Automated evaluation of quaternary structures from protein crystals
José M. Duarte, Spencer E. Bliven, Aleix Lafita, Guido Capitani, Stephen Kevin Burley · 2017
Crystallography is the most powerful technique for generating atomic level structures of proteins and other biological macromolecules. However, it does not always yield definitive insights into the quaternary structures of biological macromolecules. In order to provide better tools for determining the most likely quaternary structure in proteins, we have developed the new EPPIC 3 method. It uses evolutionary considerations as the ultimate arbiters of the biological relevance of interfaces and assemblies, thereby offering a complementary approach versus other available methods that rely on thermodynamic considerations 2. EPPIC 3 extends our previous Evolutionary Protein-Protein Interface Classifier (EPPIC)1, by going beyond classifying pairwise interfaces. It identifies all possible topologically valid assemblies present in a protein crystal and provides predictions as to likely quaternary structures. Pairwise interface classifications are based on two evolutionary scores and a single geometric score. These descriptors were trained against a large dataset of known biologically relevant and crystal interfaces to fit a logistic regression classifier that provides probabilistic scoring of interfaces together with confidence assignment. Assembly enumeration is achieved by representing the crystal lattice as a periodic graph. Finding valid assemblies is then reduced to the problem of finding subgraphs complying to a set of rules, which guarantees closed assemblies (Point Group symmetries) and isomorphism in the assembly composition and connectivity throughout the crystal. Finally the assemblies are scored based on the individual scores of the constitutive interfaces, providing in the end a single probability of an assembly being the biological one, together with a confidence estimation. The confidence values are very valuable not only for users but also for downstream analyses (e.g. docking), where only high confident predictions can be selected. The software is accessible through an easy to use web graphical interface at http://www.eppic-web.org. The graphical interface is designed to aid the crystallographer in interpreting putative quaternary structures using 2D and 3D graphical tools that operate within the browser (Figure 1). The server offers useful tools to the structural bioinformatics community such as precalculated sequence alignments for every PDB structure and visualization of conservation on protein surface with the browser embedded NGL viewer. All the data are provided via xml downloads to the community, enabling further analyses. Novel visualization tools are available as part of the web user interface, allowing the visualization of the crystal lattice via the lattice graph representation. This is done both in 2D thanks to the vis.js library and in 3D thanks to the fast NGL molecular visualization package3. The colors and labels show the different protein entities and interface types present in the lattice, allowing for a one-glance understanding of the assembly symmetry and its connectivity.