Arzeda Scales its Automated Molecule Development Pipeline

Seattle-based Arzeda, a computational and synthetic biology company that was spun out from the University of Washington labs of Prof. David Baker, recently announced that its high-throughput, automated pipeline for protein engineering and pathway discovery had been validated by the production of two keystone molecules. The announcement is a major technical milestone for Arzeda’s approach …

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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 …

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2016 IPD Newsletter from David Baker

It was a great year for the Institute for Protein Design and we couldn’t have done all of our amazing work without the support from our donors and contributors! Thank you to everyone who helped us, whether through a donation, collaboration, playing Foldit, or otherwise. We’ve filled the IPD Newsletter with all of the progress …

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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 …

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De Novo Design Makes a Splash!

A paper recently published in Science by several members of the IPD, in collaboration with others, entitled “De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity,” discusses designing proteins in a similar way to DNA so that they may be used to engineer structures. Geekwire has written up a great article about the paper; …

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Foldit Turns 8!

Over the weekend, Foldit had its 8th birthday! In celebration, they will be tweeting (@Foldit) fun facts and infographics on their feed. Haven’t heard of the game or tried playing it yet? What better time than now! Click here to learn more and to join an ever-growing community that spans the world. Who knows, maybe …

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David Baker wins a Leaders in Health Care Award, listed among ‘world’s most influential scientific minds’

David Baker wins a Leaders in Health Care Award, listed among ‘world’s most influential scientific minds’

We are proud to announce that last week, David was named winner of Seattle Business‘ 2016 Leaders in Health Care Awards for “Outstanding Achievement in Delivery of Digital Health.” The award was one of several given out, with categories ranging from “Lifetime Achievement” to “Outstanding Achievement: Health Care Delivery.” Although David was ill and unable …

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Franziska Seeger @ Ignite Seattle

On February 18th, WRF Fellow Franziska Seeger gave a talk about proteins at Ignite Seattle. Presenters have 5 minutes to speak to the audience and deliver whatever point they are trying to get across. They also cannot control their slides, so they have to have their timing perfect. Talk about pressure! However, we believe that …

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Flu Binder Paper Debuts in PLOS Pathogens

Flu Binder Paper Debuts in PLOS Pathogens

Today at 11am, the paper titled “A Computationally Designed Hemagglutinin Stem-Binding Protein Provides In Vivo Protection from Influenza Independent of a Host Immune Response” was published to the PLOS Pathogen website. This paper was contributed to by several IPD members, including Aaron Chevalier, Jorgen Nelson, Lance Stewart, Lauren Carter, and David Baker. The research was performed …

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CASP3-11 Results Published in E-Life

In the early 1990s, researchers in the field of protein structure prediction were challenged by the problem of how to impartially judge the accuracy of prediction algorithms.  This realization led the protein structure prediction the community to start the Critical Assessment of protein Structure Prediction (CASP), a community-wide, worldwide experiment for protein structure prediction taking …

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Join the IPD!

We are looking for people to join us to help achieve our goal “to engineer a whole new world of synthetic proteins that address 21st century challenges in medicine, energy, and technology.” Interested? Read on!     The newest faculty to join the IPD, Liangcai Gu, PhD, is actively recruiting postdoc fellows to work on …

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September IPD News Roundup

RESEARCH IPD Translational Investigator, Dr. Ingrid Pultz, published a paper in JACS  this month titled ‘Engineering of Kuma030: A Gliadin Peptidase That Rapidly Degrades Immunogenic Gliadin Peptides in Gastric Conditions‘. Using Rosetta to redesign the active site of the gliadin protease KumaMax – an enzyme computationally designed to break down gluten in the stomach – Dr. Pultz and …

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Cyrus hires new EVP of Sales

Cyrus Biotechnology, the first company spinout from the IPD’s Translational Investigator Program, welcomes their new EVP of Sales, Rosario Caltabiano. Follow the link to the Cyrus website to learn more: http://cyrusbio.com/2015/10/01/cyrus-welcomes-evp-rosario-caltabiano/

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August IPD News Roundup

RESEARCH Following the groundbreaking 2014 Nature paper describing the development of a computational method to design multi-component coassembling protein nanoparticles, comes a publication in Protein Science from Baker lab graduate student Jacob Bale and collaborators. Titled “Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression“, the paper reports a variant of a previously low …

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July IPD News Roundup

  RESEARCH In an article out in Structure, Baker lab postdoc Dr. Hahnbeom Park in collaboration with IPD Assistant Professor Frank DiMaio investigate the origin of protein structure refinement from structural averaging at the residue level. Structure refinement has long been a challenge in the field of protein structure prediction and it aims to improve homology …

