Prediction and Analysis for Structure and Function of Membrane Proteins

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The software systems were developed for predicting membrane proteins, signal peptides and mitochondria localization signals, analyzing amino acid sequences from total genomes. The parameters for the analysis and prediction are the electric charges, the hydrophobicity, amphiphilicity and the flexibility of polypeptides due to the density of glycine and proline. The developed systems are for (1) the improvement of membrane prediction, (2) the prediction of signal peptides and (3) the mitochondria localization of proteins. Using the methods for the membrane proteins prediction, all amino acid sequences from total genomes were analyzed and the ratio of membrane proteins was found to be almost constant. The distribution of transmembrane helices was discussed in view of the evolutionary generation of membrane proteins. The simulations of the dynamical structures and the function of light receptors and channel proteins were performed by the combination of the quantum chemistry and the molecular dynamics as well as the Brownian dynamics.