a Institute of Biophotonics, School of Biomedical Science and Engineering , National Yang-Ming University , 155, Li-Nong St., Sec. 2, Taipei 112 , Taiwan.
J Biomol Struct Dyn. 2018 Aug;36(10):2618-2627. doi: 10.1080/07391102.2017.1364671. Epub 2017 Aug 31.
Interaction of E5 of papillomavirus-16 based on its three transmembrane domains (TMDs) with a peptide mimicking the fourth TMD (TMD-A) of the 16 kDa c subunit of the human vacuolar H-ATPase, ATP6V0C, and one of its mutant is investigated. Docking reveals binding of the peptide between the second and third TMD of E5. A series of hydrophobic residues are responsible for the contact. Estimated weak binding energies based on potential of mean force calculations reveal marginal differences of the estimated binding energies between wild type (WT) and mutant peptide. Also differences in estimated binding energies of dimers of the individual TMDs of E5 with the WT peptide are marginal. Correlation of rotational data derived from coarse-grained molecular dynamics simulations of the peptides and the protein as well as from the principal component analysis reveal that the binding of TMD-A with TMD3 is enthalpy driven and binding with TMD2 is guided by entropic conditions.
研究了人空泡型质子 ATP 酶 16kDa c 亚基第 4 跨膜结构域（TMD）模拟肽 TMD-A 与 HPV-16 E5 的三个跨膜结构域（TMD）之间的相互作用及其突变体。对接揭示了 E5 中第二个和第三个 TMD 之间的肽结合。一系列疏水性残基负责接触。基于平均力势计算得出的估计弱结合能表明野生型（WT）和突变肽之间的估计结合能差异很小。E5 的各个 TMD 与 WT 肽的二聚体的估计结合能的差异也很小。从肽和蛋白质的粗粒度分子动力学模拟以及主成分分析得出的旋转数据的相关性表明，TMD-A 与 TMD3 的结合是由焓驱动的，与 TMD2 的结合则由熵条件引导。
