Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
IEEE Trans Nanobioscience. 2010 Dec;9(4):297-306. doi: 10.1109/TNB.2010.2070517. Epub 2010 Sep 13.
Molecular dynamics simulations are performed to study the physical mechanism of cobra cardiotoxin (CTX) proteins adsorption on alkanethiol self-assembled monolayers (SAMs) composed of S(CH(2))(5)CH(3) and S(CH(2))(9)CH(3). The binding energy of the CTX protein to the SAM surface of different mixing ratios of alkanethiol chains is calculated. The results show that the affinity of CTX to SAM reaches a maximum value when the ratio S(CH(2))(5)CH(3):S(CH(2))(9)CH(3) is 1:1, which agrees with the measurements of atomic force microscope obtained in Part I of our dual paper. Moreover, the binding energy is found to be linearly proportional to the CTX-SAM contact area. The hydrophobicity on CTX residues, the flexibility of SAMs and the behavior of water molecules near the SAM surface are examined to understand how these parameters affect the adsorption of a CTX protein on SAM surfaces. In addition, the importance of modeling water molecules explicitly in the study of protein adsorption is demonstrated by applying different solvent models.
采用分子动力学模拟方法研究了眼镜蛇心脏毒素（CTX）蛋白在由 S(CH(2))(5)CH(3)和 S(CH(2))(9)CH(3)组成的烷硫醇自组装单分子层（SAM）上吸附的物理机制。计算了 CTX 蛋白与不同混合比例烷硫醇链 SAM 表面的结合能。结果表明，当 S(CH(2))(5)CH(3):S(CH(2))(9)CH(3)的比例为 1:1 时，CTX 对 SAM 的亲和力达到最大值，这与我们在双篇论文的第一部分中原子力显微镜测量结果一致。此外，发现结合能与 CTX-SAM 接触面积呈线性正比关系。研究了 CTX 残基的疏水性、SAM 的柔韧性以及 SAM 表面附近水分子的行为，以了解这些参数如何影响 CTX 蛋白在 SAM 表面上的吸附。此外，通过应用不同的溶剂模型证明了在研究蛋白质吸附时显式建模水分子的重要性。
