将绝对自由能量扰动分子动力学应用于扩散结合联体
Xavier E Laracuente1, Bryan M Delfing1, Xingyu Luo1
1School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States.
Journal of chemical theory and computation
|April 7, 2025
概括
我们开发了一种新的模拟协议,用于计算难以实现的蛋白质-连接体相互作用的结合自由能量. 这种方法准确地预测了联体minNLS与importin-α的结合亲和力和结合机制.
科学领域:
- 计算化学的计算化学
- 结构生物学 结构生物学
- 生物物理学的生物物理.
背景情况:
- 与蛋白质扩散结合的配体对传统的自由能量扰动 (FEP) 模拟构成挑战.
- 了解这些结合机制对于药物发现和分子生物学至关重要.
研究的目的:
- 开发和验证一种先进的FEP协议,用于计算扩散性结合联体的结合自由能量和机制.
- 为了研究一个minNLS与importin-α的结合,一个没有明确的结合位置的系统.
主要方法:
- 开发了一种绝对自由能量扰动 (FEP) 协议,整合了全原子分子动力学,复制品交换与溶液化 (REST) 增强采样,以及球体波束.
- 应用了FEP/REST协议来模拟minNLS (KKPK) 与importin-α的结合.
- 分析模拟数据以确定结合的自由能量,结合机制和结合联体的结构组合.
主要成果:
- 通过FEP/REST协议,成功计算出了minNLS.min的融合约束性自由能量估计.
- 证明了minNLS通过一种独特的纯粹热机制与中度亲和力结合进口蛋白-α.
- 确定了从充电的氨基酸溶解中释放的水作为有利结合的主要驱动因素.
- 描述了在importin-α上的结合结构,相互作用和结合位点的分布.
结论:
- 开发的FEP/REST协议对于模拟扩散结合联体是有效的.
- minNLS与importin-α的结合主要是由有利的热带贡献,特别是水释放驱动的.
- 这项研究提供了对不同寻常的结合机制的见解,并为具有挑战性的联结蛋白系统提供了强大的计算方法.
相关概念视频
The Equilibrium Binding Constant and Binding Strength
12.7K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
12.7K
Ligand Binding Sites
12.6K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.6K
Ligand Binding and Linkage
4.7K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.7K
Cooperative Allosteric Transitions
2.3K
2.3K
Conserved Binding Sites
4.1K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.1K
Crystal Field Theory - Octahedral Complexes
25.8K
Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
25.8K


