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publication research

New publication: Gating Topology of the Proton-Coupled Oligopeptide Symporters

[Could not find the bibliography file(s) This paper [BIBCITE%%0%] is the result of a large collaboration between several groups. Since all the current crystal structures of peptide transporters are open to the cytoplasm (and hence closed to the periplasm), we wanted to investigate what bacterial peptide transporters (here PepTSo [BIBCITE%%1%] and PepTSt [BIBCITE%%2%]) looked like when they were open to the periplasm. […]

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publication 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 [BIBCITE%%3%]. The key result of that paper was that we could identify several […]

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publication research

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 […]

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research

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 […]

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publication research

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. […]

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publication research

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 […]

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publication research

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, […]

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computing research

This blog…

…is where I shall put thoughts that at least might be of interest to other people. Any opinions are my own and are not representative of my department or university in any way.