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Protein Sci. 2017 Aug;26(8):1584-1594. doi: 10.1002/pro.3194. Epub 2017 May 31.

Benchmarking a computational design method for the incorporation of metal ion-binding sites at symmetric protein interfaces.

Author information

1
Institute for Quantitative Biomedicine at Rutgers, 610 Taylor Road, Piscataway, New Jersey, 08854.
2
Center for integrative Proteomics Research, 610 Taylor Road, Piscataway, New Jersey, 08854.
3
Chemistry and Chemical Biology at Rutgers, 610 Taylor Road, Piscataway, New Jersey, 08854.

Abstract

The design of novel metal-ion binding sites along symmetric axes in protein oligomers could provide new avenues for metalloenzyme design, construction of protein-based nanomaterials and novel ion transport systems. Here, we describe a computational design method, symmetric protein recursive ion-cofactor sampling (SyPRIS), for locating constellations of backbone positions within oligomeric protein structures that are capable of supporting desired symmetrically coordinated metal ion(s) chelated by sidechains (chelant model). Using SyPRIS on a curated benchmark set of protein structures with symmetric metal binding sites, we found high recovery of native metal coordinating rotamers: in 65 of the 67 (97.0%) cases, native rotamers featured in the best scoring model while in the remaining cases native rotamers were found within the top three scoring models. In a second test, chelant models were crossmatched against protein structures with identical cyclic symmetry. In addition to recovering all native placements, 10.4% (8939/86013) of the non-native placements, had acceptable geometric compatibility scores. Discrimination between native and non-native metal site placements was further enhanced upon constrained energy minimization using the Rosetta energy function. Upon sequence design of the surrounding first-shell residues, we found further stabilization of native placements and a small but significant (1.7%) number of non-native placement-based sites with favorable Rosetta energies, indicating their designability in existing protein interfaces. The generality of the SyPRIS approach allows design of novel symmetric metal sites including with non-natural amino acid sidechains, and should enable the predictive incorporation of a variety of metal-containing cofactors at symmetric protein interfaces.

KEYWORDS:

Rosetta software; inverse rotamer kinematics; metal-ion binding sites; oligomeric proteins; protein design benchmark; protein symmetry

PMID:
28513090
PMCID:
PMC5521545
DOI:
10.1002/pro.3194
[Indexed for MEDLINE]
Free PMC Article

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