Understanding PMEs: Structure-Function Relationships of Key Brownian-motion Rectifying Enzymes

Exciting PhD Opportunites Available in Biophysics & Soft Matter in New Zealand

Several PhD openings now exist in our vibrant and international Biological Physics and Soft Matter resarch group based in the Institute of Fundamental Sciences at Massey University in Palmerston North, New Zealand (www.biophysics.ac.nz).

We now have a Riddett Institute (www.riddet.ac.nz) sponsored position in collaboration with Prof Geoff Jameson, additionally with the chance to collaborate with leading researchers in France and the USA. The project, while firmly rooted in the biological physics of nanomachines, focusses on understanding the behaviour of a processive enzyme using the tools of molecular and structural biology coupled with molecular dynamics. It would suit a student interested in solving protein structures and understanding structure-function relationships within the framework of the physics of molecular motors.


Pectin methylesterases (PMEs) modify the polysaccharide pectin, a key component of the plant cell wall. Indeed, PMEs and pectin both play key roles in structuring plant tissues at every stage of the plant life-cycle. Fungal and bacterial phytopathogens, phytophagous insects, and human-gut pathogens also express analogous PMEs for deconstructing the plant cell wall. Specifically, PMEs introduce negative charges onto the pectin molecule with controlled intramolecular distributions, from random to blockwise. Thus, the pattern of charge is modified in space and time to suit the biological purposes of the plant (or pathogen). We understand little of the subtleties of this deceptively simple reaction and how the patterning is controlled.

Our recent molecular-dynamics (MD) simulations of the interactions between pectin and a bacterial PME give insight into the correlated motions that establish this processive PME as an unconventional Brownian-ratchet nano-machine. Very recently, we have achieved the first structural and functional characterisation of a non-processive PME and, the lack of correlated motions observed by MD simulations for this PME further supports our hypothesis.

Building on this and other structural data our proposed research will deliver insight into the control of unique molecular machines, elucidate the purpose of the large numbers of plant PME isoforms, and allow the design of new pectin architectures.

PMEs, their mutants and their complexes with oligogalacturonan moieties will be investigated through a combination of techniques. High-resolution structures obtained by X-ray diffraction methods will provide the starting points for molecular dynamics simulations of PMEs complexed with substrates and inhibitor proteins. These simulations will be complemented and validated by standard biochemical measurements of PME activity and processivity, using capillary electrophoresis. X-ray diffraction measurements give a time-averaged picture of the structure, and with limitations, some information on overall dynamics. Isothermal titration calorimetry (ITC) allows full thermodynamic characterisation of substrate binding under both static conditions (to, for example, inactive PME mutants) and where substrates are undergoing enzymatic hydrolysis. SAXS and NMR techniques test congruency of X-ray structures and solution-state structures.


Check out www.biophysics.ac.nz and give Bill an email at [Email Address Removed] if you are interested. Closing date 5th November 2016.