完全优化的α-和3(10) -螺旋体与延长的β-链的比较. 一个ONIOM密度函数理论研究研究
Robert Wieczorek1, J J Dannenberg
1Department of Chemistry, City University of New York-Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10021, USA.
Journal of the American Chemical Society
|October 28, 2004
概括
我们研究了聚氨酸中的螺旋结构. 随着体大小的增加,α-螺旋变得比3(10) -螺旋更加稳定,在蛋白质折叠中显示尺寸依赖的稳定性.
科学领域:
- 计算化学是一种计算化学.
- 生物物理学的生物物理.
- 结构生物学是结构生物学.
背景情况:
- 蛋白质的二次结构,包括β-链,α-螺旋和3(10) -螺旋,对于蛋白质的折叠和功能至关重要.
- 了解中的这些基因的能量和结构稳定性对于预测蛋白质的行为至关重要.
研究的目的:
- 为了比较β-链,α-螺旋和3(10) -螺旋在加盖的聚氨酸中的结构和能量特性.
- 为了研究体大小 (N=2-18) 对螺旋稳定性和形状的影响.
主要方法:
- 使用混合密度函数理论 (DFT) 和奥斯模型1 (AM1) 计算来实现完整的优化.
- 分析了相对能量,螺旋应变,双极时刻和键长度.
主要成果:
- 在螺旋结构中观察到非偶联的附加性合作性,特别明显在α螺旋中.
- 发现由于额外的键,对于较小的多氨酸,3(10) - 螺旋更稳定.
- 证明随着聚氨酸大小的增加,α螺旋变得相对更稳定.
结论:
- 体大小显著影响不同螺旋结构的相对稳定性.
- 从3(10) - 螺旋体到α-螺旋体的稳定性过渡凸显了体构成中的能量因素的复杂相互作用.
- 计算建模为管理蛋白质二次结构形成的基本原则提供了宝贵的见解.
相关概念视频
01:13Protein Organization
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...
02:26Conservation of Protein Domains Over Different Proteins
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
02:21Globular and Fibrous Proteins
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
02:36Molecular Geometry and Dipole Moments
The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
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.