Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations
Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations
复制标题
DOI：
10.1016/j.sbi.2007.03.018
复制
发表时间：
2007-04-01
影响因子：
6.8
通讯作者：
Carloni, Paolo
中科院分区：
文献类型：
--
作者：
Dal Peraro, Matteo;Ruggerone, Paolo;Carloni, Paolo
基于密度泛函理论（DFT）的Car-Parrinello分子动力学（CPMD）模拟描述了分子系统的时间演化，而不诉诸于预定义的势能面。CPMD和混合分子力学/CPMD计划最近使计算的氧化还原性质的电子转移蛋白质在其复杂的生物环境。他们提供了靶向DNA的新型铂基抗癌药物的结构和光谱信息，也为金属损伤的力场构建奠定了基础。分子力学/CPMD也导致各种金属酶的机制假说。最近的进展，提高DFT的准确性和调查罕见事件的效率，进一步扩大了CPMD应用领域的生物分子。
Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have recently enabled the calculation of redox properties of electron transfer proteins in their complex biological environment. They provided structural and spectroscopic information on novel platinum-based anticancer drugs that target DNA, also setting the basis for the construction of force fields for the metal lesion. Molecular mechanics/CPMD also lead to mechanistic hypotheses for a variety of metalloenzymes. Recent advances that increase the accuracy of DFT and the efficiency of investigating rare events are further expanding the domain of CPMD applications to biomolecules.