Pauling and Proteins: Helices in the Air

Mounted models of the gamma helix and alpha helix, as housed in the Special Collections & Archives Research Center, Oregon State University Libraries.

Mounted models of the gamma helix and alpha helix, as housed in the Special Collections & Archives Research Center, Oregon State University Libraries.

[Part 2 of 3]

Linus Pauling sent shock waves through the scientific community when he published seven articles relating to the structure and function of proteins in the April-May 1951 issue of the Proceedings of the National Academy of Sciences. The first article of this volley was titled “The structure of proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain.” The second article was written by Pauling and Robert B. Corey, and was called “Atomic Coordinates and Structure Factors for Two Helical Configurations of Polypeptide Chains.” This paper was much more technical than was the first, and introduced two new important models developed by the Pauling group: the Gamma-helix and the Alpha-helix.

The article began by explaining in great detail Pauling’s idea for what he called the Gamma-helix (γ-helix). The γ-helix was the name assigned to the 5.1-residue helical configuration that Pauling, Corey, and Herman Branson had described in the first PNAS proteins article. The main difference between the γ-helix and the other configurations that they had proposed was that the bond angle between the C-N-C connection had been changed from 123˚ to 120˚. The authors explained that this small adjustment in the bond angle resulted in a miniscule change in the interatomic distances between various hydrogen bonds, but that these changes were significant enough to notably affect the number of residues per turn present within the structure.

51-residue

(It is worth noting that the unit used to measure the distance between molecules is the Angstrom (Å). One Å equals 10-10 m, or one ten-billionth of a meter. Considering the truly tiny sizes being measured, it is likewise worth noting that the changes between hydrogen bonds that Pauling was talking about were often measured in the thousandths of an Angstrom or ten-trillionths of a meter. One trillionth of a meter is known as a picometer.)

The article stressed that differences as small as 10 picometers could notably change bond angles, which would then change the number of residues per turn, thus dramatically affecting the shape of the helix. Next, the authors elaborated upon the likely arrangements of molecules within the helix due to symmetry or lack of symmetry in certain molecular bonds. Pauling and Corey further noted that they had used x-ray crystallography to validate their arguments and determine the crystal structures in question. From his earliest days as a scientist, Pauling had established himself as a major figure in x-ray crystallography, a technique by which an operator fires x-rays at a substance in question, then measures the way that the x-rays have deflected off of the substance. By analyzing these deflection patterns, researchers were then able to develop models of the shapes of molecular structures.

Once the γ-helix had been explained, the article moved on to discuss the Alpha-helix (α-helix). The group explained that the γ-helix and the α-helix were similar in terms of how the hydrogens bonded with other molecular groups, and how the residues fit under those configurations. They also detailed the exact interatomic distances between hydrogen and various other molecules in the structure, while pointing out that the distance between carbon and its other bonds determined the number of residues per turn. The number of turns, however, was variable; the smallest possible angle of 108.9˚ resulted in a residue of 3.6, while the largest possible angle of 110.8˚ resulted in a 3.67 residue.

37-residue

William Lawrence Bragg, an internationally famous scientist and proteins researcher of great import, was impressed by the α-helix, though he felt his rival Pauling to be overly excited about it. The α-helix was not a complete protein, except in a few cases including fibers, hair, and horn.  The structure also did not explain the functioning of proteins. As such, Bragg felt the paper to be an important first step – no more, no less. The rest of the scientific community was more enthusiastic than was Bragg and his team. Pauling received a Nobel Prize in 1954 in Chemistry “for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances,” the α-helix being among the most famous of these “complex structures.” The National Science Foundation even named a research vessel The Alpha Helix in honor of the discovery.

Bragg was even less generous regarding the γ-helix. Though in his very carefully worded congratulatory letter to Pauling he did not say so, he felt the γ-helix to be far-fetched, perhaps existing only in Pauling’s imagination. While this was not the case, the γ-helix ultimately made less of an impact on the scientific community.

Regardless, the import of Pauling’s work was felt throughout the profession.  Though Francis Crick would write that the alpha helix did not give him and Jim Watson the idea that DNA was a double helix, he did suggest that “helices were in the air,” at the time “and you would have to be either obtuse or very obstinate not to think along helical lines.”

