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Theoretical studies on protein–nucleic acid interactions. I. Interaction of positively charged amino acids with nucleic acid fragments

✍ Scribed by N. Vasant Kumar; Girjesh Govil

Publisher
Wiley (John Wiley & Sons)
Year
1984
Tongue
English
Weight
703 KB
Volume
23
Category
Article
ISSN
0006-3525

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✦ Synopsis

Coulombic interactions between the side chains of charged amino acids (Arg + , Lys-, and H i s + ) and negatively charged phosphate groups of nucleic acid fragments have been studied theoretically. Diribose monophosphate and dideoxyribose monophosphate a r e 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.

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