Molecular Dynamics Simulations - 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
(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.