Strain energies due to nonplanar distortion of fullerenes and their dependence on structural motifs

Accurate strain energies due to nonplanar distortion of 114 isolated pentagon rule (IPR) fullerenes with 60-102 carbon atoms have been calculated based on B3LYP/6-31G(d) optimized structures. The calculated values of strain energy due to nonplanar distortion (E-np) are reproduced by three simple schemes based upon counts of 8, 16, and 30 distinct structural motifs composed of hexagons and pentagons. Using C-180 (I-h) and CN (I-h) (N is very large) as test molecules, the intrinsic limitations of the motif model based on six-membered rings (6-MRs) as the central unit have been discussed. On the basis of the relationship between the contributions of motifs to E-np and the number of five-membered rings (5-MRs) in motifs, we found that IPR fullerenes with dispersed 5-MRs present smaller nonplanar distortions.

Deduction of functional peptide motifs in scorpion toxins

Scorpion toxins are important physiological probes for characterizing ion channels. Molecular databases have limited functional annotation of scorpion toxins. Their function can be inferred by searching for conserved motifs in sequence signature databases that are derived statistically but are not necessarily biologically relevant. Mutation studies provide biological information on residues and positions important for structure-function relationship but are not normally used for extraction of binding motifs. 3D structure analyses also aid in the extraction of peptide motifs in which non-contiguous residues are clustered spatially. Here we present new, functionally relevant peptide motifs for ion channels, derived from the analyses of scorpion toxin native and mutant peptides. Copyright (c) 2006 European Peptide Society and John Wiley & Sons, Ltd.

DNA Motifs Suppressing TLR9 Responses

Immune cells respond to bacterial DNA containing unmethylated CpG motifs via Toll-like receptor 9 (TLR9). Given the apparent role of TLR9 in development of systemic lupus erythernatosus (SLE), there is interest in the development of TLR9 inhibitors. TLR9-mediated responses are reported to be inhibited by a confusing variety of different DNA sequences and structures. To aid characterization, we have provisionally categorized TLR9-inhibitory oligodeoxynucleoti des (ODN) into 4 classes, on the basis of sequence and probable mode of action. Class I are short G-rich ODN, which show sequence-specific inhibition of all TLR9 responses, and may be direct competitive inhibitors for DNA binding to TLR9. Class II are telomeric repeat motifs that inhibit STAT signaling, and thus are not specific to TLR9 responses. Because Class II ODN are generally made as 24-base phosphorothioate-modified ODN (PS-ODN), they also fall into Class IV, defined as long PS-ODN, which inhibit TLR9 responses in a sequence-nonspecific manner. Class III includes oligo (dG) that forms a 4-stranded structure and inhibits DNA uptake. The Class I G-rich motifs show the most promise as selective and potent TLR9 inhibitors for therapeutic applications.

Evolving discriminative motifs for recognizing proteins imported to the peroxisome via the PTS2 pathway

Peroxisomes are small subcellular compartments that utilize proteins manufactured in the cytoplasm. Proteins use one of two peroxisomal import pathways. This paper presents a simple evolutionary search for a motif that describes the signal used by one of the two pathways: PTS2. The evolved motif has a discriminative accuracy exceeding previously manually curated motifs and can be used to screen genomic data for putative peroxisomal proteins.

Diverse functional motifs within the three intracellular loops of the CGRP1 receptor

The CGRP1 receptor exists as a heterodimeric complex between a single-pass transmembrane accessory protein (RAMP1) and a family B G-protein-coupled receptor (GPCR) called the calcitonin receptor-like receptor (CLR). This study investigated the structural motifs found in the intracellular loops (ICLs) of this receptor. Molecular modeling was used to predict active and inactive conformations of each ICL. Conserved residues were altered to alanine by site-directed mutagenesis. cAMP accumulation, cell-surface expression, agonist affinity, and CGRP-stimulated receptor internalization were characterized. Within ICL1, L147 and particularly R151 were important for coupling to Gs. R151 may interact directly with the G-protein, accessing it following conformational changes involving ICL2 and ICL3. At the proximal end of ICL3, I290 and L294, probably lying on the same face of an α helix, formed a G-protein coupling motif. The largest effects on coupling were observed with I290A; additionally, it reduced CGRP affinity and impaired internalization. 1290 may interact with TM6 to stabilize the conformation of ICL3, but it could also interact directly with Gs. R314, at the distal end of ICL3, impaired G-protein coupling and to a lesser extent reduced CGRP affinity; it may stabilize the TM6-ICL3 junction by interacting with the polar headgroups of membrane phospholipids. Y215 and L214 in ICL2 are required for cell-surface expression; they form a microdomain with H216 which has the same function. This study reveals similarities between the activation of CLR and other GPCRs in the role of TM6 and ICL3 but shows that other conserved motifs differ in their function. © 2006 American Chemical Society.

