Prediction and Analysis for Structure and Function of Membrane Proteins

膜蛋白结构与功能的预测与分析

• 批准号: 12208005
• 负责人: MITAKU Shigeki
• 金额: $ 67.07万
• 依托单位: Nagoya University (2003-2004)Tokyo University of Agriculture and Technology (2000-2002)
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research on Priority Areas
• 财政年份: 2000
• 资助国家: 日本
• 起止时间: 2000 至 2004
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-12208005/
• 关键词: membrane protein; protein structure; protein function; prediction; simulation; molecular dynamics; genome; proteome; 膜タンパク質; アミノ酸配列; 膜組み込み装置; 分子認識; シグナルペプチド; 計算機シミュレーション; 光受容膜タンパク質; ポリンチャネル; タンパク質分類; 物理的予測; 膜タンパク質予測; ドッキング; バクテリオロドプシン

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.

该软件系统用于预测膜蛋白、信号肽和线粒体定位信号，并从全基因组中分析氨基酸序列。用于分析和预测的参数是多肽的电荷、疏水性、两亲性和由于甘氨酸和脯氨酸的密度而产生的柔韧性。所开发的系统用于(1)膜预测的改进，(2)信号肽的预测和(3)蛋白质的线粒体定位。利用膜蛋白预测的方法，分析了总基因组的所有氨基酸序列，发现膜蛋白的比例几乎是恒定的。从膜蛋白的进化世代角度讨论了跨膜螺旋的分布。采用量子化学、分子动力学和布朗动力学相结合的方法，对光受体和通道蛋白的动态结构和功能进行了模拟。

项目成果

Mechanisms of secondary structure breakers in soluble proteins.

• DOI: 10.2142/biophysics.1.55
• 发表时间: 2005
• 期刊: Biophysics (Nagoya-shi, Japan)
• 作者: Imai K;Mitaku S
• 通讯作者: Mitaku S

Identification of nucleotide binding sites in V-type Na+-ATPase from Enterococcus hirae

海拉肠球菌 V 型 Na -ATP 酶核苷酸结合位点的鉴定

• 发表时间: 2004
• 期刊: Bioscience, Biotechnology, and Biochemistry 68
• 作者: T.Hosaka;T.Murata;Y.Kakinuma;I.Yamato
• 通讯作者: I.Yamato

Yokoyama et al.: "Irreversible Photobleaching of Bacteriorhodopsin from A High-Temperature Intermediate State"J. Biochem.. 131・6. 785-790 (2002)

横山等人：“来自高温中间状态的细菌视紫红质的不可逆光漂白” J. Biochem.. 131・6 (2002)

T.Hasegawa, et al.: "Analysis of Thermal Phase Transition via Time-Resolved Infrared Spectra Using Partial Least Squares Regression Modeling Parameters"Appl. Spectrosc.. (印刷中).

T. Hasekawa 等人：“使用偏最小二乘回归建模参数通过时间分辨红外光谱分析热相变”Spectrosc..（出版中）。

即活用のためのバイオインフォマティクス入門

立即使用的生物信息学简介

• 发表时间: 2004
• 作者: 美宅成樹;広川貴次
• 通讯作者: 広川貴次