From Protein Structure to Function with Bioinformatics.pdf

Chapter 7Predicting Protein Function from SurfacePropertiesNicholas J. Burgoyne and Richard M. JacksonAbstract The situation of having a protein structure with no knowledge of anassociated function is a frequent outcome of current structural genomics initiatives.Understanding the properties of the protein surface is just one of several approachesthat may be of use in characterising protein function. The analysis of the surface ofthe protein can be useful in understanding both native biological as well as proteindruginteraction partners. In this chapter we introduce the concept of protein surface.This is followed by introductions to the commonly studied surface propertiesand their use in the assignment of generic function and more specific predictionsrelating to protein-ligand, protein-drug and protein-protein interactions.7.1 Surface DescriptionsBefore considering what the surface of a protein can tell us about its function andinteraction partners, it is worth defining the different representations of the surfaceand what they mean. From a structural biology perspective there can be several differentdefinitions for a protein’s surface. Each has different characteristics thatgovern when they are used. The most commonly encountered surface descriptionsare discussed below.7.1.1 The van der Waals SurfaceAlthough rarely used to define the surface per se, it is important to introduce thevan der Waals surface as it is the foundation of the following definitions. Atoms inthe molecule are represented by overlapping spheres, with the radius of each sphereN.J. Burgoyne and R.M. Jackson*Institute of Molecular and Cellular Biology, Faculty of Biological Science,University of Leeds, Leeds, LS2 9JT, UK*Corresponding author: e-mail: r.m.jackson@leeds.ac.ukD.J. Rigden (ed.) From Protein Structure to Function with Bioinformatics, 167© Springer Science + Business Media B.V. 2009