The effects of difficulty and gain versus loss on vocal physiology and acoustics

To examine the basis of emotional changes to the voice, physiological and electroglottal measures were combined with acoustic speech analysis of 30 men performing a computer task in which they lost or gained points under two levels of difficulty. Predictions of the main effects of difficulty and reward on the voice were not borne out by the data. Instead, vocal changes depended largely on interactions between gain versus loss and difficulty. The rate at which the vocal folds open and close (fundamental frequency; f0) was higher for loss than for gain when difficulty was high, but not when difficulty was low. Electroglottal measures revealed that f0 changes corresponded to shorter glottal open times for the loss conditions. Longer closed and shorter open phases were consistent with raised laryngeal tension in difficult loss conditions. Similarly, skin conductance indicated higher sympathetic arousal in loss than gain conditions, particularly when difficulty was high. The results provide evidence of the physiological basis of affective vocal responses, confirming the utility of measuring physiology and voice in the study of emotion.

Prediction of novel and analogous folds using fragment assembly and fold recognition

A number of new and newly improved methods for predicting protein structure developed by the Jones–University College London group were used to make predictions for the CASP6 experiment. Structures were predicted with a combination of fold recognition methods (mGenTHREADER, nFOLD, and THREADER) and a substantially enhanced version of FRAGFOLD, our fragment assembly method. Attempts at automatic domain parsing were made using DomPred and DomSSEA, which are based on a secondary structure parsing algorithm and additionally for DomPred, a simple local sequence alignment scoring function. Disorder prediction was carried out using a new SVM-based version of DISOPRED. Attempts were also made at domain docking and “microdomain” folding in order to build complete chain models for some targets.

Assembling novel protein folds from super-secondary structural fragments

The results of applying a fragment-based protein tertiary structure prediction method to the prediction of 14 CASP5 target domains are described. The method is based on the assembly of supersecondary structural fragments taken from highly resolved protein structures using a simulated annealing algorithm. A number of good predictions for proteins with novel folds were produced, although not always as the first model. For two fold recognition targets, FRAGFOLD produced the most accurate model in both cases, despite the fact that the predictions were not based on a template structure. Although clear progress has been made in improving FRAGFOLD since CASP4, the ranking of final models still seems to be the main problem that needs to be addressed before the next CASP experiment

Did they talk their way out of Africa?

Corballis suggests that fully vocal communication was invented by modern humans between 170,000 and 50,000 years ago. Because this new form of communication did not require hand gestures, he wondered whether this may have facilitated the development of lithic manufacture. I cast doubt on this interesting notion but offer an enhanced version that may have more potential.

Aligning sequences to structures

Most newly sequenced proteins are likely to adopt a similar structure to one which has already been experimentally determined. For this reason, the most successful approaches to protein structure prediction have been template-based methods. Such prediction methods attempt to identify and model the folds of unknown structures by aligning the target sequences to a set of representative template structures within a fold library. In this chapter, I discuss the development of template-based approaches to fold prediction, from the traditional techniques to the recent state-of-the-art methods. I also discuss the recent development of structural annotation databases, which contain models built by aligning the sequences from entire proteomes against known structures. Finally, I run through a practical step-by-step guide for aligning target sequences to known structures and contemplate the future direction of template-based structure prediction.

Nuclear magnetic resonance structure of the N-terminal domain of nonstructural protein 3 from the severe acute respiratory syndrome coronavirus

This paper describes the structure determination of nsp3a, the N-terminal domain of the severe acute respiratory syndrome coronavirus (SARS-CoV) nonstructural protein 3. nsp3a exhibits a ubiquitin-like globular fold of residues 1 to 112 and a flexibly extended glutamic acid-rich domain of residues 113 to 183. In addition to the four beta-strands and two alpha-helices that are common to ubiquitin-like folds, the globular domain of nsp3a contains two short helices representing a feature that has not previously been observed in these proteins. Nuclear magnetic resonance chemical shift perturbations showed that these unique structural elements are involved in interactions with single-stranded RNA. Structural similarities with proteins involved in various cell-signaling pathways indicate possible roles of nsp3a in viral infection and persistence.

A self-repairing, supramolecular polymer system: healability as a consequence of donor-acceptor pi-pi stacking interactions

A novel supramolecular polymer system, in which the terminal pyrenyl groups of a polyamide intercalate into the chain-folds of a polyimide via electronically-complementary pi-pi stacking, shows both enhanced mechanical properties relative to those of its individual components and facile healing characteristics as a result of the thermoreversibility of non-covalent interactions.

Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution

Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 Angstrom. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.