ArticleProceedings of the National Academy of Sciences of the United States of America2013
Simulating the pulling of stalled elongated peptide from the ribosome by the translocon.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome.Nature communications · 2024Article
- Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines.Entropy (Basel, Switzerland) · 2022Article
- Dynamics of Co-translational Membrane Protein Integration and Translocation via the Sec Translocon.Journal of the American Chemical Society · 2020Review
- Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter.PLoS computational biology · 2018Article
- Modeling protein folding in vivo.Biology direct · 2018Article
- The FPhotosynthesis research · 2017Review
- Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids.RNA (New York, N.Y.) · 2017Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Article
- Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture).Angewandte Chemie (International ed. in English) · 2014Article
- EF-P dependent pauses integrate proximal and distal signals during translation.PLoS genetics · 2014Article
- An effective coarse-grained model for biological simulations: recent refinements and validations.Proteins · 2014Article
- On the nature of the apparent free energy of inserting amino acids into membrane through the translocon.The journal of physical chemistry. B · 2013Article
- Electrostatic origin of the unidirectionality of walking myosin V motors.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Cotranslational folding of membrane proteins probed by arrest-peptide-mediated force measurements.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The nature of the coupling between the stalling of the elongated nascent peptide chain in the ribosome and its insertion through the translocon is analyzed, focusing on the recently discovered biphasic force that overcomes the stalling barrier. The origin of this long-range coupling is explored by coarse-grained simulations that combine the translocon (TR) insertion profile and the effective chemical barrier for the extension of the nascent chain in the ribosome. Our simulation determined that the inserted H segment is unlikely to climb the TR barrier in parallel with the peptide synthesis chemical step and that the nascent chain should first overcome the chemical barriers and move into the ribosome-TR gap region before the insertion into the TR tunnel. Furthermore, the simulations indicate that the coupled TR-chemistry free energy profile accounts for the biphasic force. Apparently, although the overall elongation/insertion process can be depicted as a tug-of-war between the forces of the TR and the ribosome, it is actually a reflection of the combined free-energy landscape. Most importantly, the present study helps to relate the experimental observation of the biphasic force to crucial information about the elusive path and barriers of the TR insertion process.
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