通过非均匀尺寸修正 Poisson-Boltzmann 离子通道模型进行 VDAC 溶剂化自由能计算
VDAC Solvation Free Energy Calculation by a Nonuniform Size Modified Poisson-Boltzmann Ion Channel Model
AI总结：
该研究构建集成 nuSMPBIC 等模型的 VSFEC 软件包，纳入非均匀离子尺寸效应并改进四面体网格，用于多蛋白、多离子条件下的 VDAC 溶剂化自由能计算。
摘要：
电压依赖性阴离子通道（Voltage-Dependent Anion Channel，VDAC）蛋白是离子和代谢物受调控进出线粒体的主要通道。计算其溶剂化自由能对于理解其稳定性、功能以及在细胞环境中的相互作用至关重要。本文引入总溶剂化自由能 $E$，它是静电自由能、理想气体自由能和超额自由能之和，并加入非极性能量，以使无电荷时 $E$ 为零。我们开发了用于计算 $E$ 的数值格式，并更新了现有的网格生成软件包，以加快四面体网格的生成并提高用于计算 $E$ 的网格质量。通过将这些格式和更新后的网格软件包与我们的非均匀尺寸修正 Poisson-Boltzmann 离子通道（nuSMPBIC）、SMPBIC 和 PBIC 有限元软件包、PDB2PQR 软件包以及 OPM 数据库集成，我们创建了 VDAC 溶剂化自由能计算（VDAC Solvation Free Energy Calculation，VSFEC）软件包。利用 VSFEC 软件包，我们使用 6 种 VDAC 蛋白以及多种离子溶液，对 nuSMPBIC、SMPBIC 和 PBIC 模型进行了比较测试；这些溶液包含至多 4 种离子，其中包括 ATP$^{4-}$ 和 Ca$^{2+}$。我们还在不同中性电压和介电常数下进行测试，以探究 $E$ 的变化规律。测试结果强调了考虑非均匀离子尺寸效应的重要性，并证明了 VSFEC 软件包在计算 VDAC 蛋白溶剂化自由能方面的高性能。
英文摘要：
The Voltage-Dependent Anion Channel (VDAC) protein is the primary conduit for the regulated passage of ions and metabolites into and out of mitochondria. Calculating its solvation free energy is crucial for understanding its stability, function, and interactions within the cellular environment. In this paper, we introduce a total solvation free energy, $E$, which is the sum of electrostatic, ideal gas, and excess free energies, along with a non-polar energy to yield a zero of $E$ in the absence of charges. We develop numerical schemes for computing $E$ and update the current mesh generation package to accelerate the generation of tetrahedral meshes and improve the quality of meshes for computing $E$. By integrating these schemes and the updated mesh package with our non-uniform size modified Poisson-Boltzmann ion channel (nuSMPBIC), SMPBIC, and PBIC finite element packages, the PDB2PQR package, and the OPM database, we create the VDAC Solvation Free Energy Calculation (VSFEC) package. Using the VSFEC package, we perform comparison tests on the nuSMPBIC, SMPBIC, and PBIC models by using six VDAC proteins and various ionic solutions containing up to four ionic species, including ATP$^{4-}$ and Ca$^{2+}$. We also conduct tests with different neutral voltages and permittivity constants to explore the varying patterns of $E$. Our test results underscore the importance of considering non-uniform ionic size effects and demonstrate the high performance of the VSFEC package in calculating the solvation free energy of VDAC proteins.
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