Prediction of protein structural classes for low-homology sequences based on predicted secondary structure

<p>Abstract</p> <p>Background</p> <p>Prediction of protein structural classes (<it>α</it>, <it>β</it>, <it>α </it>+ <it>β </it>and <it>α</it>/<it>β</it>) from amino acid sequences is of great importance, as it is beneficial to study protein function, regulation and interactions. Many methods have been developed for high-homology protein sequences, and the prediction accuracies can achieve up to 90%. However, for low-homology sequences whose average pairwise sequence identity lies between 20% and 40%, they perform relatively poorly, yielding the prediction accuracy often below 60%.</p> <p>Results</p> <p>We propose a new method to predict protein structural classes on the basis of features extracted from the predicted secondary structures of proteins rather than directly from their amino acid sequences. It first uses PSIPRED to predict the secondary structure for each protein sequence. Then, the <it>chaos game representation </it>is employed to represent the predicted secondary structure as two time series, from which we generate a comprehensive set of 24 features using <it>recurrence quantification analysis</it>, <it>K-string based information entropy </it>and <it>segment-based analysis</it>. The resulting feature vectors are finally fed into a simple yet powerful Fisher's discriminant algorithm for the prediction of protein structural classes. We tested the proposed method on three benchmark datasets in low homology and achieved the overall prediction accuracies of 82.9%, 83.1% and 81.3%, respectively. Comparisons with ten existing methods showed that our method consistently performs better for all the tested datasets and the overall accuracy improvements range from 2.3% to 27.5%. A web server that implements the proposed method is freely available at <url>http://www1.spms.ntu.edu.sg/~chenxin/RKS_PPSC/</url>.</p> <p>Conclusion</p> <p>The high prediction accuracy achieved by our proposed method is attributed to the design of a comprehensive feature set on the predicted secondary structure sequences, which is capable of characterizing the sequence order information, local interactions of the secondary structural elements, and spacial arrangements of <it>α </it>helices and <it>β </it>strands. Thus, it is a valuable method to predict protein structural classes particularly for low-homology amino acid sequences.</p

Influence of interdot electronic coupling on photoluminescence spectra of self-assembled InAs/GaAs quantum dots

The influence of interdot electronic coupling on photoluminescence (PL) spectra of self-assembled InAs/GaAs quantum dots (QDs) has been systematically investigated combining with the measurement of transmission electron microscopy. The experimentally observed fast red-shift of PL energy and an anomalous reduction of the linewidth with increasing temperature indicate that the QD ensemble can be regarded as a coupled system. The study of multilayer vertically coupled QD structures shows that a red-shift of PL peak energy and a reduction of PL linewidth are expected as the number of QD layers is increased. On the other hand, two layer QDs with different sizes have been grown according to the mechanism of a vertically correlated arrangement. However, only one PL peak related to the large QD ensemble has been observed due to the strong coupling in InAs pairs. A new possible mechanism to reduce the PL linewidth of QD ensemble is also discussed

Material transport in self-assembled InAs/GaAs quantum dot ensemble

Introducing the growth interruption between the InAs deposition and subsequent GaAs growth in self-assembled quantum dot (QD) structures, the material transport process in the InAs layers has been investigated by photoluminescence and transmission electron microscopy measurement. InAs material in structures without misfit dislocations transfers from the wetting layer to QDs corresponding to the red-shift of PL peak energy due to interruption. On the other hand, the PL peak shifts to higher energy in the structures with dislocations. In this case, the misfit dislocations would capture the InAs material from the surrounding wetting layer and coherent islands leading to the reduction of the size of these QDs. The variations in the PL intensity and Linewidth are also discussed