A structural database of chain-chain and domain-domain interfaces of proteins

Abstract

In this study, we have mined the PDB and created a structural library of 178,465 interfaces that mediate protein-protein or domain-domain interactions. Interfaces involving the same CATH fold(s) were clustered together. Our analysis of the entries in the library reveals the similarity between chain-chain and domain-domain interactions. The library also illustrates how a single protein fold can interact with multiple folds using similar interfaces. The library is hence a useful resource to study the types of interactions between protein folds. Analyzing the data in the library reveals various interesting aspects of protein-protein and domain-domain interactions such as how proteins belonging to folds that interact with many other folds also have high EC values. These data could be utilized to seek potential binding partners. It can also be utilized to investigate the different ways in which two or more folds interact with one another structurally. We constructed a statistical potential of pair preferences of amino acids across the interface for chain-chain and domain-domain interactions separately. They are quite similar further lending credence to the notion that domain-domain interfaces could be used to study chain-chain interactions. Lastly and importantly, the library includes predicted small molecule binding sites at the protein-protein interfaces. This has applications as interfaces containing small molecule binding sites can be easily targeted to prevent the interaction and perhaps form a part of a therapeutic strategy.