Tables for
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 19.7, p. 464   | 1 | 2 |

Section 19.7.1. Complementary roles of NMR in solution and X-ray crystallography in structural biology

K. Wüthricha

aInstitut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, CH-8093 Zürich, Switzerland

19.7.1. Complementary roles of NMR in solution and X-ray crystallography in structural biology

| top | pdf |

X-ray diffraction in crystals and NMR in solution can both be used to determine the complete three-dimensional structure of biological macromolecules, and to date a significant number of globular protein structures have been independently determined in crystals and in solution (Billeter, 1992[link]). Particularly detailed comparisons of the two states have been made for the α-amylase inhibitor Tendamistat, which also included solving the crystal structure by molecular replacement with the NMR structure (Braun et al., 1989[link]). The dominant impression is one of near-identity of the molecular architecture in solution and in single crystals, which holds for the polypeptide backbone as well as the core side chains.

Although the presently available results show that there is usually close coincidence between both the global molecular architecture and the detailed arrangement of the molecular core in corresponding X-ray and NMR structures of globular proteins, there is also extensive complementarity in the information that is accessible with the two methods: X-ray diffraction can provide the desired information for big molecules and multimolecular assemblies, whereas NMR structure determination is limited to smaller systems [recently introduced new experiments enable solution NMR measurements for molecular weights of 100 000 and beyond (Pervushin et al., 1997[link]; Riek et al., 1999[link])]. NMR measurements in turn provide quantitative information on both very rapid motions on the subnanosecond timescale (Otting et al., 1991[link]; Peng & Wagner, 1992[link]) and slower dynamic processes (Wüthrich, 1986[link]) which are not manifested in the X-ray data. Examples of low-frequency intramolecular mobility are the ring flips of phenylalanine and tyrosine (Wüthrich & Wagner, 1975[link]), exchange of interior hydration water molecules with the bulk solvent (Otting et al., 1991[link]), and interconversion of disulfide bonds between the R and S chiral forms (Otting et al., 1993[link]). NMR studies of amide proton exchange and cis–trans isomerization of Xxx—Pro peptide bonds (Wüthrich, 1976[link], 1986[link]) afford additional insight into conformational equilibria in the protein core. Finally, in all instances where a biological macromolecule cannot be crystallized, NMR is currently the only method capable of providing a three-dimensional structure.

Overall, X-ray crystal structures and NMR solution structures provide qualitatively different information on the molecular surface. In the crystals, a sizeable proportion of surface amino-acid side chains are subject to similar packing constraints in protein–protein interfaces as the interior side chains in the protein core, and therefore they are rather precisely defined by the X-ray diffraction data. In NMR solution structures determined according to a standard protocol (Wüthrich, 1995[link]), the surface is usually largely disordered. Surface disorder in NMR structures may in part arise from scarcity of nuclear Overhauser effect (NOE) distance constraints and packing constraints near the protein surface, but, in turn, scarcity of NOE constraints is often a direct consequence of dynamic disorder. Additional NMR experiments that are not part of a standard structure determination protocol can provide information needed for more detailed characterization of the molecular surface, but care must be exercised in the data analysis because of the presence of a multitude of equilibria between two or multiple transient local conformational states, of which the relative populations are usually not independently known.


Billeter, M. (1992). Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single-crystals. Q. Rev. Biophys. 25, 325–377.Google Scholar
Braun, W., Epp, O., Wüthrich, K. & Huber, R. (1989). Solution of the phase problem in the X-ray diffraction method for proteins with the nuclear magnetic resonance solution structure as initial model. J. Mol. Biol. 206, 669–676.Google Scholar
Otting, G., Liepinsh, E. & Wüthrich, K. (1991). Protein hydration in aqueous solution. Science, 254, 974–980.Google Scholar
Otting, G., Liepinsh, E. & Wüthrich, K. (1993). Disulfide bond isomerization in BPTI and BPTI(G36S): an NMR study of correlated mobility in proteins. Biochemistry, 32, 3571–3582.Google Scholar
Peng, J. W. & Wagner, G. (1992). Mapping of spectral density functions using heteronuclear NMR relaxation measurements. J. Magn. Reson. 98, 308–332.Google Scholar
Pervushin, K., Riek, R., Wider, G. & Wüthrich, K. (1997). Attenuated T2 relaxation by mutual cancellation of dipole–dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc. Natl Acad. Sci. USA, 94, 12366–12371.Google Scholar
Riek, R., Wider, G., Pervushin, K. & Wüthrich, K. (1999). Polarization transfer by cross-correlated relaxation in solution NMR with very large molecules. Proc. Natl Acad. Sci. USA, 96, 4918–4923.Google Scholar
Wüthrich, K. (1976). NMR in biological research: peptides and proteins. Amsterdam: North Holland.Google Scholar
Wüthrich, K. (1986). NMR of proteins and nucleic acids. New York: Wiley.Google Scholar
Wüthrich, K. (1995). NMR – this other method for protein and nucleic acid structure determination. Acta Cryst. D51, 249–270.Google Scholar
Wüthrich, K. & Wagner, G. (1975). NMR investigations of the dynamics of the aromatic amino acid residues in the basic pancreatic trypsin inhibitor. FEBS Lett. 50, 265–268.Google Scholar

to end of page
to top of page