Nakayama Masamitsu, Goto Shinichi, Goto Shinya
Department of Medicine (Cardiology), Tokai University School of Medicine, Isehara, Japan.
TH Open. 2022 Dec 7;6(4):e421-e428. doi: 10.1055/a-1937-9940. eCollection 2022 Oct.
Glycoprotein (GP: HIS -PRO ) Ibɑ is a receptor protein expressed on the surface of the platelet. Its N-terminus domain binds with the A1 domain (ASP -PRO ) of its ligand protein von Willebrand factor (VWF) and plays a unique role in platelet adhesion under blood flow conditions. Single amino acid substitutions at residue 233 from glycine (G) to alanine (A), aspartic acid (D), or valine (V) are known to cause biochemically distinct functional alterations known as equal, loss, and gain of function, respectively. However, the underlying physical characteristics of VWF binding with GPIbɑ in wild-type and the three mutants exerting different biological functions are unclear. Here, we aimed to test the hypothesis: biological characteristics of macromolecules are influenced by small changes in physical parameters. The position coordinates and velocity vectors of all atoms and water molecules constructing the wild-type and the three mutants of GPIbɑ (G233A, G233D, and G233V) bound with VWF were calculated every 2 × 10 seconds using the CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field for 9 × 10 seconds. Six salt bridges were detected for longer than 50% of the calculation period for the wild-type model generating noncovalent binding energy of -1096 ± 137.6 kcal/mol. In contrast, only four pairs of salt bridges were observed in G233D mutant with noncovalent binding energy of -865 ± 139 kcal/mol. For G233A and G233V, there were six and five pairs of salt bridges generating -929.8 ± 88.5 and -989.9 ± 94.0 kcal/mol of noncovalent binding energy, respectively. Our molecular dynamic simulation showing a lower probability of salt bridge formation with less noncovalent binding energy in VWF binding with the biologically loss of function G233D mutant of GPIbɑ as compared with wild-type, equal function, and gain of function mutant suggests that biological functions of macromolecules such as GPIbɑ are influenced by their small changes in physical characteristics.
糖蛋白（GP：HIS - PRO）Ibɑ是一种在血小板表面表达的受体蛋白。其N端结构域与其配体蛋白血管性血友病因子（VWF）的A1结构域（ASP - PRO）结合，在血流条件下的血小板黏附中发挥独特作用。已知第233位残基的单个氨基酸取代，从甘氨酸（G）变为丙氨酸（A）、天冬氨酸（D）或缬氨酸（V），分别会导致生化上不同的功能改变，即功能相等、功能丧失和功能增强。然而，野生型以及发挥不同生物学功能的三个突变体中VWF与GPIbɑ结合的潜在物理特性尚不清楚。在此，我们旨在验证这一假设：大分子的生物学特性受物理参数微小变化的影响。使用CHARMM（哈佛大分子力学化学）力场，每2×10⁻⁶秒计算一次构成与VWF结合的野生型和GPIbɑ的三个突变体（G233A、G233D和G233V）的所有原子和水分子的位置坐标及速度矢量，共计算9×10⁻⁶秒。在野生型模型中检测到六个盐桥，其形成时间超过计算周期时长的50%，产生的非共价结合能为 - 1096±137.6千卡/摩尔。相比之下，在G233D突变体中仅观察到四对盐桥，非共价结合能为 - 865±139千卡/摩尔。对于G233A和G233V，分别有六对和五对盐桥，产生的非共价结合能分别为 - 929.8±88.5千卡/摩尔和 - 989.9±94.0千卡/摩尔。我们的分子动力学模拟表明，与野生型、功能相等和功能增强突变体相比，在VWF与GPIbɑ功能丧失的生物学突变体G233D结合时，盐桥形成的概率较低且非共价结合能较小，这表明诸如GPIbɑ等大分子的生物学功能受其物理特性微小变化的影响。
