标题： 纤维蛋白中突起-孔相互作用的分子机制、热力学和解离动力学 显示英文标题

标题： Molecular mechanisms, thermodynamics, and dissociation kinetics of knob-hole interactions in fibrin

摘要： 纤维蛋白的聚合，即血凝块和血栓的主要结构蛋白，通过纤维蛋白单体中心结节中的“A”和“B”突起与另一个单体的β-和γ-结节中的互补孔“a”和“b”结合而发生。 我们使用分子动力学模拟研究了在不同溶液条件下A:a和B:b突起-孔相互作用的结构模型，这些模型是纤维蛋白(原)片段D与合成肽GPRP（突起“A”模拟物）和GHRP（突起“B”模拟物）复合的结构模型。 A:a和B:b突起-孔复合物的强度大致相等，随着拉力的增加而降低；然而，解离动力学对酸度（pH=5-7）和温度（T=25-37 C）的变化敏感。 在强制解离突起-孔复合物过程中，孔“a”和“b”出现了类似的结构变化：环I的伸长、内部区域的拉伸以及可移动瓣膜的位移。 突起-孔相互作用的破坏并不是一个“全有或全无”的转变，因为它可以通过具有或不具有中间状态的两个步骤或单一步骤途径发生。 在pH=7时，突起-孔键更强、更紧密且更脆，而在pH=5时则较弱、更松散且更具适应性。 在pH=7时，B:b突起-孔键比A:a突起-孔键弱、更松散且更具适应性，但在pH=5时则更强、更紧密且适应性较差。 令人惊讶的是，由于环I的螺旋-线圈转变有助于稳定键，与T=25 C相比，在升高温度（T=37 C）下突起-孔键更强，而非更弱。 这些结果提供了关于纤维蛋白聚合中最重要非共价相互作用的详细定性和定量特征。 显示英文摘要

摘要： Polymerization of fibrin, the primary structural protein of blood clots and thrombi, occurs through binding of knobs 'A' and 'B' in the central nodule of fibrin monomer to complementary holes 'a' and 'b' in the beta- and gamma-nodules, respectively, of another monomer. We characterized the A:a and B:b knob-hole interactions under varying solution conditions using Molecular Dynamics simulations of the structural models of fibrin(ogen) fragment D complexed with synthetic peptides GPRP (knob 'A' mimetic) and GHRP (knob 'B' mimetic). The strength of A:a and B:b knob-hole complexes was roughly equal, decreasing with pulling force; yet, the dissociation kinetics were sensitive to variations in acidity (pH=5-7) and temperature (T=25-37 C). There were similar structural changes in holes 'a' and 'b' during forced dissociation of the knob-hole complexes: elongation of loop I, stretching of interior region, and translocation of the moveable flap. The disruption of the knob-hole interactions was not an "all-or-none" transition, as it occurred through distinct two-step or single-step pathways with or without intermediate states. The knob-hole bonds were stronger, tighter, and more brittle at pH=7 than at pH=5. The B:b knob-hole bonds were weaker, looser, and more compliant than the A:a knob-hole bonds at pH=7, but stronger, tighter, and less compliant at pH=5. Surprisingly, the knob-hole bonds were stronger, not weaker, at elevated temperature (T=37 C) compared to T=25 C due to the helix-to-coil transition in loop I, which helps stabilize the bonds. These results provide detailed qualitative and quantitative characteristics underlying the most significant non-covalent interactions involved in fibrin polymerization.