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Specific purine N7-nitrogens are critical for high affinity binding by the trp repressor
S A Smith1, S B Rajur, L W McLaughlin
1Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167, USA.
Nature Structural Biology
|January 1, 1994
Summary
The trp repressor binds tightly to its operator DNA sequence. Specific interactions, including water-mediated contacts, are crucial for this high-affinity binding.
Area of Science:
- Molecular Biology
- Biochemistry
- Structural Biology
Background:
- The trp repressor protein regulates gene expression by binding to the trp operator DNA sequence.
- Understanding the molecular basis of this interaction is key to comprehending gene regulation.
Purpose of the Study:
- To investigate the critical interactions between the trp repressor and its operator DNA.
- To elucidate the role of purine N7-nitrogens and water molecules in high-affinity binding.
Main Methods:
- Analysis of modified trp operator sequences containing purine analogues.
- Studying the interaction between the trp repressor and these modified operator sequences.
Main Results:
- Identified a direct contact between repressor residue Arg69 and guanine G-9.
- Discovered that three purine N7-nitrogens, through water-mediated contacts, are essential for high-affinity binding.
- Confirmed that the crystal structure reflects specific, high-affinity repressor-operator binding.
Conclusions:
- Proteins can utilize water molecules to mediate interactions and enhance binding energy.
- Water-mediated contacts play a significant role in the specificity and affinity of protein-DNA complexes.
- The trp repressor-operator interaction is a model for understanding sequence-specific DNA binding.