Tag: Institute for Protein Design

Hyper-stable Designed Peptides and the Coming of Age for De Novo Protein Design

Small constrained peptides combine the stability of small molecule drugs with the selectivity and potency of antibody-based therapeutics. However, peptide-based therapeutics have largely remained underexplored due to the limited diversity of naturally occurring peptide scaffolds, and a lack of methods to design them rationally.  New computational design and wet lab methods developed at the Institute for Protein Design have now opened the door to rational design of a whole new world of hyper-stable drug-like peptide structures.

In an article published in Nature this week, Baker lab / IPD scientists and their collaborators describe the development of computational methods for de novo design of constrained peptides with exceptional stabilities. They used these computational methods to design 18-47 residue constrained peptides with diverse shapes and sizes. The designed peptides presented in the paper cover three broad categories:

1) genetically encodable disulfide cross-linked peptides,

2) synthetic disulfide cross-linked peptides with non-canonical sequences, and

3) cyclic peptides with non-canonical backbones and sequences.

Experimentally determined structures for these peptides are nearly identical to their design models.

ehee_peptide_bhardwaj_mulligan_bahl
EHEE Designed Peptide, Visual Illustration by Vikram Mulligan. The molecular surface is shown as a transparent blue shell, and the peptide’s backbone structure is pink. The amino acid’s side chains are white (carbon atoms), blue (nitrogen atoms) and red (oxygen atoms). The crisscrossing bonds that give the peptide its constrained, stable shape are in bright white.

By including D-amino acids (mirror images of the L-amino acids), and thus expanding the palette of building blocks, Baker lab scientists designed peptides in a sequence and structure space sampled rarely by Nature. Indeed, the article describes successful design of a cyclic 2-helix peptide of mix chirality that represents a shape beyond natural secondary- and tertiary structure.

These designed peptides also exhibit exceptional stability to thermal and chemical denaturation, and thus could serve as attractive scaffolds for design of novel peptide-based therapeutics. More broadly, development of this new computational toolkit to precisely design constrained peptides opens the door for “on-demand” development of a new generation of peptide-based therapeutics.

These and other breakthroughs in computational protein design are also covered in a Nature review article by David Baker, Po-Ssu Huang, and Scott E. Boyken entitled “The coming of age of de novo protein design”, part of special supplement on The Protein World.

Illustrations of designed peptides with different configurations of two structures: tightly wound ribbons and flat, arrow-shaped ribbons.
Illustrations of designed peptides with different configurations of two structures: tightly wound ribbons and flat, arrow-shaped ribbons.

See additional news coverage

HS NewsBeat, Hutch News,

Funding Sources

The National Institutes of Health provided partial support for this work through grants P50 AG005136, T32-H600035., GM094597, GM090205, and HHSN272201200025C.  Additional funding was provided by The Three Dreamers.

Designed Protein Containers Push Bioengineering Boundaries

Earlier this month, Baker lab researchers reported the computational design of a hyperstable 60-subunit protein icosahedron in Nature (Hsia et al); icosahedral protein structures are commonly observed in natural biological systems for packaging and transport (e.g. viral capsids). The described design was composed of 60 trimeric protein building blocks that self-assembled in a nanocage.

In new work published today, Baker lab scientists and collaborators have taken this work to an exciting new level by engineering 120-subunit icosahedral nanocages that self-assemble from not one, but two distinct protein components. The new designed proteins are described in the latest issue of Science in a paper entitled “Accurate design of megadalton-scale multi-component icosahedral protein complexes”.

In this paper, former Baker lab graduate student Jacob Bale, Ph.D. and collaborators describe the computational design and experimental characterization of ten two-component protein complexes that self-assemble into nanocages with atomic-level accuracy. These nanocages are the largest designed proteins to date with molecular weights of 1.8-2.8 megadaltons and diameters comparable to small viral capsids. The structures have been confirmed by X-ray crystallography (see figure). The advantage of a multi-component protein complex is the ability to control assembly by mixing individually prepared subunits. The authors show that in vitro mixing of the designed subunits occurs rapidly and enables controlled packaging of negatively charged GFP by introducing positive charges on the interior surfaces of the two copmonents.

The ability to design, with atomic-level precision, these large protein nanostructures that can encapsulate biologically relevant cargo and that can be genetically modified with various functionalities opens up exciting new opportunities for targeted drug delivery and vaccine design. A link to the paper and additional information is below:

Link to PDF can be found here

Featured article and video in Science magazine:

This protein designer aims to revolutionize medicines and materials” – Science

Other related news items:

Virus-inspired contender design may lead to cell cargo ships” – UW Health Sciences NewsBeat

Large Protein Nanocages Could Improve Drug Design and Delivery” – HHMI News

Biggest Little Self-Assembling Protein Nanostructures Created” – DARPA News and Events

More:

Watch a short video about the designed protein nanocages

See specific descriptions on these nanoparticles from Jacob Bale, Neil King, and Yang Hsia

Abstract
Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling two-component 120-subunit icosahedral protein nanostructures with molecular weights (1.8-2.8 MDa) and dimensions (24-40 nm diameter) comparable to small viral capsids. Electron microscopy, SAXS, and X-ray crystallography show that ten designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of independently purified components reveals rapid assembly rates comparable to viral capsids and enables controlled packaging of molecular cargo via charge complementarity. The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines.

Reprinted with permission from AAAS
Reprinted with permission from AAAS

One Small Molecule Binding Protein, One Giant Leap for Protein Design

Illustration rendering of the digoxigenin binding protein was prepared by Vikram Mulligan

Reported on-line  in Nature (Sept. 4, 2013) researchers at the Institute for Protein Design describe the use of Rosetta computer algorithms to design a protein which binds with high affinity and specificity to a small drug molecule, digoxigenin a dangerous but sometimes life saving cardiac glycoside.  Learn more at this link.