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Pauling and Proteins: The Beginnings of a Revolution

Linus Pauling and Robert Corey examining models of protein structure molecules, ca. 1951.

[Part 1 of 3]

An article with the somewhat cumbersome title “The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain” appeared in the April-May, 1951 edition of the Proceedings of the National Academy of Sciences. The article was written by Linus Pauling, Robert B. Corey and Herman R. Branson, working collaboratively at the Gates and Crellin Laboratories of Chemistry at the California Institute of Technology and communicated to PNAS on Pauling’s fiftieth birthday. The article is immediately notable in that it is first of seven written by Pauling and his collaborators on the nature of protein and published in that single issue of PNAS.

And as it turns out, these seven articles were revolutionary. While the very act of mailing in all seven at once was audacious, their contents solved riddles that many researchers “believed would not be solved for decades.” Max F. Perutz, a competitor of Pauling’s in the field of biochemistry, read all seven papers in one morning, after which he immediately raced to his lab. Utilizing Pauling’s predictions, he was able to conduct experiments that validated the hypotheses proposed by the papers. He wrote to Pauling that

The fulfillment of this prediction and, finally, the discovery of this reflection in hemoglobin has been the most thrilling discovery of my life.

“The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain” was presented as the lead article in the April-May 1951 PNAS. The main question asked by the paper was: What is the structure of polypeptide chains – the backbones of proteins? Pauling, Corey, and Branson claimed that the best way to determine the answer to this question was to acquire an “accurate determination of the crystal structure of amino acids, peptides, and other simple substances related to proteins.” By determining the attributes of these components, which acted as the building blocks of polypeptide chains, the researchers could then make reasonable estimations of what the finished product would look like. Pauling’s group was specifically searching for the interatomic distances between molecules, the bond angles of the chemical bonds, and “other configurational parameters” fundamental to the structures.

Pauling and his colleagues felt that their work answered these questions and that they had determined the parameters satisfactorily. They then used their data to determine that their basic shape was a hydrogen-bonded, helical configuration. They wrote that “An amino acid residue (other than glycine) has no symmetry elements…” (In biochemistry, “residue refers to a specific monomer,” which is “a molecule that may bind chemically to other molecules…”) Because the residues lacked symmetry elements which would force the polymer chain into a symmetrical pattern, “…the only [possible] configurations for a chain…are helical configurations.”

Figures from “The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain,” 1951.

Furthermore, the group determined that, based on their calculations of bond angles, there were five possible angles for the helical turns; 165°, 120°, 108°, 97.2°, or 70.1°. Of these, only two, 97.2° and 70.1°, were “reasonable” potential configurations for the polypeptide chain, based on observed interatomic distances. Hydrogen, carbon, oxygen and nitrogen are the elements that make up the polypeptide chain. The chemical bond between C-O and C-N are both double bonds (they have four electrons instead of two). These tight bonds, along with the measured interatomic distances of other components, indicated that the interatomic distances for the chain would have to be small, otherwise the chain would very quickly become unstable. This is the reason that only the 97.2° and 70.1° configurations were acceptable. The other three angles were unstable and would have unraveled because the N-H bonds had too much space between them. Whether the helix turned at a 97.2° or a 70.1° rotation depended on the number of residues per turn in the chain. Pauling and his associates proposed either a 3.7-residue helix or a 5.1-residue helix.

The article ended by explaining why competing hypotheses on the shape of polypeptide chains were incorrect. The article specifically pointed out three hypotheses authored by William Astbury and Florence Bell, William Lawrence Bragg, John Kendrew, and Max Perutz, and Maurice Huggins as being inferior. The Caltech group asserted that each of their models assumed a set number of residues in the polypeptide chains instead of potential variables, and only gave rough estimates of interatomic distances and bond angles. While they all agreed that a helix was the correct shape, the specifics of all other helix models were incorrect because of these deficiencies.

This first paper was just a piece of the larger argument that Pauling was making. Each article was in itself useful, but only when considering the larger sum of the full publication bloc could the full import and implications of Pauling’s work be made visible. Pauling’s thinking proved to be revolutionary and controversial, as such ideas often are. William Lawrence Bragg, a key competitor of Pauling’s, was especially critical. He felt numerous of the Caltech group’s ideas to be outright false, and even the most solid of Pauling’s assertions to be just baby-steps rather than major breakthroughs. Pauling, naturally, disagreed.

