Premium
Theoretical studies on protein–nucleic acid interactions. I. Interaction of positively charged amino acids with nucleic acid fragments
Author(s) -
Kumar N. Vasant,
Govil Girjesh
Publication year - 1984
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360231013
Subject(s) - nucleic acid , chemistry , dna , rna , amino acid , interaction energy , nucleic acid structure , biochemistry , biophysics , organic chemistry , molecule , biology , gene
Coulombic interactions between the side chains of charged amino acids (Arg + , Lys + , and His + ) and negatively charged phosphate groups of nucleic acid fragments have been studied theoretically. Diribose monophosphate and dideoxyribose monophosphate are chosen as model systems for single‐stranded RNA and DNA, respectively. The interaction energies have been calculated by second‐order perturbation theory using simplified formulas for individual terms. The interaction energy in this formalism is a sum of electrostatic, polarization, dispersion, and repulsive energies. Our results show that about 90% of the total interaction energy is contributed by the electrostatic term alone. Contribution from the repulsive term exceeds that from the dispersion term. Calculated interaction energies suggest that Lys + and His + form more stable complexes with RNA than with single‐stranded DNA. On the other hand, Arg + has a higher affinity for DNA than for RNA. The affinity of nucleic acids for the three amino acids is in the order Lys + > His + > Arg + . Further, the basic amino acid residues form more stable complexes with A‐DNA than with B‐DNA. The role of the Coulombic interactions in the specific recognition of nucleic acids by proteins is discussed.