• Regulate and conquer: how do post-translational modifications regulate protein-protein interactions and molecular promiscuity?

Amino acids are the building blocks of proteins and thanks to their chemical properties, their interactions make possible the folding of a protein into a 3D structure. For most proteins, this 3D structure is well defined, whereas for others, which are called intrinsically disordered proteins (IDPs), it is less pronounced and can be mostly transient.

Nevertheless, either you have a single structure dynamically fluctuating within a set of similar conformations or multiple fluctuating conformers, biological processes require the utmost regulation.

While function is encoded into the conformational states of a protein, which are themselves linked to the amino-acid sequence composing it, regulation is very often achieved by chemical modifications of amino-acids, which change the physico-chemical properties and modify the free energy landscape of protein function.

We aim to understand how post-translational modifications contribute to the dynamics and function of proteins and protein complexes, and we do this using molecular simulations in a collaborative partnership with experimentalists.

We are studying several proteins and protein complexes to understand how PTMs regulate function and if we can extract general principles to use, in the future, to regulate the dynamics of engineered molecules fulfilling a sought-after biotechnological function.

Potential energy profile of a single de-methylesterification cycle of a processive pectin methyl esterase

Molecular motors are molecules that convert energy performing useful work, crucial for the physiological functions of cells. They come in a “wide range of shapes” (different structures), carrying out their functions through different mechanisms.

Some molecular motors are rotary, performing work rotating in a single direction and making energy. Others walk on linear molecules (tracks) like linear nucleic acids or polysaccharides. For molecular motors, performing useful work means either rotating or walking their track in a single direction.

Nevertheless, this ability is complicated by the fact that, being so tiny, their movement is always subject to considerable thermal fluctuations, which are, by definition stochastic. Usually, in order to bias thermal fluctuations and achieve unidirectionality, molecular motors use energetic co-factors such as ATP or GTP, because their binding and hydrolysis provides the necessary conditions to bias stochastic fluctuations into useful mechanical work and regenerate the motor’s cycle so that another reaction can happen in series.

Some polysaccharide-processing enzymes called Pectin methyl esterase (PME), walk along pectin linear chains removing methyl groups from the chain and modifying the physico-chemical properties of pectin, which is crucial for plants integrity and physiology.

PME are molecular motors, as they catalyse several de-methylesterification before dissociating from “their track”. They, in other words, are PROCESSIVE.

However, surprisingly they do it without the use of any energetic co-factors.

How do they do it?

We have previously studied their activity and identified the mechanism of their “molecular walking”. They use the chemical features of their product of reaction, and the dynamics of the polysaccharide chain, to walk unidirectionally along the chain.

Using the knowledge acquired in the past on these molecular systems, we now aim to rationally modify these molecules to make them perform more efficiently, and tune their application in industrial processes.

On the other hand, we also aim at developing inhibitors for PMEs used by bacteria for plant infections, as many fungi and bacteria utilize their own PMEs to break the plant cell wall and more easily penetrate the cells of the host to infect it.

To do so we employ molecular dynamics simulations, interfacing them with experimental studies involving a set of structural biology techniques, from X-ray crystallography to force spectroscopy. For this project we collaborate with Professor Geoff Jameson and Associate Professor Martin A.K. Williams at Massey University.

This project is funded by the Royal Society of New Zealand, through the award of a Marsden Grant.