Abstract:
There has been a great interest in the precise determination
of structure of DNA molecules of varying sequence and of
their complexes with protein molecules. But these biological
systems are very complex. So model systems have been
extensively used. The obvious advantage is the possibility to
investigate interactions of DNA-peptide system with
controlled amino acid composition, sequence, chain lengths
and predictable conformation which results in considerable
simplification of the system as compared to the natural
DNA-protein systems.
The present work is on a functional part of DNA binding lo
of Gene V Protein comprising of residues,
Lys -Pro-Tyr-Ser-Leu-Asn**. We have studied interaction of
this synthetic peptide with a single-stranded d(A) and
double-stranded DNA (d-GACTCGTC) by NMR techniques. One
dimensional NMR, 2D COSY and NOESY spectra are used to get
changes in chemical shift, T*., spin-spin couplings,
interproton distances, intermolecular NOEs and hence the
structural details. The results establish a role of Tyr, Lys,
Pro, and Leu residues.
We also present results obtained by theoretical calculations
using classical potential functions on the stacking of
nucleic acid bases (A,T,G,C) and base-pairs (AT,CG) with
aromatic amino acids. Intercalation of aromatic amino acids
between model dinucleotide systems such as d-CG, d-CC, d-AT,
d-AA have been studied. Unwinding and winding of DNA helix
upon intercalation have been investigated. Conformational
energy of complexes of amino acids with single- stranded DNA
have also been computed. Overlap geometries in the optimised
conformations have been obtained.
The trends in interaction energy suggest that Trp and His are
involved in the formation of more stable complex than Tyr and
Phe. Among dinucleotide model systems, homonucleotides show
strong binding to aromatic amino acids. The molecular
op
mechanisms involved in these interactions show a specificity
in protein-nucleic acid associations.
