Ultra-high resolution structure determination using only residual dipolar couplings

Structure determination using residual dipolar couplings

Ultra high resolution determination of protein structure from residual dipolar couplings

Residual dipolar couplings (RDCs), measurable under weak alignment conditions, have shown remarkable promise, predominantly for complementing nOe-based structure elucidation, but also for ab initio fold determination. In contrast to nOes, interpretation of RDCs in terms of structure and dynamics is susceptible to relatively few sources of error, and therefore should provide access to more precise structural definition.

A number of years ago we proposed an approach to solve the backbone structure of a protein using only RDCs measured from throughout the peptide chain. The method, named meccano(Molecular Engineering Calculations using Coherent Association of Non-averaged Orientations), and feasibility was initially demonstrated using the dataset from ubiquitin measured by the Bax group and then to the determination of a small strand of Methionine Sulfoxide Reductase aligned in PEG/Hexanol and Phage alignment media (see figure).

Recently we have used this approach to simultaneously determine both the solution conformation and the backbone conformational disorder of protein GB3.

Structure determined without H-H RDCs (left) and with (right) compared to known crystal structure

Although RDCs have been routinely measured between covalently bound spins of fixed internuclear distance, long-range RDCs also provide potentially very powerful structural information. It has been shown that measurement of 1H-1H RDCs can be made to high levels of precision in highly deuterated proteins, where dipolar truncation effects are avoided. We have recently shown that the backbone solution structure of perdeuterated protein GB1 can be determined to the highest possible precision using only RDCs and residual 13CÕ chemical shifts (RCSs) measured in two different alignment media, demonstrating the immense and largely unexploited power of these constraints for high precision protein structure determination.

Ultra-High Resolution Backbone Structure of Perdeuterated Protein GB1 using Residual Dipolar Couplings from Two Alignment Media. G. Bouvignies, S. Meier, S. Grzesiek and M. Blackledge. Angewandte Chemie International Edition. 45, 8166-8169 (2006).

Simultaneous Determination of Protein Structure and Dynamics using Residual Dipolar Couplings. G. Bouvignies, R.Bruschweiler and M. Blackledge. J.Am.Chem.Soc.128, 15100-15101 (2006).

Characterization of Protein Dynamics from Residual Dipolar Couplings using the Three Dimensional Gaussian Axial Fluctuation Model. Guillaume Bouvignies, Phineus R. L. Markwick and Martin Blackledge Proteins: Structure, Function and Bioinformatics71, 353-363 (2008).

De novo determination of protein backbone conformation from residual dipolar couplings J.-C.Hus, D.Marion and M.Blackledge, J. Am. Chem. Soc., 123 1541 (2001).

Reaction site conformation of methionine sulfoxide reductase in solution: Direct structure determination from dipolar couplings. Sabine Beraud, Beate Bersch, Bernhard Brutscher, Pierre Gans, Frederic Barras and Martin Blackledge J.Am.Chem.Soc. 124, 13709-13715 (2002).