Methodology
In this project we focus upon methods to improve NMR-derived structures, develop automated tools for structure quality assessment and data evaluations, and design new NMR sequences for the study of dynamics and interactions.
Improved methods for structure generation and validation
Figure 1. Improvement of structural quality in the DRESS database (before and after refinement). Using QUEEN for structure validation.
NMR structures should
adequately reflect the experimental data and be reliable in
terms of overall and local quality. In this project we
develop tools that yield better structures and tools that
help to validate data and results. Our recent analysis of a
large set of recent NMR derived structure ensembles
originating from both structural genomics projects and
individual structure determination groups suggested serious
flaws in in terms of both local and overall quality scores.
Overall, our results illustrated that the quality of NMR
structures cannot be reliably evaluated using only
traditional experimental input data as a reference and
clearly demonstrate the urgent need for a tight integration
of more sophisticated structure validation tools in NMR
structure determination projects. In contrast to common
methodologies where structures are typically evaluated as a
whole, such tools should preferentially operate on a
per-residue basis.
Key references:
■ Nabuurs, S.B., Spronk, C.A.E.M, Krieger, E.,
Maassen, H., Vriend, G. & Vuister, G.W. (2003)
“Quantitative evaluation of experimental NMR
restraints”, J. Am. Chem.
Soc.125, 12026-12034.
■ Nabuurs, S.B., Nederveen, A.J., Vranken, W.,
Doreleijers, J.F., Bonvin, A.M.J.J., Vuister, G.W., Vriend,
G. & Spronk, C.A.E.M. (2004) "DRESS, a Database of
REfined Solution nmr Structures", Proteins, Struct.,
Func., Genet. 45, 483-486.
■ Spronk, C.A.E.M., Nabuurs, S.B., Vriend, G. &
Vuister, G.W. (2004) “Validation of High-Resolution
NMR-Structures”, Prog. NMR Spectr.
45, 315-337.
■ Nabuurs, S, Krieger, E., Spronk, C.A.E.M.,
Nederveen, A.J, Vriend, G., & Vuister, G.W. (2005)
“Definition of a new information-based per-residue
quality parameter”, J. Biomol. NMR
33, 123-134.
■ Nabuurs, S, Spronk, C.A.E.M., Vuister, G.W. &
Vriend, G. (2006) “Traditional Biomolecular Structure
Determination by NMR Spectroscopy Allows for Major
Errors”, PLoS Comput. Biol.
2, e9.
New pulse sequences
Figure 2. CEESY pulse sequence element generating a pseudo-echo of SQ and MQ. The PAH2 domain in exchange with a 1% unfolded conformer.
The CEESY pulse sequence element is a new NMR method to determine the position of unobservable exited states relative to observable resonances of the major state. The CEESY element was tested for 15N and 1H resonances, but can in principle be applied to any nucleus. The sign information from the CEESY element can be combined with the information about the absolute magnitude of the chemical shift differences between observable and excited states, as obtained from relaxation dispersion elements, to characterize the nature of this excited state.
Key references:
■ Van Ingen, H., Baltussen, M.A.H, Aelen, J. & Vuister, G.W. (2006) “Role of Structural and Dynamical Plasticity in Sin3: The Free PAH2 Domain is a Folded Module in mSin3B”, J. Mol. Biol. 358, 485-497.
■ Van Ingen, H., Vuister, G.W., Wijmenga, S.S., Tessari, M. (2006) “CEESY: characterizing the conformation of unobservable protein states”, J. Am. Chem. Soc. 128, 3856-3857.