EU-STREP: Understanding Protein Misfolding and Aggregation by NMR

A detailed understanding of the processes responsible for the failure in achieving or in maintaining the normal functional structures of proteins is of crucial importance in the development of strategies to protect or enhance human health. To gain biological function, polypeptide chains generally need to fold into specific three-dimensional structures - their native states. Abberrant folding of proteins can lead to a range of other scenarios, including the development of highly organised and intractable aggregates that are deposited inside or outside cells. Such misfolding events are at the origins of a range of neurological and systemic diseases that increasingly compromise the quality and expectancy of life and the health resources of advanced societies. The focus of this application is the development of novel methods to study the structural states of proteins that are particularly relevant to understand protein misfolding and aggregation. The species involved range from highly flexible unfolded monomers to soluble oligomers and precursors of fibrillar aggregates. In most of these states, polypeptide chains acquire structures that differ substantially from those of the native proteins that are accessible from conventional approaches of structural biology or from structural genomics procedures. The major techniques that will be used to define at atomic level the structural characteristics of the range of species relevant to understanding misfolding and aggregation is NMR spectroscopy. In this STREP, a range of complementary NMR approaches will be developed by the various partners for this purpose. These approaches include a variety of NMR techniques and will be coupled with novel computational approaches able to define even the disorganised ensembles characterisitic of some of the most interesting and biologically relevant species. These approaches will then be applied to representative examples of the various types of proteins that are associated with misfolding diseases, ranging from natively unfolded species (such as alpha-synuclein associated with Parkinsons disease) and partially unfolded intermediates (such as forms of superoxide dismutase associated with motor neurone disease) to the precursors of aggregation prone fragments (such as the Alzheimer precursor protein) and the prion proteins that are uniquely associated with transmissible conditions. One of the major aims of this proposal is to provide a novel unified view of the conformational behaviour of protein molecules that will have a broad significance for understanding important aspects of functional genomics, including the fundamental links between genetic mutations and disease and the mechanisms by which normally soluble proteins can sporadically misfold, giving rise to a wide range or disorders associated with diet, medical and agricultural practices and ageing.

Publications:

Smith, Lorna J. ; Bolin, Kimberly A. ; Schwalbe, Harald ; MacArthur, Malcolm W. ; Thornton, Janet M. ; Dobson, Christopher M. : Analysis of Main Chain Torsion Angles in Proteins. Predictions of NMR Coupling Constants for Native and Denatured Conformations . In: J.Mol.Biol. 255 (1995), S. 494-506

Buck, Matthias ; Schwalbe, Harald ; Dobson, Christopher M. : Characterization of Conformational Preferences in a Partly Folded Protein by Heteronuclear NMR: Assignment and Secondary Structure Analysis of Hen Egg-White Lysozyme in Trifluoroethanol . In: Biochemistry 34 (1995), S. 13219-13232

Buck, Matthias ; Schwalbe, Harald ; Dobson, Christopher M. : Determinants of Mainchain Dynamics of a Partially Folded Protein: 15N NMR Relaxation Measurements of Hen Egg White Lysozyme Denatured in Trifluoroethanol . In: J.Mol.Biol. 254 (1995), S. 7532-7539

Smith, Lorna J. ; Fiebig, Klaus M. ; Schwalbe, Harald ; Dobson, Christopher M. : The concept of a random coil. Residual structure in peptides and denatured proteins . In: Folding and Design 1 (1996), S. 95-106

Schwalbe, Harald ; Fiebig, Klaus M. ; Buck, Matthias ; Jones, Jonathan A. ; Grimshaw, Shaun B. ; Glaser, Steffen J. ; Smith, Lorna J. ; Dobson, Christopher M. : Structural and Dynamical Properties of Lysozyme Denatured in 8M Urea. Heteronuclear 3D NMR Experiments and Theoretical Simulations . In: Biochemistry 36 (1997), S. 8977-8991

Kühn, Till ; Schwalbe, Harald: Monitoring the Kinetics of Ion Dependent Protein Folding by Time Resolved NMR at Atomic Resolution . In: J. Am. Chem. Soc. 122 (2000), S. 6169-6174

Peti, Wolfgang ; Hennig, Mirko ; Smith, Lorna J. ; Schwalbe, Harald: NMR Spectroscopic Investigation of Torsion Angle Distribution in Unfolded Ubiquitin from Analysis of 3J(Calpha ,Calpha) Coupling Constants and Cross-Correlated Relaxation Rates . In: J. Am. Chem. Soc. 122 (2000), S. 12017-12018

Peti, Wolfgang ; Smith, Lorna ; Redfield, Christina ; Schwalbe, Harald: Chemical Shifts in Denatured Proteins: Resonance Assignments for Denatured Ubiquitin and Comparisons with other Denatured Proteins . In: J. Biomol. NMR 19 (2001), S. 153-165