Dennis S, Camacho C J, Vajda S
Department of Biomedical Engineering, Boston University, Massachusetts 02215, USA.
Proteins. 2000 Feb 1;38(2):176-88.
To understand water-protein interactions in solution, the electrostatic field is calculated by solving the Poisson-Boltzmann equation, and the free energy surface of water is mapped by translating and rotating an explicit water molecule around the protein. The calculation is applied to T4 lysozyme with data available on the conservation of solvent binding sites in 18 crystallographically independent molecules. The free energy maps around the ordered water sites provide information on the relationship between water positions in crystal structure and in solution. Results show that almost all conserved sites and the majority of nonconserved sites are within 1.3 A of local free energy minima. This finding is in sharp contrast to the behavior of randomly placed water molecules in the boundary layer, which, on the average, must travel more than 3 A to the nearest free energy minimum. Thus, the solvation sites are at least partially determined by protein-water interactions rather than by crystal packing alone. The characteristic water residence times, obtained from the free energies at the local minima, are in good agreement with nuclear magnetic resonance experiments. Only about half of the potential sites show up as ordered water in the 1.7 A resolution X-ray structure. Crystal packing interactions can stabilize weak or mobile potential sites (in fact, some ordered water positions are not close to free energy minima) or can prevent water from occupying certain sites. Apart from a few buried water molecules that are strong binders, the free energies are not very different for conserved and nonconserved sites. We show that conservation of a water site between two crystals occurs if the positions of protein atoms, primarily contributing to the free energy at the local minimum, do not substantially change from one structure to the other. This requirement can be correlated with the nature of the side chain contacting the water molecule in the site.
为了理解溶液中的水 - 蛋白质相互作用，通过求解泊松 - 玻尔兹曼方程来计算静电场，并通过在蛋白质周围平移和旋转一个明确的水分子来绘制水的自由能表面。该计算应用于T4溶菌酶，有关于18个晶体学上独立分子中溶剂结合位点保守性的数据可用。有序水位点周围的自由能图提供了晶体结构和溶液中水位置之间关系的信息。结果表明，几乎所有保守位点和大多数非保守位点都在局部自由能最小值的1.3埃范围内。这一发现与边界层中随机放置的水分子的行为形成鲜明对比，随机放置的水分子平均而言必须移动超过3埃才能到达最近的自由能最小值。因此，溶剂化位点至少部分由蛋白质 - 水相互作用决定，而不仅仅由晶体堆积决定。从局部最小值处的自由能获得的特征水停留时间与核磁共振实验结果吻合良好。在1.7埃分辨率的X射线结构中，只有大约一半的潜在位点显示为有序水。晶体堆积相互作用可以稳定弱的或可移动的潜在位点（实际上，一些有序水的位置并不靠近自由能最小值），或者可以阻止水占据某些位点。除了少数作为强结合剂的埋藏水分子外，保守位点和非保守位点的自由能并没有太大差异。我们表明，如果主要对局部最小值处的自由能有贡献的蛋白质原子位置在两种结构之间没有实质性变化，那么两个晶体之间就会出现水位点的保守性。这一要求可以与位点中与水分子接触的侧链性质相关联。
