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Daniel Bearup


Comparative flux control through the cytoplasmic stages of cell wall biosynthesis


Supervisors: Prof Chris Dowson[1], Dr Mike Chappell[2]

Advisory Committee: Prof Tim Bugg[3], Dr Markus Kirkilionis[4], Dr Dave Roper[1]


For the sake of completeness:-


Mini-project Supervisors: Prof Chris Dowson, Dr Dave Roper and Dr Mike Chappel


(Yes, my mini-projects did bear a striking resemblance to my current project.)


Project summary


Peptidoglycan is an essential structural component of the bacterial cell wall, protecting the cell from mechanical (principally osmotic) stress. Its synthesis is a target for numerous clinically important antibiotics; however resistance to these drugs is increasing. An improved understanding of the biosynthetic pathway producing peptidoglycan is essential to determining the potential efficacy of new drugs.


Peptidoglycan is a polysaccharide of alternating N-acetyl-glucosamine (NAG) and N-acetyl muramate (MurNac) residues, cross linked by pentapeptide chains (L-Ala-D-GLu-L-lys [or -D,L diaminopimelic acid, DAP]-D- Ala-D- Ala) and is synthesised in a three stage process. The cytoplasmic phase is catalysed by murA-murF and forms the MurNac-pentapeptide residues. In the second phase the MurNac pentapeptide enters a series of steps on the intracellular face of the cell membrane, where it is attached to a lipid carrier and glycosylated. In the third phase, the product of this sequence of reactions is flipped to the extracellular face of the membrane where the final crosslinking reactions (transglycosylation and transpeptidation) furnish the final peptidoglycan. The principal focus of this project is the cytoplasmic phase of the synthesis. While inhibitors for each of the enzymes in this process have been developed they are as yet ineffective antibacterials.


Pathways from S. pneumoniae, P. aeruginosa, S. aureus and E. coli are under investigation. Concentrations of relevant reaction species are monitored in vitro using real time spectroscopic techniques. These data are used to derive kinetic characterisations of the enzymes using a combination of initial rate and curve-fitting techniques guided by structural identifiability and indistinguishability analyses. The resulting constants are used to construct in silico models of the reactions which can then be combined to simulate the complete pathway.


Flux through constructed pathways is monitored using similar experimental techniques. These pathways are then challenged using specific inhibitors and changes in flux measured. These results are used to validate the in silico model which can then be used, in conjunction with steady state and robustness analyses, to optimise combinations of inhibitors to maximise disruption of the pathway.




A year on and I still haven't given this website the attention it deserves ... .

Well in an attempt to rectify the situation I'm going to ramble on for a couple of paragraphs in a vain (in oh so many ways) attempt to tell you a little something about me and what I do. Having discovered a love of mathematics in my formative years I went on to do a four years maths degree right here at Warwick. Abstract mathematics was all very well but it didn't really seem to be going anywhere. So by a series of relatively unlikely coincidences I found my way to MOAC.

The taught sections are perhaps of little interest to you, unless you're a new MSc student looking to crib, in which case tut tut. Well perhaps not I doubt he would have liked it and crocodiles aren't particularly forgiving. My miniprojects were chosen with malice aforethought to satisfy my bias towards medical applications and to lead naturally into a PhD project, after all why would I want to learn yet another new subject before I could get on with research. All of them concerned the cytoplasmic phase of peptidoglycan biosynthesis. So for those of you for whom this is so much Greek, we're looking at the way that bacterial cell walls are constructed.


Setting up a VPN

Go to here. You'll need to sign in, once you have you'll be able to set up a password for use on the VPN. It ought to be different from the one you have at the moment.

Go to here. Follow the instructions.

Internet phenomena

In an attempt to feed an internet phenomenon

"Jar Jar, you're a genius"

If you know what I'm talking about you geek you ... . Hey it might increase awareness of my research ... that's what I'll be telling university PR if they complain about this little addition.


Departmental Affiliation

[1] Biology

[2] Engineering

[3] Chemistry

[4] Mathematics


Contact Details


Alternatively send mail to: Daniel Bearup,
Coventry House,
University of Warwick,
Gibbet Hill Road,

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