambiguities which complicate the identification of its management units. One of...     

Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA

DNA intercalators bind nucleic acids by stacking between adjacent basepairs. This causes a considerable elongation of the DNA backbone as well as untwisting of the double helix. In the past few years, single-molecule mechanical experiments have become a common tool to characterize these deformations and to quantify important parameters of the intercalation process. Parameter extraction typically relies on the neighbor-exclusion model, in which a bound intercalator prevents intercalation into adjacent sites. Here, we challenge the neighbor-exclusion model by carefully quantifying and modeling the force-extension and twisting behavior of single ethidium-complexed DNA molecules. We show that only an anticooperative ethidium binding that allows for a disfavored but nonetheless possible intercalation into nearest-neighbor sites can consistently describe the mechanical behavior of intercalator-bound DNA. At high ethidium concentrations and elevated mechanical stress, this causes an almost complete occupation of nearest-neighbor sites and almost a doubling of the DNA contour length. We furthermore show that intercalation into nearest-neighbor sites needs to be considered when estimating intercalator parameters from zero-stress elongation and twisting data. We think that the proposed anticooperative binding mechanism may also be applicable to other intercalating molecules.     

Neuronal and muscular alterations caused by two wheat endosperm proteins,puroindoline-a and alpha1-purothionin,are due to ion pore formation

Using the patch-clamp technique it was found that the toxicity of the two wheat endosperm proteins puroindoline-a and alpha1-purothionin probably results from the dissipation of ion concentration gradients essential for the maintenance of cellular homeostasis.Abbreviations PIN-a puroindoline-a - PTH alpha1-purothionin Presented at the Biophysical Society Meeting on Ion Channels—from structure to disease held in May 2003, Rennes, France     

Echocardiographic measurement of cardiac output in rats

The systematic evaluation of different transthoracic echocardiographic (TTE) methods to determine cardiac output (CO) and the effect of changes in intravascular volume on echocardiographically determined indexes of cardiovascular structure in the rat has not been documented. With the use of 11 Wistar rats, simultaneous echocardiographic and thermodilution measurements of CO were compared at baseline and after blood withdrawal or transfusion at 43 different levels of intravascular volume and using 10 different echocardiographic approaches. The best correlation (r = 0.93; P < 0.0001), least bias (-3 ml/min), and best precision (16 ml/min) between thermodilution and echocardiographic methods were obtained at the level of aortic annulus using pulsed Doppler. In conclusion, CO could be accurately assessed in rats using TTE and pulsed Doppler at the level of the aortic annulus. This annulus was demonstrated to remain stable, but pulmonary annulus, thoracic aorta, mitral valve, and left ventricular diameters were found to be more modifiable during volumic changes.     

The control of the proventriculus in the honeybee (Apis mellifera carnica L.) II. Feedback mechanisms

The mechanisms underlying the control of solution transport rates through the proventriculus in foraging honeybees were investigated in individuals trained to collect defined amounts of sugar solutions. Following feeding, bees were injected either with metabolisable (glucose, fructose, trehalose), or non-metabolisable (sorbose) sugars, in order to distinguish between haemolymph osmolarity and haemolymph sugar levels as factors controlling the solution transport rates through the proventriculus. After a fixed period, workers were dissected in order to measure crop content and haemolymph sugar titers. Between feeding and dissection, the metabolic rate of every investigated forager was measured using open-flow respirometry. Bees injected with metabolisable sugars 15 min after feeding were observed to reduce their solution transport rates through the proventriculus, but injection of non-metabolisable sugars had no influence on them. This suggests that the solution transport rate through the proventriculus is controlled by the concentration of metabolisable compounds in the haemolymph, and not by the haemolymph osmolarity. A period of 10 min after injection of metabolisable sugars was enough to observe reduced solution transport rates. However, if bees were injected only 5 min after feeding, no reduced solution transport rates were observed 10 min after injection.     

The influence of amino acid side chains on water binding to the copper(II) in bis(N,N-dimethyl-L-alpha-isoleucinato)-copper(II): an EPR and molecular mechanics study

Simulations were done of the electron paramagnetic resonance (EPR) spectra for bis(N,N-dimethyl-L-alpha-isoleucinato)copper(II) dissolved in deuterated methanol as a function of temperature. They indicated different behaviour of the complex below and above 300 degrees K. The effect was examined by the conformational analysis of the copper(II) complex with a new molecular mechanics force field.     

<Emphasis Type="SmallCaps">l</Emphasis>-Homoarginine suppresses exocrine pancreas in rats

Summary.  Previously, we found that guanidinated casein, a l-homoarginine-containing protein, was a more potent stimulator of pancreatic enzyme secretion than intact casein in rats. In this study, we examined secretory response and adaptation of the exocrine pancreas to the administration of free l-homoarginine in normal and bile-pancreatic juice (BPJ)-diverted rats. An intraperitoneal injection of l-homoarginine (10 mg/rats) produced immediate and transient reduction in pancreatic secretion in BPJ-diverted rats, but not in normal rats. The BPJ-diverted rats were fed with either a 25% casein, 45% casein, or 45% casein diet supplemented with l-homoarginine (19 g/kg diet) for 4 days. Feeding of a diet containing l-homoarginine inhibited the pancreatic adaptation induced by the high-protein diet. These results indicate that l-homoarginine has an inhibitory effect on the secretion and production of exocrine pancreatic enzyme in BPJ-diverted rats, and l-homoarginine may have an antagonistic effect on CCK receptors. Received July 1, 2002 Accepted August 28, 2002 Published online December 20, 2002 Authors' address: Dr. Hiroshi Hara, Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan E-mail: hara@chem.agr.hokudai.ac.jp     

Oxidative stress tolerance and longevity in Arabidopsis: the late‐flowering mutant gigantea is tolerant to paraquat

Recent genetic analyses of longevity in animals have revealed that long-lived strains are more tolerant to environmental stresses. To investigate whether extended longevity in Arabidopsis also correlates with an increase in stress tolerance, the response was tested of 11 late-flowering mutants to the superoxide radical-generating herbicide paraquat. A tight correlation between flowering time and paraquat tolerance was found when plants were exposed to low doses of herbicide. Furthermore, the mutant gigantea (gi-3) with the longest delay in flowering time had a high tolerance level to paraquat-induced oxidative stress. All the tested gi alleles had an increased tolerance to paraquat toxicity compared to wild-type, although the actual levels of tolerance differed. In addition, the gi-3 mutant was more tolerant to hydrogen peroxide. These results suggest that the link between longevity and oxidative stress resistance in plants is similar to that found in animals, implying that this phenomenon may be general for all aerobic organisms.