ArticleJournal of the American Chemical Society2012
Direct simulation of early-stage Sec-facilitated protein translocation.
Article in Journal of the American Chemical Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum.International journal of molecular sciences · 2021Review
- Molecular Modeling of Signal Peptide Recognition by Eukaryotic Sec Complexes.International journal of molecular sciences · 2021Review
- Characterization of the Features of Water Inside the SecY Translocon.The Journal of membrane biology · 2021Review
- Dynamics of Co-translational Membrane Protein Integration and Translocation via the Sec Translocon.Journal of the American Chemical Society · 2020Review
- Energy landscape underlying spontaneous insertion and folding of an alpha-helical transmembrane protein into a bilayer.Nature communications · 2018Article
- Forces on Nascent Polypeptides during Membrane Insertion and Translocation via the Sec Translocon.Biophysical journal · 2018Article
- Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method.The Journal of membrane biology · 2018Article
- Improving membrane protein expression by optimizing integration efficiency.The Journal of biological chemistry · 2017Article
- Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration.PLoS computational biology · 2017Article
- A Link between Integral Membrane Protein Expression and Simulated Integration Efficiency.Cell reports · 2016Article
- Article
- 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
- Allosteric response and substrate sensitivity in peptide binding of the signal recognition particle.The Journal of biological chemistry · 2014Article
- Article
- Functional asymmetry within the Sec61p translocon.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Native states of fast-folding proteins are kinetic traps.Journal of the American Chemical Society · 2013Article
- Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion.Journal of the American Chemical Society · 2013Article
- Exploring the nature of the translocon-assisted protein insertion.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Direct simulations reveal key mechanistic features of early-stage protein translocation and membrane integration via the Sec-translocon channel. We present a novel computational protocol that combines non-equilibrium growth of the nascent protein with microsecond timescale molecular dynamics trajectories. Analysis of multiple, long timescale simulations elucidates molecular features of protein insertion into the translocon, including signal-peptide docking at the translocon lateral gate (LG), large lengthscale conformational rearrangement of the translocon LG helices, and partial membrane integration of hydrophobic nascent-protein sequences. Furthermore, the simulations demonstrate the role of specific molecular interactions in the regulation of protein secretion, membrane integration, and integral membrane protein topology. Salt-bridge contacts between the nascent-protein N-terminus, cytosolic translocon residues, and phospholipid head groups are shown to favor conformations of the nascent protein upon early-stage insertion that are consistent with the Type II (N(cyt)/C(exo)) integral membrane protein topology, and extended hydrophobic contacts between the nascent protein and the membrane lipid bilayer are shown to stabilize configurations that are consistent with the Type III (N(exo)/C(cyt)) topology. These results provide a detailed, mechanistic basis for understanding experimentally observed correlations between integral membrane protein topology, translocon mutagenesis, and nascent-protein sequence.
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