Details
| Original language | English |
|---|---|
| Article number | e130 |
| Number of pages | 7 |
| Journal | Nucleic acids research |
| Volume | 46 |
| Issue number | 22 |
| Early online date | 10 Aug 2018 |
| Publication status | Published - 14 Dec 2018 |
| Externally published | Yes |
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.
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Genetics
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In: Nucleic acids research, Vol. 46, No. 22, e130, 14.12.2018.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - Decomposition of time-dependent fluorescence signals reveals codon-specific kinetics of protein synthesis
AU - Haase, Nadin
AU - Holtkamp, Wolf
AU - Lipowsky, Reinhard
AU - Rodnina, Marina
AU - Rudorf, Sophia
N1 - Publisher Copyright: © The Author(s) 2018.
PY - 2018/12/14
Y1 - 2018/12/14
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85058916325&partnerID=8YFLogxK
U2 - 10.1093/nar/gky740
DO - 10.1093/nar/gky740
M3 - Article
C2 - 30364963
AN - SCOPUS:85058916325
VL - 46
JO - Nucleic acids research
JF - Nucleic acids research
SN - 0305-1048
IS - 22
M1 - e130
ER -