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首页> 外文期刊>The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory >Conformational simulations of aqueous solvated alpha-conotoxin GI and its single disulfide analogues using a polarizable force field model
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Conformational simulations of aqueous solvated alpha-conotoxin GI and its single disulfide analogues using a polarizable force field model

机译：使用极化力场模型对水性溶剂化α-芋螺毒素GI及其单二硫类似物的构象模拟

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The solution conformation of alpha-conotoxin GI and its two single disulfide analogues are simulated using a polarizable force field in combination with the molecular fragmentation quantum chemical calculation. The polarizability is explicitly described by allowing the partial charges and fragment dipole moments to be variables, with values coming from the linear-scaling energy-based molecular fragmentation calculations at the B3LYP/6-31G(d) level. In comparison with the full quantum chemical calculations, the fragmentation approaches can yield precise ground-state energies, dipole moments, and static polarizabilities for peptides. The B3LYP/6-31G(d) charges and fragment-centered dipole moments are introduced in calculations of electrostatic terms in both AmberFF03 and OPLS force fields. Our test calculations on the gas-phase glucagon (PDB code: 1gcn) and solvated alpha-conotoxin GI (PDB code: 1not) demonstrate that the present polarization model is capable of describing the structural properties (such as the relative conformational energies, intramolecular hydrogen bonds, and disulfide bonds) with accuracy comparable to some other polarizable force fields (ABEEM/MM and OPLS-PFF) and the quantum mechanics/molecular mechanics (QM/MM) hybrid model. The employment of fragment-centered dipole moments in calculations of dipole-dipole interactions can save computational time in comparison with those polarization models using atom-centered dipole moments without much loss of accuracy. The molecular dynamics simulations using the polarizable force field demonstrate that two single disulfide GI analogues are more flexible and less structured than the native a-conotoxin GI, in agreement with NMR experiments. The polarization effect is important in simulations of the folding/unfolding process of solvated proteins.
机译：使用极化力场结合分子碎裂量子化学计算，模拟了α-芋螺毒素GI及其两个单一的二硫键类似物的溶液构象。通过允许部分电荷和碎片偶极矩为变量来明确描述极化率，其值来自B3LYP / 6-31G（d）级别基于线性缩放能量的分子碎片计算。与完整的量子化学计算相比，裂解方法可以产生精确的基态能量，偶极矩和多肽的静态极化率。在AmberFF03和OPLS力场的静电项计算中引入了B3LYP / 6-31G（d）电荷和以碎片为中心的偶极矩。我们对气相胰高血糖素（PDB代码：1gcn）和溶剂化的α-芋螺毒素GI（PDB代码：1not）的测试计算表明，本极化模型能够描述结构特性（例如相对构象能，分子内氢键和二硫键的精度可与其他一些极化力场（ABEEM / MM和OPLS-PFF）和量子力学/分子力学（QM / MM）混合模型相媲美。与使用以原子为中心的偶极矩的极化模型相比，在以偶极-偶极相互作用的计算中采用以碎片为中心的偶极矩可以节省计算时间，而不会损失很多精度。使用可极化力场的分子动力学模拟表明，与NMR实验相符，两个单一的二硫化物GI类似物比天然的α-芋螺毒素GI更灵活，结构更少。极化效应在溶剂化蛋白质折叠/展开过程的模拟中很重要。

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