ArticleJournal of the American Chemical Society2013
Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Folding and Insertion of Transmembrane Helices at the ER.International journal of molecular sciences · 2021Review
- Molecular Modeling of Signal Peptide Recognition by Eukaryotic Sec Complexes.International journal of molecular sciences · 2021Review
- Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis.The journal of physical chemistry. A · 2021Article
- Characterization of the Features of Water Inside the SecY Translocon.The Journal of membrane biology · 2021Review
- Recent Insights from Molecular Dynamics Simulations for G Protein-Coupled Receptor Drug Discovery.International journal of molecular sciences · 2019Review
- Membrane Protein Integration and Topogenesis at the ER.The protein journal · 2019Review
- A molecular dynamics study on the resilience of Sec61 channel from open to closed state.RSC advances · 2019Article
- Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis.Chemical reviews · 2019Article
- Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.Chemical reviews · 2019Article
- Interaction mapping of the Sec61 translocon identifies two Sec61α regions interacting with hydrophobic segments in translocating chains.The Journal of biological chemistry · 2018Article
- Cotranslational protein targeting to the membrane: Nascent-chain transfer in a quaternary complex formed at the translocon.Scientific reports · 2018Article
- Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method.The Journal of membrane biology · 2018Article
- Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models.PeerJ · 2018Article
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.Biochimica et biophysica acta · 2016Review
- Structure of the native Sec61 protein-conducting channel.Nature communications · 2015Article
- Anomalous behavior of water inside the SecY translocon.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Peptide Folding in Translocon-Like Pores.The Journal of membrane biology · 2015Article
- Lateral opening of the bacterial translocon on ribosome binding and signal peptide insertion.Nature communications · 2014Article
- Lateral opening and exit pore formation are required for BamA function.Structure (London, England : 1993) · 2014Article
- Functional asymmetry within the Sec61p translocon.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
For the vast majority of membrane proteins, insertion into a membrane is not direct, but rather is catalyzed by a protein-conducting channel, the translocon. This channel provides a lateral exit into the bilayer while simultaneously offering a pathway into the aqueous lumen. The determinants of a nascent protein's choice between these two pathways are not comprehensively understood, although both energetic and kinetic factors have been observed. To elucidate the specific roles of some of these factors, we have carried out extensive all-atom molecular dynamics simulations of different nascent transmembrane segments embedded in a ribosome-bound bacterial translocon, SecY. Simulations on the μs time scale reveal a spontaneous motion of the substrate segment into the membrane or back into the channel, depending on its hydrophobicity. Potential of mean force (PMF) calculations confirm that the observed motion is the result of local free-energy differences between channel and membrane. Based on these and other PMFs, the time-dependent probability of membrane insertion is determined and is shown to mimic a two-state partition scheme with an apparent free energy that is compressed relative to the molecular-level PMFs. It is concluded that insertion kinetics underlies the experimentally observed thermodynamic partitioning process.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.