The pragmatic motifs of the Jespersen cycle: default, activation, and the history of negation in French

The purpose of this article is to delimit the role of pragmatic specialization in the evolution of negation in French. The change in the marking of sentential negation is believed to proceed in characterized stages that would together constitute the Jespersen cycle. As a marker becomes the default expression of negation, the other markers do not necessarily fade away, and are maintained with specialized roles that include pragmatic functions. One such pragmatic function is that of activation (Dryer 1996), by which a proposition is presented as accessible to the hearer. Activation is shown to motivate the use of preverbal non that competes with 'ne' for several centuries. The claims that the emergence of postverbal pas in early French and the loss of 'ne' in contemporary spoken French are associated with activation are considered on the basis of novel data. It is concluded that pragmatic functions contribute to language change by providing marked options that may be conferred the default status in a grammatical paradigm.

The development of heat recovery equipment from conception to commercialisation

A comprehensive survey of industrial sites and heat recovery products revealed gaps between equipment that was required and that which was available. Two heat recovery products were developed to fill those gaps: a gas-to-gas modular heat recovery unit; a gas-to-liquid exhaust gas heat exchanger. The former provided an entire heat recovery system in one unit. It was specifically designed to overcome the problems associated with existing component system of large design commitment, extensive installation and incompatibility between parts. The unit was intended to recover heat from multiple waste gas sources and, in particular, from baking ovens. A survey of the baking industry defined typical waste gas temperatures and flow rates, around which the unit was designed. The second unit was designed to recover heat from the exhaust gases of small diesel engines. The developed unit differed from existing designs by having a negligible effect on engine performance. In marketing terms these products are conceptual opposites. The first, a 'product-push' product generated from site and product surveys, required marketing following design. The second, a 'market-pull' product, resulted from a specific user need; this had a captive market and did not require marketing. Here marketing was replaced by commercial aspects including the protection of ideas, contracting, tendering and insurance requirements. These two product development routes are compared and contrasted. As a general conclusion this work suggests that it can be beneficial for small companies (as was the sponsor of this project) to undertake projects of the market-pull type. Generally they have a higher probability of success and are less capital intensive than their product-push counterparts. Development revealed shortcomings in three other fields: British Standards governing heat exchangers; financial assessment of energy saving schemes; degree day procedure of calculating energy savings. Methods are proposed to overcome these shortcomings.

Pre-conception care : current practice and methods of provision

This thesis examines the present provisions for pre-conception care and the views of the providers of services. Pre-conception care is seen by some clinicians and health educators as a means of making any necessary changes in life style, corrections to imbalances in the nutritional status of the prospective mother (and father) and the assessment of any medical problems, thus maximizing the likelihood of the normal development of the baby. Pre-conception care may be described as a service to bridge the gap between the family planning clinic and the first ante-natal booking appointment. There were three separate foci for the empirical research - the Foresight organisation (a charity which has pioneered pre-conception care in Britain); the pre-conception care clinic at the West London Hospital, Hammersmith; and the West Midlands Regional Health Authority. The six main sources of data were: twenty five clinicians operating Foresight pre-conception clinics, couples attending pre-conception clinics, committee members of the Foresight organisation, staff of the West London Hospital pre-conception clinic, Hammersmith, District Health Education Officers working in the West Midlands Regional Health Authority and the members of the Ante-Natal Care Action Group, a sub-group of the Regional Health Advisory Group on Health Promotion and Preventive Medicine. A range of research methods were adopted. These were as follows: questionnaires and report forms used in co-operation with the Foresight clinicians, interviews, participant observation discussions and informal meetings and, finally, literature and official documentation. The research findings illustrated that pre-conception care services provided at the predominantly private Foresight clinics were of a rather `ad hoc' nature. The type of provision varied considerably and clearly reflected the views held by its providers. The protocol which had been developed to assist in the standardization of results was not followed by the clinicians. The pre-conception service provided at the West London Hospital shared some similarities in its approach with the Foresight provision; a major difference was that it did not advocate the use of routine hair trace metal analysis. Interviews with District Health Education Officers and with members of the Ante Natal Care Action Group revealed a tentative and cautious approach to pre-conception care generally and to the Foresight approach in particular. The thesis concludes with a consideration of the future of pre-conception care and the prospects for the establishment of a comprehensive pre-conception care service.