Shinobu Ai, Agmon Noam
The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel.
J Phys Chem B. 2015 Feb 26;119(8):3464-78. doi: 10.1021/jp5127255. Epub 2015 Feb 13.
Internal water molecules in proteins are conceivably part of the protein structure, not exchanging easily with the bulk. We present a detailed molecular dynamics study of the water molecule bound to the green fluorescent protein (GFP) chromophore that conducts its proton following photoexcitation. It readily exchanges above 310 K through a hole that forms between strands 7 and 10, due to fluctuations in the 6-7 loop. As the hole widens, rapid succession of water exchange events occur. The exiting water molecule passes three layers of atoms, constituting the binding, internal, and surface sites. Along this pathway, hydrogen bonding protein residues are replaced with water molecules. The mean squared displacement along this pathway is initially subdiffusive, becomes superdiffusive as the water traverses the protein wall in a flip-flop motion, and reverts to normal diffusion in the bulk. The residence correlation function for the bound state decays biexponentially, supporting this three-site scenario. For a favorable orientation of the Thr203 side-chain, the hole often fills with a single file of water molecules that could indeed rapidly conduct the photodissociated proton outside the protein. The activation enthalpy for its formation, 26 kJ/mol, agrees with the experimental value for a protein conformation change suggested to gate proton escape.
蛋白质内部的水分子可以想象是蛋白质结构的一部分，不易与主体水分子交换。我们对与绿色荧光蛋白（GFP）发色团结合的水分子进行了详细的分子动力学研究，该发色团在光激发后会传导质子。由于6 - 7环的波动，在310 K以上，它会通过7链和10链之间形成的一个孔快速交换。随着孔变宽，水交换事件快速连续发生。离开的水分子穿过三层原子，分别构成结合位点、内部位点和表面位点。沿着这条路径，与蛋白质形成氢键的残基会被水分子取代。沿着这条路径的均方位移最初是亚扩散的，当水分子以翻转运动穿过蛋白质壁时变为超扩散，然后在主体中恢复为正常扩散。结合态的停留相关函数呈双指数衰减，支持了这种三位点的情况。对于苏氨酸203侧链的有利取向，孔中常常会充满一排水分子，这些水分子确实可以将光解离的质子快速传导到蛋白质外部。其形成的活化焓为26 kJ/mol，与推测为质子逃逸门控的蛋白质构象变化的实验值相符。
