Electrostatic surface potential analysis of the dhax3 superhelical
assembly shows positively charged amino acids (e.g. Lys16 and
Gln17) running along the its inner surface. The
amino acids, positioned at the start of each “b” helix repeat, enable
the accommodation of
the negatively charged phosphate groups
on the DNA sense strand into surface pockets, encouraging interactions
mediated by hydrogen bonds between the DNA duplex and
the dHax3 repeats.
Figure 4.1 The positively charged
inner surface (blue) interacting with the negatively charged sugar
phosphate backbone of DNA sense strand.
Residues 12 and 13 on the RVD loop are found close to the major groove of the sense DNA strand and have different
biochemical functions in dHax3. The His or Asn side chains at
position 12 does not directly contact
or recognise the DNA, but
actually points away from the bases forming H bonds with the
carbonyl oxygen atom of the regular Ala8 present at each
TAL repeat’s C-terminal. In addition water-mediated H bonds between the His12 imidazole
in TAL repeat 1 and the Asp13 carboxylate oxygen atom of
repeat 2 demonstrate that the 12th residue
aids in stabilising the RVD loop
conformations and indirectly contributes to DNA binding, while residue 13 chiefly recognises the DNA bases.
Figure 4.2 1 to 4 TALE repeats of dHax3. The side chain of each 12th amino acid of each repeat hydrogen bonded to the 8th Alanine amino acid.
dHax3 TAL repeats predominantly use three codes
located at the hypervariable residues to recognise DNA bases. These are the amino acids HD, NG
and NS, which specifically identify the DNA bases C, T, and A respectively, and have
structurally sound reasons within DNA-bound dHax3 for this. For HD (His12, Asp13)
to recognise the Cytosine DNA
base the carboxylate oxygen of
Asp13 must accept a H bond from the amine
group of cytosine. For NS (Asn12,
Ser13) the hydroxyl group of Ser13 donates a H bond to the adenine DNA base N7 atom identifying
it. Recognition of DNA base guanine is thought to be similar to
adenine differentiation with
the use of the Ser13 residue.
However, distinguishing Thymine DNA base with NG (Asn12,
Gly13) residues is different to the others due to the Gly13 providing
the thymine’s 5-methyl group with sufficient space to
exist in that position without causing any steric clashes, allowing van
der Waal interactions to occur between
the Cα of
Gly13 and the thymine 5-methyl group. This suggests why Glycine
is often required for thymine recognition, but could mean that mutation of Gly13 to
a short side chained amino acid will also permit thymine identification.
Figure 4.3 The interaction of residue 13 of repeat 1 to 4 of
dHax3 with DNA bases.
With many other blogs choosing to fill their pages up to their capacity, I thought the minimal layout of the pages with was a key feature of this blog. It allowed me to focus on the detailed content and great structural images. However navigation around the blog was hard work and there was a lack of interactive links, which could easily be addressed.
ReplyDelete