Self-Assembly of a Designed Nucleoprotein Architecture through Multimodal Interactions

Abstract

The co-self-assembly of proteins and nucleic acids (NAs) produces complex biomolecular machines (e.g., ribosomes and telomerases) that represent some of the most daunting targets for biomolecular design. Despite significant advances in protein and DNA or RNA nanotechnology, the construction of artificial nucleoprotein complexes has largely been limited to cases that rely on the NA-mediated spatial organization of protein units, rather than a cooperative interplay between protein- and NA-mediated interactions that typify natural nucleoprotein assemblies. We report here a structurally well-defined synthetic nucleoprotein assembly that forms through the synergy of three types of intermolecular interactions: Watson–Crick base pairing, NA–protein interactions, and protein–metal coordination. The fine thermodynamic balance between these interactions enables the formation of a crystalline architecture under highly specific conditions.

Stimulus-responsive Self-Assembly of Protein-Based Fractals by Computational Design

“…Self-assembly of engineered proteins 23 provides a general framework for the controllable and bottom-up fabrication of novel biomaterials with chosen supramolecular topologies but these approaches have, thus far, been applied to the design of integer (two or three)-dimensional ordered patterns such as layers, lattices, and polyhedra 24–30 . While external triggers such as metal ions and redox conditions have been used to trigger synthetic protein and peptide assemblies 20,21,31–34 , phosphorylation – a common biological stimulus used for dynamic control over protein function – has yet to be utilized for controlling protein assembly formation.…”

Strategies to Build Hybrid Protein–DNA Nanostructures

“…The reported proteins (lacking DNA-binding capabilities) conjugated covalently to DNA include (multimeric) enzymes used as structural templates [ 19 , 20 , 21 ], metal-binding proteins [ 22 ], coiled-coil peptides [ 23 ], and elastine-like peptides [ 24 ]. By contrast, proteins that exhibit a DNA binding affinity in a sequence-dependent or independent mode include cationic peptides [ 25 , 26 , 27 , 28 ], cationic polymer proteins [ 29 , 30 , 31 ], ribosomal proteins [ 32 ], transcription activator-like (TAL) effectors [ 17 ], transcription factors [ 33 ], viral proteins [ 34 , 35 , 36 ], histones, and polymerases [ 37 ].…”

Strategies to Build Hybrid Protein-DNA Nanostructures

“…However, the resultant complexes can have low stability and be more susceptible to the environmental conditions than chemically linked complexes; thus, the control of these types of interaction represents a great challenge. The reported proteins (lacking DNA-binding capabilities) conjugated covalently to DNA include (multimeric) enzymes used as structural templates [19][20][21], metal-binding proteins [22], coiled-coil peptides [23], and elastine-like peptides [24]. By contrast, proteins that exhibit a DNA binding affinity in a sequence-dependent or independent mode include cationic peptides [25][26][27][28], cationic polymer proteins [29][30][31], ribosomal proteins [32], transcription activator-like (TAL) effectors [17], transcription factors [33], viral proteins [34][35][36], histones, and polymerases [37].…”

“…Other reports followed similar approaches. For example, protein dimers that coassemble through metal-directed protein-protein self-assembly were further polymerized through complementary ssDNA strands (Figure 4b) [22]. Analogously, proteins covalently conjugated to ssDNA strands positioned on opposing faces have been harnessed to create large one-dimensional nanotubes or fibrous nanomaterials (Figure 4c) [19,20,47].…”