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KcsA closed and open: modelling and simulation studies

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Abstract

Bacterial homologues of mammalian potassium channels provide structures of two states of a gated K channel. Thus, the crystal structure of KcsA represents a closed state whilst that of MthK represents an open state. Using homology modelling and molecular dynamics simulations we have built a model of the transmembrane domain of KcsA in an open state and have compared its conformational stability with that of the same domain of KcsA in a closed state. Approximate Born energy calculations of monovalent cations within the two KcsA channel states suggest that the intracellular hydrophobic gate in the closed state provides a barrier of height ~5 kT to ion permeation, whilst in the open state the barrier is absent. Simulations (10 ns duration) in an octane slab (a simple membrane mimetic) suggest that closed- and open-state models are of comparable conformational stability, both exhibiting conformational drifts of ~3.3 Å Cα RMSD relative to the respective starting models. Substantial conformational fluctuations are observed in the intracellular gate region during both simulations (closed state and open state). In the simulation of open-state KcsA, rapid (<5 ns) exit of all three K+ ions occurs through the intracellular mouth of the channel. Helix kink and swivel motion is observed at the molecular hinge formed by residue G99 of the M2 helix. This motion is more substantial for the open- than for the closed-state model of the channel.

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Acknowledgements

We thank the Wellcome Trust and the BBSRC for funding, and the Oxford Supercomputing Centre for access to computing facilities. Our thanks to all of our colleagues for their interest in this work, and especially to Declan Doyle and to Nigel Unwin.

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  1. Joanne N. Bright

    Present address: Research School of Chemistry, The Australian National University, 0200, Canberra, ACT , Australia

Authors and Affiliations

  1. Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford , OX1 3QU, UK

    John Holyoake, Carmen Domene, Joanne N. Bright & Mark S. P. Sansom

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  1. John Holyoake
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Correspondence to Mark S. P. Sansom.

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Holyoake, J., Domene, C., Bright, J.N. et al. KcsA closed and open: modelling and simulation studies. Eur Biophys J 33, 238–246 (2004). https://doi.org/10.1007/s00249-003-0355-2

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