纳入物理来克服蛋白质功能的预测建模中的数据稀缺:BK通道的案例研究
Erik Nordquist1, Guohui Zhang2, Shrishti Barethiya1
1Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA.
bioRxiv : the preprint server for biology
|July 10, 2023
概括
这项研究结合了物理和机器学习来预测大 (BK) 通道电压门,克服数据稀缺. 该模型准确地预测了突变效应,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
- 蛋白质科学 蛋白质科学
背景情况:
- 机器学习在丰富的数据方面表现出色,但在复杂的蛋白质功能预测方面却面临着稀缺问题.
- 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 (473个位点) 现有的实验数据太稀少,无法进行强大的预测建模.
研究的目的:
- 使用有限的实验数据开发BK通道电压封闭的预测模型.
- 将基于物理的功能与机器学习相结合,以克服数据稀缺.
- 为了揭示管理BK通道电压门的基本物理原理.
主要方法:
- 利用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.
- 纳入了来自原子模拟的动态性质和来自罗塞塔计算的能量量.
- 使用物理衍生描述符和实验突变数据训练随机森林模型.
主要成果:
- 该模型准确地预测了门电压 (ΔV1/2) 的变化,其中RMSE ∼32 mV和R ∼0.7.
- 确定了BK通道电压关中疏水关的重要作用.
- 成功预测了四种新型突变对S5螺旋 (R = 0.92,RMSE = 18 mV) 的影响,证实了模型在数据稀疏地区的预测能力.
结论:
- 将基于物理学的特征与机器学习相结合,有效地克服了蛋白质功能预测中的数据稀缺性.
- 开发的模型准确地预测了BK通道电压封闭特性,并揭示了关键的生物物理原理.
- 这种方法表明,在实验数据有限的情况下,预测复杂蛋白质功能的潜力很大.
相关概念视频
Physiological Pharmacokinetic Models: Assumption with Protein Binding
75
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...
75
Protein-protein Interfaces
12.6K
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...
12.6K
Nonlinear Pharmacokinetics: Bioavailability and Protein-Drug Binding
212
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 .
212
Protein Dynamics in Living Cells
2.2K
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...
2.2K
Intrinsically Disordered Proteins
17.9K
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
17.9K
Model Approaches for Pharmacokinetic Data: Physiological Models
78
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...
78


