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Study on the Dynamic and Static Effects of Sulfur Atoms on Protein Structure

硫原子对蛋白质结构动静态影响的研究

基本信息

批准号：
16350092
负责人：
IWAOKA Michio
金额：
$ 10.11万
依托单位：
Tokai University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (B)
财政年份：
2004
资助国家：
日本
起止时间：
2004 至 2006
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-16350092/
关键词：
Protein Structure Sulfur Nonbonded Interaction Electronic Effect Protein Data Bank Selenium Reagents Protein Folding Molecular Simulation

项目摘要

In this research project, we tried to thoroughly elucidate the principles that dictate the dynamic behavior and the stability of protein structures by means of several methods from an organic-chemistry point of view. As the result, we could point out for the first time the possibility of the sulfur atoms in proteins playing roles on the functions as well as the evolution.Four sub-projects were simultaneously run in order to approach the unprecedented roles of the sulfur.1. Static roles of sulfur atoms in proteins.2. Dynamic roles of sulfur atoms in proteins.3. Chemical modification of sulfur atoms in proteins.4. Theoretical approach by molecular simulation.In sub-project 1, molecular structures of phospholipase A2 were analyzed by using the coordination data obtained from protein data bank, and four S…O and one S…N nonbonded interactions were characterized. It was found that these weak interactions exist near the active site and have strong correlation with molecular evolution of phosphilipase A2. In sub-project 2, new selenium reagents were applied to oxidative folding experiments of ribonuclease A that has four SS bonds. Significant importance of SS rearrangement processes for formation of the stable native-like structures was clearly demonstrated. In sub-project 3, the transformation reactions from cystine to selenocysteine derivatives were developed. The reaction would be useful for the design and synthesis of various peptides and proteins containing selenium atoms instead of the sulfur atoms. In sub-project 4, a high-speed molecular simulation program was developed based on the single amino acid potential (SAAP) force field. The SAAP potentials in water were shown to be a very important factor for determining folded structures of proteins.

在本研究项目中，我们试图从有机化学的角度，通过多种方法彻底阐明决定蛋白质结构的动态行为和稳定性的原理。结果，我们首次指出了蛋白质中硫原子在功能和进化上发挥作用的可能性。为了探讨硫原子的前所未有的作用，我们同时进行了四个子项目。硫原子在蛋白质中的静态作用.硫原子在蛋白质中的动力学作用.蛋白质中硫原子的化学修饰.子项目1利用蛋白质数据库中的配位数据对磷脂酶A2的分子结构进行了分析，确定了4个S…O和1个S…N非键相互作用。研究发现，这些弱相互作用存在于活性中心附近，与磷脂酶A2的分子进化有很强的相关性。在子项目2中，将新的硒试剂应用于具有四个SS键的核糖核酸酶A的氧化折叠实验。SS重排过程的稳定的天然样结构的形成的重要性被清楚地证明。在子项目3中，开发了从胱氨酸到硒代半胱氨酸衍生物的转化反应。该反应将有助于设计和合成含有硒原子而不是硫原子的各种肽和蛋白质。在子项目4中，开发了基于单氨基酸势（SAAP）力场的高速分子模拟程序。水溶液中的SAAP电位是决定蛋白质折叠结构的一个重要因素。