Intrinsically disordered proteins and protein folding : A challenge for structural biology

Presentation

Intrinsically disordered proteins : A challenge for structural biology.

Around 35% of the human proteome does not fold into stable three-dimensional structures but are either fully unfolded, or contain unfolded regions of significant length. The inherent flexibility of this class of proteins is essential for their function in a vast range of biomolecular processes such as molecular recognition, signal transduction and trscription and replication. Natively unfolded proteins also appear to play major roles in important human diseases such as neurodegenerative disorders and cancer (see examples by clicking on the left of the page). Despite the importance of characterizing this class of proteins, standard, single conformer-based approaches to structure determination necessarily fail to adequately describe such highly flexible systems. It has therefore become essential to develop new tools for characterizing their rapidly fluctuating conformational behaviour.

Our group is currently developing methods to determine local and long-range structural behaviour in intrinsically unfolded proteins from experimental NMR data. We are using NMR and complementary biophysical techniques such as molecular simulation and small angle scattering to study in fine detail the presence of local conformational preferences in a number of biologically and medically important unfolded proteins that have until recently remained inaccessible to structural biology. Some examples are detailed in the accompanying sections.

A structural model for unfolded proteins from residual dipolar couplings and small angle X-ray scattering. P. Bernado, L. Blanchard, P. Timmins, D. Marion, R. Ruigrok and M. Blackledge Proc. Natl. Acad. Sci. 102, 17002-17007 (2005)

Conformational distributions of unfolded polypeptides from novel NMR techniques. Sebastian Meier, Martin Blackledge and Stephan Grzesiek. J. Chem. Phys.128, 052204.(2008)

Structural Characterization of Flexible Proteins Using Small-Angle X-ray Scattering. P. Bernado, E. Mylonas , M. V. Petoukhov, M. Blackledge and D. I. Svergun. J.Am.Chem.Soc. 129, 5656-5664 (2007)

Highly Populated Turn Conformations in Natively Unfolded Tau Protein Identified from Residual Dipolar Couplings and Molecular Simulation. M. D. Mukrasch, P.R.L. Markwick, J. Biernat, M. von Bergen, P. Bernado, C. Griesinger, E. Mandelkow, M. Zweckstetter and M. Blackledge J.Am.Chem.Soc. 129, 5235-5243 (2007)

Defining long-range order and short-range disorder in native alpha-synuclein using residual dipolar couplings. P. Bernado, C. Bertoncini, C. Griesinger, M. Zweckstetter and M. Blackledge. J.Am.Chem.Soc. 127, 17968-17969 (2005)

A structural model for unfolded proteins from residual dipolar couplings and small angle X-ray scattering. P. Bernado, L. Blanchard, P. Timmins, D. Marion, R. Ruigrok and M. Blackledge Proc. Natl. Acad. Sci. 102, 17002-17007 (2005)

Understanding protein folding at atomic resolution.

The methods that we are developing for studying unfolded proteins provide exquisitely sensitive probes for understanding the molecular basis of protein folding and stability. In collaboration with Prof Grzesiek from the University of Basel Biozentrum we are trying to understand the level of local and tertiary structure present in urea-denatured proteins using extensive measurements of residual dipolar couplings and extensive simulation of the conformational sampling regime of the protein backbone. Initial results strongly suggest that the protein backbone samples more extended conformations in the presence of urea while retaining amino acid specific conformational wells.

Mapping the Conformational Landscape of Urea-Denatured Ubiquitin using Residual Dipolar Couplings. Sebastian Meier, Stephan Grzesiek and Martin Blackledge J.Am.Chem.Soc.129, 9799-9807(2007).

Direct observation of dipolar couplings and hydrogen bonds across a beta-hairpin in 8 M urea. S. Meier, M. Strohmeier, M. Blackledge and S. Grzesiek J.Am.Chem.Soc. 129, 754-755 (2007).