Biological Assembly of Modular Protein Building Blocks as Sensing, Delivery, and Therapeutic Agents

Nature has evolved a wide range of strategies to create self-assembled protein nanostructures with structurally defined architectures that serve a myriad of highly specialized biological functions. With the advent of biological tools for site-specific protein modifications and de novo protein design, a wide range of customized protein nanocarriers have been created using both natural and synthetic biological building blocks to mimic these native designs for targeted biomedical applications. In this review, different design frameworks and synthetic decoration strategies for achieving these functional protein nanostructures are summarized. Key attributes of these designer protein nanostructures, their unique functions, and their impact on biosensing and therapeutic applications are discussed.

Download Full-text

Protein designer David Baker: I like doing things that seem like magic

National Science Review ◽

10.1093/nsr/nwaa071 ◽

2020 ◽

Vol 7 (8) ◽

pp. 1410-1412

Author(s):

Weijie Zhao ◽

Chu Wang

Keyword(s):

Protein Design ◽

De Novo ◽

Protein Structures ◽

Computational Prediction ◽

Biological Functions ◽

Personal Experiences ◽

De Novo Protein Design ◽

And Function ◽

The University ◽

Opening Up

Abstract Search ‘de novo protein design’ on Google and you will find the name David Baker in all results of the first page. Professor David Baker at the University of Washington and other scientists are opening up a new world of fantastic proteins. Protein is the direct executor of most biological functions and its structure and function are fully determined by its primary sequence. Baker's group developed the Rosetta software suite that enabled the computational prediction and design of protein structures. Being able to design proteins from scratch means being able to design executors for diverse purposes and benefit society in multiple ways. Recently, NSR interviewed Prof. Baker on this fast-developing field and his personal experiences.

Download Full-text

Designed for life: biocompatible de novo designed proteins and components

Journal of The Royal Society Interface ◽

10.1098/rsif.2018.0472 ◽

2018 ◽

Vol 15 (145) ◽

pp. 20180472 ◽

Cited By ~ 8

Author(s):

Katie J. Grayson ◽

J. L. Ross Anderson

Keyword(s):

Protein Design ◽

De Novo ◽

Building Blocks ◽

De Novo Design ◽

Biochemical Processes ◽

Designed Proteins ◽

De Novo Protein Design ◽

Protein Molecules ◽

And Function

A principal goal of synthetic biology is the de novo design or redesign of biomolecular components. In addition to revealing fundamentally important information regarding natural biomolecular engineering and biochemistry, functional building blocks will ultimately be provided for applications including the manufacture of valuable products and therapeutics. To fully realize this ambitious goal, the designed components must be biocompatible, working in concert with natural biochemical processes and pathways, while not adversely affecting cellular function. For example, de novo protein design has provided us with a wide repertoire of structures and functions, including those that can be assembled and function in vivo . Here we discuss such biocompatible designs, as well as others that have the potential to become biocompatible, including non-protein molecules, and routes to achieving full biological integration.

Download Full-text

A bottom-up approach for the de novo design of functional proteins

10.1101/2020.03.11.988071 ◽

2020 ◽

Cited By ~ 2

Author(s):

Che Yang ◽

Fabian Sesterhenn ◽

Jaume Bonet ◽

Eva van Aalen ◽

Leo Scheller ◽

...

Keyword(s):

Protein Design ◽

Mammalian Cells ◽

De Novo ◽

Protein Structures ◽

Functional Protein ◽

Regular Secondary Structure ◽

Bottom Up ◽

Binding Motifs ◽

Wide Range ◽

Novel Protein

AbstractDe novo protein design has enabled the creation of novel protein structures. To design novel functional proteins, state-of-the-art approaches use natural proteins or first design protein scaffolds that subsequently serve as templates for the transplantation of functional motifs. In these approaches, the templates are function-agnostic and motifs have been limited to those with regular secondary structure. Here, we present a bottom-up approach to build de novo proteins tailored to structurally complex functional motifs. We applied a bottom-up strategy to design scaffolds for four different binding motifs, including one bi-functionalized protein with two motifs. The de novo proteins were functional as biosensors to quantify epitope-specific antibody responses and as orthogonal ligands to activate a signaling pathway in engineered mammalian cells. Altogether, we present a versatile strategy for the bottom-up design of functional proteins, applicable to a wide range of functional protein design challenges.

