The RNA-protein complex: direct probing of the interfacial recognition dynamics and its correlation with biological functions.
The N protein from bacteriophage lambda is a key regulator of transcription antitermination. It specifically recognizes a nascent mRNA stem loop termed boxB, enabling RNA polymerase to read through downstream terminators processively. The stacking interaction between Trp-18 of WT N protein and A7 of boxB RNA is crucial for efficient antitermination. Here, we report on the direct probing of the dynamics for this interfacial binding and the correlation of the dynamics with biological functions. Specifically, we examined the influence of structural changes in four peptides on the femtosecond dynamics of boxB RNA (2-aminopurine labeled in different positions), through mutations of critical residues of N peptide (residues 1-22). We then compare their in vivo (Escherichia coli) transcription antitermination activities with the dynamics. The results demonstrate that the RNA-peptide complexes adopt essentially two dynamical conformations with the time scale for interfacial interaction in the two structures being vastly different, 1 ps for the stacked structure and nanosecond for the unstacked one; only the weighted average of the two is detected in NMR by nuclear Overhauser effect experiments. Strikingly, the amplitude of the observed ultrafast dynamics depends on the identity of the amino acid residues that are one helical turn away from Trp-18 in the peptides and is correlated with the level of biological function of their respective full-length proteins.
Xia
Tianbing
T
Laboratory for Molecular Sciences, Arthur Amos Noyes Laboratory of Chemical Physics, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Becker
Hans-Christian
HC
Wan
Chaozhi
C
Frankel
Adam
A
Roberts
Richard W
RW
Zewail
Ahmed H
AH
D010582:Bacteriophage lambda / Q000235:genetics* / Q000502:physiology; D001665:Binding Sites; D004926:Escherichia coli / Q000235:genetics / Q000821:virology; D015967:Gene Expression Regulation, Viral; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D012261:Ribonucleoproteins / Q000737:chemistry*; D013329:Structure-Activity Relationship; D014158:Transcription, Genetic; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry* / Q000378:metabolism
C059417:N protein, Bacteriophage lambda; D012333:RNA, Messenger; D012367:RNA, Viral; D012261:Ribonucleoproteins; D054334:Viral Regulatory and Accessory Proteins