Message from the editor
Brian W. Matthews
Myoglobin and the Origins of Structural Biology
It is 50 years since Kendrew and his group determined the structure of myoglobin - the first detailed image of any protein.1 My colleague, Peter von Hippel, was at the Proteins Gordon Conference at which Kendrew first described the results. Pete well-remembers the scene. Many in the audience had spent their careers studying proteins and had put forth their own theories regarding the structure, stability, folding and function of these large molecules. Now would come the moment of truth. The first opportunity to “see” a real protein. It was as if Kendrew was Saint Peter, standing at the pearly gates, and deciding which theories had been true, and who could be admitted into scientific heaven.
This virtual issue of Protein Science is intended to commemorate the 50th anniversary of the myoglobin structure determination. It is made up of articles selected exclusively from the first six years of the journal’s publication (1992-1997). As such, the coverage is not all-inclusive. Nevertheless, it does provide a remarkable historical overview not only of the myoglobin structure determination, per se, but other pioneers who have shaped the field of protein science as we now understand it.
We commence this virtual issue with Dick Dickerson’s recollection2* of the myoglobin structure determination in which Dick played a major role. [References marked with an asterisk are included in the virtual issue.] The recollection of Michael Rossmann, who played an equally important part in Max Perutz’s parallel studies of hemoglobin, is also presented.3* The specific achievements of Max Perutz are highlighted by David Eisenberg.4* This introductory group of articles is concluded with the obituary for John Kendrew following his death at age 80 and written by Max Perutz.5* Although Kendrew was Perutz’s first doctoral student, and they subsequently shared a Nobel Prize, their personalities were very different. Perutz lived to do science and was personally active until the day he died. Even though he was extraordinarily successful as Chair of the MRC Laboratory, and, in later years, became a well-regarded author, these activities seemed to take a second place to his own scientific endeavors. In contrast, shortly after Kendrew had determined the structure of myoglobin (and had received his Nobel Prize) he was drawn to administrative roles. Among other accomplishments he became the founding Editor of the Journal of Molecular Biology and the first Director of the European Molecular Biology Laboratory in Heidelberg.
Pioneers of Protein Science
Shortly after Protein Science was established, the journal introduced a “Recollections” feature. These reminiscences provide fascinating insights into the early understanding of protein structure and function, often written by the key protagonists. We have included a selection of these contributions. The first, by Fred Richards,6* describes the contributions of Linderstrom-Lang and the Carlsberg Laboratory.
Linus Pauling’s extraordinary accomplishments, including the use of a rolled-up sheet of paper to discover the alpha-helix, are well known. What is perhaps less well appreciated is that Pauling delayed publishing his model because it predicted a helical repeat distance of 5.4 Å, whereas the experimental X-ray photographs suggested a pitch of 5.1 Å. It was only after Pauling had seen the paper of Bragg, Kendrew and Perutz, and had dismissed all of their models for helical structures as incorrect, that he wrote up his own work. In his Recollection, Pauling7* attributes the mistake of the Cambridge group to their lack of appreciation of structural chemistry [i.e. being “physicists working in a physics department” rather than (in Pauling’s case) practicing X-ray crystallography in a chemistry department].
The early memories of three of the pioneers of the physical chemistry of proteins are provided in the Recollections of John Edsall,8* Charles Tanford9* and Ephraim Katchalski-Katzir.10*
James Manning11* overviews the contributions of Stein and Moore in protein sequencing. Their determination of the amino acid sequence of ribonuclease was a key stepping off point for Chris Anfinsen’s demonstration that the amino acid sequence of the protein was sufficient to direct its refolding to the native structure, reviewed by Michael Young.12*
The Recollections of Mildred Cohn,13* Arthur Kornberg14* and Dan Koshland15* give insights into their personal histories and some of their contributions in understanding proteins as enzymatic catalysts.
Finally, Bruce Merrifield16* traces the circuitous route that led him from attempts to quantitate cytosine and uracil in RNA to the chemical synthesis of proteins.
Evolution of the Science of Proteins
At the time that Kendrew determined the structure of myoglobin its amino acid sequence was unknown. Indeed, only a handful of such sequences had been determined. In one very early study, however, Sanger and his colleagues had shown that the amino acid sequences of cow, sheep and pig insulin were identical except for just one or two substitutions at three specific sites.17 This clearly suggested that much might be learned from sequence comparison. Furthermore, the comparison of Kendrew’s X-ray structure of myoglobin with Perutz’s lower resolution structures of hemoglobin showed striking similarities. In particular, the overall alpha-helical fold of myoglobin was seen to occur in both the alpha- and beta-subunits of hemoglobin, notwithstanding that myoglobin and hemoglobin had different functions, and one protein came from whale and the other from horse.
The acquisition of additional sequences and additional structures have led to entirely new subfields of protein analysis. In the third part of this issue we include selected articles from Protein Science published between 1992 and 1996 that herald some of these newer developments.
As the amino acid sequences of more and more proteins became available it became clear that sequence comparison would, for the first time, allow the process of evolution to be reconstructed at the molecular level. At the same time, tracing the ancestry of a given protein could be complicated by the finding that the rate of change of amino acid sequence can vary greatly from one protein family to another. Russ Doolittle’s classic review summarizes the state of the field at the time that this journal was established.18*
As more structures were determined, protein structure comparison also began to play a central role. Today every “new” structure is routinely compared with every other entry in the Protein Data Bank, often resulting in important functional insights. The report of Holm et al.19* introduced one of the first data bases of protein structure families.
