How Nobel Prize-winning computational methods have contributed to structural biology

How Nobel Prize-winning computational methods have contributed to structural biology

The 2013 Nobel Prize in Chemistry has been awarded jointly to Martin Karplus, Michael Levitt and Arieh Warshel "for the development of multiscale models for complex chemical systems".

In the 1970’s Karplus, Levitt and Warshel laid the foundation for powerful computer programs that model chemical behaviour and are used to understand and predict large complex chemical systems and reactions. Today, computers and theoretical models are essential components of every chemist’s and biologist’s toolbox.

This year’s Nobel laureates have developed hybrid approaches that combined classical and quantum physics and they have shown how these can be used to successfully model dynamical properties of real biological systems, ranging from protein-folding to electron transfer reactions. Consider simulations of how a drug binds to its target protein: quantum theoretical calculations are performed on those atoms in the target protein that interact directly with the drug, whereas the rest of the protein is simulated using less computationally demanding classical physics.

Among other developments, such hybrid approaches have led to more accurate atomic force fields, a crucial component of structure determination by structural biology techniques, such as X-ray crystallography and NMR.

 

In addition to developing computational methods, all three Nobel Laureates have experimentally determined structures and deposited them in the PDB. Shown above is the recently determined crystal structure of the eukaryotic chaperonin CCT published by Kalisman, Schroder, and Levitt in the journal Structure. These large nanomachines are essential for correct and efficient protein folding in both eukaryotes and archaea. Their 3D structures can be explored further in the PDB (entries 4aol and 4apk).