Small angle X‐ray scattering‐assisted protein structure prediction in CASP13 and emergence of solution structure differences

Abstract

Small angle X‐ray scattering (SAXS) measures comprehensive distance information on a protein's structure, which can constrain and guide computational structure prediction algorithms. Here, we evaluate structure predictions of 11 monomeric and oligomeric proteins for which SAXS data were collected and provided to predictors in the 13th round of the Critical Assessment of protein Structure Prediction (CASP13). The category for SAXS‐assisted predictions made gains in certain areas for CASP13 compared to CASP12. Improvements included higher quality data with size exclusion chromatography‐SAXS (SEC‐SAXS) and better selection of targets and communication of results by CASP organizers. In several cases, we can track improvements in model accuracy with use of SAXS data. For hard multimeric targets where regular folding algorithms were unsuccessful, SAXS data helped predictors to build models better resembling the global shape of the target. For most models, however, no significant improvement in model accuracy at the domain level was registered from use of SAXS data, when rigorously comparing SAXS‐assisted models to the best regular server predictions. To promote future progress in this category, we identify successes, challenges, and opportunities for improved strategies in prediction, assessment, and communication of SAXS data to predictors. An important observation is that, for many targets, SAXS data were inconsistent with crystal structures, suggesting that these proteins adopt different conformation(s) in solution. This CASP13 result, if representative of PDB structures and future CASP targets, may have substantive implications for the structure training databases used for machine learning, CASP, and use of prediction models for biology.

Assessment of protein assembly prediction in CASP13

“…SAXS data was collected for all seven of the targets, while cross‐link data was collected for five of them and NMR data for one ( H0980 ). The experimental details and data‐assisted specific assessment is discussed in the respective articles . Here, as part of our assembly analysis, we looked into how the data‐assisted assembly predictions compare with the regular ones, using the regular evaluation strategy.…”

“…The experimental details and data-assisted specific assessment is discussed in the respective articles. 35,42 Here, as part of our assembly analysis, we looked into how the data-assisted assembly predictions compare with the regular ones, using the regular evaluation strategy. All seven targets were selected from the difficult group, for which there is little homology information available to perform traditional modeling.…”

“…The other subunit attaches on either side of the beta sheets experimental data and structural data (crystallography), which is discussed in the accompanying articles in this issue. 35,42…”

How good are comparative models in the understanding of protein dynamics?

“…Here, we provide an assessment of dynamics features of comparative models of proteins of known crystal structures by comparing the dynamics inferred from the corresponding crystal structures (targets). Although, some conformational differences are observed among experimental structures of the same protein determined by different techniques, the extent of differences in the conformation is expected to be lower than the extent of errors in 3D models generated using comparative modeling . It has also been shown that X‐ray crystal structures are more reliable templates as compared to NMR structures .…”

Conformational States of Exchange Protein Directly Activated by cAMP (EPAC1) Revealed by Ensemble Modeling and Integrative Structural Biology

“…Considering the important but non-redundant roles that EPAC1 and EPAC2 play under both physiological and pathological conditions, it is essential to comprehend the structural, dynamic, and functional differences between the EPAC isoforms. Thus, we have employed solution X-ray scattering combined with homology modeling and structure prediction [38] to study the full-length EPAC1 molecule in its apo-, cAMP-bound, and substrate-bound states. Herein, we show that SAXS can elucidate the conformational states of EPAC1 activation as Cells 2020, 9, 35 3 of 18 it proceeds from the compact inactive apo conformation to the extended active cAMP-bound form, and finally to an effector-bound ternary complex.Cells 2019, 8, x 3 of 18 conformational states of EPAC1 activation as it proceeds from the compact inactive apo conformation to the extended active cAMP-bound form, and finally to an effector-bound ternary complex.…”