Once the first protein structures were known, one could ask “how do they fold?”. We have chosen to include two classical reviews of the subject; first the experimentally-focused analysis of Barrick and Baldwin20* and second Dill and coworkers’ perspective from computer simulations of lattice models.21*
As the accuracy of protein structures increased, and more examples became available, one could begin to catalog the “fine structure” of protein architecture. As examples, we include the survey by Janet Thornton and her group of buried water and internal cavities in proteins,22* together with George Rose’s analysis of the “capping box”, a common motif at the N-terminus of alpha-helices.23*
The knowledge of specific protein structures also made it possible to contemplate protein design, either de novo, or via the redesign of a known template. Early (and contemporary) attempts have yielded some striking successes, but the fact remains that this is an extremely challenging problem. Ideally, the design procedure should reflect both the conformational and energetic adaptability of native proteins. An important first step in this direction is described in the report of Desjarlais and Handel.24*
“Domain swapping” was at first thought to be a quirk present in an occasional dimeric structure. The thoughtful analysis of David Eisenberg and his group, however, coupled with increasingly common examples, have led to the appreciation that domain swapping is a general mechanism for oligomer assembly.25*
We conclude this virtual issue with Peter Colman’s overview of the influenza virus neuraminidase.26* Colman’s determination of the neuraminidase structure is generally recognized as the first example in which the knowledge of the structure of a target protein was used to rationally design a lead compound which led directly to a clinically effective drug.
Against all odds, Perutz and Kendrew established the field of protein crystallography. The structure of myoglobin, now 50 years ago, vindicated their efforts. More important, however, was the revolution in structural biology that they made possible. This volume celebrates their achievement.
REFERENCES
1. Kendrew JC, Dickerson RE, Strandberg BE, Hart RG, Davies DR, Phillips DC, Shore VC (1960) Structure of myoglobin: A three-dimensional Fourier synthesis at 2 Å resolution. Nature 185:422-427.
2*. Dickerson RE (1992) A little ancient history. Protein Sci 1:182-186.
3*. Rossmann MG (1994) The beginnings of structural biology. Protein Sci 3:1731-1733.
4*. Eisenberg D (1994) Max Perutz’s achievements: How did he do it? Protein Sci 3:1625-1628.
5*. Perutz M (1997) Obituary: Sir John Kendrew (1917-1997). Protein Sci 6:2684-2685.
6*. Richards FM (1992) Linderstrom-Lang and the Carlsberg Laboratory: The view of a postdoctoral fellow in 1954. Protein Sci 1:1721-1730.
7*. Pauling L (1993) How my interest in proteins developed. Protein Sci 2:1060-1063.
8*. Edsall JT (1992) Memories of early days in protein science, 1926-1940. Protein Sci 1:1526-1530.
9*. Tanford C (1994) Macromolecules. Protein Sci 3:857-861.
10*. Katchalski-Katzir E (1993) Poly--amino acids as the simplest protein models: Recollections of a retired state president. Protein Sci 2:476-482.
11*. Manning JM (1993) The contributions of Stein and Moore to protein science. Protein Sci 2:1188-1191.
12*. Young M (1995) Christian B. Anfinsen (1916-1995). Remembering his life and his science. Protein Sci 4:2237-2239.
13*. Cohn M (1995) Some early tracer experiments with stable isotopes. Protein Sci 4:2444-2447.
14*. Kornberg A (1993) ATP and inorganic pyro- and polyphosphate. Protein Sci 2:131-132.
15*. Koshland DE Jr (1993) The joys and vicissitudes of protein science. Protein Sci 2:1364-1368.
16*. Merrifield B (1996) The chemical synthesis of proteins. Protein Sci 5:1947-1951.
17. Brown H, Sanger F, Kitai F (1955) The structure of pig and sheep insulins. Biochem J 60:556-565.
18*. Doolittle RF (1992) Reconstructing history with amino acid sequences. Protein Sci 1:191-200.
19*. Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G (1992) A database of protein structure families with common folding motifs. Protein Sci 1:1691-1698.
20*. Barrick D, Baldwin RL (1993) The molten globule intermediate of apomyoglobin and the process of protein folding. Protein Sci 2:869-876.
21*. Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS (1995) Principles of protein folding - a perspective from simple exact models. Protein Sci 4:561-602.
22*. Williams MA, Goodfellow JM, Thornton JM (1994) Buried waters and internal cavities in monomeric proteins. Protein Sci 3:1224-1235.
23*. Seale JW, Srinivasan R, Rose GD (1994) Sequence determinants of the capping box, a stabilizing motif at the N-termini of -helices. Protein Sci 3:1741-1745.
24*. Desjarlais JR, Handel TM (1995) De novo design of the hydrophobic cores of proteins. Protein Sci 4:2006-2018.
25*. Bennett MJ, Schlunegger MP, Eisenberg D (1995) 3D domain swapping: A mechanism for oligomer assembly. Protein Sci 4:2455-2468.
26*. Colman PM (1994) Influenza virus neuraminidase: Structure, antibodies and inhibitors. Protein Sci 3:1687-1696.
References marked with an asterisk are included in the virtual issue.
