将物理纳入蛋白质功能的预测建模中,以克服数据稀缺:BK通道的案例研究
Erik Nordquist1, Guohui Zhang2, Shrishti Barethiya1
1Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America.
PLoS computational biology
|September 15, 2023
概括
这项研究将基于物理的建模与机器学习相结合,以预测大 (BK) 通道电压门,克服数据稀缺. 这种方法准确地模拟了突变效应,揭示了关键的物理原理,如疏水性门.
科学领域:
- 生物物理学的生物物理.
- 计算生物学 计算生物学
- 分子建模分子建模
背景情况:
- 机器学习在数据丰富的生物物理问题上表现出色,但在数据稀缺方面扎.
- 大 (BK) 通道对心血管和神经系统至关重要,与疾病相关的突变.
- 对于BK通道突变的现有实验数据不足以进行预测建模.
研究的目的:
- 通过将基于物理的描述符与机器学习相结合,开发BK通道电压封闭的预测模型.
- 为了克服预测蛋白质功能的数据稀缺性挑战.
- 为了揭示BK通道封锁的基础物理原理.
主要方法:
- 基于物理的建模来量化BK通道开放和关闭状态上的突变效应.
- 原子模拟用于导出动态性质.
- 随机森林模型在物理描述器上进行训练,以预测门电压 (ΔV1/2) 的变化.
主要成果:
- 该模型准确地预测了实验测量的 ΔV1/2 转移 (RMSE ~ 32 mV,R ~ 0.7).
- 该方法确定了疏水性门作为BCK通道功能的关键原则.
- 与新突变的验证显示出高量的量化协议 (R = 0.92,RMSE = 18 mV),证明了数据稀疏地区的预测能力.
结论:
- 结合基于物理学的建模和机器学习,有效地解决了预测复杂蛋白质功能的数据稀缺问题.
- 开发的模型准确地预测了BK通道电压封闭特性,并揭示了重要的生物物理见解.
- 这种综合方法具有很大的潜力,可以促进对非碎蛋白质功能的预测.
相关概念视频
Physiological Pharmacokinetic Models: Assumption with Protein Binding
70
Physiological models with protein binding in pharmacokinetics offer a sophisticated approach to understanding drug disposition. These models consider drug-protein interactions, enabling them to effectively predict drug concentrations in different organs and tissues. This precision aids in accurate drug dosing, providing a significant advantage over conventional models. A key process within these models is equilibration, which ensures that drug concentrations achieve a steady state within the...
70
Protein-protein Interfaces
12.5K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.5K
Nonlinear Pharmacokinetics: Bioavailability and Protein-Drug Binding
209
When a drug follows nonlinear pharmacokinetics, its bioavailability, the amount of the drug that reaches the systemic circulation, can change with different doses. This is due to the presence of a saturable pathway. The pathway becomes saturated as the drug concentration increases, decreasing the absorption rate. Consequently, the drug's bioavailability may be lower than expected at higher doses.
To quantify the extent of bioavailability, pharmacologists often use a parameter called .
To quantify the extent of bioavailability, pharmacologists often use a parameter called .
209
Model Approaches for Pharmacokinetic Data: Physiological Models
72
Physiological models in pharmacokinetics are instrumental in understanding the distribution and elimination of drugs within the body. These models describe the drug concentration within target organs, influenced by factors such as drug uptake, tissue volume, and blood flow. Drug uptake is governed by the partition coefficient, which signifies the drug concentration ratio in tissue to that in the blood. The blood flow rate to a specific tissue is expressed as Qt, and the rate of change in tissue...
72
Protein Dynamics in Living Cells
2.1K
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
2.1K
Protein-Drug Binding: Mechanism and Kinetics
577
Protein-drug binding refers to the interaction between drugs and proteins within the body. This binding process can occur intracellularly, involving drug interactions with enzymes or receptors within cells, or extracellularly, involving plasma proteins in the blood.
Various forces drive these interactions, including hydrogen bonds, hydrophobic interactions, ionic bonds, electrostatic interactions, and van der Waals forces. These bonds enable drugs to bind to specific sites on proteins,...
Various forces drive these interactions, including hydrogen bonds, hydrophobic interactions, ionic bonds, electrostatic interactions, and van der Waals forces. These bonds enable drugs to bind to specific sites on proteins,...
577


