Waldauer Steven A, Stucki-Buchli Brigitte, Frey Lukas, Hamm Peter
Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland.
J Chem Phys. 2014 Dec 14;141(22):22D514. doi: 10.1063/1.4897975.
By covalently binding a photoswitchable linker across the binding groove of the PDZ2 domain, a small conformational change can be photo-initiated that mimics the allosteric transition of the protein. The response of its binding groove is investigated with the help of ultrafast pump-probe IR spectroscopy from picoseconds to tens of microseconds. The temperature dependence of that response is compatible with diffusive dynamics on a rugged energy landscape without any prominent energy barrier. Furthermore, the dependence of the kinetics on the concentration of certain viscogens, sucrose, and glycerol, has been investigated. A pronounced viscosity dependence is observed that can be best fit by a power law, i.e., a fractional viscosity dependence. The change of kinetics when comparing sucrose with glycerol as viscogen, however, provides strong evidence that direct interactions of the viscogen molecule with the protein do play a role as well. This conclusion is supported by accompanying molecular dynamics simulations.
通过在PDZ2结构域的结合凹槽上共价连接一个可光开关的连接子，可以光引发一个小的构象变化，该变化模拟了蛋白质的变构转变。借助从皮秒到数十微秒的超快泵浦-探测红外光谱研究了其结合凹槽的响应。该响应的温度依赖性与崎岖能量景观上的扩散动力学兼容，没有任何明显的能垒。此外，还研究了动力学对某些粘性剂（蔗糖和甘油）浓度的依赖性。观察到明显的粘度依赖性，其最适合用幂律拟合，即分数粘度依赖性。然而，当将蔗糖与甘油作为粘性剂进行比较时，动力学的变化提供了强有力的证据，表明粘性剂分子与蛋白质的直接相互作用也起到了作用。这一结论得到了伴随的分子动力学模拟的支持。
