蛋白质结构和动态与跨键的标尺合的相关性
Hans-Jürgen Sass1, Franziska Fang-Fang Schmid, Stephan Grzesiek
1Biozentrum and Department Chemie, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland. juergen.sass@unibas.ch
Journal of the American Chemical Society
|April 14, 2007
概括
核磁共振 (NMR) 标尺合量化了蛋白质中的键动态. 使用明确水的分子动力学模拟提高了对低分辨率结构的实验数据的一致性.
科学领域:
- 结构生物学 结构生物学
- 计算生物物理学的计算生物物理学
- 生物分子NMR光谱学 生物分子NMR光谱学
背景情况:
- 通过NMR可观测的标尺合提供了对生物分子中的键几何学和动态学的洞察.
- 之前的研究已经探讨了标尺合和键特性之间的关系.
研究的目的:
- 调查分子动力学 (MD) 模拟与不同的力场和溶解模型对理论h3JNC'标量合的精度的影响.
- 评估实验h3JNC'数据与静态,高分辨率结构模型相比时间平均结构的兼容性.
主要方法:
- 使用各种力场对ubiquitin,GB1和SMN Tudor域进行了深入的分子动力学 (MD) 模拟.
- 使用密度函数理论和几何参数化方法,从MD快照中计算了理论平均h3JNC'标量合.
- 将理论值与实验h3JNC'数据和高分辨率X射线结构进行比较.
主要成果:
- 用明确的水溶解进行的MD模拟显著改善了对较低分辨率蛋白质结构的实验和理论h3JNC'值之间的一致性.
- 在MD模拟中隐含的水模型恶化了协议,可能是由于人造的键延长.
- 实验h3JNC'值与静态的高分辨率结构模型一致,MD平均精炼低分辨率结构.
结论:
- 在MD模拟中,明确的水对于准确预测键动态和改善对低分辨率结构的实验性NMR数据的一致性至关重要.
- 这项研究验证了使用h3JNC'标量合作为蛋白质中键表征的定量探针.
- 使用明确溶解的MD平均值使低分辨率结构与实验性NMR观测相协调.
相关概念视频
Protein Folding
Overview
Protein 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...
Structural Protein Function
Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Protein 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.
Protein 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...
Structural Protein Function
Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...


