![]() ![]() ![]() ![]() Proteins are polymers, and using idealized bond lengths and bond angles, the conformation of a polypeptide chain can be represented as a series of backbone dihedral angle triplets (φ, ψ, and ω). The 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. Nevertheless, I was able to design amino-acid sequences that were predicted to fold into the target topologies that contained these α-GBB-α motifs, which suggests such topologies that are difficult to build by ABEGO-based simulations are designable once the backbone structures are modeled by some means. I also found that α-GBB-α motifs caused a loss of efficiency in the ABEGO-based fragment-assembly simulations for de novo protein backbone design. I found that two well-known local motifs αα-hairpins and αα-corners are both represented as α-GBB-α and thus indistinguishable in the ABEGO representation, although they show distinct arrangements of the flanking α-helices. Here, I show a nontrivial example of two local motifs that could not be distinguished by their ABEGO representations. Although the ABEGO representation is widely used in backbone building simulation for de novo protein design, it cannot capture minor differences in backbone dihedral angles, which potentially leads to ambiguity between two structurally distinct fragments. 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. ABEGO is a coarse-grained representation for polypeptide backbone dihedral angles. ![]()
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