Cheng A, Merz K M
Department of Chemistry, The Pennsylvania State University, University Park 16802-2801, USA.
Biophys J. 1997 Dec;73(6):2851-73. doi: 10.1016/S0006-3495(97)78315-2.
We have studied the winter flounder antifreeze protein (AFP) and two of its mutants using molecular dynamics simulation techniques. The simulations were performed under four conditions: in the gas phase, solvated by water, adsorbed on the ice (2021) crystal plane in the gas phase and in aqueous solution. This study provided details of the ice-binding pattern of the winter flounder AFP. Simulation results indicated that the Asp, Asn, and Thr residues in the AFP are important in ice binding and that Asn and Thr as a group bind cooperatively to the ice surface. These ice-binding residues can be collected into four distinct ice-binding regions: Asp-1/Thr-2/Asp-5, Thr-13/Asn-16, Thr-24/Asn-27, and Thr-35/Arg-37. These four regions are 11 residues apart and the repeat distance between them matches the ice lattice constant along the (1102) direction. This match is crucial to ensure that all four groups can interact with the ice surface simultaneously, thereby, enhancing ice binding. These Asx (x = p or n)/Thr regions each form 5-6 hydrogen bonds with the ice surface: Asn forms about three hydrogen bonds with ice molecules located in the step region while Thr forms one to two hydrogen bonds with the ice molecules in the ridge of the (2021) crystal plane. Both the distance between Thr and Asn and the ordering of the two residues are crucial for effective ice binding. The proper sequence is necessary to generate a binding surface that is compatible with the ice surface topology, thus providing a perfect "host/guest" interaction that simultaneously satisfies both hydrogen bonding and van der Waals interactions. The results also show the relation among binding energy, the number of hydrogen bonds, and the activity. The activity is correlated to the binding energy, and in the case of the mutants we have studied the number of hydrogen bonds. The greater the number of the hydrogen bonds the greater the antifreeze activity. The roles van der Waals interactions and the hydrophobic effect play in ice binding are also highlighted. For the latter it is demonstrated that the surface of ice has a clathratelike structure which favors the partitioning of hydrophobic groups to the surface of ice. It is suggested that mutations that involve the deletion of hydrophobic residues (e.g., the Leu residues) will provide insight into the role the hydrophobic effect plays in partitioning these peptides to the surface of ice.
我们使用分子动力学模拟技术研究了冬比目鱼抗冻蛋白（AFP）及其两种突变体。模拟在四种条件下进行：气相、水合状态、气相中吸附在冰（2021）晶面上以及水溶液中。这项研究提供了冬比目鱼AFP冰结合模式的详细信息。模拟结果表明，AFP中的天冬氨酸（Asp）、天冬酰胺（Asn）和苏氨酸（Thr）残基在冰结合中很重要，并且Asn和Thr作为一组协同结合到冰表面。这些冰结合残基可分为四个不同的冰结合区域：Asp-1/Thr-2/Asp-5、Thr-13/Asn-16、Thr-24/Asn-27和Thr-35/Arg-37。这四个区域相隔11个残基，它们之间的重复距离与沿（1102）方向的冰晶格常数相匹配。这种匹配对于确保所有四个基团能够同时与冰表面相互作用至关重要，从而增强冰结合。这些Asx（x = p或n）/Thr区域各自与冰表面形成5 - 6个氢键：Asn与位于台阶区域的冰分子形成约三个氢键，而Thr与（2021）晶面脊部的冰分子形成一到两个氢键。Thr和Asn之间的距离以及这两个残基的排列顺序对于有效的冰结合都至关重要。合适的序列对于生成与冰表面拓扑结构兼容的结合表面是必要的，从而提供同时满足氢键和范德华相互作用的完美“主/客”相互作用。结果还显示了结合能、氢键数量和活性之间的关系。活性与结合能相关，在我们研究的突变体情况下，还与氢键数量相关。氢键数量越多，抗冻活性越高。范德华相互作用和疏水效应在冰结合中所起的作用也得到了突出体现。对于后者，证明了冰表面具有笼状结构，有利于疏水基团分配到冰表面。有人提出，涉及疏水残基（如亮氨酸残基）缺失的突变将有助于深入了解疏水效应在将这些肽分配到冰表面中所起的作用。
