Aqvist J, Leijonmarck M, Tapia O
Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala.
Eur Biophys J. 1989;16(6):327-39. doi: 10.1007/BF00257881.
The crystallographic dimer of the C-terminal fragment (CTF) of the L7/L12 ribosomal protein has been subjected to molecular dynamics (MD) simulations. A 90 picosecond (ps) trajectory for the protein dimer, 19 water molecules and two counter ions has been calculated at constant temperature. Effects of intermolecular interactions on the structure and dynamics have been studied. The exact crystallographic symmetry is lost and the atomic fluctuations differ from one monomer to the other. The average MD structure is more stable than the X-ray one, as judged by accessible surface area and energy calculations. Crystal (non-dimeric) interactions have been simulated in another 40 ps trajectory by using harmonic restraints to represent intermolecular hydrogen bonds. The conformational changes with respect to the X-ray structure are then virtually suppressed. The unrestrained dimer trajectory has been scanned for cooperative motions involving secondary structure elements. The intrinsic collective motions of the monomer are transmitted via intermolecular contacts to the dimer structure. The existence of a stable dimeric form of CTF, resembling the crystallographic one, has been documented. At the cost of fairly small energy expenditure the dimer has considerable conformational flexibility. This flexibility may endow the dimer with some functional potential as an energy transducer.
对L7/L12核糖体蛋白C末端片段（CTF）的晶体学二聚体进行了分子动力学（MD）模拟。在恒定温度下计算了该蛋白二聚体、19个水分子和两个抗衡离子的90皮秒（ps）轨迹。研究了分子间相互作用对结构和动力学的影响。精确的晶体学对称性丧失，且两个单体的原子波动情况不同。通过可及表面积和能量计算判断，平均MD结构比X射线结构更稳定。通过使用谐波约束来表示分子间氢键，在另一条40 ps轨迹中模拟了晶体（非二聚体）相互作用。相对于X射线结构的构象变化随后几乎被抑制。对无约束的二聚体轨迹进行扫描，以寻找涉及二级结构元件的协同运动。单体的固有集体运动通过分子间接触传递到二聚体结构。已证明存在一种类似于晶体学二聚体的稳定CTF二聚体形式。以相当小的能量消耗为代价，二聚体具有相当大的构象灵活性。这种灵活性可能赋予二聚体作为能量转换器的一些功能潜力。
