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Theoretical Study on Phase Space Landscapes Acquired by Evolution

进化获得的相空间景观的理论研究

基本信息

批准号：
17540383
负责人：
KIKUCHI Macoto
金额：
$ 2.18万
依托单位：
Osaka University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
2005
资助国家：
日本
起止时间：
2005 至 2006
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-17540383/
关键词：
Ecosystem Protein Biophysics Molecular machine Computational physics

项目摘要

Mainly for ecosystems and proteins, characteristics of the evolutionarily-organized phase-space landscapes are studied using statistical and computational physics.For ecosystems, general evolutionary dynamics models are analyzed. In special, abundance distributions, e.g. for species in ecosystem, metabolites in cells, proteins and mRNA, is analytically obtained for some parameters of productivity, maturity and abundance of resources. Evolutionary dynamics of HIV virus and human immune system is also studied and the length of the asymptomatic term is obtained for some parameters.For proteins, we studied free-energy landscape of motor proteins and obtained the following results: (1)We found that large structural fluctuations of kinesin and tubulin are localized at functionally important regions. In particular, our results imply that the microtuble, which is composed of tubulin and plays a role of rail for kinesin, is not just a rail but acts cooperatively in stepping motion of kinesin (papers were submitted). (2) We investigate cooperativity of structural relaxation and nucleotide unbinding of myosin. Our results imply that the binding and unbinding of nucleotide switches the the structures of free-energy landscape (a paper was submitted).On the above resuls, five papers have been appeard on international journals listed in 11.REFERENCES.

主要针对生态系统和蛋白质，利用统计和计算物理方法研究了进化组织相空间景观的特征。对于生态系统，分析了一般的进化动力学模型。特别地，通过分析得到了生态系统中物种、细胞中代谢物、蛋白质和mRNA的丰度分布，以及生产力、成熟度和资源丰度的一些参数。研究了HIV病毒与人体免疫系统的进化动力学，得到了一些参数的无症状期长度。对于蛋白质，我们研究了运动蛋白的自由能景观，得到以下结果：(1)我们发现运动蛋白和微管蛋白的大结构波动集中在功能重要的区域。特别是，我们的研究结果表明，微管是由微管蛋白组成的，对驱动蛋白起轨道作用，它不仅仅是一个轨道，而且在驱动蛋白的步进运动中起协同作用（论文已提交）。(2)研究了肌球蛋白的结构松弛和核苷酸解结合的协同性。我们的结果表明，核苷酸的结合和解结合改变了自由能景观的结构（已提交论文）。以上研究成果已在11.REFERENCES所列国际期刊上发表5篇论文。