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antimicrobial resistance molecular dynamics publication research

New Publication: Predicting whether mutations confer resistance to an antibiotic

Due to the rise of antibiotic resistance, it is increasingly important that your clinician knows which antibiotics will work (and which will not). Traditionally, this is done in hospital microbiology labs by growing a sample taken from the infection site, and then testing how a range of antibiotics affect its growth, or, ideally, kill it. […]

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citizen science clinical microbiology computing research tuberculosis

Automated detection of bacterial growth on 96-well plates (AMyGDA)

I am involved in an international collaboration, the Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC), that is collecting 30-50,000 clinical samples from patients with tuberculosis (TB). Although often viewed as a historical disease, TB kills more people globally than any other infectious disease, with 1.7 million people dying from it in 2016. The ultimate […]

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publication research

New Publication: Protein crowding affects the organisation of ion channels

Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes It is difficult to look at the dynamic spatial organisation of ion channels in cell membranes, but this is something coarse-grained molecular dynamics simulations can offer insights. This work, led by Anna Duncan, shows how altering the lipid composition of […]

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publication research

New Publication: Effect of SAO mutation on Band 3

There is a lovely story behind this paper just published earlier this week in Biochemistry. Reinhart Reithmeier came to visit Mark Sansom in Oxford whilst on sabbatical back in 2002. Now Reinhart, if you don’t know, is a world-expert on Band 3 which is the transmembrane protein in the membrane of red blood cells that […]

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publication research

New Publication: Lipids can form anti-registered phases

When we think of lipids phase separating in a cell membrane we usually think of this process occurring symmetrically, i.e. with like on top of like (this is described as a registered phase). If we consider the simplest case of two lipids, one saturated (A), one unsaturated (B), then if their lengths are sufficiently different […]

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publication research

New Publication: Proteins Alter the Stiffness of Membranes

Although there have been many studies of proteins whose primary function is to ‘sculpt’ the surface of membranes e.g. BAR domains, there have been very few investigations of what effect regular membrane proteins have on the stiffness of membranes. Here we show via very large simulations, using the MARTINI coarse-grained forcefield, that ‘regular’ integral membrane […]

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publication research

New Publication: Membrane Compartmentalization Reduces the Mobility of Lipids.

Lipids are not free to diffuse around the cell membrane. Rather they are constrained not just by all the embedded proteins but also by the cytoskeleton, which, it has been suggested, corral the lipids. In this paper, we show by very large coarse-grained simulations of a realistic model of the plasma membrane how compartmentalisation leads […]

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computing molecular dynamics publication research

New Publication: Predicting affinities for peptide transporters

PepT1 is a nutrient transporter found in the cells that line your small intestine. It is not only responsible for the uptake of di- and tai-peptides, and therefore much of your dietary proteins, but also the uptake of most β-lactam antibiotics. This serendipity ensures that we can take (many of) these important drugs orally. Our […]

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publication research

New Publication: The Extra-Cellular Domain of PepT1 and PepT2

PepT1 is a nutrient transporter found in the cells that line your small intestine. It is not only responsible for the uptake of di- and tai-peptides, and therefore much of your dietary proteins, but also the uptake of most β-lactam antibiotics. This serendipity ensures that we can take (many of) these important drugs orally. Our […]

Categories
molecular dynamics publication research

New Publication: Alchembed

In much of my research I’ve looked at how proteins embedded in cell membranes behave. An important part in any simulation of a membrane protein is, obviously, putting it into a model membrane, often a square patch of several hundred lipid molecules. This is surprisingly difficult: although a slew of methods have been published, none of […]