Related proteins as phasing models

Direct methods work if the molecules, and thus the unit cells and numbers of reflections, are relatively small. Isomorphous replacement works if the molecules are large enough that a heavy atom does not disturb their structures significantly. The most difficult structures for crystallographers are those that are too large for direct methods and too small to remain isomorphous despite the intrusion of a heavy atom. If a medium-size protein naturally contains a heavy atom, like iron or zinc, or if a selenomethionine derivative can be produced, the structure can often be solved by MAD phasing (Section IV.E). [NMR methods (see Chapter 10) are also of great power for small and medium-size molecules ] 

Our last phasing method applies to all molecules, regardless of size, but it requires knowledge that the desired structure is similar to a known structure. 

Molecular replacement Related proteins as phasing models 

The crystallographer can sometimes use the phases from structure factors of a known protein as initial estimates of phases for a new protein. If this method is feasible, then the crystallographer may be able to determine the structure of the new protein from a single native data set. The known protein in this case is referred to as a phasing model, and the method, which entails calculating initial phases by placing a model of the known protein in the unit cell of the new protein, is called molecular replacement. 

For instance, the mammalian serine proteases — trypsin, chymotrypsin, and elastase—are very similar in structure and conformation. If a new mammalian serine protease is discovered, and sequence homology with known proteases 

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V. Molecular replacement Related proteins as phasing models... 

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