Matthew Cliff

Address:
Manchester Institute of Biotechnology,
University of Manchester,
Princess St,
MANCHESTER.
M1 7DN
email: matthew.cliff@manchester.ac.uk

Tel: 0161 3065179

Tweet: @drmattcliff

Research

Enzyme Catalysis.

My principal research area is the biological catalysis of phosphoryl transfer.

Enzymes are proteins which accelerate the rates of chemical reactions without being modified themselves, i.e. they are catalysts. The increases in reaction rate that an enzyme induces can be up to 1020-fold, for example in phosphoryl transfer reactions. The mechanisms by which enzymes achieve these accelerations is far from well understood. Convention says that the enzyme stabilises a transition state-like conformation, which resembles the mid-point of the reaction. This is supported by phosphoryl transfer enzymes binding metal fluoride complexes that resemble the putative transferring, pentavalent conformation of phosphate (AlF4 and MgF3). However, the dissociation constants and enthalpies for these complexes are much above the required values (i.e. less favourable) for binding alone to induce the rate enhancement. Other contributions may come from non-local effects imposed by the protein structure, for example quantum tunneling, protein dynamics and "enthalpic chelate" effects have been proposed to have a significant impact on catalytic rates. My research, carried out in the labs of Anthony Clarke and Jon Waltho, has focused on phosphoglycerate kinase, which transfers a phosphate group from bisphosphoglycerate to ADP (see animated gif above), and on β-phosphoglucomutase, which interconverts glucose 6-phosphate and β-glucose 1-phosphate.


Coupled folding and binding

There are an increasing number of examples of proteins that do not form a conventional, well-defined 3 dimensional structure in physiological conditions. However, many of these proteins do fold upon interaction with small molecules, or forming protein- protein interactions. The thermodynamic consequence of this is a decrease in the apparent dissociation constant. The extent to which this is an evolutionary accident, or imparts a physiological benefit, has not been determined. My work (with John Ladbury and Mark Williams) established this behaviour in the TPR domain of protein phosphatase 5.

Protein Folding.

Protein folding is the study of how the linear polymer that makes up a protein is arranged to form the defined 3 dimensional arrangement required for activity. This process is spontaneous (Anfinsen hypothesis) and non-random (Levinthal calculation). The study of protein folding attempts to characterise the properties of the folding pathway that define the non-randomness. There are a number of models for the process which have different processes dominating the pathway: the hydrophobic effect leads to compaction (collapse); specific sequence distant (tertiary) contacts (nucleation); backbone hydrogen bonding (secondary structure) (framework). The "new view" which appeared in the 1990's, on the basis of computational work, suggested many pathways were possible, and the route taken may vary from molecule to molecule in a population, and one effect will not dominate completely over the others. It is very difficult to model the hydrophobic effect realistically, and so computational work has struggled to describe the process properly. My work, carried out in the labs of Anthony Clarke, and Jonathan Waltho, has focussed on two protein domains; CD2.d1 and N-PGK. My most recent protein folding work focused on defining the structural biases in unfolded protein states and how these change with denaturing conditions, using paramagnetic relaxation enhancement and chemical shifts.

Publications

Link to recent publications on pubmed