Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States.
Biochemistry. 2014 Oct 21;53(41):6473-95. doi: 10.1021/bi500904f. Epub 2014 Oct 7.
Intrinsically disordered proteins (IDPs) often rely on electrostatic interactions to bind their structured targets. To obtain insight into the mechanism of formation of the electrostatic encounter complex, we investigated the binding of the peptide Sos (PPPVPPRRRR), which serves as a minimal model for an IDP, to the c-Crk N-terminal SH3 domain. Initially, we measured ¹⁵N relaxation rates at two magnetic field strengths and determined the binding shifts for the complex of Sos with wild-type SH3. We have also recorded a 3 μs molecular dynamics (MD) trajectory of this complex using the Amber ff99SB*-ILDN force field. The comparison of the experimental and simulated data shows that MD simulation consistently overestimates the strength of salt bridge interactions at the binding interface. The series of simulations using other advanced force fields also failed to produce any satisfactory results. To address this issue, we have devised an empirical correction to the Amber ff99SB*-ILDN force field whereby the Lennard-Jones equilibrium distance for the nitrogen-oxygen pair across the Arg-to-Asp and Arg-to-Glu salt bridges has been increased by 3%. Implementing this correction resulted in a good agreement between the simulations and the experiment. Adjusting the strength of salt bridge interactions removed a certain amount of strain contained in the original MD model, thus improving the binding of the hydrophobic N-terminal portion of the peptide. The arginine-rich C-terminal portion of the peptide, freed from the effect of the overstabilized salt bridges, was found to interconvert more rapidly between its multiple conformational states. The modified MD protocol has also been successfully used to simulate the entire binding process. In doing so, the peptide was initially placed high above the protein surface. It then arrived at the correct bound pose within ∼2 Å of the crystallographic coordinates. This simulation allowed us to analyze the details of the dynamic binding intermediate, i.e., the electrostatic encounter complex. However, an experimental characterization of this transient, weakly populated state remains out of reach. To overcome this problem, we designed the double mutant of c-Crk N-SH3 in which mutations Y186L and W169F abrogate tight Sos binding and shift the equilibrium toward the intermediate state resembling the electrostatic encounter complex. The results of the combined NMR and MD study of this engineered system will be reported in the next part of this paper.
无规则蛋白质 (IDPs) 通常依赖静电相互作用来结合其结构靶标。为了深入了解静电遭遇复合物形成的机制,我们研究了肽 Sos (PPPVPPRRRR) 的结合情况,该肽是 IDP 的最小模型,与 c-Crk N 端 SH3 结构域结合。最初,我们在两个磁场强度下测量了 ¹⁵N 弛豫率,并确定了 Sos 与野生型 SH3 复合物的结合位移。我们还使用 Amber ff99SB*-ILDN 力场记录了这个复合物的 3 μs 分子动力学 (MD) 轨迹。实验数据和模拟数据的比较表明,MD 模拟始终高估了结合界面上盐桥相互作用的强度。使用其他先进力场的一系列模拟也没有产生任何令人满意的结果。为了解决这个问题,我们对 Amber ff99SB*-ILDN 力场进行了经验修正,其中 Arg 到 Asp 和 Arg 到 Glu 盐桥的氮氧对的 Lennard-Jones 平衡距离增加了 3%。实施此修正后,模拟与实验结果吻合较好。调整盐桥相互作用的强度消除了原始 MD 模型中包含的一定应变,从而改善了肽的疏水性 N 端部分的结合。肽的富含精氨酸的 C 端部分不受过稳定盐桥的影响,发现其在多种构象状态之间快速转换。改进后的 MD 方案还成功地用于模拟整个结合过程。在此过程中,肽最初被放置在蛋白质表面上方。然后,它在与晶体坐标相差约 2 Å 的范围内到达正确的结合位置。这种模拟使我们能够分析动态结合中间物,即静电遭遇复合物的细节。然而,对这种瞬态、低丰度状态的实验表征仍然难以实现。为了克服这个问题,我们设计了 c-Crk N-SH3 的双突变体,其中突变 Y186L 和 W169F 消除了 Sos 的紧密结合,并将平衡向类似于静电遭遇复合物的中间状态转移。该工程系统的 NMR 和 MD 联合研究的结果将在下一部分中报告。