Physical characterization of protein phase transitions
Proteins are essentially nanosolids. They have the same properties as molecular solids of nanometer dimensions (density, compactness, vibrations etc). Proteins have two additional properties: they consist of a (usually) single polymer chain with a defined sequence and proteins “self assemble” – the polymer chain can fold itself into the solid-like “native” state. In this folding process, the polymer goes from a “spaghetti-like” unfolded state to the native state. The former is an ensemble of states (possibly a random polymer chain) while the latter has a well-defined three-dimensional structure that is amenable to crystallization and characterization by x-ray crystallography. This structural change resembles a first order phase transition.
Proteins are life’s molecular machines. All processes in living systems are (usually) effected by protein machines. These range from molecular transitions catalysed by enzymes to directed movement along a track powered by a protein engine. The way proteins machines work usually involves structural changes in the protein. These transitions may be phase transitions or just rigid body segmental motion.
The central portion of this project is to experimentally characterise the transition between the solid-like folded native state and the unfolded state for a set of proteins. For small proteins, this transition is essentially a reversible equilibrium process, while for larger proteins the system is not in equilibrium. We have previously characterised the protein CLIC1 and shown that the experimental data for CLIC1 melting can be described by a three-state non-equilibrium model.
The aim of this project is to experimentally characterise the melting of at least two other (unrelated) proteins and determine whether the experimental data can be fit by the same three-state non-equilibrium model as per CLIC1. If the model fits, then it will allow the determination of many key energetic and kinetic parameters for the unfolding transitions of these proteins. The key experimental tool for monitoring protein folding will be circular dichroism (CD) spectroscopy (as a function of temperature). CD measures chirality, which is enhanced in a folded protein. Additionally, differential scanning calorimetry may be used to monitor thermodynamic parameters.
The project will be hands on experimental. There are no prerequisites, no background in proteins, biology or chemistry is needed. What is important is dexterity in a laboratory situation and an ease with sophisticated experimental equipment. The experimental results obtained will be amenable to theoretical modelling, if this is an area which the student wishes to pursue. The results obtained will contribute to larger projects aimed at understanding molecular machines.