Assessment of protein assembly prediction in CASP13

We present the assembly category assessment in the 13th edition of the CASP community-wide experiment. For the second time, protein assemblies constitute an independent assessment category. Compared to the last edition we see a clear uptake in participation, more oligomeric targets released, and consistent, albeit modest, improvement of the predictions quality. Looking at the tertiary structure predictions we observe that ignoring the oligomeric state of the targets hinders modelling success. We also note that some contact prediction groups successfully predicted homomeric interfacial contacts, though it appears that these predictions were not used for assembly modelling. Homology modelling with sizeable human intervention appears to form the basis of the assembly prediction techniques in this round of CASP. Future developments should see more integrated approaches to modelling where multiple subunits are a natural part of the modelling process, which would benefit the structure prediction field as a whole

Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm

Many proteins fold into highly regular and repetitive three dimensional structures. The analysis of structural patterns and repeated elements is fundamental to understand protein function and evolution. We present recent improvements to the CE-Symm tool for systematically detecting and analyzing the internal symmetry and structural repeats in proteins. In addition to the accurate detection of internal symmetry, the tool is now capable of i) reporting the type of symmetry, ii) identifying the smallest repeating unit, iii) describing the arrangement of repeats with transformation operations and symmetry axes, and iv) comparing the similarity of all the internal repeats at the residue level. CE-Symm 2.0 helps the user investigate proteins with a robust and intuitive sequence-to-structure analysis, with many applications in protein classification, functional annotation and evolutionary studies. We describe the algorithmic extensions of the method and demonstrate its applications to the study of interesting cases of protein evolution

Biological and functional relevance of CASP predictions.

Our goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo-sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo-sites), and ten sites containing important motifs, loops, or key residues with important disease-associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best-ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand-binding sites, most prediction methods have higher performance on apo-sites than holo-sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein-protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein-protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template

Periscope Proteins are variable length regulators of bacterial cell surface interactions

Changes at the cell surface enable bacteria to survive in dynamic environments, such as diverse niches of the human host. Here, we reveal “Periscope Proteins” as a widespread mechanism of bacterial surface alteration mediated through protein length variation. Tandem arrays of highly similar folded domains can form an elongated rod-like structure; thus, variation in the number of domains determines how far an N-terminal host ligand binding domain projects from the cell surface. Supported by newly available long-read genome sequencing data, we propose that this class could contain over 50 distinct proteins, including those implicated in host colonization and biofilm formation by human pathogens. In large multidomain proteins, sequence divergence between adjacent domains appears to reduce interdomain misfolding. Periscope Proteins break this “rule,” suggesting that their length variability plays an important role in regulating bacterial interactions with host surfaces, other bacteria, and the immune system

Computational discovery and modelling of tandem domain repeats in proteins

Domains are functional and evolutionary units of proteins that typically fold into stable globular structures. A small subset of natural multidomain proteins contain large arrays of nearly identical domains repeated in tandem, challenging some of our assumptions about protein folding and evolution. In this study, I aim to discover new tandem domain repeats, characterise their sequence and structural properties and understand their roles in the function of proteins. I start by using computational sequence analysis tools across large datasets of proteins and bacterial genomes to survey the prevalence and distribution of tan- dem domain repeats across organisms and domain families. Next, I computation- ally analyse and compare structures of domains found as tandem repeats, several of which have been experimentally determined by our collaborators in the course of this study. I finally develop two computational methods to systematically model the structure and misfolding energetics of tandem domain repeats. Nearly identical tandem domain repeats are rare in natural proteins (below 0.1%) and their sequences are highly biased in amino acid composition. Many of them have structural roles in bacterial surface proteins implicated in biofilm for- mation and host colonisation; new examples of such proteins, named "Periscope proteins", show rapid domain repeat number variation, a molecular mechanism used to modulate bacterial phenotype. Tandem domain repeat structures reveal unusual structural malleability, with numerous cases of domain atrophy (loss of core secondary structures) and elaboration. They are also predicted to be more resistant to misfolding via tandem domain swapping, with potential misfolding- resistant mechanisms such as the domain topology and length. This study improves our understanding of the prevalence, type and function of tandem domain repeats in proteins, in particular their role as structural ele- ments in bacterial surface proteins, and suggests new protein and domain targets for further experimental characterisation. It also has important implications for protein misfolding and for the design and engineering of multidomain proteins.EMBL International PhD fellowshi

Automated evaluation of quaternary structures from protein crystals

A correct assessment of the quaternary structure of proteins is a fundamental prerequisite to understanding their function, physico-chemical properties and mode of interaction with other proteins. Currently about 90% of structures in the Protein Data Bank are crystal structures, in which the correct quaternary structure is embedded in the crystal lattice among a number of crystal contacts. Computational methods are required to 1) classify all protein-protein contacts in crystal lattices as biologically relevant or crystal contacts and 2) provide an assessment of how the biologically relevant interfaces combine into a biological assembly. In our previous work we addressed the first problem with our EPPIC (Evolutionary Protein Protein Interface Classifier) method. Here, we present our solution to the second problem with a new method that combines the interface classification results with symmetry and topology considerations. The new algorithm enumerates all possible valid assemblies within the crystal using a graph representation of the lattice and predicts the most probable biological unit based on the pairwise interface scoring. Our method achieves 85% precision (ranging from 76% to 90% for different oligomeric types) on a new dataset of 1,481 biological assemblies with consensus of PDB annotations. Although almost the same precision is achieved by PISA, currently the most popular quaternary structure assignment method, we show that, due to the fundamentally different approach to the problem, the two methods are complementary and could be combined to improve biological assembly assignments. The software for the automatic assessment of protein assemblies (EPPIC version 3) has been made available through a web server at http://www.eppic-web.org.ISSN:1553-734XISSN:1553-735