Database For Binding Sites Of Intrinsically Disordered Proteins With Other Substances

Intrinsically disordered proteins (IDPs) is a class of proteins with flexible structure and they don’t have stable structure in natural stations. Because of the widely spread in organisms and participating in many important life processes such as signal transduction, as well as having relationship with a variety of important diseases, IDPs has become a focus of research in life sciences. Interacting with many other substances and changing their structure is one of the important ways of IDPs to play a variety of biological functions. However, the study of IDPs through experience is difficult and there is none database for binding sites of IDPs. Therefore, we collect the information of binding sites in IDPs interacting with other molecules based on the databases of Disprot, Uniprot and PDB, and we construct the first database for binding sites of IDPs with other substances. On this basis, the information of secondary structure in disordered regions that based on DSSP database also be collected and be put into the database. The database is available to users free of charge and the web site is http://biophy.dzu.edu.cn/bssdidps/index.php.226 IDPs entries,465 ordered regions,428 disordered regions and 3572 binding sites are released in the database on current version. Besides, the database also contains secondary structure information of 98 IDPs entries’disordered regions and the number of amino acids in disordered regions with secondary structure information is 3590.In order to reveal the feature of binding sites of IDPs with other substances, three kinds of mathematical models are used to analyze amino acids usage basis of binding site in disordered regions and ordered regions. The results indicate that binding sites in ordered regions prefer Y, W, F, H, N and M and most of the amino acids with big volume of side chain. Binding sites in disordered regions prefer basic amino acid just as R and K. For IDPs with different binding types, the amino acids usage basis of binding sites is different between ordered regions and disordered regions. For IDPs that interact with DNA, binding sites in ordered regions prefer W, K, N, F, T and Y, and binding sites in disordered regions prefer R, H, C, S and Y; For IDPs that interact with RNA, binding sites in ordered regions prefer R, Y, M, I, N and C, and binding sites in disordered regions prefer K, H, S, F, G and T; For IDPs that interact with proteins, binding sites in ordered regions prefer Y, R, H, F, M and N, and binding sites in disordered regions prefer W, D, Q and I. So binding sites in ordered regions share a similar basis and they all prefer polar amino acids with positive charge and long side chain. However, for binding sites in disordered regions, the binding sites interact with proteins is bigger than binding sites interact with nucleic on polarity% volume of side chain and solvent accessibility surface area. When the binding sites interact with DNA compared with binding sites interact with RNA, the former prefer amino acids with polarity and long side chain. At the same time, features of secondary structure in disordered regions after combination also be analyzed and the result indicates that there are still some disordered regions keep disorder structures after IDPs binding other molecules. Besides, the structures of IDPs mainly exist as alpha helix and ring or random coil and secondary structure in disordered regions prefer amino acids with charge and amino acids with the annular structure are not preferred. In addition, the amino acids share different preference when they formatting different types of secondary structure. Therefore, our research provides a reliable data platform for research of IDPs interactions and also plays an important role in promoting the drug research that based on IDPs.