Download Full-text

Intracellular artificial supramolecules based on de novo designed Y15 peptides

Nature Communications ◽

10.1038/s41467-021-23794-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Takayuki Miki ◽

Taichi Nakai ◽

Masahiro Hashimoto ◽

Keigo Kajiwara ◽

Hiroshi Tsutsumi ◽

...

Keyword(s):

Mammalian Cells ◽

Actin Polymerization ◽

Fluorescent Protein ◽

De Novo ◽

Adaptor Protein ◽

Building Blocks ◽

Vaccine Adjuvants ◽

Functional Protein ◽

Self Assembling ◽

Wide Range

AbstractDe novo designed self-assembling peptides (SAPs) are promising building blocks of supramolecular biomaterials, which can fulfill a wide range of applications, such as scaffolds for tissue culture, three-dimensional cell culture, and vaccine adjuvants. Nevertheless, the use of SAPs in intracellular spaces has mostly been unexplored. Here, we report a self-assembling peptide, Y15 (YEYKYEYKYEYKYEY), which readily forms β-sheet structures to facilitate bottom-up synthesis of functional protein assemblies in living cells. Superfolder green fluorescent protein (sfGFP) fused to Y15 assembles into fibrils and is observed as fluorescent puncta in mammalian cells. Y15 self-assembly is validated by fluorescence anisotropy and pull-down assays. By using the Y15 platform, we demonstrate intracellular reconstitution of Nck assembly, a Src-homology 2 and 3 domain-containing adaptor protein. The artificial clusters of Nck induce N-WASP (neural Wiskott-Aldrich syndrome protein)-mediated actin polymerization, and the functional importance of Nck domain valency and density is evaluated.

Download Full-text

Hierarchical design of multi-scale protein complexes by combinatorial assembly of oligomeric helical bundle and repeat protein building blocks

10.1101/2020.07.27.221333 ◽

2020 ◽

Author(s):

Yang Hsia ◽

Rubul Mout ◽

William Sheffler ◽

Natasha I. Edman ◽

Ivan Vulovic ◽

...

Keyword(s):

Protein Design ◽

De Novo ◽

Protein Complexes ◽

Building Blocks ◽

Hierarchical Design ◽

X Ray ◽

Helical Bundle ◽

X Ray Crystallography ◽

Repeat Proteins ◽

Wide Range

AbstractA goal of de novo protein design is to develop a systematic and robust approach to generating complex nanomaterials from stable building blocks. Due to their structural regularity and simplicity, a wide range of monomeric repeat proteins and oligomeric helical bundle structures have been designed and characterized. Here we describe a stepwise hierarchical approach to building up multi-component symmetric protein assemblies using these structures. We first connect designed helical repeat proteins (DHRs) to designed helical bundle proteins (HBs) to generate a large library of heterodimeric and homooligomeric building blocks; the latter have cyclic symmetries ranging from C2 to C6. All of the building blocks have repeat proteins with accessible termini, which we take advantage of in a second round of architecture guided rigid helical fusion (WORMS) to generate larger symmetric assemblies including C3 and C5 cyclic and D2 dihedral rings, a tetrahedral cage, and a 120 subunit icosahedral cage. Characterization of the structures by small angle x-ray scattering, x-ray crystallography, and cryo-electron microscopy demonstrates that the hierarchical design approach can accurately and robustly generate a wide range of macromolecular assemblies; with a diameter of 43nm, the icosahedral nanocage is the largest structurally validated designed cage to date. The computational methods and building block sets described here provide a very general route to new de novo designed symmetric protein nanomaterials.

Download Full-text