Sakuma, K. | Search bioRxiv

bioRxiv2021

Design of complicated all-α protein structures

A wide range of de novo protein structure designs have been achieved, but the complexity of naturally occurring protein structures is still far beyond these designs. To expand the diversity and complexity of de novo designed protein structures, we sought to develop a method for designing "difficult-to-describe"-helical protein structures composed of irregularly aligned -helices like globins. Backbone structure libraries consisting of a myriad of -helical structures with 5- or 6-helices were generated by combining 18 helix-loop-helix motifs and canonical -helices, and five distinct topologies were selected for de novo design. The designs were found to be monomeric with high thermal stability in solution and fold into the target topologies with atomic accuracy. This study demonstrated that complicated -helical proteins are created using typical building blocks. The method we developed would enable us to explore the universe of protein structures for designing novel functional proteins.

biophysics↗

bioRxiv2021

Limitations of the ABEGO representation: ambiguity between αα-corner and αα-hairpin

ABEGO is a coarse-grained representation for polypeptide backbone dihedral angles. The Ramachandran map is divided into four segments denoted as A, B, E, and G to represent the local conformation of polypeptide chains in the character strings. Although the ABEGO representation is widely used in structural informatics and protein design, it cannot capture minor differences in backbone dihedral angles, which potentially leads to ambiguity between two structurally distinct fragments. Here, we show a nontrivial example of two local motifs that could not be distinguished by their ABEGO representations. We found that two well-known local motifs -hairpins and -corners are both represented as -GBB- and thus indistinguishable in the ABEGO representation, although they show distinct arrangements of the flanking -helices. We also found that -GBB- motifs caused a loss of efficiency in the ABEGO-based fragment-assembly simulations for protein backbone design. Nevertheless, we designed amino-acid sequences that were predicted to fold into the target topologies that contained these -GBB- motifs. Our finding that certain local motifs bottleneck the ABEGO-based fragment-assembly simulations for construction of backbone structures suggests that finer representations of backbone torsion angles are required for efficiently generating diverse topologies containing such indistinguishable local motifs.

bioinformatics↗