Tag: Institute for Protein Design

Graphic: Possu Huang

Open Philanthropy Project Awards $11.3 Million to Institute for Protein Design at UW Medicine

Gift seeks universal flu vaccine and will advance Rosetta software        

Seattle — The Institute for Protein Design (IPD) at UW Medicine in Seattle has been awarded $11.3 million from the Open Philanthropy Project to support the institute’s technological revolution in protein design and support its work on the development of a universal flu vaccine.

The Open Philanthropy Project is based in San Francisco, California. The gift is:

  • One of Open Philanthropy Project’s largest awards in the sciences to date.
  • Its first scientific gift in the Seattle area.
  • Its first investment at UW Medicine.

The gift comes in two parts:

  • $5.6 million to refine and advance Rosetta, the software platform for protein design originally developed at UW
  • $5.7 million for the institute’s program to develop a universal flu vaccine.

“We’re excited to help move science forward in ways not seen before with proteins, which are essential to life. This grant recognizes that UW Medicine is at the forefront of unlocking the keys to the use of proteins in medical settings,” says Chris Somerville, a Program Officer for Scientific Research at the Open Philanthropy Project. “The universal flu vaccine is a tough nut to crack, but David Baker has shown the ability to pioneer life-changing scientific research. It’s exciting that whether a universal flu vaccine is developed or not, this gift will build techniques and technologies that will advance science and have a huge variety of implications in medicine and industry.”

Proteins are the workhorses of all living creatures, fulfilling the instructions of DNA. Existing proteins are the products of billions of years of evolution and carry out all the important functions in our body—digesting food, building tissue, transporting oxygen through the bloodstream, dividing cells, firing neurons, and powering muscles.

“This gift is speeding up a technological revolution in how we design proteins. Our team can now custom design proteins from scratch, creating entirely novel molecules that can be used for new treatments, new diagnostics and new biomaterials. The Open Philanthropy Project’s generous gift will transform our ability to design proteins from scratch,” said David Baker, the institute’s director as well as professor of biochemistry at the University of Washington School of Medicine and Howard Hughes Medical Institute investigator. Baker is the Henrietta and Aubrey Davis Endowed Professor in Biochemistry.

Computer-based protein design

The gift will accelerate the institute’s efforts to advance protein design on computers with the Rosetta software originally developed in Baker’s lab. Baker said the gift will transform’s the institute’s ability to design proteins on computers, test them by creating the actual proteins in the lab, and then repeat the process at an enormous scale. “By speeding up this cycle of design, building and testing, we will be able to systematically improve protein design methods,” Baker said.

The results and new Rosetta software will be shared with the scientific community through the Rosetta Commons. The Rosetta Commons is a collaboration founded by  Baker with almost 100 developers from 23 universities and laboratories who regularly contribute to and share the Rosetta source code, currently over 3 million lines.

This project is in collaboration with Frank DiMaio, assistant professor of biochemistry at the University of Washington School of Medicine.

Universal flu vaccine

Current flu vaccines are intended to protect only against currently circulating strains, requiring the vaccines to be reformulated every year as the virus mutates, and are only partially protective. With Open Philanthropy Project support, Baker and his collaborators, Neil King and David Veesler, both assistant professors of biochemistry at the University of Washington School of Medicine, will be leading an effort to design universal flu vaccine candidates that provide durable protection against multiple virus strains, including strains that have the potential to cause pandemic outbreaks. The vaccine candidates will be based on the self-assembling protein nanoparticle technology Baker and King have developed. To ensure that the vaccine candidates are thoroughly and efficiently tested, they will work in close collaboration with the groups of Dr. Barney Graham and Dr. Masaru Kanekiyo at the Vaccine Research Center of the National Institute of Allergy and Infectious Diseases at the National Institutes of Health.

The goal is to design a nanoparticle vaccine that can trigger an effective immune response to many existing flu strains as well as new strains that might appear in the future. Researchers hope such a universal vaccine might need to be administered no more than every five years, ending the need for annual flu vaccinations.

