准确预测非极性溶解的自由能量需要明确考虑结合场所的水化
Samuel Genheden1, Paulius Mikulskis, LiHong Hu
1Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden.
Journal of the American Chemical Society
|July 7, 2011
概括
连续溶解方法难以准确预测非极性溶解对蛋白质-联体结合的自由能量,特别是在暴露于溶剂的地点. 对于可靠的结合亲和度计算,需要改进.
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.
- 分子建模分子建模
背景情况:
- 连续性溶解方法被广泛用于计算化学中近似的自由能量计算.
- 估计非极性溶解的自由能量变化在蛋白质 - 配体结合期间对于理解结合亲和关系至关重要.
- 这些方法的准确性可能受到它们对溶剂相互作用的简化表示的限制.
研究的目的:
- 评估不同连续溶解方法在估计非极性溶解中蛋白质-联体结合的自由能量变化时的准确性.
- 调查结合点溶剂暴露对这些方法性能的影响.
- 确定当前连续性方法的局限性,并建议潜在的改进.
主要方法:
- 评估了三个连续溶解方法:极化连续模型 (PCM),腔和分散 (CD) 和溶剂可访问的表面积 (SASA).
- 使用双解热力学集成作为严格的基准.
- 研究了四种蛋白质 - 配体复合物 (费里 - ,阿维丁 - 生物类型,二 - 氨基胺,二 - 甲胺,三 - 甲胺) 具有不同的结合部位溶剂暴露.
主要成果:
- 连续性方法提供了合理准确的非极性溶解自由能量隐藏的结合点 (ferritin,avidin),当水排除被强制执行.
- 对于暴露于溶剂的结合点 (trypsin,galectin-3),无论水排除设置如何,都没有获得准确的估计.
- 在不同连续方法之间的约束能量估计中观察到显著差异 (绝对高达200kJ/mol,相对高达75kJ/mol).
结论:
- 连续溶解方法无法准确预测具有显著溶剂暴露的系统的结合自由能量,因为缺乏微观水合和信息.
- 当前的方法可能会导致不可靠的结合亲和力预测,根据所选择的方法有很大的差异.
- 纳入明确的溶剂暴露或水合信息显示了改善连续溶解模型的希望.
更多相关视频
06:50Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
Published on: January 26, 2024
10:29Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
Published on: May 9, 2025
相关概念视频
Conserved Binding Sites
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 analyses the...
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 analyses the...
Conserved Binding Sites
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 analyses the...
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 analyses the...
Ligand 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...
Aqueous Solutions and Heats of Hydration
Water and other polar molecules are attracted to ions. The electrostatic attraction between an ion and a molecule with a dipole is called an ion-dipole attraction. These attractions play an important role in the dissolution of ionic compounds in water.
When ionic compounds dissolve in water, the ions in the solid separate and disperse uniformly throughout the solution because water molecules surround and solvate the ions, reducing the strong electrostatic forces between them. This process...
When ionic compounds dissolve in water, the ions in the solid separate and disperse uniformly throughout the solution because water molecules surround and solvate the ions, reducing the strong electrostatic forces between them. This process...
Entropy and Solvation
The process of surrounding a solute with solvent is called solvation. It involves evenly distributing the solute within the solvent. The rule of thumb for determining a solvent for a given compound is that like dissolves like. A good solvent has molecular characteristics similar to those of the compound to be dissolved. For example, polar solutions dissolve polar solutes, and apolar solvents dissolve apolar solutes. A polar solvent is a solvent that has a high dielectric constant (ϵ ≥ 15); an...
Chemical and Solubility Equilibria
The free energy change associated with dissolving a solute in a liter of solvent is called the free energy of a solution, ΔGsolution. The overall ΔGsolution is expressed as the balance of ΔGinteraction against the always-favorable free-energy of mixing, ΔGmixing. Solution formation is favorable if ΔGsolution is less than zero, whereas it is unfavorable if ΔGsolution is greater than zero. In short, for a solution to form and complete dissolution to take place, the Gibbs energy change must be...
