Sequence-specific interactions with

Figure 9.10 Schematic diagrams illustrating the complex between DNA (orange) and one monomer of the homeodomain. The recognition helix (red) binds in the major groove of DNA and provides the sequence-specific interactions with bases in the DNA. The N-terminus (green) binds in the minor groove on the opposite side of the DNA molecule and arginine side chains make nonspecific interactions with the phosphate groups of the DNA. (Adapted from C.R. Kissinger et al Cell 63 579-590, 1990.)...

Figure 9.19 shows the sequence of the DNA that was used for the structure determination of the p53-DNA complex the bases involved in sequence-specific binding to the protein are shaded. One molecule of the DNA-bind-ing domain of p53 binds to the minor and the major grooves of the DNA making sequence-specific interactions with both strands (Figure 9.20). 

Figure 10.4 Detailed view of the binding of the second zinc finger of Zif 268 to DNA. Two side chains, Arg 46 and His 49, form sequence-specific interactions with DNA. There are also three nonspecific interactions between phosphate groups of the DNA and the side chains of Arg 42, Ser 45, and His 53.

Three residues in the recognition helix provide the sequence-specific interactions with DNA... 

There is only one sequence-specific interaction with an amino acid side chain, which is provided by Lys 18 (red). The linker region is an extended chain that follows one strand of the DNA and provides several nonspecific contacts (blue) to the DNA. The numbering of the base pairs starts from the center of the DNA fragment. (Adapted from R. Matmorstein et al., Nature 356 408 14, 1992.)... 

Figure 16.19 Schematic drawing illustrating the structure and sequence of the RNA fragment that is recognized and bound by the coat protein of bacteriophage MS2. The RNA fragment forms a base-paired stem with a bulge at base -10 and a loop of four bases. Bases that form sequence-specific Interactions with the coat protein are red. (Adapted from a diagram provided by L. Llljas.)...

DNA has a MAJOR AND MINOR GROOVE because the bases attach at an angle that is not 180° apart around the axis of the helix. The major groove has more of the bases exposed. Sequence-specific interactions with DNA often occur along the major groove. Since the helix is right-handed, the next ribose shown... 

The high density of negative charges in heparan sulfate brings positively charged molecules of lipoprotein lipase into the vicinity and holds them by electrostatic interactions as well as by sequence-specific interactions with S domains. Such interactions are also central in the first step in the entry of certain viruses (such as herpes simplex viruses HSV-1 and HSV-2) into cells. 

Strand invasion, an alternative approach to obstructing transcription by formation of triple strands, has been shown to be feasible if analogs with sufficient affinity can be synthesized. PNAs have been shown to have very hyi affinity and be capable of strand invasion of double-stranded DNA under some conditions (51). Additionally, progress in develop-irg sequence-specific minor groove binders has been reported (52) (for review, see Ref 53). Thus, progress in developing the basic tools with which to evaluate the potential of sequence-specific interactions with DNA has bcai reported, although much remains to be dene. 

Figure 9.7 Sequence specific interactions between TBP and the TATA box. Asn 69 and Thr 124 from one domain and the equivalent residues Asn 159 and Thr 215 from the second domain interact with the palindromic TATA sequence of the central region of the TATA box.

Figure 9.20 Diagram iliustrating the sequence-specific interactions between DNA and p53. The C-terminai a helix and loop LI of p53 bind in the major groove of the DNA. Arg 280 from the a helix and Lys 120 from LI form important specific interactions with bases of the DNA. In addition, Arg 248 from loop L3 binds to the DNA in the minor groove. (Adapted from Y. Cho et al.. Science 265 346-355, 1994.)...

Figure 10.11 Sequence-specific interactions between DNA (yellow) and the recognition helix (red) of the glucocorticoid receptor. Three residues, Lys 461, Val 462 and Arg 466 make specific contacts with the edges of the bases In the major groove.

Three residues. His 28, Glu 32 and Arg 36, form specific interactions with the edges of the bases in the major groove of DNA. Like MyoD, a Glu residue recognizes the first two bases, C and A, of the recognition sequence. 

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