De novo design of protein–protein interactions through modification of inter-molecular helix–helix interface residues

Yagi, Sota; Akanuma, Satoshi; Yamagishi, Manami; Uchida, Tatsuo; Yamagishi, Akihiko

doi:10.1016/j.bbapap.2016.02.008

Cited by 5 publications

(6 citation statements)

References 28 publications

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“…When the cysLARFH variant and the sulerythrin mutant, each with the designed hydrophobic interface, were mixed, thin fibers were observed by atomic force microscopy (Fig. 5a) (Yagi et al 2016). The average length of the self-assembled fibers was 90 nm.…”

Section: Construction Of Artificial Protein Fibers Through Helix-helimentioning

confidence: 99%

“…We engineered the exposed α-helices of two helical bundle proteins, a dimeric sulerythrin and a monomeric cysLARFH (Fig. 3) (Yagi et al 2016). Six leucine residues and six aspartate or glutamate residues were introduced onto the surface formed by two antiparalleled α-helices of sulerythrin.…”

Section: Design Of Ppis Mediated By Inter-helical Interactionsmentioning

confidence: 99%

“…3 The modeled structure of the designed complex between homodimeric sulerythrin (white) and two monomeric cysLARFHs molecules (black). The interaction between the proteins was created by modification of the sequences of their exposed α-helices (Yagi et al 2016). The image was generated from the crystal structures of sulerythrin (PDB ID 1 J30) and the four-helix bundle domain of the lac repressor (PDB ID 3EDC) from which cysLARFH was derived.…”

Section: Construction Of An Artificial Peptide Fiber Using Helix-helimentioning

confidence: 99%

“…5 a The modeled structure of artificial protein fibers. The fiber comprised sulerythrin homodimers (white) and cysLARFH monomers (black) (Yagi et al 2016). b The crystal structure of a protein-DNA hybrid fiber (PDB ID 4QTR) (Mou et al 2015b) Construction of a more complex structure Self-assembling complexes designed using a computational PPI design strategy…”

Section: Construction Of Artificial Protein Fibers Through Helix-helimentioning

confidence: 99%

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Creation of artificial protein–protein interactions using α-helices as interfaces

2017

Self Cite

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Designing novel protein-protein interactions (PPIs) with high affinity is a challenging task. Directed evolution, a combination of randomization of the gene for the protein of interest and selection using a display technique, is one of the most powerful tools for producing a protein binder. However, the selected proteins often bind to the target protein at an undesired surface. More problematically, some selected proteins bind to their targets even though they are unfolded. Current state-of-the-art computational design methods have successfully created novel protein binders. These computational methods have optimized the non-covalent interactions at interfaces and thus produced artificial protein complexes. However, to date there are only a limited number of successful examples of computationally designed de novo PPIs. De novo design of coiled-coil proteins has been extensively performed and, therefore, a large amount of knowledge of the sequence-structure relationship of coiled-coil proteins has been accumulated. Taking advantage of this knowledge, de novo design of inter-helical interactions has been used to produce artificial PPIs. Here, we review recent progress in the in silico design and rational design of de novo PPIs and the use of α-helices as interfaces.

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Section: Construction Of Artificial Protein Fibers Through Helix-helimentioning

confidence: 99%

Section: Design Of Ppis Mediated By Inter-helical Interactionsmentioning

confidence: 99%

Section: Construction Of An Artificial Peptide Fiber Using Helix-helimentioning

confidence: 99%

Section: Construction Of Artificial Protein Fibers Through Helix-helimentioning

confidence: 99%

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Creation of artificial protein–protein interactions using α-helices as interfaces

2017

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“…Various self-assembling nanostructures have been constructed using designed coiled-coil peptide modules as building blocks: self-assembling cages from coiled-coil peptide modules (Fletcher et al 2013); modular designed self-assembling peptide nanotubes using α-helical barrels with tunable internal cavities as building blocks (Burgess et al 2015); and peptide nanotubes with control of the lateral association and the longitudinal assembly (Thomas et al 2016); and self-assembling protein cages using de novo-designed short coiled-coil domains to mediate assembly by a flexible, symmetry-directed approach (Sciore et al 2016). In addition, the design of protein-protein interactions through modification of inter-molecular helix-helix interface residues was reported (Yagi et al 2016(Yagi et al , 2017.…”

Section: Hierarchical Design Of Quaternary and Supra-quaternary Strucmentioning

confidence: 99%

Hierarchical design of artificial proteins and complexes toward synthetic structural biology

Arai

2017

Biophys Rev

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In multiscale structural biology, synthetic approaches are important to demonstrate biophysical principles and mechanisms underlying the structure, function, and action of bio-nanomachines. A central goal of "synthetic structural biology" is the design and construction of artificial proteins and protein complexes as desired. In this paper, I review recent remarkable progress of an array of approaches for hierarchical design of artificial proteins and complexes that signpost the path forward toward synthetic structural biology as an emerging interdisciplinary field. Topics covered include combinatorial and protein-engineering approaches for directed evolution of artificial binding proteins and membrane proteins, binary code strategy for structural and functional de novo proteins, protein nanobuilding block strategy for constructing nano-architectures, protein-metal-organic frameworks for 3D protein complex crystals, and rational and computational approaches for design/creation of artificial proteins and complexes, novel protein folds, ideal/optimized protein structures, novel binding proteins for targeted therapeutics, and self-assembling nanomaterials. Protein designers and engineers look toward a bright future in synthetic structural biology for the next generation of biophysics and biotechnology.

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Protein Nanostructures with Purpose-Designed Properties in Biotechnology and Medicine

Chronopoulou

Ioannou

Perperopoulou

et al. 2020

Microbial Enzymes and Biotechniques

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De novo design of protein–protein interactions through modification of inter-molecular helix–helix interface residues

Cited by 5 publications

References 28 publications

Creation of artificial protein–protein interactions using α-helices as interfaces

Creation of artificial protein–protein interactions using α-helices as interfaces

Hierarchical design of artificial proteins and complexes toward synthetic structural biology

Protein Nanostructures with Purpose-Designed Properties in Biotechnology and Medicine

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