Building better fibrin knob mimics: an investigation of synthetic fibrin knob peptide structures in solution and their dynamic binding with fibrinogen/fibrin holes
Building better fibrin knob mimics: an investigation of synthetic fibrin knob peptide structures in solution and their dynamic binding with fibrinogen/fibrin holes
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DOI：
10.1182/blood-2009-11-251801
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发表时间：
2010-08-26
期刊：
影响因子：
20.3
通讯作者：
Barker, Thomas H.
中科院分区：
文献类型：
--
作者：
Stabenfeldt, Sarah E.;Gossett, J. Jared;Barker, Thomas H.
凝血酶通过凝血酶暴露的“球”与互补的“孔”的非共价和动态缔合而聚合。“合成的旋钮肽作为理解纤维蛋白组装机制和抑制纤维蛋白聚合的手段已经受到了极大的关注。然而，不能结晶短肽显着限制了我们的理解旋钮肽的结构特征，调节动态旋钮：孔相互作用。在这项研究中，我们使用分子模拟来生成纤维蛋白孔接合之前溶液中合成旋钮的第一个预测结构。结合表面等离子体共振（SPR），我们探讨了结构和静电性质的旋钮“A”模拟物在调节旋钮：空穴结合动力学的作用。SPR的结果表明，协会率是最深刻的影响，存在额外的脯氨酸以及带电残基在第六至第七位。重要的是，通过模拟分析肽的结构动力学表明，3Arg侧链取向和肽骨架稳定性各自对功能性结合有显著贡献。这些发现提供了对早期纤维蛋白原纤维组装动力学的见解，以及建立高亲和力旋钮模拟物的基本设计参数，其更有效地竞争空穴占据，这里通过一种新型旋钮模拟物实现的参数显示出比当前模拟物高10倍的缔合速率。（血。2010; 116（8）：1352-1359）
Fibrin polymerizes via noncovalent and dynamic association of thrombin-exposed "knobs" with complementary "holes." Synthetic knob peptides have received significant interest as a means for understanding fibrin assembly mechanisms and inhibiting fibrin polymerization. Nevertheless, the inability to crystallize short peptides significantly limits our understanding of knob peptide structural features that regulate dynamic knob: hole interactions. In this study, we used molecular simulations to generate the first pre-dicted structure(s) of synthetic knobs in solution before fibrin hole engagement. Combining surface plasmon resonance (SPR), we explored the role of structural and electrostatic properties of knob "A" mimics in regulating knob: hole binding kinetics. SPR results showed that association rates were most profoundly affected by the presence of both additional prolines as well as charged residues in the sixth to seventh positions. Importantly, analyzing the structural dynamics of the peptides through simulation indicated that the 3Arg side chain orientation and peptide backbone stability each contribute significantly to functional binding. These findings provide insights into early fibrin protofibril assembly dynamics as well as establishing essential design parameters for high-affinity knob mimics that more efficiently compete for hole occupancy, parameters realized here through a novel knob mimic displaying a 10-fold higher association rate than current mimics. (Blood. 2010; 116(8): 1352-1359)