Secondary and tertiary restraints in assembly of protein structures

1 Secondary and tertiary restraints in assembly of protein structures 

The meaning of the reduced models of protein structures is discussed in more detail later in this chapter however, we stress here that the minimal requirements for a low-resolution structure prediction to be correct are (A). The overall topology (the shape of the main chain trace) of the fold is the same as that seen in the experimental structure (B). The obtained secondary structure is very close to that seen in the native structure and the alpha carbon trace root mean square deviation (RMSD) from the native structure is in the range of 3-7 A depending on protein size. This level of accuracy may be of some use for application to protein function annotation [179]. 

To assemble a nativelike structure at a given resolution, a good protein model with an efficient force field should require fewer restraints than a more generic model that relies solely on the driving force derived from the restraints. Obviously, when the number of restraints is small, the resolution of the obtained structures will depend mostly on the quality of the protein model and its force field. In contrast, when the number of restraints is very large, then, the model quality will depend on the restraint representation and the intrinsic resolution of the model. Different classes of globular proteins of a similar size may require a different number of restraints to achieve models of comparable 

Models with exact secondary structure but no tertiary restraints 

One of the common ways of predicting protein tertiary structure assumes that the secondary structure has to be known before the prediction of a three-dimensional fold can be attempted [154-157]. While this view as a paradigm for protein structure prediction could be challenged, it certainly provides a straightforward framework that may sometimes prove to be useful. Indeed, there were a number of early attempts to apply such a methodology to low resolution protein fold predictions that were quite successful in some specific cases [154-157]. However, only recently has the problem of protein structure assembly, given its secondary structure, been more systematically addressed. 

---