The Institute for Protein Design, founded in 2012 at UW Medicine in Seattle, is a research center that focuses on creating custom-designed proteins to improve human health and address 21st-century challenges in medicine, energy, industry and technology. In the human body, proteins are chains of amino acids directed by genes to perform essential life functions in every cell including in the brain, muscles and internal organs. Proteins also have implications for the design of new materials outside of the human body such as new kinds of fibers. The institute’s team of 120 faculty, staff, postdoctoral fellows and graduate students work on designing entirely novel proteins from scratch to create, for example, new, safer and more potent vaccines and therapeutics to prevent or treat people with serious diseases. The institute has assembled some of the world’s top experts in protein science, computer science, biochemistry and biological structure, pharmacology, immunology and clinical medicine.

About the Open Philanthropy Project

The Open Philanthropy Project identifies outstanding giving opportunities, makes grants, follows the results, and publishes its findings. Its main funders are Cari Tuna and Dustin Moskovitz, a co-founder of Facebook and Asana.

See news in UW Medicine Newsroom. For more information on the IPD check out this video!

De Novo Design of Membrane Proteins

It is now possible to create complex, custom-designed transmembrane proteins from scratch !   Today Baker lab members published in Science  “Accurate computational design of multipass transmembrane proteins

Designed Membrane Protein:  (Left) Side view showing the designed membrane protein inside the membrane.  (Right)  Top view of same.

The Abstract reads as follows:

The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer—a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices—are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions.

 

 

 

 

End-of-year profile in The New York Times

At the end of a historic year for protein design, the Baker lab was honored to be profiled in the New York Times by famed science writer Carl Zimmer. Zimmer writes about the technology, progress and promise in the field, noting the contributions from our wonderful crowdsource participants.

Graphic: John Hersey / New York Times

On the technology front, Rosetta continues to improve year over year thanks to the hard work of the RosettaCommons. Given ongoing advances in DNA synthesis and protein screening technology, there is still so much more we can design and discover.

Progress in the field of protein design was staggering in 2017. Thousands of de novo proteins were produced, with new features, folds and functions. From immunotherapy, drug delivery, anti-viral activity and more, this truly was an awesome year for applied protein design.

The promise of the field has never been greater. As David says at the close of the article, “As we understand more and more of the basic principles, we ought to be able to do far better.”

Read the full profile here: Scientists Are Designing Artisanal Proteins for Your Body

A New World of Designed Macrocycles

Today marks another major step forward for peptide based drug discovery.  IPD researchers report in Science the computational design of a new world of small cyclic peptides, “Macrocycles”,  increasing the number of the known kinds of these molecules by multiple fold.  The conceptual art image below “Illuminating the energy landscape” shows the power of computational design to explore and illuminate structured peptides across the vast energy landscape.

Small peptides have the benefits of small molecule drugs, like aspirin, and large antibody therapies, like rituximab, with fewer drawbacks.  They are stable like small molecules and potent and selective like antibodies.

Image by Vikram Mulligan. Computational design calculations reveal the peptide macrocycle energy landscape.

Abstract reads as follows.

Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with L-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of L- and D-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods.

Check out these additional news items from UW Medicine, and Science

Read more and download the paper at the Baker lab web site.

Synthetic Nucleocapsids Have Arrived

Published today in Nature, IPD researchers describe the first synthetic protein assemblies — dubbed synthetic nucleocapsids — that encapsulate their own genome and evolve in complex environments.

Computationally Designed Synthetic Nucleocapsid
Computationally Designed Synthetic Nucleocapsid, Illustration by Institute for Protein Design & Cognition Studio

Synthetic nucleocapsids are built to resemble viral capsids and could be used in future to deliver therapeutics to specific cells and tissues. These icosahedral protein assemblies are based off of previously reported results from the Institute for Protein Design.

The image above visualizes the de novo creation of synthetic nucleocapsids from computationally designed proteins and their evolution to acquire properties that could be useful for drug delivery and other biomedical applications. The narrative was designed as a futuristic hologram projection realized through spiraling DNA composed of binary zeros and ones. The projection and computational imagery evoke futuristic technology and design, while calling out natural evolution through the DNA spiral “time-scale” motif. The heads-up display iconography showing a blood bag, mouse, and RNase A convey the challenges we used to evolve the synthetic nucleocapsids. The single net impression of this image is engaging + enlightening and shows that we are entering the next epoch of synthetic biology in which biological systems can be designed and created from scratch.

