Protein structure determination by NMR

K. Wuthrich, Six years of protein structure determination by NMR spectroscopy What have we learned in Protein Conformation. Ciba Foundation Symposium 161, John Wiley Sons, Chichester, 1991, pp. 136-149. 

Although in the past years, significant progress has been made in generating dynamically relevant ensembles, these methods are still not used widely used. Such calculations require efforts beyond the current routine of protein structure determination by NMR both from the experimental side, as heteronuclear relaxation and /or... 

The accuracy of protein structures determined by NMR is very dependent on the quantity and quality of data that can be obtained. It has been known that the highest quality NMR structures have accuracies comparable to the medium-resolution X-ray structures (2.0-2.5A) for protein backbone atomic coordinates.3 To improve the structural qualities and utilize them for biological system studies, it is important to re-emphasize factors having a critical impact on quality as summarized below. 

The high-resolution protein structure determination by NMR is possible and becomes more and more feasible. There are many obstacles, but there... 

The volume opens with a report by L.D. Field on Multiple Quantum NMR of Partially Aligned Molecules following this is an account on Solid-State NMR Studies of Molecular Motion by M.J. Duler C. Odin reviews NMR Studies of Phase Transitions Application of Multi-way Analysis to 2D NMR Data is covered by H.T. Pedersen, M. Dyrby, S.B. Engelsen and R. Bro the final contribution is on High Resolution Protein Structure Determination by NMR and it is provided by H. Takashima. My sincere thanks go to all of these reporters and to the production staff at Elsevier for their assistance in the creation of this volume. 

Box 2.2 Stages in a Typical Protein Structure Determination by NMR (courtesy of Nicola Meenan)... 

Aramini JM, Rossi P, Anklin C, Xiao R, Montelione GT (2007) Microgram-scale protein structure determination by NMR. Nat Methods 4 491 93... 

H. Takashima, High-Resolution Protein Structure Determination by NMR , Annu. Rep. NMR Spectrosc., 2006, 59, 235. 

The secondary structure elements, formed in this way and held together by the hydrophobic core, provide a rigid and stable framework. They exhibit relatively little flexibility with respect to each other, and they are the best-defined parts of protein structures determined by both x-ray and NMR techniques. Functional groups of the protein are attached to this framework, either directly by their side chains or, more frequently, in loop regions that connect sequentially adjacent secondary structure elements. We will now have a closer look at these structural elements. 

Protein Data Bank (PDB) Protein structures determined by X-ray and NMR http //www.rcsb.org/pdb/... 

Protein structures determined by X-ray or neutron diffraction or NMR which may include co-factors, substrates, inhibitors, or other ligands... 

F. 3.6 This is a stereo view of the SAM structure determined by NMR. The characteristic five helices are shown. (The nbbon structure is reproduced from ref. 61, with permission of the authors and Protein SiSence.)... 

Biomolecular NMR spectroscopy is applicable to both liquid-and solid-state samples. Liquid-state NMR spectroscopy, in which molecules are dissolved in a variety of different solvents and studied at ambient temperatures, is a powerful tool to derive information on the stmcture of proteins and nucleic acids, as well as their complexes with each other and small molecules, ions, and solvents. Liquid-state NMR can be applied not only to native folded states of proteins, but also to intrinsically unstmctured proteins as well as proteins in their unfolded state and under nonphysiological conditions (i.e., in organic solvents). Figure 1 provides an overview on the number of protein structures determined by liquid-state NMR spectroscopy. 

The molecular mass of the complex hetween a domain of protein G and an Fab or an Fc fragment of IgG is approximately 58 kDa, so that a complete structure determination by nmr is not feasible. However, since the structure of each component of the complex is known, it is possible to obtain a medium-resolution model of the complex if the residues in each component involved in the interaction can be identified, at a simple level by using appropriately isotope-labelled proteins to identify residues whose chemical shifts are affected by complex formation. 

Clearly, additional efforts to streamline 3D protein structure determination by MAS NMR are necessary. Novel concepts may make extensive use of the rapidly increasing power of bioinformatics and computational chemistry. Already, general approaches have appeared to predict 3D structure from a limited set of solution-state NMR data. " In parallel, the ability to relate molecular structure to NMR detectable parameters by ab initio quantum chemistry calculations and DFT approaches is dramatically improving.These techniques already have empowered novel material science applications of solid-state NMR and will greatly expand the use of MAS solid-state NMR for the study of polypeptides and proteins. Complementary to crystallographic... 

---