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首页> 外文期刊>The Journal of Chemical Physics >A many-body model to study proteins. II. Incidence of many-body polarization effects on the interaction of the calmodulin protein with four Ca~(2+) dications and with a target enzyme peptide
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A many-body model to study proteins. II. Incidence of many-body polarization effects on the interaction of the calmodulin protein with four Ca~(2+) dications and with a target enzyme peptide

机译：用于研究蛋白质的多体模型。二。多体极化作用对钙调蛋白与四个Ca〜（2+）指示剂和靶酶肽相互作用的影响

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摘要

The origin of the interactions occurring in the calmodulin protein interacting with one of its target peptide and counterions, and binding four calcium dications, has been investigated in the gas phase, using the many-body model presented in Paper I [Masella and Cuniasse, J. Chem. Phys. 119, 1866 (2003)] and a classical pairwise force field. As compared to the latter force field, the many-body model is shown to provide a geometrical description of the calmodulin/target peptide structure in better agreement with the x-ray experimental one,and a better description of the Ca~(2+) binding sites (as compared to "small molecule" structures reported in the Cambridge Structural Database). Regarding the energy, both models provide qualitatively a similar description of the interactions occurring in the calmodulin/target peptide system. However, quantitatively, the pairwise model predicts interaction energies greater by about 25% as compared to the many-body one in the case of calmodulin/Ca~(2+) interactions. This is due to the inability of pairwise force fields to account for the strong anticooperative effects predicted to occur in [Ca, (carboxylate)_n]~(2-n) systems by both the many-body model and quantum computations. Hence, thenew many-body model appears to be well suited for describing proteinic systems interacting with cations, both in terms of geometry and energy.
机译：在气相中，使用论文I中所述的多体模型研究了钙调蛋白与它的靶肽和抗衡离子之一相互作用并结合四种钙离子的相互作用的起源。[Masella and Cuniasse，J化学物理119，1866（2003）]和经典的成对力场。与后一个力场相比，多体模型显示了钙调蛋白/靶标肽结构的几何描述，与X射线实验结果更加吻合，并且对Ca〜（2+）具有更好的描述。结合位点（与剑桥结构数据库中报道的“小分子”结构相比）。关于能量，两个模型在质量上都提供了钙调蛋白/靶标肽系统中相互作用的类似描述。但是，从数量上说，成对模型预测在钙调蛋白/ Ca〜（2+）相互作用的情况下，与多体相互作用能相比，相互作用能提高约25％。这是由于成对力场无法解释通过多体模型和量子计算预测在[Ca，（羧酸盐）_n]〜（2-n）系统中发生的强烈的反协同作用。因此，新的多体模型似乎非常适合描述在几何形状和能量方面与阳离子相互作用的蛋白质系统。

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