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The new face of vaccine development

of cross-immunity, Woods developed a computer simulation model that can predict how the atoms in the long-chain sugars interact with the body's antibodies. The model takes into account factors such as the various attractive forces between and among the sugar molecules, the attraction between the sugar molecules and the thousands of water molecules and ions that surround them and the motion and folding patterns of the sugar chains.

A simulation running for more than 700 hours – about a month – of computing time on a cluster of 16 machines lead to the observation that the acidic side chains give the backbone of the surface sugars in type III Group B Streptococcus an extended, corkscrew-like shape that is not rigid, but coils around like a phone cord. When the immune system "sees" this helical shape, it produces antibodies that recognize this shape.

The surface sugars of Streptococcus pneumoniae 14, on the other hand, lack the extended corkscrew shape and so aren't recognized by antibodies against type III Group B Streptococcus. Instead, antibodies against Streptococcus pneumoniae 14 are forced to recognize a short sequence of surface sugars.

In the past, researchers have only been able to infer such relationships. Now that they can be clearly demonstrated, these binding patterns can potentially be exploited to create new vaccines. Woods' team examined Group B Streptococcus and Streptococcus penumoniae, but he stressed that the technique is in no way limited to those bacteria.

He and his team are now working with Neisseria meningitidis, the bacteria that causes meningitis. Neisseria has evolved some strains that have a coat that bears the same sugars that human cells do – the bacteriological equivalent of a wolf in sheep's clothing – so that the body is slow to mount a strong immune response. Once an accurate model of its sugar chains is created, those chains could potentially be altered in a way that allows the body to
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