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Visualising Targets for Novel Antibiotics

Scientists have taken significant strides towards the development of new antibiotics in our battle against resistant strains of bacteria. Researchers at Oxford, Trinity College Dublin, Diamond and the University of East Anglia have visualised, in high definition, proteins that are crucial to bacterial survival.

Indeed one of these proteins is so important that bacteria designed a natural antibiotic, globomycin, as a weapon to kill its competitors, by binding to this protein.

LspA-cover
Globomycin inhibits LspA

The protein in question is LspA: a key enzyme in both gram-negative bacteria, like E. coli, where resistance is rapidly on the rise, and gram-positive bacteria like the infamous MRSA and and multi-drug resistant tuberculosis.

Martin Caffrey’s group at Trinity College Dublin, in collaboration with Dr Phill Stansfeld in the Department of Biochemistry, University of Oxford, have perceived and studied how globomycin binds to LspA.

The study, which is published in the journal Science, provides a means to design new drugs that are similar to globomycin, thereby paving the way for novel antibiotics to kill the resistant and infectious bacteria in the future.

Lipoprotein-pathway
The Lipoprotein Pathway

Globomycin works by preventing the correct development of ‘bacterial lipoproteins’. These proteins perform critical roles in behaviour, pathogenicity, and antibiotic resistance of bacteria. Processing of these proteins requires the LspA enzyme to cut off part of the protein, whilst other enzymes stick the proteins to the outside of the cell through fatty anchors.

In bacteria, such as E. coli, the lipoprotein complex called LptDE is the bacteria’s bricklayer and is essential for the formation of the fortifications of the bacterial cell. The first structure of this complex was reported in Nature in 2014 by Chanjiang Dong’s group, at University of East Anglia, with Dr Phill Stansfeld a key component of the collaboration.

BamABCDE
The BAM Complex

The same team have now visualised and assessed another essential lipoprotein complex, called BAM, which is also reported in Nature. This protein is crucial to the building of proteins that permit the entry of nutrients into the bacterial cell, and also pump out hazardous compounds, such as antibiotics.

Disruption of this complex provides another route to the development of new antimicrobial agents.

LspA – the processing enzyme for lipoproteins, inhibited by the antibiotic Globomycin: 
http://science.sciencemag.org/content/351/6275/876

BAM – the protein responsible for inserting proteins into the bacterial outer membrane: 
http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature17199.html

LptDE – the bacterial bricklayer: 
http://www.nature.com/nature/journal/v511/n7507/full/nature13464.html

Structure & Simulations of Antibiotic Inhibition of a Signal Peptidase

Lipoproteins make up only a small fraction of a bacteria’s genome, however they perform critical roles in bacterial physiology, pathogenicity, and antibiotic resistance. Their roles include modulation of the cell envelope structure, signal transduction and transport. Like the majority of membrane proteins, Lipoproteins are targeted to the cell envelope by a  signal peptide, which affixes them to the inner bacterial cell membrane. This orients the protein so that its lipoprotein domain is in the periplasm or outside the cell. Post-translational processing of these proteins requires requires a signal peptidase II (also known as LspA) to remove the signal peptide, whilst retaining the lipoprotein’s lipid anchor.

The crystal crystal structure of LspA from the gram-negative bacteria Pseudomonas aeruginosa has been solved by Martin Caffrey’s group at Trinity College Dublin (TCD). This 2.8 angstrom resolution structure is complexed with the antimicrobial globomycin. We have taken this structure and computationally reincorporated it back into its host membrane. In doing so we have developed molecular parameters for globomycin and simulated the inhibition of the enzyme by this natural antibiotic. We have also used molecular modelling techniques to predict how the native lipoprotein substrates of LspA engage with the enzyme, and to propose mechanisms by which the signal peptide is cleaved.

Bioinformatic analyses illustrate the conservation of a pair of aspartic acid residues, stabilised by a network of asparagine sidechains. Their importance is confirmed by mutagenesis studies, which firmly suggest LspA as an aspartyl peptidase.  In an example of molecular mimicry, globomycin appears to inhibit by acting as a noncleavable peptide that sterically blocks the active site. This structure should inform rational  drug discovery of novel antibiotics in our combat against drug resistant infections.

The link to the article is here.

Molecular Simulations of Diacylglycerol Kinase

A fantastic new structure of the integral membrane protein Diacylglycerol Kinase (DgkA) has been solved by Martin Caffrey’s group at Trinity College Dublin. This is a direct follow-up to their original study that appeared in Nature, two years previous [1]. The new structure not only shows the three-dimensional structure of the protein, but also reveals the mechanism of interaction of the substrates ATP and the lipid Monoacylglycerol within the catalytic site.

We have complemented this study by illustrating how the protein sits within a biological membrane, its molecular stability and how it dynamically interacts with substrates, products and potential molecular intermediates. More details can be found at Nature Communications [2]. To explore the structure in more detail go to the links at the PDB or MemProtMD.

References:

[1] Li, D. et al. (2013) Crystal structure of the integral membrane diacylglycerol kinase. Nature

[2] Li, D, Stansfeld, P.J. et al. (2015) Ternary structure reveals mechanism of a membrane diacylglycerol kinase. Nature Comms. 6: 10140