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TitleDesign of multi-scale protein complexes by hierarchical building block fusion.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 2294, Year 2021
Publish dateApr 16, 2021
AuthorsYang Hsia / Rubul Mout / William Sheffler / Natasha I Edman / Ivan Vulovic / Young-Jun Park / Rachel L Redler / Matthew J Bick / Asim K Bera / Alexis Courbet / Alex Kang / T J Brunette / Una Nattermann / Evelyn Tsai / Ayesha Saleem / Cameron M Chow / Damian Ekiert / Gira Bhabha / David Veesler / David Baker /
PubMed AbstractA systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two ...A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials.
External linksNat Commun / PubMed:33863889 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.4 - 19.0 Å
Structure data

EMDB-22305, PDB-6xss:
CryoEM structure of designed helical fusion protein C4_nat_HFuse-7900
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-22306:
CryoEM map of designed helical fusion protein C5_HFuse-3921
Method: EM (single particle) / Resolution: 8.06 Å

EMDB-23168:
Dihedral ring D2_Wm-01
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-23169:
Dihedral ring D2_Wm-02
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-23170:
Dihedral ring D2_Wm-01_trunc
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-23171:
Point Group nanocage T_Wm-1606
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-23172:
Point Group nanocage I32_Wm-42
Method: EM (single particle) / Resolution: 9.62 Å

EMDB-23173:
Crown C5_Crn_HF-12_26
Method: EM (single particle) / Resolution: 6.0 Å

EMDB-23174:
Crown C5_Crn_HF-12_26
Method: EM (single particle) / Resolution: 6.5 Å

PDB-6xh5:
Hierarchical design of multi-scale protein complexes by combinatorial assembly of oligomeric helical bundle and repeat protein building blocks
Method: X-RAY DIFFRACTION / Resolution: 3.32 Å

PDB-6xi6:
Hierarchical design of multi-scale protein complexes by combinatorial assembly of oligomeric helical bundle and repeat protein building blocks
Method: X-RAY DIFFRACTION / Resolution: 2.69 Å

PDB-6xns:
C3_crown-05
Method: X-RAY DIFFRACTION / Resolution: 3.19 Å

PDB-6xt4:
C3_HD-1069 (1BH-69) - fusion protein of helical bundle and repeat protein
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

Chemicals

ChemComp-HOH:
WATER

Source
  • synthetic construct (others)
KeywordsDE NOVO PROTEIN / helical fusion / de novo design / HELICAL BUNDLE REPEAT PROTEIN / helical bundle / helical repeat

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