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Abstract
Inflammation of vessels is partially caused by tumour necrosis factor (TNF). Although the pharmacological understanding of the main inflammatory protein data is well characterised, basic structural information is rare. For this reason, we developed a method for the representation and analysis of the macromolecular interface between TNF and its receptor, enabling a better understanding of their interaction. In this paper we use structural information on the TNF–receptor complex in the protein (PDB) database as input to calculate an interface contact matrix, based on the distance between individual residues of each counterpart. The two-dimensional matrix is a plot of pairwise interactions between adjacent residues of the two chains in the protein complex. The residue names within each chain are plotted on the respective axis and an entry is made wherever two residues come into close contact. The matrix elements are annotated with physicochemical properties. The interface contact matrix is linked to a 3D visualisation of the macromolecular structure in such a way that mouse clicking on the appropriate part of the interface contact matrix highlights the corresponding residues in the 3D structure. Additionally the residues in the matrix are used to define the molecular surface at the interface. The interface contact matrix enables an overview representation of the residue distribution at the macromolecular interface and an evaluation of interfacial 'hot spots'. The selection of the residues in the interface contact matrix and the highlighting in the 3D structure allow an easy retrieval of the desired information out of the wealth of structural information. The representation with molecular surfaces shows complementary shapes. Many forms of treatment have been developed to reduce excessive TNF activity and their success is based on knowledge of the active sites of TNF. Our macromolecular interface analysis system will help us to define better receptor and acceptor molecules for the neutralisation and excretion of TNF.