FIGURE 2
A computer model of NMR GR DBD dimer in complex with the 29 bp nucleotide sequence of MMTV GRE from GENBANK locus MMTPRGR1. The protein is docked at a distance of about 10 angstroms from the DNA for visual clarity. Color coding for nucleotides and amino acids is as in figure 1. Amino acids of the GR DBD which are oriented toward the GRE are labelled using the Dayhoff one letter code (51) and are numbered as in the rat GR (52) . The following amino acids are labeled: Exon 3 encoded amino acids of the first "zinc finger", H 451 and Y 452, exon 3 encoded DNA recognition helix amino acids, K 461, K 465, R 466, E 469, and G 470, exon 4 encoded beta strand amino acids, Q 471, H 472, N 473, Y 474, L 475, and C 476 and finally, exon 5 encoded predicted alpha helix amino acids, R 510, K 511, K 513, K 514, K 515, and K 517. The nucleotide sequence of the DNA model was derived from a GRE within GeneBank locus MMTPRGR1 which shared maximal nucleotide subsequence similarity with subsequences within the GR cDNA encoding the DNA recognition helix in exon 3, a beta strand in exon 4 and a predicted alpha helix in exon 5 (22). Above the DNA model is a schematic of the MMTPRGR1 GRE and flanking regions, numbered above and below with the 5' sense strand read left to right, starting at -190 upstream from the mouse mammary tumor virus (MMTV) transcription start site and ending at -162 = 1 to 29. The antisense strand reads right to left from -162 to -190 = 30 to 58. GR binding sites have been detected with nuclease footprinting studies by others and are shown as large boxes (53) and dashed underlines and overlines (32-33). Small boxes contain the two glucocorticoid receptor binding half-sites GTTACA and TGTTCT respectively. Methylation inhibition studies by others (32) are summarized with the following symbols: Triangles show nucleotides where methylation inhibits receptor binding. The circles show nucleotides which, when methylated, do not inhibit receptor binding but cannot be methylated after receptor is bound. The square shows a guanine that is hypermethylated in the presence of bound receptor. The GR/GRE model shown is to be used as a key for locating interactions from molecular dynamics found between the GR DBD amino acids and nucleotides of the GRE and its flanks (see Table I). The color coding and numbering scheme in this figure is used in all subsequent molecular models.