Ionic Coulomb blockade oscillations and the physical origins of permeation, selectivity, and their mutation transformations in biological ion channels

We will apply physics to elucidate the operation of biological ion channels including the long-standing problem of how their function emerges from their structure. These natural nanotubes exist in the membranes of all biological cells. They control a vast range of biological functions and are crucially important for life. Just lifting a finger requires the coordinated operation of billions of ion channels. Understanding ion channels is relevant to curing many diseases, and may also provide the future basis for bio-computers and their integration with nano-electronics.

The project promises significant contributions to the EPSRC Physics Grand Challenges (a) "Understanding the Physics of Life" and (b) "Emergence and Physics Far from Equilibrium" - and it has been inspired and encouraged by their associated NetworksPlus.

Channels are extraordinarily complex devices, built of thousands of atoms, and operating under non-equilibrium conditions. They conduct selected ions discretely on "one-by-one" basis. Channels can be very selective, e.g. the calcium channel discriminates between Ca++ and Na+ ions by a factor of 1000, even though they are of almost identical size. Yet a channel conducts almost at the rate of free diffusion, like an open hole. Modelling channels is an innately difficult many-body problem with long range interactions and widely-varying timescales, ranging from ps atomic motion to ms gating dynamics. The detailed structures of some channels are now known, but this knowledge has helped much less than expected/hoped in understanding how they actually work.

Our recent research has involved the analysis of a generic ion channel of very simple form: an open nanotube with some fixed charge around its middle, using both analytic theory and modelling with self-consistent electrostatic Brownian dynamics. We complemented this mesoscale description with molecular dynamics simulations that take account of individual atoms and provide the parameters needed by the analytic description.

One outcome was our discovery of an emergent phenomenon: a periodic sequence of conduction-bands and stop-bands dependent on the fixed charge. We hypothesise that it is a manifestation of Ionic Coulomb blockade, closely analogous to Coulomb blockade oscillations in quantum dots. In the context of ion channels, this brings an entirely fresh vision of the conduction process. Our new model based on ionic Coulomb blockade seems potentially able to account for numerous earlier observations on wild-type channels and their mutants that have hitherto been regarded as mysterious and puzzling, bringing them together within a consistent, unified, picture.

We now request the funding needed to exploit this scientific break-through. We will develop an analytic model of ionic Coulomb blockade oscillations, accounting for resonant fluctuation-induced permeation. We will validate the model through an experimental investigation of bacterial sodium channels and their mutants, comparing the measurements with model predictions, and seeking evidence for for Ca2+ and Ba2+ conduction bands, stop-bands and selectivity. By extending the ionic Coulomb blockade model to include the discreteness of the hydration shells around the ion, we can expect to account for selectivity between alike ions, i.e. of equal charge like Na+ and K+.

From the perspective of our reduced model based on ionic Coulomb blockade, there is no inherent difference between an ion channel and an artificial charged nanopore. So we expect most of our results to be equally applicable to nanopores, if values of charge and dimensions are adjusted appropriately.

The investigations bring ideas from far-from-equilibrium physics to bear on problems in biology that are also applicable to nanotechnology. The work will draw freely on the consortium's special expertise in experiments on ion channels, nonlinear dynamics, fluctuation theory, and molecular dynamics.

The expected beneficiaries are: (a) industry, and especially the pharmaceutical industry; (b) the medical profession; and (c) the public. We consider these in turn -

(a) BENEFITS TO INDUSTRY -

The work proposed is basic research, seeking to understand how biological ion channels function. Nonetheless, the chain leading from discovery to practical benefits in the long term is so clear, and so well established by recent successes, that the case is easy to make. There are two books by Frances Ashcroft FRS ("The Spark of Life: Electricity in the Human Body", Norton, 2012; and "Ion Channels and Disease", New York, Academic Press, 1999) focussed on just this subject.

The path from channel research to public benefit lies mainly in medical progress. There are literally thousands of diseases that result directly from single-molecule defects in ion channel proteins. If the protein can be modified, e.g. by means of a drug, the disease can be cured. For this reason, ion channels are a primary target of the pharmaceutical industry: in many cases, modification of the protein, by drugs or mutation, can cure the disease; in most cases, modification can greatly ameliorate symptoms.

Thus the long-term medical impacts relate to the possibility that a deeper appreciation of the physical mechanisms of permeation will yield better drugs targeted on ion channels (like calcium channel blockers) and a better understanding of diseases related to ion channel dysfunction. In particular our discovery of forbidden gaps is likely to be important.

After being validated and further developed, our model will provide a simple and efficient way to calculate the properties of ion channels from a knowledge of their structure, and vice versa to infer the probable structure from the functionality/dysfunctionality. An understanding of the physical reason for the dysfunction of a particular ion channel is likely to help in the optimisation of treatment.

Another likely path from ion channels to public benefit lies in technology. A wide variety of single molecule sensors is being developed using artificial ion channels as the key devices, including methods to allow cheap and easy reading of DNA sequences. Again, better understanding of how the channels function will almost certainly lead to improved devices. The impact will come from the possibility of calculating and predicting selected nanotube properties from predefined structure/geometry, and vice versa to determine the optimal structure of artificial nanotubes needed to provide the required properties. These possibilities can be used in the exponentially growing industrial applications of nano-filters including artificial ion channels, industrial pollution filters, fast DNA sequencing, and numerous other applications of ion-selective nanotubes.

(b) BENEFITS FOR MEDICAL PRACTITIONERS
In the long term, medical practitioners stand to gain from the improved drugs on offer from the pharmaceutical companies. Channelopathies include some of the scourges of mankind (cystic fibrosis, influenza, and diabetes), so that the potential benefits are nontrivial. In other cases, natural properties of ion channels (like the sensitivity of the herg channel to commonly used pharmaceuticals) has profound public health consequences. In still other (frustrating) cases, small changes in the current through a channel, e.g. the calcium current through the CaV L-type calcium channel, can exert a dramatic influence on longevity. Hundreds of thousands of people die each year from cardiac arrhythmias that would be converted to normal rhythms if one could simply double or triple the calcium current through this type of channel.

(c) BENEFITS TO THE PUBLIC
The public stand to benefit from the proposed research programme : (i) in the longer term, through improved medical treatment and technological possibilities (see above); and (ii) culturally during the research itself from our website and outreach activities.