Linus Pauling and the Structure of Proteins: A Documentary History

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Today is Linus Pauling’s birthday – he would have been 112 years old.  Every year on February 28th we try to do something special and this time around we’re pleased to announce a project about which we’re all very excited: the sixth in our series of Pauling documentary history websites.

Launched today, Linus Pauling and the Structure of Proteins is the both latest in the documentary history series and our first since 2010’s The Scientific War Work of Linus C. Pauling. (we’ve been a little busy these past few years)  Like Pauling’s program of proteins research, the new website is sprawling and multi-faceted.  It features well over 200 letters and manuscripts, as well as the usual array of photographs, papers, audio and video that users of our sites have come to expect.  A total of more than 400 primary source materials illustrate and provide depth to the site’s 45-page Narrative, which was written by Pauling biographer Thomas Hager.

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Warren Weaver, 1967.

That narrative tells a remarkable story that was central to many of the twentieth century’s great breakthroughs in molecular biology.  Readers will, for example, learn much of Pauling’s many interactions with Warren Weaver and the Rockefeller Foundation, the organization whose interest in the “science of life” helped prompt Pauling away from his early successes on the structure of crystals in favor of investigations into biological topics.

So too will users learn about Pauling’s sometimes caustic confrontations with Dorothy Wrinch, whose cyclol theory of protein structure was a source of intense objection for Pauling and his colleague, Carl Niemann.  Speaking of colleagues, the website also delves into the fruitful collaboration enjoyed between Pauling and his Caltech co-worker, Robert Corey.  The controversy surrounding Pauling’s interactions with another associate, Herman Branson, are also explored on the proteins website.

Linus Pauling shaking hands with Peter Lehman in front of two models of the alpha-helix. 1950s.

Linus Pauling shaking hands with Peter Lehman in front of two models of the alpha-helix. 1950s.

Much is known about Pauling’s famously lost “race for DNA,” contested with Jim Watson, Francis Crick and a handful of others in the UK.  Less storied is the long running competition between Pauling’s laboratory and an array of British proteins researchers, waged several years before Watson and Crick’s breakthrough.  That triumph, the double helix, was inspired by Pauling’s alpha helix, discovered one day when Linus lay sick in bed, bored and restless as he fought off a cold. (This was before the vitamin C days, of course.)

Illustration of the antibody-antigen framework, 1948.

Illustration of the antibody-antigen framework, 1948.

Many more discoveries lie in waiting for those interested in the history of molecular biology: the invention of the ultracentrifuge by The Svedberg; Pauling’s long dalliance with a theory of antibodies; his hugely important concept of biological specificity; and the contested notion of coiled-coils, an episode that once again pit Pauling versus Francis Crick.

Linus Pauling and the Structure of Proteins constitutes a major addition to the Pauling canon. It is an enormously rich resource that will suit the needs of many types of researchers, students and educators. It is, in short, a fitting birthday present for history’s only recipient of two unshared Nobel Prizes.

Happy birthday, Dr. Pauling!

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The Alpha Helix

Space-filling model of the alpha helix.

[The Paulings in England: Part 5 of 5]

It has been said that sometimes blessings come in disguise, and so it may be that we have the damp English spring to thank for the elucidation of the alpha-helix structure of alpha-keratin – a fundamental and ubiquitous secondary structure pattern found in many proteins.

Linus Pauling was plagued by sinusitis for much of his time in England, and for three days in March 1948 it had become severe enough to put him in bed (as he was fond of saying over the years, this was before his vitamin C days). After a day spent devouring mystery novels, Pauling asked Ava Helen if she would bring him some paper and his slide rule, at which point he started trying to figure out how polypeptide chains might fold up into a satisfactory protein structure.

Pauling’s canvas was just an ordinary 8 1/2 by 11 inch sheet of paper. His first step was to draw the correct bond angles and distances onto the sheet, as determined from previous x-ray crystallographic work on polypeptides. Next he folded the sheet along parallel lines into a sort of squared-off tube. Doing so allowed him to add in representations of hydrogen bonds, which the impromptu model suggested would form between amino acid residues and, as a result, hold the turns of the polypeptide together.

