Molecular Dynamics Simulations - Figure 2
FIGURE 2
(a) A schematic of the maximally similar nucleotide sequence alignment for exons 2 and 3:
898 to 1116 bp of the ER DBD c-DNA
(GenBank locus HSERR) vs Xenopus laevis vitellogenin
A1 ERE
(GenBank locus XLVITA15)
nucleotides ranging from -428 to
-278 upstream from the vitellogenin gene transcription start site.
Diagonal lines represent the maximally similar subsequence between VITA1ERE
(-373 TO -302) and HSERR (923 to 1002) respectively.
Sequence alignments were computed using LOCAL (39)
.
(b) At the top of figure 2b is shown the
VITA1 ERE which contains the maximally similar nucleotide sequence from figure 1a.
Small boxes contain the four
estrogen receptor binding half-sites: the distal, non-consensus ERE left and
right major groove half-sites AGTCA, TGACT and
and the proximal consensus ERE left and right major groove half-sites
GGTCA, TGACC respectively.
Nuclecotide base pair matches between VITA1ERE and HSERR c-DNA are starred.
Vertical bars indicate purine/pyrimidine matches.
Below the HSERR cDNA sequence is shown the corresponding
amino acid sequence in Dayhoff (36)
one-letter code with the amino acids numbered
as in the human ER (37). The recognition helix in the exon 2 alignment is underlined.
(c) The nucleotide sequence of the distal non-consensus VITA1 ERE
(see 2b) is translated to amino acids (in Dayhoff one-letter code) in all
reading frames (F1, F2, and F3), on both strands: top (rightward: sense 5'-3') and
bottom (leftward: antisense 5'-3'). Circles and triangles indicate codons in
the DNA sequence with which cognate amino acids from the ER DBD are aligned.
Circles = codons for exon 2 encoded DNA recognition helix amino acids, triangles
= codons for exon 3 encoded beta strand amino acids. The amino acid sequences of
these structures are shown at the bottom of the figure. Amino acids aligned with
cognate codons are indicated with dots.