Lamoureux Guillaume, Klein Michael L, Bernèche Simon
Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Biophys J. 2007 May 1;92(9):L82-4. doi: 10.1529/biophysj.106.102756. Epub 2007 Mar 9.
The accessibility of water molecules to the pore of the AmtB ammonium transporter is studied using molecular dynamics simulations. Free energy calculations show that the so-called hydrophobic pore can stabilize a chain of water molecules in a well of a few kcal/mol, using a favorable electrostatic binding pocket as an anchoring point. Moreover, the structure of the water chain matches precisely the electronic density maxima observed in x-ray diffraction experiments. This result questions the general assumption that the AmtB pore only contains ammonia (NH(3)) molecules diffusing in a single file fashion. The probable presence of water molecules in the pore would influence the relative stability of NH(3) and NH(4)(+), and thus calls for a reassessment of the overall permeation mechanism in ammonium transporters.
利用分子动力学模拟研究了水分子进入AmtB铵转运蛋白孔道的可及性。自由能计算表明，所谓的疏水孔道可以利用一个有利的静电结合口袋作为锚定点，在几千卡/摩尔的势阱中稳定一串水分子。此外，水链的结构与X射线衍射实验中观察到的电子密度最大值精确匹配。这一结果对AmtB孔道仅包含以单列方式扩散的氨（NH₃）分子这一普遍假设提出了质疑。孔道中可能存在的水分子会影响NH₃和NH₄⁺的相对稳定性，因此需要重新评估铵转运蛋白的整体渗透机制。
