ArticleBiophysical journal2008
End-point targeted molecular dynamics: large-scale conformational changes in potassium channels.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Article
- Conduction through a narrow inward-rectifier KThe Journal of general physiology · 2019Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Hydrophobic plug functions as a gate in voltage-gated proton channels.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Mutations in the S6 gate isolate a late step in the activation pathway and reduce 4-AP sensitivity in shaker K(v) channel.Biophysical journal · 2014Article
- Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.BMC structural biology · 2013Article
- Probing the energy landscape of activation gating of the bacterial potassium channel KcsA.PLoS computational biology · 2013Article
- Article
- Being flexible: the voltage-controllable activation gate of kv channels.Frontiers in pharmacology · 2012Article
- Shape-Dependent Global Deformation Modes of Large Protein Structures.Journal of molecular structure · 2010Article
- Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations.Proteins · 2010Article
- Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.Journal of molecular biology · 2009Article
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Authors and funding
2 authors.
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Abstract
Large-scale conformational changes in proteins that happen often on biological time scales may be relatively rare events on the molecular dynamics time scale. We have implemented an approach to targeted molecular dynamics called end-point targeted molecular dynamics that transforms proteins between two specified conformational states through the use of nonharmonic "soft" restraints. A key feature of the method is that the protein is free to discover its own conformational pathway through the plethora of possible intermediate states. The method is applied to the Shaker K(v)1.2 potassium channel in implicit solvent. The rate of cycling between the open and closed states was varied to explore how slow the cycling rate needed to be to ensure that microscopic reversibility along the transition pathways was well approximated. Results specific to the K(+) channel include: 1), a variation in backbone torsion angles of residues near the Pro-Val-Pro motif in the inner helix during both opening and closing; 2), the identification of possible occlusion sites in the closed channel located among Pro-Val-Pro residues and downstream; 3), a difference in the opening and closing pathways of the channel; and 4), evidence of a transient intermediate structural substate. The results also show that likely intermediate conformations during the opening-closing process can be generated in computationally tractable simulation times.
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