Gu W, Schoenborn B P
Department of Biochemistry, University of New Mexico, Albuquerque 87545, USA.
Proteins. 1995 May;22(1):20-6. doi: 10.1002/prot.340220104.
This study was carried out to evaluate the stability of the 89 bound water molecules that were observed in the neutron diffraction study of CO myoglobin. The myoglobin structure derived from the neutron analysis was used as the starting point in the molecular dynamics simulation using the software package CHARMM. After solvation of the protein, energy minimization and equilibration of the system, 50 ps of Newtonian dynamics was performed. This data showed that only 4 water molecules are continuously bound during the length of this simulation while the other solvent molecules exhibit considerable mobility and are breaking and reforming hydrogen bonds with the protein. At any instant during the simulation, 73 of the hydration sites observed in the neutron structure are occupied by water.
本研究旨在评估在一氧化碳肌红蛋白的中子衍射研究中观察到的89个结合水分子的稳定性。源自中子分析的肌红蛋白结构被用作使用CHARMM软件包进行分子动力学模拟的起点。在蛋白质溶剂化、系统能量最小化和平衡之后，进行了50皮秒的牛顿动力学模拟。该数据表明，在该模拟过程中，只有4个水分子持续结合，而其他溶剂分子表现出相当大的流动性，并且正在与蛋白质断裂和重新形成氢键。在模拟过程中的任何时刻，中子结构中观察到的73个水合位点被水占据。
