Mechanisms of Membrane Ion Channels
Ion channels are fundamental for life. They are proteins that allow ions to pass through biological membranes (e.g. cell walls) in a controlled manner, and understanding the mechanisms of ion channels is a fundamental problem in biology. Usually an ion channel has two important characteristics, namely (1) selective conduction of a particular ion, and (2) a gating response, i.e. a change of conductivity in response to some external stimulus. Such stimuli include voltage across the membrane, pH of the external fluid, presence of particular molecules (ligands), and mechanical stress in the membrane.
The field of biological ion channels has developed rapidly in the last few years, with breakthroughs in the crystallographic determination of molecular structures of membrane proteins (earning a 2003 Nobel Prize) and advances in computer simulation of biomolecules. These developments have finally enabled the long-awaited goal of relating the function of a channel to its underlying atomic structure. Crystallographic structures of several new classes of channel have become available recently, which in turn are driving new approaches and improvements in simulation methods, and creating many opportunities for informative large-scale simulations on supercomputer systems. The results may help researchers to find the causes of, and possibly cures for, many neurological and muscular disorders.
This project x65 is a recent offshoot of other projects of the ANU computational biophysics group led by Shin-Ho Chung, but with a greater emphasis on gating mechanisms in terms of channel physics, and a greater use of molecular dynamics in terms of computational methods.
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Principal Investigator David BissetTheoretical Physics, RSPhysSE Australian National University |
Project x65 |
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Co-Investigators Stephen McMahonANU Supercomputer Facility Australian National University Jean-Fang Gwan Matthew Hoyles Megan O'Mara Melissa Tacy Taira Vora Theoretical Physics, RSPhysSE Australian National University |
RFCD Codes 270104 |
Significant Achievements, Anticipated Outcomes and Future Work
Since this project began during the third quarter of 2003, the bulk of the work has been (and will continue to be) the investigation of various forms of ion channel gating. This involves two questions: (1) What changes occur within the channel structure in reponse to the gating stimulus? (2) How do those changes affect channel conduction properties? We are mainly using Molecular Dynamics (MD) for simulations of gating. However, the timeframe for simulating the conduction of ions is out of reach for MD on current computers, so we simulate the conduction process using Brownian Dynamics (BD) programs written in-house. An important question for BD is the effective dielectric constant of water in narrow pores, which has only been inferred indirectly. We are now in the process of determining suitable dielectric values directly by comparing results from the Poisson-Boltzmann equation against MD results in typical channels such as the chloride channel CLC0 and the potassium channel KCSA.
Chloride channels such as CLC0 and CLC1 exhibit fast gating in response to the concentration of chloride in the extracellular solution. We have demonstrated via MD that a postulated mechanism for this gate, i.e. sidechain movement of protein residue GLU148, can indeed behave in a manner that leads to gating. Results have been incorporated into a video made at the ANUSF Vizlab.
Many important ion channels are voltage-gated, and the recent publication of the structure of the voltage-gated potassium channel KVAP was a major development. We have constructed a channel-membrane-water system of almost 100,000 atoms (very large for practical MD) incorporating a closed KVAP structure, and are part-way through a very long simulation of KVAP opening in response to voltage depolarization.
As a general procedure, we use MD to manipulate channel protein structure, and then determine the ionic conductivity using BD. Thus we can infer likely open and closed channel conformations from the conductivity results. We are currently using this approach for certain ligand-gated channels (nAch, GABA) and the mechanosensitive channel MSCS. The gating mechanism appears to be fairly simple in the latter case, so we are planning a full MD simulation of gating with a channel-membrane-water system.
Computational Techniques Used
For molecular dynamics we use the semi-commercial program Charmm, running in parallel on four processors of sc, and on multiple single processors on lc. For direct simulations of ion conduction we use stochastic Brownian dynamics programs written in-house, running many single-processor jobs simultaneously.
Publications, Awards and External Funding
External Funding and Awards
ARC and NH&MRC funding as for project d32 (Shin-Ho Chung)
Publications
B. Corry, M. O'Mara and S. H. Chung. Conduction mechanisms of chloride ions in ClC-type channels. Biophysical Journal,
86, 2004, 846-860.
B. Corry, M. O'Mara and S. H. Chung. 2004. Permeation dynamics of chloride ions in the ClC-0 and ClC-1 channels.
Chemical Physics Letters, 386, 2004, 233-238.