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June IPD News Roundup

RESEARCH A new Science paper is out from Dr. David Baker and IPD collaborator Dr. Tamir Gonen (HHMI Janelia Campus) titled Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces. Graduate student Shane Gonen and Dr. Frank DiMaio describe a new computational approach to design two-dimensional protein arrays with a number of exciting potential applications …

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New Science paper: Designed 2-D protein arrays

A new Science paper is out from IPD faculty Dr. David Baker titled Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces. Read the abstract below and the article at the link: http://www.sciencemag.org/content/348/6241/1365 We describe a general approach to designing two-dimensional (2D) protein arrays mediated by noncovalent protein-protein interfaces. Protein homo-oligomers are placed into one of the …

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IPD Launches First Company Spinout

Seattle, WA Today, we are announcing that Cyrus Biotechnology, has been successfully launched from the UW Institute for Protein Design (IPD) to pursue commercialization of an innovative user friendly software as a service (SaaS) cloud computing solution for distribution of the powerful “Rosetta” protein structure prediction and design algorithms. “Cyrus is the first new IPD …

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New structure solved for hyperthermophilic DNA virus

A new Science paper is out from IPD faculty Dr. Frank DiMaio titled A virus that infects a hyperthermophile encapsidates A-form DNA. Read the abstract below and the article at the link: http://www.sciencemag.org/content/348/6237/914.full.pdf Extremophiles, microorganisms thriving in extreme environmental conditions, must have proteins and nucleic acids that are stable at extremes of temperature and pH. The nonenveloped, …

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AAAS 2015 Plenary Lecture by David Baker

David Baker, IPD Director and Professor of Biochemistry at the UW was the Plenary Speaker at this year’s AAAS meeting in San Francisco. A video of his talk, titled ‘Post-Evolutionary Biology: Design of Novel Protein Structures, Functions, and Assemblies’ covers a breadth of information on ongoing IPD research and can be viewed at the following …

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Translational Investigator awarded LSDF Matching Grant Award for Celiac Disease Therapy

            Please make a tax deductible donation at this LINK.  IPD Translational Investigator Dr. Ingrid Swanson Pultz was awarded a Matching Grant award of $250K from the Life Sciences Discovery Fund (LSDF) for her project ‘In vivo assessment of an oral therapeutic for celiac disease‘! We need to raise an additional $74K …

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November IPD News Roundup

Staff and scientists of the IPD and Foldit volunteered at Pacific Science Center’s Life Sciences Research Weekend this month – teaching budding scientists about the awesomeness of protein folding! Pics from the event and more Institute news at the link.

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Custom design of novel alphahelical bundles

A new paper is out in this week’s issue of Science entitled High thermodynamic stability of parametrically designed helical bundles. Using novel computational design methods, extremely stable helical bundles can be custom designed with fine-tuned structural geometries for a number of applications. Read more about this exciting work at this link.

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Targeting Ebola

The Foldit community to targets Ebola. Click here to learn more. Watch grad student Brian Koepnick and IPD Director David Baker talk about this work on this KOMO TV news segment. See the Seattle Times article here. Make a donation to help us fund our anti-Ebola effort.

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Designer Proteins to Target Cancer Cells

What if scientists could design a completely new protein that is precision-tuned to bind and inhibit cancer-causing proteins in the body? Collaborating scientists at the UW Institute for Protein Design (IPD) and Molecular Engineering and Sciences Institute (MolES) have made this idea a reality with the designed protein BINDI. BINDI (BHRF1-INhibiting Design acting Intracellularly) is a completely novel protein, based …

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Accurate Design of Co-Assembling Multi-Component Protein Nanomaterials

A new paper is out in the June 5 issue of Nature entitled Accurate design of co-assembling multi-component protein nanomaterials. Scientists at the Institute for Protein Design (IPD), in collaboration with researchers at UCLA and HHMI, have built upon their previous work constructing single-component protein nanocages and can now design and build self-assembling protein nanomaterials made up of …

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Women in Science Lunch Discussion

A recent Nature issue exposed the dismaying fact that many women are deterred from pursuing a career in science, especially at the highest levels (postdoctoral positions, faculty position, scientific advisory boards to start up companies, etc). To talk about this significant gender gap in science and the issues female scientists face, Baker lab members participated …

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WRF Awards $8M for the IPD Innovation Fellows Program