The model made sense and pretty quickly it was clear that Pauling had discovered something important.  As he later wrote, his folded creation “turned out to be the structure of hair and horn and fingernail, and also present in myoglobin and hemoglobin and other globular proteins, a structure called the alpha-helix .”

Reconstruction of the alpha-helix paper model. Drawn and folded by Linus Pauling, 1982.

Pauling kept this idea to himself until his return to the United States because something didn’t match up quite right with the current laboratory data. Specifically, the turns of Pauling’s helix didn’t mirror the 5.1 angstrom repeat found in all of William T. Astbury‘s x-ray patterns. Pauling’s structure came close, but made a turn every 5.4 angstroms, or every 3.7 amino acid residues.

After his return home, with the assistance of colleagues Robert Corey and Herman Branson, Pauling continued refining his alpha helix structure and developing others, including the beta sheet. Simultaneously, the Caltech group’s chief British rivals at the Cavendish Laboratory published a paper titled “Polypeptide Chain Configurations in Crystalline Proteins.” The paper promised more than it delivered though, and while it listed many possible structures, Pauling found none of them to be likely. The competition was still on.

Pauling was finally convinced to publish when he received word that a British chemical firm called Courtaulds had created a synthetic polypeptide chain that showed no sign of Astbury’s 5.1 angstrom reflection in x-ray diffraction images. This was enough evidence for Pauling to decide that the 5.1 angstrom repeat was, perhaps, not a vital component of all polypeptide chains.  And so it was that in April 1951 Pauling, Corey and Branson published “The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain,” in the Proceedings of the National Academy of Sciences.

After devouring the Pauling group’s results shortly after their publication, Max Perutz headed to the Cavendish lab at Cambridge to check the data himself. Having confirmed the structure in images of horsehair, porcupine quill, synthetic polypeptides, hemoglobin and, for good measure, some old protein films that had been tucked away, Perutz wrote to Pauling, “The fulfillment of this prediction and, finally, the discovery of this reflection in hemoglobin has been the most thrilling discovery of my life.” He then published an analysis of his own data, concluding, “The spacing at which this reflexion appears excludes all models except the 3.7 residue helix of Pauling, Corey and Branson, with which it is in complete accord.”

Video Link: Pauling Recounts His Discovery of the Alpha Helix


It wasn’t until a year later that the mystery of Astbury’s 5.1 angstrom reflection was finally solved. In 1952, on a visit to the Cavendish, Pauling met Francis Crick, the then-graduate student who would go on to play a huge part in the discovery of the structure of DNA. The two maintained similar interests and during a taxi ride around Cambridge found themselves discussing the matter of the alpha helix. “Have you thought about the possibility,” Crick asked Pauling, “that alpha helixes are coiled around one another?” Whether Pauling had or had not considered this possibility remains a point of contention, but Pauling remembered replying that he had, because he had been considering a number of higher-level schemes for his helixes, including some which wound around each other.

Regardless, Pauling returned to Caltech and both he and Crick set to work on the problem. With help from Corey, Pauling discovered a means by which the alpha helixes could wrap around each other in a coiled-coil to produce the problematic 5.1 angstrom found in Astbury’s pictures of natural keratin.  Crick, in the meantime, was conducting a very similar study.  Pauling and Crick, independent of one another, ultimately submitted the solution to this puzzle for publication within days of each other, and at first there was a bit of grumbling as to whom the credit should be awarded. Though Crick’s note was published first, the Cavendish camp eventually conceded that Pauling’s paper included considerably more detail of consequence, and it was finally settled that both scientists had independently come to the same general conclusion.


Pauling receiving his honorary degree from the University of Paris, 1948.

After Pauling’s two fruitful terms as Eastman Professor at Oxford were up in July, the family split their remaining time between travels in Amsterdam, Switzerland and Paris. Pauling rounded off the trip by receiving yet another honorary degree from the University of Paris, and on August 25, 1948, the Paulings set sail once more on the Queen Mary.

His eight months in Europe had been productive and enlightening, but Pauling was ready to return to Pasadena where he could share the myriad ideas he had generated and gathered during his time away from Caltech. As we have seen, he was especially eager to get back to work on proteins, writing shortly before his departure that “I have continued to work on my theory of metals, and have been doing nothing about proteins. However, I am looking forward to being back home, and to thinking about that subject again.”