Hyre David E, Amon Lynn M, Penzotti Julie E, Le Trong Isolde, Stenkamp Ronald E, Lybrand Terry P, Stayton Patrick S
Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA.
Nat Struct Biol. 2002 Aug;9(8):582-5. doi: 10.1038/nsb825.
The streptavidin-biotin system has provided a unique opportunity to investigate the molecular details of ligand dissociation pathways. An underlying mechanistic question is whether ligand dissociation proceeds with a relatively ordered process of bond breaking and ligand escape. Here we report a joint computational and crystallographic study of the earliest events in biotin dissociation. In molecular dynamics potential of mean force simulations, a water molecule from a defined access channel intercalated into the hydrogen bond between Asp 128 and biotin, bridging them and stabilizing an intermediate state. In forced biotin dissociation simulations, this event led to subsequent bond breaking steps and ligand escape. In equilibrium simulations, the water molecule was sometimes observed to move back to the access channel with re-formation of the biotin hydrogen bond. Analysis of streptavidin crystal structures revealed a close overlap of crystallographically defined and simulated waters in the water access channel. These results suggest that biotin dissociation is initiated by stochastic coupling of water entry with lengthening of a specific biotin hydrogen-bonding interaction.
链霉亲和素-生物素系统为研究配体解离途径的分子细节提供了独特的机会。一个潜在的机制问题是，配体解离是否通过相对有序的键断裂和配体逸出过程进行。在此，我们报告了一项关于生物素解离早期事件的联合计算和晶体学研究。在分子动力学平均力势模拟中，来自特定进入通道的一个水分子插入到天冬氨酸128与生物素之间的氢键中，连接二者并稳定一个中间状态。在强制生物素解离模拟中，这一事件导致了随后的键断裂步骤和配体逸出。在平衡模拟中，有时会观察到水分子回到进入通道，生物素氢键重新形成。对链霉亲和素晶体结构的分析揭示了在水进入通道中晶体学定义的水和模拟的水有紧密重叠。这些结果表明，生物素解离是由水进入与特定生物素氢键相互作用延长的随机耦合引发的。
