Guo Weihua, Lampoudi Sotiria, Shea Joan-Emma
Department of Chemistry, University of California, Santa Barbara, California 93106, USA.
Biophys J. 2003 Jul;85(1):61-9. doi: 10.1016/S0006-3495(03)74454-3.
The folding thermodynamics of the src-SH3 protein domain were characterized under refolding conditions through biased fully atomic molecular dynamics simulations with explicit solvent. The calculated free energy surfaces along several reaction coordinates revealed two barriers. The first, larger barrier was identified as the transition state barrier for folding, associated with the formation of the first hydrophobic sheet of the protein. phi values calculated from structures residing at the transition state barrier agree well with experimental phi values. The microscopic information obtained from our simulations allowed us to unambiguously assign intermediate phi values as the result of multiple folding pathways. The second, smaller barrier occurs later in the folding process and is associated with the cooperative expulsion of water molecules between the hydrophobic sheets of the protein. This posttransition state desolvation barrier cannot be observed through traditional folding experiments, but is found to be critical to the correct packing of the hydrophobic core in the final stages of folding. Hydrogen exchange and NMR experiments are suggested to probe this barrier.
通过带有显式溶剂的有偏全原子分子动力学模拟，在重折叠条件下对src-SH3蛋白结构域的折叠热力学进行了表征。沿着几个反应坐标计算得到的自由能面显示出两个障碍。第一个更大的障碍被确定为折叠的过渡态障碍，与蛋白质第一个疏水片层的形成有关。从处于过渡态障碍的结构计算得到的φ值与实验得到的φ值吻合良好。从我们的模拟中获得的微观信息使我们能够明确地将中间φ值归因于多种折叠途径。第二个较小的障碍出现在折叠过程的后期，与蛋白质疏水片层之间水分子的协同排出有关。这种过渡态后去溶剂化障碍无法通过传统的折叠实验观察到，但被发现对折叠最后阶段疏水核心的正确堆积至关重要。建议通过氢交换和核磁共振实验来探测这一障碍。
