May 30, 2007

The Structure of Proteins

Max Perutz, et al., Structure of Haemoglobin: a Three-Dimensional Fourier Synthesis at 5.5-Å Resolution, Obtained by X-Ray Analysis, 1960

The unravelling of the structures of the first proteins is a great example of the way scientific discoveries are built on and interlock with each other. Proteins like Haemoglobin are the workhorses of living systems. They are created by the translation of strands of DNA into chains of amino acids, while almost all other types of molecules in cells are assembled by proteins. They perform a myriad of functions, acting as targeted chemical messengers (hormones), enzymes which speed the rate of otherwise improbable chemical reactions, structural components of cells, pumps, valves, and turbines embedded in cell membranes, contractile fibres in muscles, and many other roles. Until the three-dimensional structure of a protein is worked out, scientists can only know what a protein does, not how. Understanding of protein structures leads to some unifying principles that help explain their diverse properties.

Haemoglobin is a relatively small protein, at only 10,000 atoms, that transports oxygen from the lungs of vertebrate animals to their cells, there to be fed into the Krebs Cycle. It's formed of four chains of amino acids of roughly equal length, all of which are quite similar to each other and to another protein called Myoglobin. Myoglobin is the second stage of oxygen transport in the body: where Haemoglobin binds strongly to oxygen at the concentration found in blood near the lungs and releases it at the concentrations found in blood near oxygen consuming cells, myoglobin binds strongly at the concentrations where Haemoglobin releases, and only relinquishes oxygen when very low concentrations are present, inside active cells.

The chemical similarity between Haemoglobin's four amino acid sub-chains and Myoglobin makes the difference between their oxygen binding properties mysterious. As it turns out, it is the three-dimensional arrangement of the four sub-chains that makes all the difference. To figure out the structure of Haemoglobin, Max Perutz and his team used (and improved) X-ray crystallography. This involved making crystals of the oxygenated and deoxygenated forms of Haemoglobin (actually Haemoglobin crystallized in a matrix of much smaller molecules), taking pictures of the diffractions produced by shining X-rays through them at several hundred different angles, repeating this process many times with specific atoms in the Haemoglobin crystal replaced with heavier atoms (to help locate particular parts of the amino acid chain), and putting all the results together with what computing power was available in the UK in the 1950s (including Cambridge's Edsac II).

The diffraction pictures produced were much larger than von Laue's initial trials. They contained thousands of spots of differing intensities, each of which had to be quantified one-by-one, by eye, in much the same way that Henrietta Leavitt determined the brightness of stars by comparing spots on a photographic plate. And the mathematical effort required to combine all this data into a three-dimensional model was staggering. The whole process took more than a decade the first time around. (Not including WWII, during which Perutz, an Austrian living in Britain, was imprisoned, then banished to Newfoundland. On the way across the Atlantic, the liner he was travelling on, the Arandora Star, was torpedoed by a U-boat, killing almost all of the 1,800 aboard. Perutz was one of the few to be fished out of the water alive. Needless to say, no work on Haemoglobin got done during this interlude.)

The payoff was a plastic model, built up slice-by-slice, showing the way the four sub-chains fold up and fit together.

The circular plates are heme groups, non-protein molecules that serve as the actual binding sites for oxygen. Many proteins have bits and pieces of non-amino-acid molecules embedded in them, often to act as binding sites, while the bulk of the protein acts as structural support. In Haemoglobin's case, when oxygen is bound to a heme group, the structure of the whole molecule shifts in a small but significant way, making its binding properties different from Myoglobin. (Animated GIF)

These days, with massively improved automation and computer support, thousands of protein structures are mapped every year (although understanding of their significance, as always, still takes time), and there are some indications that we may someday be able to predict the configuration of a protein from its amino acid sequence alone (and therefore from the DNA that encodes it).


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