ArticleProceedings of the National Academy of Sciences of the United States of America2012
Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 53 citations in OpenAlex.
- Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids.Journal of molecular biology · 2022Review
- Peptide Dynamics and Metadynamics: Leveraging Enhanced Sampling Molecular Dynamics to Robustly Model Long-Timescale Transitions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives.Advances and applications in bioinformatics and chemistry : AABC · 2022Review
- Looking for a safe haven: tail-anchored proteins and their membrane insertion pathways.Plant physiology · 2021Review
- Scalable molecular dynamics on CPU and GPU architectures with NAMD.The Journal of chemical physics · 2020Article
- A structural perspective on tail-anchored protein biogenesis by the GET pathway.Current opinion in structural biology · 2018Review
- A protean clamp guides membrane targeting of tail-anchored proteins.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Mechanisms of Tail-Anchored Membrane Protein Targeting and Insertion.Annual review of cell and developmental biology · 2017Review
- Decoupled side chain and backbone dynamics for proton translocation - M2 of influenza A.Journal of molecular modeling · 2017Article
- Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications.Annual reports in computational chemistry · 2017Article
- Accelerated molecular dynamics simulations of the octopamine receptor using GPUs: discovery of an alternate agonist-binding position.Proteins · 2016Article
- Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies.ChemMedChem · 2016Review
- Article
- A single residue substitution accounts for the significant difference in thermostability between two isoforms of human cytosolic creatine kinase.Scientific reports · 2016Article
- Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor.Quarterly reviews of biophysics · 2015Review
- Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.Journal of chemical theory and computation · 2015Article
- Accelerated molecular dynamics simulations of protein folding.Journal of computational chemistry · 2015Article
- Transcriptional regulation of secretory capacity by bZip transcription factors.Frontiers in biology · 2015Article
- Functional loop dynamics of the streptavidin-biotin complex.Scientific reports · 2015Article
- Theoretical Insights Reveal Novel Motions in Csk's SH3 Domain That Control Kinase Activation.PloS one · 2015Article
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2 authors at 1 institution in 1 country.
Funding
Abstract
The unique topology of tail-anchored (TA) proteins precludes them from utilizing the well-studied cotranslational translocation mechanism of most transmembrane proteins, forcing them into a distinct, posttranslational pathway. In yeast, this process is the guided entry of TA-proteins (GET) pathway, which utilizes a combination of cytosolic and transmembrane proteins to identify a TA protein, transfer it, and insert it into the endoplasmic reticulum membrane. At the center of this mechanism is the Get3 homodimer, which transfers a TA protein between the two GET phases by leveraging energy gained in ATP binding and hydrolysis to undergo significant structural changes from "open" to "closed" conformations. We present all-atom molecular dynamics simulations of Get3 in multiple nucleotide states, and through rigorous potential of mean force calculations, compute the free energy landscape of the Get3 opening/closing pathway. Results agree well with experiments on the nucleotide bias of Get3 open and closed structures in the crystallographically observed no-nucleotide, two ATP, and two ADP states, and also reveal their populations in the asymmetric one ATP and one ADP cases. Structures also compare well with the recently observed "semiopen" conformation and suggest that Get3 may sample this state free in solution and not just when bound to Get1, as observed in experiments. Finally, we present evidence for a unique, "wide-open" conformation of Get3. These calculations describe the nucleotide-dependent thermodynamics of Get3 in solution, and improve our understanding of its mechanism in each phase of the GET cycle.
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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.