ArticleProceedings of the National Academy of Sciences of the United States of America2009
Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Machines on Genes through the Computational Microscope.Journal of chemical theory and computation · 2023Review
- Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Simulating the directional translocation of a substrate by the AAA+ motor in the 26S proteasome.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Revisiting the protomotive vectorial motion of FProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- The FPhotosynthesis research · 2017Review
- Simulating the dynamics of the mechanochemical cycle of myosin-V.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Protein-DNA and ion-DNA interactions revealed through contrast variation SAXS.Biophysical reviews · 2016Article
- Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions.Journal of chemical theory and computation · 2015Article
- Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution.Journal of the American Chemical Society · 2015Article
- Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor.Nature communications · 2014Article
- Simulating the pulling of stalled elongated peptide from the ribosome by the translocon.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Why nature really chose phosphate.Quarterly reviews of biophysics · 2013Review
- Electrostatically accelerated encounter and folding for facile recognition of intrinsically disordered proteins.PLoS computational biology · 2013Article
- Electrostatically accelerated coupled binding and folding of intrinsically disordered proteins.Journal of molecular biology · 2012Article
- Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Frustration in protein-DNA binding influences conformational switching and target search kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Capturing the essence of folding and functions of biomolecules using coarse-grained models.Nature communications · 2011Review
- Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks.The journal of physical chemistry. B · 2011Article
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Authors and funding
4 authors.
Funding
Abstract
The molecular origin of the action of helicases is explored, starting with a model built based on the different X-ray structures of the large tumor antigen (LTag) hexameric helicase and a simplified model containing the ionized phosphate backbones of a single-strand DNA. The coupling between the protein structural changes and the translocation process is quantified using an effective electrostatic free-energy surface for the protein/DNA complex. This surface is then used in Langevin dynamics simulations of the time dependence of the translocation process. Remarkably, the simulated motion along the free-energy surface results in a vectorial translocation of the DNA, consistent with the biological process. The electrostatic energy of the system appears to reproduce the directionality of this process. Thus, we are able to provide a consistent structure-based molecular description of the energetic and dynamics of the translocation process. This analysis may have general implications for relating structural models to translocation directionality in helicases and other DNA translocases.
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