Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin

A growing number of solved protein structures display an elongated structural domain, denoted here as alpha-rod, composed of stacked pairs of anti-parallel alpha-helices. Alpha-rods are flexible and expose a large surface, which makes them suitable for protein interaction. Although most likely originating by tandem duplication of a two-helix unit, their detection using sequence similarity between repeats is poor. Here, we show that alpha-rod repeats can be detected using a neural network. The network detects more repeats than are identified by domain databases using multiple profiles, with a low level of false positives (<10%). We identify alpha-rod repeats in approximately 0.4% of proteins in eukaryotic genomes. We then investigate the results for all human proteins, identifying alpha-rod repeats for the first time in six protein families, including proteins STAG1-3, SERAC1, and PSMD1-2 & 5. We also characterize a short version of these repeats in eight protein families of Archaeal, Bacterial, and Fungal species. Finally, we demonstrate the utility of these predictions in directing experimental work to demarcate three alpha-rods in huntingtin, a protein mutated in Huntington's disease. Using yeast two hybrid analysis and an immunoprecipitation technique, we show that the huntingtin fragments containing alpha-rods associate with each other. This is the first definition of domains in huntingtin and the first validation of predicted interactions between fragments of huntingtin, which sets up directions toward functional characterization of this protein. An implementation of the repeat detection algorithm is available as a Web server with a simple graphical output: http://www.ogic.ca/projects/ard. This can be further visualized using BiasViz, a graphic tool for representation of multiple sequence alignments

Investigation of Ramsdellite Titanates as Possible New Negative Electrode Materials for Li Batteries

Transition metal oxides with ramsdellite and spinel structures have been the subject of considerable investigation as candidate electrode materials for lithium-ion batteries. Good ionic conductivity has been reported for the ramsdellite Li2Ti3O7, and the spinel Li4Ti5O12 has been shown to exhibit good electrochemical properties as a Li-anode material. We have recently demonstrated that ramsdellite series Li1+xTi2-2xO4 displays a complete range of solubility at high temperatures between compositions LiTi2O4 and Li2Ti3O7 and that these phases can be preserved to room temperature by quenching. In this study we report on the electrochemical properties of members of this series of ramsdellite phases and the ramsdellite form of TiO2. Comparison is made with the electrochemical properties of the spinel phase Li4Ti5O12 In cyclic voltammetry, spinel Li4Ti5O12 showed a major, reversible peak at about 1.55 V vs. Li. The ramsdellite phases showed a similar reversible peak at just less than -1.5 V; however, a number of additional reversible peaks were observed at up to 2.0 V. As the x value in Li1+xTi2-2xO4 increased, these extra peaks moved to smaller potentials, and they were observed to merge with the 1.5 V peak for Li2Ti3O7 The presence of these extra peaks is thought to reflect the availability of additional sites in the ramsdellites. On charging and discharging, the potential was in the range from 1.5 to 2.5 V, although the, behavior was not as flat as for the spinel, sigh capacities were observed, typically approaching 200 mAh/g. initial cycling efficiencies were generally on the order of 80-90%, although no attempt has yet been made to optimize morphology. On cycling TiO2 ramsdellite, capacity generally faded from an initial value of 300 mAh g(-1) to a stable capacity of 190 mAh g(-1) by cycle ten. (C) 1999 The Electrochemical Society. S0013-4651(99)07-058-5. All rights reserved.</p