Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

Abstract

The CAPRI and CASP prediction experiments have demonstrated the power of community wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting there may be important physical chemistry missing in the energy calculations. 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the non-polar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were on average structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a non-binder.

Redesign of a cross-reactive antibody to dengue virus with broad-spectrum activity and increased in vivo potency

“…Detailed comparison against other docking algorithms, which goes beyond the scope of this study, should be performed for a systematic evaluation. Because ZRANK is widely used and has shown considerable success in critical assessment of predicted interactions (CAPRI) experiments (35,36), we believe our method will perform comparatively well when evaluated against other top docking algorithms. The benchmarked test dataset contained a diverse set of 44 different targets that varied in size and in secondary and tertiary structures (SI Appendix, Table S3); these difficult test cases provided an opportunity to comprehensively validate the MLRbased structure discrimination.…”

Computational design and experimental verification of a symmetric protein homodimer

“…These candidates are then used as the basis for computational design, with the top designs screened experimentally (e.g., for target binding affinity or catalytic activity). This approach has the advantage of providing a large amount of data that can be used to test design protocols (22,40). Alternatively, focusing on a single scaffold allows the design to take specific features of the scaffold into account.…”

“…Several studies have shown that it is possible to achieve atomiclevel accuracy in the de novo design of protein dimers (12, 13, 16), as well as highly symmetric nanomaterials (17-20). However, the success rate of protein interface design is rather low (21), and protein interface modeling and design remain significant challenges (22).Homodimers are the most common type of protein assembly and are well represented in the Protein Data Bank (PDB). Compared with heterodimers, homodimers have a larger surface area; fewer hydrogen bonds; higher hydrophobicity; and, typically, C2 symmetry (23).…”

“…Several studies have shown that it is possible to achieve atomiclevel accuracy in the de novo design of protein dimers (12,13,16), as well as highly symmetric nanomaterials (17)(18)(19)(20). However, the success rate of protein interface design is rather low (21), and protein interface modeling and design remain significant challenges (22).…”

Using Molecular Dynamics Simulations as an Aid in the Prediction of Domain Swapping of Computationally Designed Protein Variants

“…For example, Fleishman et al [5] recently showed that only 2 of 88 CPD-designed variants from different protein scaffolds bound to the target molecule, influenza hemagglutinin. A community-wide assessment of this study suggested that many of the failed designs do not adopt the target fold [11]. In addition, only half express solubly [12], likely due to poor stability.…”