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RNA-protein recognition: single-residue ultrafast dynamical control of structural specificity and function
Tianbing Xia1, Chaozhi Wan, Richard W Roberts
1Laboratory for Molecular Sciences, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125, USA.
Summary
The bacteriophage lambda N protein
Area of Science:
- Molecular Biology
- Biophysics
Background:
- The transcription antiterminator N protein from bacteriophage lambda binds a specific RNA hairpin (boxB) via its arginine-rich motif.
- A key interaction involves a tryptophan (Trp-18) and adenosine (A7) in the RNA loop, crucial for antitermination.
- Previous studies showed the N/boxB complex exists in a dynamic equilibrium between stacked and unstacked states, influenced by residues 14 and 15.
Purpose of the Study:
- To investigate the sequence-dependent conformational dynamics of the N/boxB complex.
- To elucidate the specific molecular interactions governing the stacked and unstacked states.
- To correlate femtosecond dynamics with in vivo antitermination activity.
Main Methods:
- Femtosecond fluorescence up-conversion spectroscopy.
- Transient absorption spectroscopy.
- Analysis of mutant N protein complexes.
Main Results:
- Hydrophobic interactions of residue 14's beta-carbon with A7's ribose stabilize the stacked conformation.
- A positive charge at residue 14 plays a minor role in stacking.
- A positive charge at residue 15 disfavors stacking but maintains binding energy.
Conclusions:
- Conformational dynamics of the N/boxB complex are sequence-dependent.
- Specific hydrophobic and charged interactions dictate the balance between stacked and unstacked states.
- These dynamics directly correlate with and control antitermination activity in vivo.