Decoy structures

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

A plausible interpretation of this result is that these rare sites are used to enhance recognition in some cases, due to specific homologous features. In Table Va we examined the type of contacts (in terms of the number of neighbors) for native and decoy structures. 

It is evident that native structures tend to have more contacts but that the difference is not profound. The deviations are the result of threading short sequences through longer stmctures (we have more threading of this kind). Such threading suggests a small number of contacts for the set of decoy structures. A sharper difference between native and decoy stmctures is observed when the contacts are separated to hydrophobic and polar (Table Vb). The difference in hydrophobic and polar contacts is very small at the decoy stmctures and much more significant for the native shapes. 

The stability of each decoy structure is determined by the sum of the intra-complex energy and the solvation free energy A//. Figure 6.3 shows A// and (Ec + A/i) against RMSDj for the IPPE complex. The complex structures with low RMSDj have smaller E that the other decoys, and with addition of the solvation term, the (E + Afi) value for the equilibrium structure in solution becomes distinctively the smallest. The right structure for IPPE can thus be singled out from Fig. 6.3. It should be noted that the crystal structure is a close but not the right one in solution. The protein structure in solution deviates from that in crystal t3q)icaUy by a few A. 

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