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Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR
Liskin Swint-Kruse1, Christopher Larson, B Montgomery Pettitt
1Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA. lsk@bioc.rice.edu
Protein Science : a Publication of the Protein Society
|March 23, 2002
Summary
LacI and PurR repressors, homologous proteins, show distinct hinge structures influencing DNA binding. Molecular dynamics simulations reveal sequence differences impacting allosteric regulation and repressor function.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- LacI and PurR are homologous transcriptional repressors with similar DNA-binding domains.
- Hinge region structural changes upon DNA dissociation are critical but experimentally challenging to study.
Purpose of the Study:
- To investigate the initial steps of hinge unfolding in LacI and PurR.
- To understand how sequence variations in the hinge region affect protein structure and function.
- To elucidate the mechanism behind the opposite allosteric responses of LacI and PurR.
Main Methods:
- Molecular dynamics simulations of a truncated, chimeric protein (LacI HTH/N-linker and PurR hinge).
- Disulfide bond formation for monitoring dimerization.
- Structural comparison of DNA-bound LacI, truncated LacI(1-62), and PurR structures.
- Correlation with mutational analysis and sequence data.
Main Results:
- Hinge primary sequence differences influence hinge-hinge interface quaternary structure.
- N-linker and hinge contacts to the core domain affect DNA-binding domain juxtapositions.
- Significant differences exist in core and C-linker interactions between LacI and PurR.
- LacI and PurR exhibit opposite allosteric responses to effectors.
Conclusions:
- Sequence variations in the hinge and linkers fine-tune repressor function and allosteric regulation.
- Structural distinctions correlate with functional differences in DNA-binding proteins.
- A mechanism for differential repressor activity is proposed based on structural and simulation data.