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 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.