在蛋白质水化层中,键的二次结构灵敏度和生命周期动态
Sanjoy Bandyopadhyay1, Sudip Chakraborty, Biman Bagchi
1Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India. sanjoy@chem.iitkgp.ernet.in
Journal of the American Chemical Society
|November 25, 2005
概括
蛋白质表面水化动态影响生物活动. 带正电荷的残留物形成稳定的水键,而-3的柔性水化层与HP-36的功能相关.
科学领域:
- 生物物理学的生物物理.
- 计算化学计算化学
- 结构生物学 结构生物学
背景情况:
- 蛋白质表面异质性对于生物活性和分子识别至关重要.
- 周围的水分子调解蛋白质-连接体相互作用和功能.
研究的目的:
- 调查水合层动态和蛋白质-水键寿命之间的关系.
- 在蛋白质表面分析水分子的动态平衡.
主要方法:
- 在水溶液中对HP-36进行原子分子动力学模拟.
- 使用卢扎-钱德勒形式主义对非指数级键寿命相关函数的分析.
- 在准结合和自由水分子之间的相互转换率的量化.
主要成果:
- 负电荷的残留物与水形成更长寿命的键,不论蛋白质分段.
- 在三个α螺旋体中观察到蛋白质-水键放松的显著差异.
- 螺旋体-3 呈现出较少刚性的水合层,与更快的键放松和水动力学相关.
结论:
- 补水层的动态与蛋白质的结构和功能密切相关.
- 螺旋-3的灵活的水化层,具有更快的水动力学,与HP-36的活点残留物的位置有关.
- 了解蛋白质水化动态是阐明生物识别和活动的关键.
相关概念视频
01:13Protein Organization
Overview
01:22Protein Folding
Overview
02:15Protein and Protein Structure
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...
01:22Protein Folding
Overview
01:24Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
01:25Protein Folding
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...