对小分子蛋白质配体的单态和多态结合的NMR区分
Mikhail Reibarkh1, Thomas J Malia, Gerhard Wagner
1Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
Journal of the American Chemical Society
|February 16, 2006
概括
本研究提出了一种方法来区分针对蛋白相互作用的小分子的单键和多键结合模式. 了解结合模式对于优化药物发现和化学遗传学研究至关重要.
科学领域:
- 生物化学 生物化学
- 化学生物学 化学生物学
- 药物发现 药物发现 药物发现
背景情况:
- 识别蛋白质与蛋白质相互作用的小分子抑制剂 (PPI) 对药物发现和理解生物通路至关重要.
- 最初的小分子抑制剂通常表现出较低的微分子亲和力,并导致NMR光谱中的线条扩大,使优化复杂化.
- 在基于结构的化合物开发中,区分动力线扩展和多重结合模式至关重要.
研究的目的:
- 开发和演示一种实验方法,以区分单模式结合与中间交换动力学和多模式结合.
- 将这种方法应用于分析针对Bcl-xL的两个类似的小分子连接体的结合行为.
主要方法:
- 利用核磁共振 (NMR) 谱学来分析小分子子与Bcl-xL.xL的结合.
- 研究了连接物度对NMR光谱线扩展的影响,以推断结合模式和动力学.
- 应用了适用于各种生物分子相互作用的可概括方法.
主要成果:
- 一个Bcl-xL连接体显示单模结合,线路扩大仅由于中间解离动力学,这被过多的连接体减轻了.
- 第二个,类似的连接体表现出因分离动力学和多重结合形态之间的交换引起的线路扩展,过多的连接体无法克服这种情况.
- 使用开发的基于NMR的方法,证明了区分这些约束场景的能力.
结论:
- 这种方法有效地区分了小分子与蛋白质的单模式和多模式结合.
- 这种方法对于准确的基于结构的药物候选物和化学探针的优化至关重要.
- 该方法广泛适用于描述PPI和蛋白质-核酸相互作用.
相关概念视频
02:40Ligand Binding Sites
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...
02:18The Equilibrium Binding Constant and Binding Strength
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:
00:49Ligand Binding and Linkage
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 the...
01:58Cooperative Allosteric Transitions
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
00:49Ligand Binding and Linkage
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 the...
02:40Ligand Binding Sites
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...