Target selection and determination of function in structural genomics

Abstract

The first crucial step in any structural genomics project is the selection and prioritization of target proteins for structure determination. There may be a number of selection criteria to be satisfied, including that the proteins have novel folds, that they be representatives of large families for which no structure is known, and so on. The better the selection at this stage, the greater is the value of the structures obtained at the end of the experimental process. This value can be further enhanced once the protein structures have been solved if the functions of the given proteins can also be determined. Here we describe the methods used at either end of the experimental process: firstly, sensitive sequence comparison techniques for selecting a high-quality list of target proteins, and secondly the various computational methods that can be applied to the eventual 3D structures to determine the most likely biochemical function of the proteins in question.

Figure 1

Outline of the target selection protocol for MCSG. Algorithms and functional databases are italicised (see text for references). For simplicity, methods for handling domains within sequences are not addressed in the diagram.

Figure 2

Outline of the semi-automated functional analysis pipeline we have developed, illustrating the types of information that can be inferred from the combination of procedures.

Figure 3

The various ‘success’ levels of each of the major stages in our functional analysis pipeline are shown. The results are based on the analysis of 24 out of 60 deposited MCSG structures.