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Structural studies of the engrailed homeodomain
N D Clarke1, C R Kissinger, J Desjarlais
1Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205.
Protein Science : a Publication of the Protein Society
|October 1, 1994
Summary
The Drosophila engrailed homeodomain structure reveals unique features in its unbound state, including aromatic packing and salt bridges. These findings offer insights into DNA-binding protein stability and function.
Area of Science:
- Structural biology
- Molecular genetics
- Protein science
Background:
- The engrailed homeodomain is a crucial DNA-binding protein family.
- Understanding its structure is key to deciphering gene regulation.
Purpose of the Study:
- To determine the high-resolution structure of the unbound Drosophila engrailed homeodomain.
- To compare the unbound structure with its DNA-bound form.
- To identify novel structural features and stabilizing elements.
Main Methods:
- X-ray crystallography for structure determination (molecular replacement, refinement to 2.1 A resolution).
- Comparison with existing 2.8-A resolution structure of engrailed-DNA complex.
- Circular dichroism (CD) and thermal denaturation studies on a protein variant.
Main Results:
- High-resolution structure (2.1 A) of the unbound Drosophila engrailed homeodomain was solved.
- Significant structural differences noted compared to the DNA-bound state, including a more compact conformation.
- Novel features identified: 'herringbone' aromatic packing in the core and extensive salt bridge network.
- Stabilizing interactions include buried carbonyls and preferred side-chain angles.
- A 51-amino acid variant showed structural and thermodynamic similarity to the full-length domain.
Conclusions:
- The unbound engrailed homeodomain possesses distinct structural characteristics influencing its DNA-binding capabilities.
- Identified structural features contribute to protein stability and may play roles in its native state.
- The study provides a detailed molecular view of an important class of transcription factors.