research

New publication: Insights into the structural nature of the transition state in the Kir channel gating pathway.

[Could not find the bibliography file(s)

We recently examined how Kir1.1, an inwardly-rectifying potassium channel that is found in the kidneys, opens and closes in response to being stimulated by changes in pH or the presence of absence of PIP2, a signalling lipid [1]. The key result of that paper was that we could identify several networks of residues that came together to form one large gate when the channel was open. In this addendum paper, we examine how mutating several of these residues affected the kinetics of gating [2]. By comparing the on- and off-rates we are able to infer that the transition state more closely resembles that pre-open, rather than open, state. This paper is open access and is freely available to download.

References

[1] [doi] M. K. Bollepalli, P. W. Fowler, M. Rapedius, L. Shang, M. S. P. Sansom, S. J. Tucker, and T. Baukrowitz, “State-dependent network connectivity determines gating in a K+ channel.,” Structure, vol. 22, pp. 1037-1046, 2014.
[Bibtex]
@article{Bollepalli2014,
abstract = {X-ray crystallography has provided tremendous insight into the different structural states of membrane proteins and, in particular, of ion channels. However, the molecular forces that determine the thermodynamic stability of a particular state are poorly understood. Here we analyze the different X-ray structures of an inwardly rectifying potassium channel (Kir1.1) in relation to functional data we obtained for over 190 mutants in Kir1.1. This mutagenic perturbation analysis uncovered an extensive, state-dependent network of physically interacting residues that stabilizes the pre-open and open states of the channel, but fragments upon channel closure. We demonstrate that this gating network is an important structural determinant of the thermodynamic stability of these different gating states and determines the impact of individual mutations on channel function. These results have important implications for our understanding of not only K+ channel gating but also the more general nature of conformational transitions that occur in other allosteric proteins.},
author = {Bollepalli, Murali K. and Fowler, Philip W. and Rapedius, Markus and Shang, Lijun and Sansom, Mark S P and Tucker, Stephen J. and Baukrowitz, Thomas},
doi = {10.1016/j.str.2014.04.018},
journal = {Structure},
pages = {1037-1046},
pmid = {24980796},
title = {{State-dependent network connectivity determines gating in a K+ channel.}},
volume = {22},
year = {2014}
}
[2] [doi] P. W. Fowler, M. K. Bollepalli, M. Rapedius, E. Nematian, L. Shang, M. S. P. Sansom, S. J. Tucker, and T. Baukrowitz, “Insights into the structural nature of the transition state in the Kir channel gating pathway,” Channels, vol. 8, pp. 551-555, 2014.
[Bibtex]
@article{Fowler2014,
abstract = {In a previous study we identified an extensive gating network within the inwardly rectifying Kir1.1 (ROMK) channel by combining systematic scanning mutagenesis and functional analysis with structural models of the channel in the closed, pre-open and open states. This extensive network appeared to stabilize the open and pre-open states, but the network fragmented upon channel closure. In this study we have analyzed the gating kinetics of different mutations within key parts of this gating network. These results suggest that the structure of the transition state (TS), which connects the pre-open and closed states of the channel, more closely resembles the structure of the pre-open state. Furthermore, the G-loop, which occurs at the centre of this extensive gating network, appears to become unstructured in the TS because mutations within this region have a ‘catalytic’ effect upon the channel gating kinetics.},
author = {Fowler, Philip W and Bollepalli, Murali K. and Rapedius, Markus and Nematian, Ehsan and Shang, Lijun and Sansom, Mark S. P. and Tucker, Stephen J. and Baukrowitz, Thomas},
doi = {10.4161/19336950.2014.962371},
journal = {Channels},
pages = {551-555},
title = {{Insights into the structural nature of the transition state in the Kir channel gating pathway}},
volume = {8},
year = {2014}
}

New Publication: State-Dependent Network Connectivity Determines Gating in a K+ Channel

In an earlier paper we showed that the closed state of Kir1.1, a important potassium ion channel found in the kidneys, was stabilised by a single hydrogen bond. This paper builds on that work by looking for any interactions that stabilise either the open or closed state of the channel by systematically mutating the majority of the residues to alanine. We were surprised to find that 47 mutations destabilised the open state but only 2 destabilised the closed state, one of which was the one we’d found before. Modelling suggests that this is because open conformations of the channel are more optimised and compact hence mutations tend to be more disruptive. The work was partly funded by the Wellcome Trust and hence the paper is free to download.

fig-k11-2

So…. I’m a Software Sustainability Fellow

I’m pleased to announce that I am one of the Software Sustainability Fellows for 2014. I met all the other fellows when we were being selected and it is an amazing group with very diverse research interests and backgrounds. This means I have a responsibility to try and improve the development and use of software in my field, computational biophysics. My plan is to

New Publication: Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY

In this paper we examine how the lactose permease, LacY, changes its structure to shuttle molecules of lactose across a cell membrane. The change in conformation is modelled usinga biased computational method called dynamic importance sampling (DIMS) and the results compared to the results of some previously published double electron electron spin resonance (DEER) experiments. We conclude that LacY, as expected, does pass through an occluded intermediate and this is incompatible a simple rigid-body motion as implied by a “rocker-switch” mechanism.

It is published in the Journal of Molecular Biology and is free to download (open access).

New Publication: Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels

Can we predict the conductance of a potassium ion channel from an experimental structure?

In this paper we examine the kinetic barriers experienced by potassium ions (and waters) as they move through the narrowest part of two different potassium ion channels. We examine the reproducibility of our results and test the sensitivity of the approach to changes in the method. We conclude that we are currently unable to accurately calculate the kinetic barriers to conduction for potassium channels and that other channels (such as sodium channels) may be more amenable to this approach.

This article is published in the Journal of Chemical Theory and Computation and is free to download (open access). It carries out the preparatory work necessary for a second paper on how potassium ions and water molecules move through the selectivity filter of a voltage-gated potassium ion channel.

New Publication: Detailed examination of a single conduction event in a potassium channel.

What can we learn using computational methods about how potassium ions and water molecules move through the narrowest part of a potassium channel?

In this paper, we calculate the average force experienced by three potassium ions as they move through the selectivity filter of a voltage-gated potassium channel. This allows us to identify the most probably mechanism, which includes two “knock-on” events, just like a Newton’s cradle. By examining the behaviour of the conducting waters and the protein in detail we can see how the waters rotate to coordinate one or other of the conducting potassium ions, and even get squeezed between two potassium ions during a knock-on event. We also see how the coordination number of each potassium ion changes.

This article is published in the Journal of Physical Chemistry Letters and is free to download (open access). There is an accompanying paper that is published in the Journal of Chemical Theory and Computation.