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Theoretical studies on protein–nucleic acid interactions. III. Stacking of aromatic amino acids with bases and base pairs of nucleic acids

✍ Scribed by N. Vasant Kumar; Girjesh Govil

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

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✦ Synopsis

Stacking of aromatic amino acids tryptophan (Trp), tyrosine (Tyr), phenylalanine (Phe), and histidine (His) with bases and base pairs of nucleic acids has been studied. Stacking energies of the amino acid-base (or base pair) complexes have been calculated by second-order perturbation theory. Our results show that, in general, the predominant contribution to the total stacking energy comes from the dispersion term. In these cases, repulsion energy is greater than the sum of electrostatic and polarization energies. In contrast to this, interaction of histidine with the bases and base pairs is largely Coulombic in nature. The complexes of guanine with aromatic amino acids are more stable than the corresponding complexes of adenine. Among pyrimidines, cytosine forms the most stable complexes with the aromatic amino acids. The G C base pair has the highest affinity with aromatic amino acids among various sets of base pairs. Optimized geometries of the stacked complexes show that the aromatic moieties overlap only partially. The heteroatom of one residue generally overlaps with the other aromatic moiety. There is a considerable degree of configurational freedom in the stacked geometries. The role of stacking in specific recognition of base sequences by proteins is discussed.

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