4DAC

Crystal Structure of Computationally Designed Protein P6d

Summary for 4DAC

• Entry DOI: 10.2210/pdb4dac/pdb
• Descriptor: Computationally designed crystal forming protein P6d (2 entities in total)
• Functional Keywords: alpha-helix, three-helix bundle, coiled-coil protein, de novo design, computational protein design, computationally designed protein, three helix coiled coil, acylated n-terminus, synthetic, de novo protein
• Total number of polymer chains: 4
• Total formula weight: 12066.06

Authors

Lanci, C.J.,MacDermaid, C.M.,Saven, J.G. (deposition date: 2012-01-12, release date: 2012-05-02, Last modification date: 2024-10-30)

Primary citation

Lanci, C.J.,Macdermaid, C.M.,Kang, S.G.,Acharya, R.,North, B.,Yang, X.,Qiu, X.J.,Degrado, W.F.,Saven, J.G.
Computational design of a protein crystal.
Proc.Natl.Acad.Sci.USA, 109:7304-7309, 2012

PubMed Abstract: Protein crystals have catalytic and materials applications and are central to efforts in structural biology and therapeutic development. Designing predetermined crystal structures can be subtle given the complexity of proteins and the noncovalent interactions that govern crystallization. De novo protein design provides an approach to engineer highly complex nanoscale molecular structures, and often the positions of atoms can be programmed with sub-Å precision. Herein, a computational approach is presented for the design of proteins that self-assemble in three dimensions to yield macroscopic crystals. A three-helix coiled-coil protein is designed de novo to form a polar, layered, three-dimensional crystal having the P6 space group, which has a "honeycomb-like" structure and hexameric channels that span the crystal. The approach involves: (i) creating an ensemble of crystalline structures consistent with the targeted symmetry; (ii) characterizing this ensemble to identify "designable" structures from minima in the sequence-structure energy landscape and designing sequences for these structures; (iii) experimentally characterizing candidate proteins. A 2.1 Å resolution X-ray crystal structure of one such designed protein exhibits sub-Å agreement [backbone root mean square deviation (rmsd)] with the computational model of the crystal. This approach to crystal design has potential applications to the de novo design of nanostructured materials and to the modification of natural proteins to facilitate X-ray crystallographic analysis.

PubMed: 22538812
DOI: 10.1073/pnas.1112595109

Experimental method

X-RAY DIFFRACTION (2.1 Å)