一个可转移和强大的计算框架,用于A类GPCR激活自由能量
Simone Aureli1,2,3, Nicola Piasentin1,2, Thorben Fröhlking1,2,3
1School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, CH, Switzerland.
The journal of physical chemistry letters
|March 3, 2026
概括
研究人员开发了一种简化方法来模拟G蛋白合受体 (GPCR) 激活. 这种方法简化了对分子模拟的集体变量 (CV) 的定义,使得可靠的自由能量计算成为可能,并揭示了对受体激活机制的新见解.
科学领域:
- 生物化学 生物化学
- 计算生物学 计算生物学
- 药理学 药理学是指药理学的学科.
背景情况:
- G-蛋白合受体 (GPCRs) 调解关键的细胞功能,但由于需要进行局部和全球运动捕获,模拟它们的激活是复杂的.
- 以前用于GPCR激活模拟的方法虽然对β1-上腺素受体 (ADRB1) 等特定受体成功,但需要进行广泛和易出错的集体变量 (CV) 改进.
研究的目的:
- 在GPCR激活的分子模拟中引入简化和用户友好的CVs定义策略.
- 减少用户在CV选择和精炼过程中的干预,同时确保强大的自由能源融合.
- 将新方法应用于药理上相关的阿波-GPCR,特别是ADRB1和μ-阿片类受体.
主要方法:
- 开发了用于定义集体变量 (CVs) 的进化策略,尽量减少用户输入.
- 将增强的CV定义策略应用于ADRB1和μ-阿片类受体的分子模拟.
- 使用多重复制增强采样方法与新的CV策略相结合.
主要成果:
- 新方法成功地重建了ADRB1激活的自由能量,与以前的量身定制方法相一致.
- 获得了对μ-阿片类受体激活机制的新生物学见解.
- 该策略在实现两个研究受体的自由能量趋同方面表现出强大.
结论:
- 提出的简化CV定义策略对于模拟GPCR激活是有效的.
- 这种方法显著降低了在准备GPCR分子模拟时的复杂性和错误的可能性.
- 该方法很容易适用于其他A类GPCR,促进对药物位激活机制的系统研究.
更多相关视频
相关概念视频
Gibbs Free Energy
41.3K
One of the challenges of using the second law of thermodynamics to determine if a process is spontaneous is that it requires measurements of the entropy change for the system and the entropy change for the surroundings. An alternative approach involving a new thermodynamic property defined in terms of system properties only was introduced in the late nineteenth century by American mathematician Josiah Willard Gibbs. This new property is called the Gibbs free energy (G) (or simply the free...
41.3K
Calculating Standard Free Energy Changes
26.8K
The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
26.8K
Gibbs Free Energy and Thermodynamic Favorability
9.1K
The spontaneity of a process depends upon the temperature of the system. Phase transitions, for example, will proceed spontaneously in one direction or the other depending upon the temperature of the substance in question. Likewise, some chemical reactions can also exhibit temperature-dependent spontaneities. To illustrate this concept, the equation relating free energy change to the enthalpy and entropy changes for the process is considered:
9.1K
Activation and Inactivation of G Proteins
12.5K
Heterotrimeric G proteins are guanine nucleotide-binding proteins. As the name suggests, heterotrimeric G proteins are composed of three subunits: alpha, beta, and gamma. They remain GDP-bound or GTP-bound inside the cells and switch between inactive/active states. The Gα subunit possesses the nucleotide-binding pocket that binds guanine nucleotides and switches between GDP or GTP-bound states. In contrast, the Gꞵ and Gγ subunits are always bound together with high...
12.5K
Thermodynamic Potentials
1.8K
Thermodynamic potentials are state functions that are extremely useful in analyzing a thermodynamic system. They have dimensions of energy. The four important thermodynamic potentials are internal energy, enthalpy, Helmholtz free energy, and Gibbs free energy. These thermodynamic potentials can be expressed using two of the following variables: pressure, volume, temperature, and entropy. These two variables are expressed as the rate of change of the thermodynamic potential with respect to other...
1.8K
Thermodynamics: Chemical Potential and Activity
2.0K
The effective concentration of a species in a solution can be expressed precisely in terms of its activity. Activity considers the effect of electrolytes present in the vicinity of the species of interest and depends on the ionic strength of the solution. The activity of a species is expressed as the product of molar concentration and the activity coefficient of the species.
The thermodynamic equilibrium constant is more accurately defined in terms of activity rather than concentration.
The thermodynamic equilibrium constant is more accurately defined in terms of activity rather than concentration.
2.0K


