‘Leaves of Crystals’ or ‘Crystals of Leaves’

A small gallery of the shapes and forms present in the atomic structures of proteins. This represents a simplified rendering of a few of the thousands of ‘atomic sculptures’ available from the Protein Data Bank. Further details can be found on Crystals and Life Plates 12.3, 13.1,14.1,20.1,20.2. Helices are represented by helical coils and beta sheets by ribbons. Various software packages can go from the atomic coordinates from the PDB to this schematic and artistic representation of protein structures. Each coordinate set has a four character accession code that annotates uniquely each coordinate set. Browse the PDB website for further details.

Atomic-sculptures-2 On August 1999, crystallographers from all over the world met in Glasgow, Scotland for the XVIIIth International Congress of Crystallography sponsored by the International Union of Crystallography (IUCr). The IUCr is the international association of crystallographic societies that was formed in 1948 to disseminate and promote the study and practice of crystallography all over the world. Towering figures of the field such as John D. Bernal, P. P. Ewald, the Braggs (W.L.Bragg and W.H. Bragg) and many others were the moving forces behind this association when the nations of the world were swept by a wind of internationalism after the trauma of WWII [1].

I took a day off from the sessions of the Congress to visit Edinburgh. I walked along the historic mile with special interest in the cathedral. The castle did not interest me at all. On a side alley, I discovered something interesting: ‘Writers Museum’. I walked into the house, visited the different rooms and up the stairs there was a special exhibit of a poet totally unknown to me until them. The name was quite plain: George Mackay Brown (1921-1996). What immediately caught my attention were those two poignant lines in one of the posters illustrating the work of GMB:

See this tall finger of science
Scratch the stars out! [2]

As a scientist, I felt as if I was – personally – the one scratching with my own fingernails the stars out of the sky. I was hooked! Why was he saying that?

Who was this George M. Brown anyway? You can find more details about this sensitive poet of the land and the sea at http://www.georgemackaybrown.co.uk. I learned later that he was referring to the presence of oil refineries in the solitude of the Orkney Islands in Scotland, occluding the limpidness of the night sky.

The animosity and tension between science and the arts has had a long history, particularly in the modern era when the exponential expansion of our knowledge has demanded specialization in almost all activities of the human mind. The influential essay about the ‘two cultures’ by C.P. Snow is widely known. I had encountered ‘anti-science’ poems before and I will illustrate a few at the end of this essay. From the disappointment of J. Keats in the poem Lamia, where he laments that Mr. Newton destroyed the rainbow by ‘unweaving’ it (reference to ‘Unweaving the Rainbow’, lines 229-238), to the boring explanations that Walt Whitman had to endure from the ‘Learned Astronomer’ (poem When I Heard the Learn’d Astronomer included in Leaves of Grass).
This latter one was particularly interesting to me because one day, I was inspired to modify it in relation to the beautiful macromolecular structures that protein crystallographers unveil from their crystal structures. The DNA double helix is probably the best-known icon of intrinsic splendor but many other structures illustrate the cover of specialized journals of biochemistry, molecular biology, cellular biology and so many other fields. The best way to have sense of the beauty and variety of these atomic sculptures is to access the Protein Data Bank web site (http://www.rcsb.org/pdb/home/home.do ) and use their educational and outreach tools (see Figs. 1,2). I recommend the tab Molecule of the Month (http://www.rcsb.org/pdb/101/motm_archive.do ) by David S. Goodsell for an amazing collection of shapes and forms.

For the layperson, crystals mean something solid, rock-solid, as in the crystals of quartz, pyrite, calcite, gypsum and others that are so common in the mineral stores. However, the crystals containing the molecules that make possible the biological world are so different: fragile, vulnerable and susceptible to damage by their surroundings (i.e., moisture, concentration of alien ions, temperature). Their properties reflect the delicacy and elegance of the materials necessary to sustain life. In a way they relate to the subtlety of poetry, as described by the poem of George M. Brown also reproduced briefly in my book [3-4]:

The mingling’s of sea and earth
Creel and plough
Fish and cornstalk
Shore people and shepherds
Are the warp and weft that go
To make the very stuff of poetry.

The revised version of Walt Whitman’s poem is included in my modest book about crystallography (Crystals and Life: A Personal Journey, IUL, 2002) and is reproduced below. I must confess that I was often tempted to change the title of the book to ‘Leaves of Crystals’ (or ‘Crystals of Leaves’) to convey the beauty and fragility of crystals of macromolecules such as proteins, nucleic acids and their complexes. I thought that the dichotomy suggested by the ‘organic’ and ‘inorganic’, or ‘biological’ and ‘mineral’, was perfectly reflected and condensed in those two words, using them with a slight alteration of the title of the inimitable poetry book by Walt Withman, Leaves of Grass. The purpose of the poem is certainly not to make a poetic ‘anti-science’ pronouncement. Quite to the contrary. It is to emphasize that behind the hard science of crystallography required to unveil the structures of these molecules and to analyze their function, there is the beauty of their atomic structure that reveals itself as a unique ‘atomic sculpture’ of singular and subtle properties.

When I Heard The Learn’d Crystallographer

When I heard the learn’d crystallographer
When the bonds, the angles, were ranged in columns before me,
When I was shown the charts and diagrams, to add, divide, and measure them,
When I sitting hear the crystallographer where he lectured
with much applause in the lecture room,
How soon unaccountable I became tired and sick,
Til rising and gliding out wander’d off by myself
In the mystical dim-lighted room, and from time to time,
Look’d up in perfect silence at the protein fold.

Adapted from When I Heard the Learn’d Astronomer (W. Whitman) by C. Abad-Zapatero.
Extracted from his book Crystals and Life: A Personal Journey. Chapter 27. pg. 207.



Excerpt from Lamia (J. Keats, 1795-1821)
lines 229–238

Do not all charms fly
At the mere touch of cold philosophy?
There was an awful rainbow once in heaven:
We know her woof, her texture; she is given
In the dull catalogue of common things.
Philosophy will clip an Angel’s wings,
Conquer all mysteries by rule and line,
Empty the haunted air, and gnomèd mine—
Unweave a rainbow, as it erewhile made
The tender-person’d Lamia melt into a shade

[1] Kamminga, K. Acta Cryst. (1989). The International Union of Crystallography: Its Formation and Early Development. A45, 581-601.
[2] from Flotta Flare ORKNEY: Pictures & Poems, 1996 and 1998,
published by Colin Baxter Photography Ltd. Grantown-on-Spey, Scotland.
[3] Quote from the introduction by GMB to
George Mackay Brown, Selected Poems 1954-1992
published enlarged edition 1996, reprinted 1998
by John Murray Publishers Ltd.
Used on one of the posters at the Edinburgh exhibition.
[4] Before my departure from Scotland, I purchased several books by George M. Brown and once at home in Lake Forest, Illinois (USA), I ordered – and subsequently treasured – ORKNEY, Pictures & Poems by GMB and Gunnie Moberg. The combination of images and poems is magnificent.

About Cele Abad-Zapatero

Biophysicist, Protein Crystallographer, Drug Designer and Science Writer. Licenciado Degree, University of Valladolid, Spain, 1969. Physics, Mathematics. Graduate work, University of Salamanca, 1969-1972. Biological Sciences. Fullbright Scholarship for Graduate studies in the USA (1972). Ph. D. University of Texas at Austin, 1978. Biophysics Postdoc with M.G.Rossmann, Purdue University, 1979-1985. Group Leader-Associate Research Fellow, Abbott Laboratories-Retired 2008. Adjunct Professor to the Graduate Faculty, University of Illinois at Chicago. current
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