Abstract:

The challenges of evolution in a complex biochemical environment, coupling genotype to phenotype and protecting the genetic material, are solved elegantly in biological systems by the encapsulation of nucleic acids. In the simplest examples, viruses use capsids to surround their genomes. Although these naturally occurring systems have been modified to change their tropism and to display proteins or peptides, billions of years of evolution have favoured efficiency at the expense of modularity, making viral capsids difficult to engineer. Synthetic systems composed of non-viral proteins could provide a ‘blank slate’ to evolve desired properties for drug delivery and other biomedical applications, while avoiding the safety risks and engineering challenges associated with viruses. Here we create synthetic nucleocapsids, which are computationally designed icosahedral protein assemblies with positively charged inner surfaces that can package their own full-length mRNA genomes. We explore the ability of these nucleocapsids to evolve virus-like properties by generating diversified populations using Escherichia coli as an expression host. Several generations of evolution resulted in markedly improved genome packaging (more than 133-fold), stability in blood (from less than 3.7% to 71% of packaged RNA protected after 6 hours of treatment), and in vivo circulation time (from less than 5 minutes to approximately 4.5 hours). The resulting synthetic nucleocapsids package one full-length RNA genome for every 11 icosahedral assemblies, similar to the best recombinant adeno-associated virus vectors. Our results show that there are simple evolutionary paths through which protein assemblies can acquire virus-like genome packaging and protection. Considerable effort has been directed at ‘top-down’ modification of viruses to be safe and effective for drug delivery and vaccine applications; the ability to design synthetic nanomaterials computationally and to optimize them through evolution now enables a complementary ‘bottom-up’ approach with considerable advantages in programmability and control.

Read more and obtain a PDF of the paper from the Baker lab web site.  Also read additional news items from Science Daily, GeekWire, UW Newsroom, CEN

The Matrix of Protein Design

The Matrix movie (1999) depicts a future in which the reality perceived by most humans is actually a computer simulated reality called “the Matrix”.  Published today in Sciencethe Baker lab and collaborators report on a new kind of Matrix –  a new reality for large scale computational protein design which can achieve massive data driven improvements in our ability to design highly stable, small proteins from scratch.

Illustration by Gabe Rocklin

 

Following the White Rabbit, Postdoctoral fellow Dr. Gabe Rocklin led a group of scientists to design and test over 15,000 new mini-proteins (which do not exist in nature) to see whether they form stable folded structures. Even major protein design studies in the past few years have generally examined only 50 to 100 designs.  Synthetic DNA technology and high throughput screening permitted the group to conduct large-scale testing of structural stability of multitudes of computationally designed proteins.  In turn, this allows them to perform a “Global analysis of protein folding using massively parallel design, synthesis and testing“.  

Through iterative improvements in the design process, the group arrived at 2,788 stable mini-protein structures, which is at least 50-fold more proteins than have ever been characterized from natural sources for similar sized proteins.  Their small size and stability may be advantageous for treating diseases when the drug needs to avoid the immune system and reach the inside of a cell.

The publication Abstract is a step into the Matrix as Morpheus explains,

Proteins fold into unique native structures stabilized by thousands of weak interactions that collectively overcome the entropic cost of folding. Though these forces are “encoded” in the thousands of known protein structures, “decoding” them is challenging due to the complexity of natural proteins that have evolved for function, not stability. Here we combine computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for over 15,000 de novo designed miniproteins, 1,000 natural proteins, 10,000 point-mutants, and 30,000 negative control sequences, identifying over 2,500 new stable designed proteins in four basic folds. This scale — three orders of magnitude greater than that of previous studies of design or folding—enabled us to systematically examine how sequence determines folding and stability in uncharted protein space. Iteration between design and experiment increased the design success rate from 6% to 47%, produced stable proteins unlike those found in nature for topologies where design was initially unsuccessful, and revealed subtle contributions to stability as designs became increasingly optimized. Our approach achieves the long-standing goal of a tight feedback cycle between computation and experiment, and promises to transform computational protein design into a data-driven science.

The research has been recognized by opinion leaders and media outlets as a major step for computational protein design.  See articles in Science, Science Daily, Chemistry WorldPhys.orgGEN, and C&E News.

 

 

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.  See In the Pipeline.

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.