CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering

Abstract

CyBase was originally developed as a database for backbone-cyclized proteins, providing search and display capabilities for sequence, structure and function data. Cyclic proteins are interesting because, compared to conventional proteins, they have increased stability and enhanced binding affinity and therefore can potentially be developed as protein drugs. The new CyBase release features a redesigned interface and internal architecture to improve user-interactivity, collates double the amount of data compared to the initial release, and hosts a novel suite of tools that are useful for the visualization, characterization and engineering of cyclic proteins. These tools comprise sequence/structure 2D representations, a summary of grafting and mutation studies of synthetic analogues, a study of N- to C-terminal distances in known protein structures and a structural modelling tool to predict the best linker length to cyclize a protein. These updates are useful because they have the potential to help accelerate the discovery of naturally occurring cyclic proteins and the engineering of cyclic protein drugs. The new release of CyBase is available at http://research1t.imb.uq.edu.au/cybase.

Figure 1.

Sequence graphical representations incorporated into CyBase. Panel (A) shows a Diversity Wheel representation of sequence diversity from a multiple sequence alignment, where the consensus sequence is positioned in the inner circle and the spike protruding from each position represents the amino acid variation observed at that position. Panel (B) is a Collier de Perles representation of the prototypical cyclotide, kalata B1, showing the sequence and disulphide connectivity. Collier de Perles representations can be generated for proteins belonging to the cyclotide or trypsin squash inhibitor classes. Panel (C) shows a Cyclic Seqplot, which is a representation for NOE data measured from an NMR experiment. The sequence of the peptide is shown on the outside of the circle. Backbone NOEs are drawn as dark bars, where the height of the bar is relative to the strength of the NOE. Medium range and long NOEs are drawn as arcs and lines. 134 × 47mm (600 × 600 DPI)

Figure 2.

Cyclization tools incorporated into CyBase. By scanning the distribution of N- to C-termini distances from the PDB as shown in panel (A), the conotoxin MII was identified as a potential target for backbone cyclization. Its relatively short N- to C-termini distance of 9.8 Å means that it is potentially more amenable to backbone cyclization compared to a protein with a longer termini distance. Panel (B) shows a model of a cyclic MII using its native linear structure as a template (PDB ID: 1MII) (37), which has been cyclized in silico using a seven-residue poly-alanine linker (coloured in white). 83 × 136 mm (600 × 600 DPI)