Department of Chemical Engineering, Dankook University, Yongin-si, Gyeonggi-do, 16890, South Korea.
J Mol Graph Model. 2019 Mar;87:48-55. doi: 10.1016/j.jmgm.2018.11.006. Epub 2018 Nov 20.
Tenebrio molitor antifreeze protein (TmAFP) was simulated with growing ice surfaces such as primary prism, secondary prism, basal, and pyramidal planes. The ice-binding site of TmAFP, which is full of threonine (Thr), binds to the primary-prism plane but does not bind to other ice planes, in agreement with experiments showing the fast adsorption of TmAFP to the primary-prism plane. To mimic the ice-binding site of shorthorn sculpin AFP (ssAFP; type I) that predominantly consists of alanine (Ala) and has the binding affinity to the secondary-prism plane, the ice-binding site of TmAFP was mutated by replacing a few Thr residues with Ala residues, showing that mutated TmAFP binds to the secondary-prism plane, similar to the ice-binding affinity of ssAFP. Ala residues are located at the cavity of ice, while Thr residues form hydrogen bonds with water molecules. When the mutated TmAFP is further modified by removing Thr, it does not bind to the secondary-prism plane. These findings indicate that simulations can successfully capture the experimentally observed binding affinity of AFP to specific ice planes, to an extent dependent on hydrophobicity of the ice-binding site. In particular, the addition of hydrophobic residues influences the ice-binding affinity of TmAFP, while a certain amount of hydrophilic residue is still required for hydrogen-bond interactions, which supports experimental observations regarding the key roles of hydrophobic and hydrophilic interactions on the AFP-ice binding.
黄粉虫抗冻蛋白（TmAFP）与初生棱柱、次生棱柱、基底和金字塔面等生长冰面进行了模拟。富含苏氨酸（Thr）的 TmAFP 的冰结合位点与初生棱柱面结合，但不与其他冰面结合，这与实验结果一致，表明 TmAFP 快速吸附到初生棱柱面。为了模拟主要由丙氨酸（Ala）组成且与次生棱柱面结合亲和力较强的短须拟蜥 AFP（ssAFP；I 型）的冰结合位点，通过用 Ala 残基替换 TmAFP 中的几个 Thr 残基来突变 TmAFP 的冰结合位点，表明突变的 TmAFP 与次生棱柱面结合，类似于 ssAFP 的冰结合亲和力。Ala 残基位于冰的腔中，而 Thr 残基与水分子形成氢键。当进一步通过去除 Thr 对突变的 TmAFP 进行修饰时，它不再与次生棱柱面结合。这些发现表明，模拟可以成功地捕获 AFP 与特定冰面结合的实验观察到的结合亲和力，在一定程度上取决于冰结合位点的疏水性。特别是，疏水性残基的添加会影响 TmAFP 的冰结合亲和力，而氢键相互作用仍需要一定数量的亲水性残基，这支持了关于 AFP-冰结合中疏水性和亲水性相互作用关键作用的实验观察。
