The overall objective of our research is to understand the principles governing protein homeostasis - the ability of cells to generate and regulate the levels of proteins in terms of conformations, interactions, concentrations and cellular localisation. By adopting the strategy of analysing the origins of specific diseases to inform us about normal biology, we have set up an interdisciplinary programme that involves bringing together methods and concepts from chemistry, physics, engineering, genetics and medicine. We are using a combination of in vitro, in silico and in vivo approaches to study protein homeostasis through the analysis of the effects that result from its alteration in a select group of specific proteins, from either amino acid mutations, or changes in concentration and solubility, or the interactions with other molecules. This programme is generating new insights into the mechanism through which physical and chemical sciences can address biological questions in order to understand the normal behaviour of living systems. In addition it is increasing our understanding of the nature and consequences of the failure to maintain homeostasis, which is associated with such phenomena as ageing and neurodegenerative disorders.



LATEST RESEARCH


Cyclophilin A catalyses proline isomerization by an electrostatic handle mechanism. Proc. Natl. Acad. Sci. USA 111, 10203-10208 (2014).

One of the most widespread molecular switches in biochemical pathways is based on the isomerization of the amino acid proline, a process that normally is facilitated by enzymes known as 'proline isomerases'. We show that cyclophilin A, one of the most common proline isomerases, acts by a simple mechanism, which we describe as an 'electrostatic handle'. In this mechanism, the enzyme creates an electrostatic environment in its catalytic site that rotates a peptide bond in the substrate by pulling the electric dipole associated with the carbonyl group preceding the peptide bond itself. Our results thus identify a specific mechanism by which electrostatics is exploited in enzyme catalysis.


Statistical mechanics of the denatured state of a protein using replica-averaged metadynamics. J. Am. Chem. Soc. 136, 8982-8991 (2014).

The characterization of denatured states of proteins is challenging because the lack of permanent structure in these states makes it difficult to apply to them standard methods of structural biology. In this work we use all-atom replica-averaged metadynamics (RAM) simulations with NMR chemical shift restraints to determine an ensemble of structures representing an acid-denatured state of the 86-residue protein ACBP. This approach has enabled us to reach convergence in the free energy landscape calculations, obtaining an ensemble of structures in relatively accurate agreement with independent experimental data used for validation. By observing at atomistic resolution the transient formation of native and non-native structures in this acid-denatured state of ACBP, we rationalize the effects of single-point mutations on the folding rate, stability, and transition-state structures of this protein, thus characterizing the role of the unfolded state in determining the folding process.

NEW TOOLS


CamSol: A method of rational design of protein variants with enhanced solubility.



P. Sormanni, F. A. Aprile and M. Vendruscolo. J. Mol. Biol. in press.



UPDATED TOOLS


d2D: Determination of secondary structure populations in disordered states of proteins using NMR chemical shifts.



C. Camilloni, A. De Simone, W. Vranken and M. Vendruscolo. Biochemistry 51, 2224-2231 (2012).



BOOKS


Networks in Cell Biology



M. Buchanan, G. Caldarelli, P. De Los Rios, F. Rao and M. Vendruscolo (Eds). Cambridge University Press, Cambridge (2010).