PDB_Amyloid: an extended live amyloid structure list from the PDB

Abstract

The Protein Data Bank (PDB) contains more than 135 000 entries at present. From these, relatively few amyloid structures can be identified, since amyloids are insoluble in water. Therefore, most amyloid structures deposited in the PDB are in the form of solid state NMR data. Based on the geometric analysis of these deposited structures, we have prepared an automatically updated web server, which generates a list of the deposited amyloid structures, and also entries of globular proteins that have amyloid-like substructures of given size and characteristics. We have found that by applying only appropriately selected geometric conditions, it is possible to identify deposited amyloid structures and a number of globular proteins with amyloid-like substructures. We have analyzed these globular proteins and have found proof in the literature that many of them form amyloids more easily than many other globular proteins. Our results relate to the method of Stanković et al. [Stanković I et al. (2017) IPSI BgD Tran Int Res 13, 47-51], who applied a hybrid textual-search and geometric approach for finding amyloids in the PDB. If one intends to identify a subset of the PDB for certain applications, the identification algorithm needs to be re-run periodically, since in 2017 on average 30 new entries per day were deposited in the data bank. Our web server is updated regularly and automatically, and the identified amyloid and partial amyloid structures can be viewed or their list can be downloaded from the following website https://pitgroup.org/amyloid.

Keywords: PDB; amyloid; amyloid‐precursor; human chorionic gonadotropin; thymidylate synthase; web server.

Figure 1

Protein structures 1HCN, 1BSF, 3FJ5 and 2OCT, with partial amyloid‐like substructures. All of these entries are documented as amyloidogenic in the literature.