Sequence and structural duality: designing peptides to adopt two stable conformations

To improve our understanding of conformational transitions in proteins, we are attempting the de novo design of peptides that switch structural state. Here, we describe coiled-coil peptides with sequence and structural duality; that is, features compatible with two different coiled-coil motifs superimposed within the same sequence. Specifically, we promoted a parallel leucine-zipper dimer under reducing conditions, and a monomeric helical hairpin in an intramolecularly disulfide bridged state. Using an iterative process, we engineered peptides that formed stable structures consistent with both targets under the different conditions. Finally, for one of the designs, we demonstrated a one-way switch from the helical hairpin to the coiled-coil dimer upon addition of disulfide-reducing agents.     

Effect of ionic strength and pH on hydraulic properties and structure of accumulating solid assemblages during microfiltration of montmorillonite suspensions

The structure and hydraulic behaviour of colloidal montmorillonite assemblages formed during constant-pressure microfiltration of feed suspensions under various pH and ionic strengths have been investigated with flux versus time data analysed using both conventional cake filtration theory and a more rigorous sorptivity-diffusivity approach. Size distribution and fractal dimension analyses revealed a shift in assemblage structure from porous to compact as a result of a step-increase in electrolyte concentrations. The hydraulic conductivity of the filter cakes was dramatically affected by suspension ionic strength with significantly higher hydraulic conductivity observed at the higher ionic strengths compared to that observed at lower ionic strengths. Results obtained using the sorptivity-diffusivity model were consistent with conventional cake filtration theory and provided useful insights into the bulk properties of the filter cakes. Cake moisture ratio profiles of the montmorillonite system showed that high suspension ionic strength resulted in denser or less voluminous filter cakes that retained less water than was the case at the low ionic strength. These results suggest that, under low ionic strength conditions, the clay particles associate in suspension in assemblages of high aspect ratio which subsequently form highly "cross-linked" voluminous honeycomb type structures of low permeability once deposited upon the membrane. However, under sufficiently high ionic strength conditions, the high aspect ratio montmorillonite assemblages form nematic structures on deposition on the membrane that are denser yet more permeable than the structures formed at lower salt concentration. The distinct change in properties of the deposited clay on increase in salt concentration may well be indicative of transition from a gel to a nematically ordered phase.     

Resilience in reaction-diffusion systems

Reaction-diffusion systems with zero-flux Neumann boundariesare widely used to model various kinds of interaction in, forexample, the scientific fields of ecology, biology, chemistry,medicine and industry. The physical systems within these fieldsare often known to be (conditionally or unconditionally) resilientwith respect to shocks, disturbances or catastrophies in theimmediate environment. In order to be good mathematical modelsof such situations the reaction-diffusion systems must havethe same resilient or asymptotic behaviour as that of the physicalsituation. Three fundamentally different kinds of reaction termsare usually distinguished according to the entry signs of thereaction Jacobian: mutualism, mixed (predator-prey) interactionand competition. The asymptotic stability (in the Poincarésense) of mutualistic systems has already been studied extensively,but the results cannot be generalized (globally) to the othertwo fundamental types, which are not order-preserving. A partial(local) generalization is, however given here for these twotypes, involving simple Jacobian inequalities and knowledge(often prompted by the underlying physical situation) of invariantsets in solution space. The return time of resilient systemsand the approach rate of asymptotically stable solutions arealso estimated.     

Metals and the integrity of a biological coating: the cuticle of mussel byssus

The cuticle of mussel byssal threads is a robust natural coating that combines high extensibility with high stiffness and hardness. In this study, fluorescence microscopy and elemental analysis were exploited to show that the 3,4-dihydroxyphenyl-l-alanine (dopa) residues of mussel foot protein-1 colocalize with Fe and Ca distributions in the cuticle of Mytilus galloprovincialis mussel byssal threads. Chelated removal of Fe and Ca from the cuticle of intact threads resulted in a 50% reduction in cuticle hardness, and thin sections subjected to the same treatment showed a disruption of cuticle integrity. Dopa-metal complexes may provide significant interactions for the integrity of composite cuticles deformed under tension.     

The photocurrent response of human cones is fast and monophasic

Background  

The precise form of the light response of human cone photoreceptors in vivo has not been established with certainty. To investigate the response shape we compare the predictions of a recent model of transduction in primate cone photoreceptors with measurements extracted from human cones using the paired-flash electroretinogram method. As a check, we also compare the predictions with previous single-cell measurements of ground squirrel cone responses.     

Efficient Hydrolysis of RNA by a PNA - Diethylenetriamine Adduct

The introduction of a urea bond linking a protected diethylenetriamine (DETA) unit and the terminal amino group of a resin-bound peptide nucleic acid (PNA) decamer gave access to a PNA - DETA adduct (shown here), which hydrolyzed the target 25-mer RNA rapidly and sequence specifically.     

Classical model studies of dissociation following linear to bent triatomic photoexcitation

Using classical trajectory calculations, we show that photodissociation involving a transition from a linear ground state to a bent excited state can account for the gross structure in the rotational distributions of the CN fragment from ClCN and ICN. If one excited state dominates in the ICN spectrum, its potential energy surface must be characterized by a bending angle near but not equal to the linear configuration.