A fragment-based protein interface design algorithm for symmetric assemblies

Abstract

Theoretical and experimental advances in protein engineering have led to the creation of precisely defined, novel protein assemblies of great size and complexity, with diverse applications. One powerful approach involves designing a new attachment or binding interface between two simpler symmetric oligomeric protein components. The required methods of design, which present both similarities and key differences compared to problems in protein docking, remain challenging and are not yet routine. With the aim of more fully enabling this emerging area of protein material engineering, we developed a computer program, nanohedra, to introduce two key advances. First, we encoded in the program the construction rules (i.e. the search space parameters) that underlie all possible symmetric material constructions. Second, we developed algorithms for rapidly identifying favorable docking/interface arrangements based on tabulations of empirical patterns of known protein fragment-pair associations. As a result, the candidate poses that nanohedra generates for subsequent amino acid interface design appear highly native-like (at the protein backbone level), while simultaneously conforming to the exacting requirements for symmetry-based assembly. A retrospective computational analysis of successful vs failed experimental studies supports the expectation that this should improve the success rate for this challenging area of protein engineering.

A structural database of chain-chain and domain-domain interfaces of proteins

“…The interfaces here could prove useful in constructing the structures of protein complexes or even building a whole protein structure from individually solved domains. Our library could also be used in conjugation with fragment based interface design algorithms such as nanohedra [71]. With the rapid growth of structures resolved using cryo-EM, a library such as ours could also prove useful in refining such structures.…”

A structural database of chain–chain and domain–domain interfaces of proteins

“…Our library could also be used in conjugation with fragment-based interface design algorithms such as nanohedra. 86 With the rapid growth of structures resolved using cryo-EM, a library such as ours could also prove useful in refining such structures. The information presented in this study would soon be available as a queryable relational database on a webserver (work in progress).…”

“…The interfaces here could prove useful in constructing the structures of protein complexes or even building a whole protein structure from individually solved domains. Our library could also be used in conjugation with fragment‐based interface design algorithms such as nanohedra 86 . With the rapid growth of structures resolved using cryo‐EM, a library such as ours could also prove useful in refining such structures.…”

Engineering Self-Assembling Protein Nanoparticles for Therapeutic Delivery

“…Recent advances in protein engineering have enabled the bottom-up design of purpose-built protein nanoparticles, drastically expanding the protein nanoparticle design space. These methods typically apply principles of symmetry to arrange natural or de novo designed cyclic oligomers into protein nanoparticles through interface design or rigid genetic fusion, reviewed in Khmelinskaia, Wargacki, and King (2021). − Padilla, Colovos, and Yeates et al (2001) reported an early example of a self-assembling protein nanoparticle constructed using the rigid fusion of several oligomeric domains . Recently computational protein design has been applied to interface and rigid fusion methods enabling the design of increasingly complex protein nanoparticles with improving success rates. ,, King and Baker et al (2012) reported self-assembling protein nanoparticles with a variety of symmetries using computational protein interface design to arrange existing cyclic oligomers into the desired assemblies (Figure B) .…”