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The RNA–protein complex: Direct probing of the interfacial recognition dynamics and its correlation with biological functions

Xia, Tianbing and Becker, Hans-Christian and Wan, Chaozhi and Frankel, Adam and Roberts, Richard W. and Zewail, Ahmed H. (2003) The RNA–protein complex: Direct probing of the interfacial recognition dynamics and its correlation with biological functions. Proceedings of the National Academy of Sciences of the United States of America, 100 (14). pp. 8119-8123. ISSN 0027-8424. http://resolver.caltech.edu/CaltechAUTHORS:XIApnas03

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Abstract

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.


Item Type:Article
Additional Information:Contributed by Ahmed H. Zewail, May 22, 2003. This work was financially supported by the National Science Foundation. H.-C. B. is supported in part by the Wenner-Gren Foundation in Stockholm.
Record Number:CaltechAUTHORS:XIApnas03
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:XIApnas03
Alternative URL:http://dx.doi.org/10.1073/pnas.1433099100
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:497
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:11 Jul 2005
Last Modified:14 Nov 2014 19:18

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