Modeling large regions in proteins: applications to loops, termini, and folding

Template-based methods for predicting protein structure provide models for a significant portion of the protein but often contain insertions or chain ends (InsEnds) of indeterminate conformation. The local structure prediction "problem" entails modeling the InsEnds onto the rest of the protein. A well-known limit involves predicting loops of ≤12 residues in crystal structures. However, InsEnds may contain as many as ~50 amino acids, and the template-based model of the protein itself may be imperfect. To address these challenges, we present a free modeling method for predicting the local structure of loops and large InsEnds in both crystal structures and template-based models. The approach uses single amino acid torsional angle "pivot" moves of the protein backbone with a C(β) level representation. Nevertheless, our accuracy for loops is comparable to existing methods. We also apply a more stringent test, the blind structure prediction and refinement categories of the CASP9 tournament, where we improve the quality of several homology based models by modeling InsEnds as long as 45 amino acids, sizes generally inaccessible to existing loop prediction methods. Our approach ranks as one of the best in the CASP9 refinement category that involves improving template-based models so that they can function as molecular replacement models to solve the phase problem for crystallographic structure determination.     

Chestnut pellicle for the recovery of gold

Recovery of Au(III) from hydrochloric acid medium by using crosslinked chestnut pellicle (CCP) gel was studied. Strong selectivity was observed for Au(III) showing negligible affinity for other precious metals and some base metal ions tested. The adsorption isotherm study exhibited the maximum loading capacity of the gel as high as 10.6 mol or about 2.1 kg gold per kg dry weight of gel. The reduction of Au(III) ion to elemental form during adsorption process is expected to be the reason of high selectivity and high capacity for Au(III). Kinetic studies at various temperatures confirm an endothermic adsorption process following the pseudo-first order rate law.     

A 2H solid-state NMR spectroscopic investigation of biomimetic bicelles containing cholesterol and polyunsaturated phosphatidylcholine

Deuterium solid-state NMR spectroscopy was used to qualitatively study the effects of both 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLiPC) and cholesterol on magnetically aligned phospholipid bilayers (bicelles) as a function of temperature utilizing the chain-perdeuterated probe 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC-d54) in DMPC/dihexanoylPC (DHPC) phospholipid bilayers. The results demonstrate that polyunsaturated PC and cholesterol were successfully incorporated into DMPC/DHPC phospholipid bilayers, leading to a bicelle that will be useful for investigations of eukaryotic membrane protein-lipid interactions. The data indicate that polyunsaturated PC increases membrane fluidity and decreases the minimum magnetic alignment temperature for DMPC/DHPC bicelles. Conversely, the introduction of cholesterol into aligned DMPC/DHPC bilayers decreases fluidity in the membrane and increases the minimum temperature necessary to magnetically align the phospholipid bilayers. Finally, the addition of Tm3+ to magnetically aligned DMPC/DMPC-d54/PLiPC/DHPC bilayers doubles the quadrupolar splittings, indicating that this unique bicelle system can be aligned with the bilayer normal parallel to the static magnetic field.     

In vitro anti-herpetic activity of sulfated polysaccharide fractions from Caulerpa racemosa

A sulfated polysaccharide fraction was isolated from the hot water extract of the green alga Caulerpa racemosa and designated HWE. This polymer, which contained galactose, glucose, arabinose and xylose as the major component sugars, had [alpha](D)(30) + 46.2 degrees in water and contained 9% sulfate hemiester groups. Sugar linkage analysis indicates that HWE was branched and mainly contained 1,3- and 1,3,6-linked galactose, 1,3,4-linked arabinose, 1,4-linked glucose and terminal- and 1,4-linked xylose residues. Sulfation was deduced from infrared spectroscopy and methylation analysis to occur on O-6 of galactose and O-3 of arabinose. The native polysaccharide could be fractionated by size exclusion chromatography into two overlapping fractions and the major fraction has a hydrodynamic volume similar to that of 70 kDa dextran. HWE was a selective inhibitor of reference strains and TK(-) acyclovir-resistant strains of herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) in Vero cells, with antiviral effective concentration 50% (EC(50)) values in the range of 2.2-4.2 microg/ml and lacking cytotoxic effects. Furthermore, HWE did not exhibit anticoagulant properties at concentrations near the EC(50).     

Theoretical simulation of the calcium action potential in squid giant synapse: Repetitive stimulation

A biophysical model of the experimentally observed calcium action potential (CAP) in squid giant synapse is proposed. Whereas the inclusion of the inward calcium current in the Hodgkin-Huxley model can generate the rising phase of CAP, to account for the observed termination of the action potential, a repolarizing process needs to be introduced. Adding a term representing Ca-activated K current, the observed features of CAP can be reproduced. However, one feature of CAP, namely the gradual shortening of the plateau duration on repetitive stimulation, cannot be simulated by this model. In this paper, it is proved that both the termination of the action potential and the gradual shortening of the plateau cannot be accounted for by inclusion of a single repolarizing process. One more repolarizing process, namely a slow voltage-dependent Ca-inactivation, is therefore proposed to account for all the observed features of CAP.     

Dynamic behaviors of microtubules in cytosol

Highly anisotropic microtubules (MTs) immersed in cytosol are a central part of the cytoskeleton in eukaryotic cells. The dynamic behaviors of an MT–cytosol system are of major interest in biomechanics community. Such a solid–fluid system is characterized by a Reynolds number of the order 10^?3 and a slip ionic layer formed at the MT–cytosol interface. In view of these unique features, an orthotropic shell-Stokes flow model with a slip boundary condition has been developed to explore the distinctive dynamic behaviors of MTs in cytosol. Three types of motions have been identified, i.e., (a) undamped and damped torsional vibration, (b) damped longitudinal vibration, and (c) overdamped bending and radial motions. The exponentially decaying bending motion given by the present model is found to be in qualitative agreement with the existing experimental observation [Felgner et al., 1996. Flexural rigidity of microtubules measured with the use of optical tweezers, Journal of Cell Science 109, 509–516 ].     

Population and conservation of Sapria himalayana Griffith. in Namdapha national park, Arunachal Pradesh, India

Sapria himalayana Griffith. (Rafflesiaceae), a root parasitic plant, is one of the lesser known and poorly understood taxons, which is at the brink of extinction due to incessant human interventions in the natural forest environment. This note deals with the population of Sapria in the buffer zone of Namdapha national park in Arunachal Pradesh, northeastern India. The host plant was a woody climber, Tetrastigma sp. Two patches of Sapria were observed at Hornbill (primary and relatively undisturbed forest) and four patches in Zero camp (disturbed secondary forest). Presently the species is prone to extirpation due to habitat loss through encroachments and massive NTFP extraction in the park area. All attempts to reintroduce or translocate the species will be in vain due to its phytogeographical limitations and host-specificity. A viable approach could be in situ conservation by effective protected area management.