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  Decomposition of time-dependent fluorescence signals reveals codon-specific kinetics of protein synthesis

Haase, N., Holtkamp, W., Lipowsky, R., Rodnina, M., & Rudorf, S. (2018). Decomposition of time-dependent fluorescence signals reveals codon-specific kinetics of protein synthesis. Nucleic Acids Research (London), 46(22), e130. doi:10.1093/nar/gky740.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0001-EDB5-8 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-36AB-0
Genre: Journal Article

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 Creators:
Haase, Nadin1, Author              
Holtkamp, Wolf, Author
Lipowsky, Reinhard2, Author              
Rodnina, Marina, Author
Rudorf, Sophia1, Author              
Affiliations:
1Sophia Rudorf, Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society, ou_2205637              
2Reinhard Lipowsky, Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society, ou_1863327              

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 Abstract: During protein synthesis, the nascent peptide chain traverses the peptide exit tunnel of the ribosome. We monitor the co-translational movement of the nascent peptide using a fluorescent probe attached to the N-terminus of the nascent chain. Due to fluorophore quenching, the time-dependent fluorescence signal emitted by an individual peptide is determined by co-translational events, such as secondary structure formation and peptide-tunnel interactions. To obtain information on these individual events, the measured ensemble fluorescence signal has to be decomposed into position-dependent intensities. Here, we describe mRNA translation as a Markov process with specific fluorescence intensities assigned to the different states of the process. Combining the computed stochastic time evolution of the translation process with a sequence of observed ensemble fluorescence time courses, we compute the unknown position-specific intensities and obtain detailed information on the kinetics of the translation process. In particular, we find that translation of poly(U) mRNAs dramatically slows down at the fourth UUU codon. The method presented here detects subtle differences in the position-specific fluorescence intensities and thus provides a novel approach to study translation kinetics in ensemble experiments.

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Language(s): eng - English
 Dates: 2018-08-10
 Publication Status: Published in print
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 Identifiers: DOI: 10.1093/nar/gky740
DOI: 10.1093/nar/gky1101
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Title: Nucleic Acids Research (London)
  Other : Nucleic Acids Res
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 46 (22) Sequence Number: - Start / End Page: e130 Identifier: ISSN: 0305-1048