ABINITIO FORCE-FIELD FOR SIMULATIONS OF PROTEINS AND NUCLEIC-ACIDS
ABINITIO FORCE-FIELD FOR SIMULATIONS OF PROTEINS AND NUCLEIC-ACIDS
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DOI：
10.1002/qua.560420514
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发表时间：
1992-06-05
影响因子：
2.2
通讯作者：
CLEMENTI, E
中科院分区：
文献类型：
--
作者：
AIDA, M;CORONGIU, G;CLEMENTI, E
我们提出了一个新的自洽的从头算分析对电位来预测特定的非键相互作用的蛋白质与核酸，蛋白质与蛋白质，核酸与核酸。 本研究的目的是代表生物分子之间的相互作用的准确性相当于从头算分子轨道计算，这是用来作为参考数据，以获得对电位。 核酸和蛋白质中的原子根据其化学环境进行分类。 一个“有效电荷”，从Mulliken人口分析获得的电荷的修改，被引入并用于代表静电能。 计算了30，000多个SCF相互作用能，为我们在势参数化中采用的拟合方法提供了参考数据。 对于跨越约-220 kcal/mol至+20 kcal/mol范围的相互作用能，标准偏差为1.61 kcal/mol。 分子动力学模拟，使用上述一套新的力场，已成功地进行了适当的治疗特定的相互作用的系统中，需要：的稳定性的α-螺旋的C-肽和精胺与寡核苷酸的相互作用作为初步的例子进行检查。
We present a new self-consistent set of ab initio analytical pair potential to predict specific nonbonded interactions of protein with nucleic acid, of protein with protein, and of nucleic acid with nucleic acid. The purpose of this study is to represent the interaction between biological molecules with an accuracy equivalent to the ab initio molecular orbital calculations, which are used as reference data to obtain the pair potentials. Atoms in nucleic acids and proteins are classified according to their chemical environments. An "effective charge," a modification of a charge obtained from the Mulliken population analysis, is introduced and used to represent the electrostatic energy. More than 30,000 SCF interaction energies have been calculated to provide the reference data for the fitting procedure that we have adopted in the parameterization of the potentials. The standard deviation is 1.61 kcal/mol for interaction energies spanning the range from about -220 kcal/mol to +20 kcal/mol. Molecular dynamics simulations, using the above new set of force field, have been performed successfully for the systems where adequate treatments of specific interactions are required: The stability of alpha-helix of C-peptide and the interaction of spermine with oligonucleotide are examined as preliminary examples.