From Protein Structure to Function with Bioinformatics.pdf

10 Integrated Servers for Structure-Informed Function Prediction 269fold comparison method, such as SSM. However, far from being redundant, thereverse template method provides much more specific information about thesimilarities between any two structures. Furthermore, it identifies the regionssharing the highest similarity and consequently most likely to be the functionalsite. Also, it provides stronger confirmatory evidence for a putative functionshowing, as it does, the key residues involved.Of course, the only true way of validating a prediction is to confirm it experimentally.This is difficult, time-consuming and expensive although some progresshas been made towards development of high-throughput functional assays (Yakuninet al. 2004).10.4 ConclusionHere we have described ProKnow and ProFunc, two integrated servers that use acombination of structure- and sequence-based matching methods to try to predictthe function of a protein from an uploaded 3D structural model. In most cases, theyare able to offer some suggestions about possible function, although these maysometimes be rather vague (e.g. DNA-binding activity). In other cases, however, alltheir methods draw a blank and they fail completely. The most challenging casesare structures belonging to uncharacterized protein families possessing a novel fold.So, all one may be left with is the knowledge that the structure has an interestinglookingcleft in its surface, lined by highly conserved residues, but with no hint ofwhat might bind there. For cases such as these, new methods need to be developedand incorporated into the servers. Of most utility would be methods that can predictwhat a given protein’s likely substrate is from an analysis of the structure alone.That is, the methods should not rely on a match to an existing structure as, for novelfolds, there is by definition no such match. At present, such methods are very computeintensiveand tend to commence with some idea of class of substrate at least(e.g. Hermann et al. 2006). So, for the time being, prediction of a protein’s functionwill continue to rely on clever sleuthing and deduction.Acknowledgement The author would like to thank Debnath Pal for help with ProKnow and forhis useful comments on this chapter.Fig. 10.8 (continued) interesting or functionally informative, deriving from elements of the crystallizationsolution, and comprise 12 nitrate ions and one molecule of glycerol. (b) Topologydiagram of the 2fck protein chain. The diagram illustrates how the β-strands, represented by thelarge pink arrows, join up, side-by-side, to form the domain’s central β-sheet. The diagram alsoshows the relative locations of the α-helices, here represented by the red cylinders. The small bluearrows indicate the directionality of the protein chain, from the N- to the C-terminus. The numberswithin the secondary structural elements correspond to the residue numbering given in the PDB file.The diagram is generated from the output of the Hera program (Hutchinson and Thornton 1990)