Hydration of Biological Macromolecules in Solution: Surface Structure and Molecular Recognition

Abstract

The presently available three-dimensional protein and nucleic acid structures at atomic resolution have, with few exceptions, been determined either by X-ray diffraction in protein crystals (Blundell and Johnson 1976) or by nuclear magnetic resonance (NMR) spectroscopy in protein solutions (Wuthrich 1986). These two techniques produce a rapidly growing pool of data (Hendrickson and Wuthrich 1991, 1992, 1993), which represent today's structural basis for detailed investigations on the functionality of biological macromolecules. NMR spectroscopy and X-ray diffraction can provide complementary information on the same molecule, which results primarily from the facts that the time scales of the two types of measurements are widely different, and that the two techniques use, respectively, proteins in solution and protein single crystals (see, e.g., Wuthrich 1990, 1991). Since protein structure determinations by NMR or by X-ray diffraction can be performed independently (Blundell and Johnson 1976; Wuthrich 1986), meaningful comparisons of corresponding structures in single crystals and in noncrystalline states can be obtained. This is highly relevant, since the solution conditions for NMR studies may coincide closely with the physiological fluids, and comparative studies of corresponding crystal and solution structures promise to result in more relevant ways of analyzing crystal data with regard to protein functions in physiological milieus. Providing this kind of fundamental information may well turn out to be the major impact of NMR in structural biology, considering that X-ray crystallography continues to provide a dominant fraction of the new macromolecular structures (Hendrickson and Wuthrich 1993). Although NMR structure determination in solution will foreseeably be limited to proteins with molecular weights below about 30,000-40,000 (see, e.g., Wuthrich 1990), many conclusions from comparative studies with relatively small proteins should also be applicable to crystal structures of bigger molecules. In comparisons of corresponding crystal and solution structures of proteins, both global conformational rearrangements and extensive conservation between the two states have been observed. Major rearrangements are usually seen in nonglobular polypeptides (see, e.g., Braun et al. 1983) and on the surface of globular proteins, whereas close coincidence is commonly encountered for the core of globular proteins (Billeter 1992). However, even for proteins with virtually identical molecular architecture in crystals and in solution, the two techniques provide different information on the internal mobility of the molecular core. NMR can provide direct, quantitative measurements of the frequencies of certain high-activation-energy motional processes in the interior of globular proteins, and at least semiquantitative information on additional, higher-frequency processes. The corresponding information from X-ray structure determinations commonly consists of an outline of the conformation space covered by the combination of static disorder and high-frequency structure fluctuations. The protein surface is most likely to be influenced by crystal packing, or by solvent interactions, respectively, and it is thus of special interest to investigate these effects by combined use of NMR and crystallography. On the one hand, a detailed description of the protein surface in near-physiological solution represents a proper reference for investigating mechanistic aspects of intermolecular interactions with proteins, and novel NMR techniques enabling the observation of hydration water on the molecular surface (Otting et al. 1991a) have greatly added to the characterization of protein surfaces in solution. On the other hand, the structural basis of intermolecular recognition between different macromolecules can be investigated in a large sample of X-ray crystal structures of proteins in binary complexes or multimolecular assemblies, and even the influence of crystal-packing effects on the protein surface may be indicative of the types of protein-protein interactions that are important in physiological recognition processes. In this paper, I survey novel insights into protein structures in solution that result from NMR investigations of protein hydration. Special emphasis is on protein surface hydration in aqueous solution and comparison with corresponding data from diffraction experiments with protein crystals. As an illustration, hydration data on a homeodomain-DNA complex (Billeter et al. 1993; Qian et al. 1993a) are discussed.