| Nucleic acids and proteins are composed of two important material in organisms. Synthesis of protein depends on the nucleic acid, and the synthesis of nucleic acid is also dependent on the role of the protein. Interactions between bases and protein participate in many biological processes in the life. Studies on the interaction make people understand the specific mechanism of gene expression, also it is the key to reveal the arcanum of life.There are two types of nucleic acids, deoxynucleic acid (DNA) and ribonucleic acid (RNA), these two types of nucleic acids that contain five bases. DNA replication, repairing and recombination must depend on the interaction with the protein. NMA(N-methylacetamide) is one of the typical unit in protein. Taking NMA and the bases in nucleic acids as the studied objects, we investigate their interaction properties including geometry, charge distribution and binding energy of these NMA-base complexes in terms of the ABEEMσπ/MM method and the ab initio MP2 method. The geometry optimizations are performed at the B3LYP/6-311++G(d,p) level. We compared the results of ABEEMσπ/MM and ab initio methods. It shows that the results from ABEEMσπ/MM and ab initio methods have good agreement. The order of relative binding ability of interaction between NMA and bases holds: guanine >thymine >cytosine >uracil >adenine. The parameters of ABEEMσπ/MM have good transferability. This study provides a solid foundation for the research of interaction between the protein and nucleic acid by using the ABEEMσπ/MM model.1-2 waters are added to the NMA-bases complexes. The 59 geometries optimizations are performed at the B3LYP/6-31++G(d,p) level. the binding energies are calculated by ab initio (MP2/6-311 + + G (d, p)) method. The order of relative binding ability of interaction between NMA-base and water holds: guanine> cytosine> adenine> thymine> uracil. This work will lay a solid foundation for simulating the interaction between NMA and bases in water. |
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