Section 1.2.5. The first protein structures (1957 to the 1970s)

By the time three-dimensional structures of proteins were being solved, Linderström-Lang (Linderström-Lang & Schellman, 1959) had introduced the concepts of `primary', `secondary' and `tertiary' structures, providing a basis for the interpretation of electron-density maps. The first three-dimensional protein structure to be solved was that of myoglobin at 6 Å resolution (Fig. 1.2.5.1) in 1957 (Kendrew et al., 1958). It clearly showed sausage-like features which were assumed to be α-helices. The iron-containing haem group was identified as a somewhat larger electron-density feature. The structure determination of haemoglobin at 5.5 Å resolution in 1959 (Cullis et al., 1962) showed that each of its two independent chains, α and β, had a fold similar to that of myoglobin and, thus, suggested a divergent evolutionary process for oxygen transport molecules. These first protein structures were mostly helical, features that could be recognized readily at low resolution. Had the first structures been of mostly β structure, as is the case for pepsin or chymotrypsin, history might have been different.

Figure 1.2.5.1| top | pdf | A model of the myoglobin molecule at 6 Å resolution. Reprinted with permission from Bodo et al. (1959). Copyright (1959) Royal Society of London.

The absolute hand of the haemoglobin structure was determined using anomalous dispersion (Cullis et al., 1962) in a manner similar to that used by Bijvoet. This was confirmed almost immediately when a 2 Å-resolution map of myoglobin was calculated in 1959 (Kendrew et al., 1960). By plotting the electron density of the α-helices on cylindrical sections (Fig. 1.2.5.2), it was possible to see not only that the Pauling prediction of the α-helix structure was accurately obeyed, but also that the atoms were consistent with laevo amino acids and that all eight helices were right-handed on account of the steric hindrance that would occur between the atom and carbonyl oxygen in left-handed helices.

Figure 1.2.5.2| top | pdf | Cylindrical sections through a helical segment of a myoglobin polypeptide chain. (a) The density in a cylindrical mantle of 1.95 Å radius, corresponding to the mean radius of the main-chain atoms in an α-helix. The calculated atomic positions of the α-helix are superimposed and roughly correspond to the density peaks. (b) The density at the radius of the β-carbon atoms; the positions of the β-carbon atoms calculated for a right-handed α-helix are marked by the superimposed grid (Kendrew & Watson, unpublished). Reprinted with permission from Perutz (1962). Copyright (1962) Elsevier Publishing Co.

The first enzyme structure to be solved was that of lysozyme in 1965 (Blake et al., 1965), following a gap of six years after the excitement caused by the discovery of the globin structures. Diffusion of substrates into crystals of lysozyme showed how substrates bound to the enzyme (Blake, Johnson et al., 1967), which in turn suggested a catalytic mechanism and identified the essential catalytic residues.

From 1965 onwards, the rate of protein-structure determinations gradually increased to about one a year: carboxypeptidase (Reeke et al., 1967), chymotrypsin (Matthews et al., 1967), ribonuclease (Kartha et al., 1967; Wyckoff et al., 1967), papain (Drenth et al., 1968), insulin (Adams et al., 1969), lactate dehydrogenase (Adams et al., 1970) and cytochrome c (Dickerson et al., 1971) were early examples. Every new structure was a major event. These structures laid the foundation for structural biology. From a crystallographic point of view, Drenth's structure determination of papain was particularly significant in that he was able to show an amino-acid sequencing error where 13 residues had to be inserted between Phe28 and Arg31, and he showed that a 38-residue peptide that had been assigned to position 138 to 176 needed to be transposed to a position between the extra 13 residues and Arg31.

The structures of the globins had suggested that proteins with similar functions were likely to have evolved from a common precursor and, hence, that there might be a limited number of protein folding motifs. Comparison of the active centres of chymotrypsin and subtilisin showed that convergent evolutionary pathways could exist (Drenth et al., 1972; Kraut et al., 1972).

The variety of structures that were being studied increased rapidly. The first tRNA structures were determined in the 1960s (Kim et al., 1973; Robertus et al., 1974), the first spherical virus structure was published in 1978 (Harrison et al., 1978) and the photoreaction centre membrane protein structure appeared in 1985 (Deisenhofer et al., 1985). The rate of new structure determinations has continued to increase exponentially. In 1996, about one new structure was published every day. Partly in anticipation and partly to assure the availability of results, the Brookhaven Protein Data Bank (PDB) was brought to life at the 1971 Cold Spring Harbor Meeting (H. Berman & J. L. Sussman, private communication). Initially, it was difficult to persuade authors to submit their coordinates, but gradually this situation changed to one where most journals require coordinate submission to the PDB, resulting in today's access to structural results via the World Wide Web.

The growth of structural information permitted generalizations, such as that β-sheets have a left-handed twist when going from one strand to the next (Chothia, 1973) and that `cross-over' β-α-β turns were almost invariably right-handed (Richardson, 1977). These observations and the growth of the PDB have opened up a new field of science. Among the many important results that have emerged from this wealth of data is a careful measurement of the main-chain dihedral angles, confirming the predictions of Ramachandran (Ramachandran & Sasisekharan, 1968), and of side-chain rotamers (Ponder & Richards, 1987). Furthermore, it is now possible to determine whether the folds of domains in a new structure relate to any previous results quite conveniently (Murzin et al., 1995; Holm & Sander, 1997).