May 15, 2014 With a very generous $8 M gift from the Washington Research Foundation (WRF), the IPD has launched the WRF-IPD Innovation Fellows Program supporting research partnerships between the IPD and other Seattle-area research institutes or UW departments.  We are recruiting exceptionally talented researchers who have just finished their PhD to join expert laboratories at local institutions where they …

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Beyond Evolution: Protein Design News and Art

Re/Code writer James Temple has written an interesting article on David Baker’s efforts to design a new world of proteins.  The article covers the IPD efforts to design proteins that neutralize the flu virus, Alzheimer’s disease amyloid protein, and how the IPD is engaging citizen scientists in the Rosetta@home and Foldit projects.  Learn more at …

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Design of Activated Serine-Containing Catalytic Triads with Atomic-Level Accuracy

Baker lab members published in Nature Chemical Biology a paper entitled “Design of activated serine-containing catalytic triads with atomic-level accuracy“, describing the computational design of proteins with idealized serine-containing catalytic triads which can capture and neutralize organophosphate probes.  This work has utility in design of scavengers of environmental toxins. Learn more at this link.

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A Computationally Designed Metalloprotein Using an Unnatural Amino Acid

What if scientists could design proteins to capture specific metals from our environment?  The utility for cleaning up metals from waste water, soils, and our bodies could be tremendous.  Dr. Jeremy Mills and collaborators in Dr. Baker’s group at the University of Washington’s Institute for Protein Design (IPD) address this challenge in the first reported …

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Computational Design of a pH Sensitive Antibody Binder

Purification of antibody IgG from crude serum or culture medium is required for virtually all research, diagnostic, and therapeutic antibody applications.  Researchers at the Institute for Protein Design (IPD) have used computational methods to design a new protein (called “Fc-Binder”) that is programed to bind to the constant portion of IgG (aka “Fc” region) at basic …

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KumaMax: Winner of C4C Recognition as a Novel Oral Therapeutic for Celiac Disease

  Dr. Ingrid Swanson Pultz, a Translational Investigator at the Institute for Protein Design won first prize at the UW Center for Commercialization 2013 Innovator Recognition Event, for KumaMax, an enzyme designed in the Baker lab to efficiently break down gluten within the acidic environment of the stomach, before it can reach the small intestine where intact gluten …

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Computational Protein Design To Improve Detoxification Rates Of Nerve Agents

V-type nerve agents are among the most toxic compounds known, and are chemically related to pesticides widespread in the environment. Using an integrated approach, described in an ACS Chemical Biology paper entitled Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries, Dr. Izhack Cherny, Dr. Per Greisen, and collaborators increased the rate of nerve …

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Computational Design Of A Protein That Binds Polar Surfaces

In a Journal of Molecular Biology publication entitled Computational design of a protein-based enzyme inhibitor, Dr. Erik Procko and collaborators describe the computational design of a protein-based enzyme inhibitor that binds the polar active site of hen egg lysosome (HEL).  Computational design of a protein that binds polar surfaces has not been previously accomplished.  Learn …

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Life Sciences Discovery Fund Awards $1.4M to the Institute for Protein Design

The Life Sciences Discovery Fund  (LSDF) today announced its latest round of Opportunity Grants, and awarded $1.4 M to the University of Washington (UW) to “Launch of the Institute for Protein Design for Creating New Therapeutics, Vaccines and Diagnostics.”   This LSDF Opportunity Grant Award will enable the IPD Translational Investigators to improve upon protein design discoveries so that they …

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

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

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.    

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IPD Researchers Publish New Protocols for Preparing Protein Scaffold Libraries for Functional Site Design

IPD researchers in the Baker group have published new computational protocols for preparing protein scaffold libraries for functional site design.  Their paper entitled “A Pareto-optimal refinement method for protein design scaffolds“ improves the search for amino acids with the lowest energy subject to a set of constraints specifying function.  Learn more at this link.

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Centenary Award and Frederick Gowland Hopkins Memorial Lecture

Dr. David Baker, Director of the IPD delivered the Centenary Award and Frederick Gowland Hopkins Memorial Lecture at  at the MRC Laboratory of Molecular Biology, Cambridge, UK, on December, 13, 2012.   Baker’s lecture entitled “Protein folding, structure prediction and design”  can be read at this published link.   See:  Baker, D. (2014).  Protein folding, structure prediction and design.. Biochemical Society …

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Proteins Made to Order. Researchers at the IPD Design Proteins from Scratch with Predictable Structures

A team from David Baker’s laboratory at the University of Washington in Seattle have described a set of “rules” for the design of proteins from scratch, and have demonstrated the successful design of five new proteins that fold reliably into predicted conformations.  Their work was published Nature.  Learn more at this link.

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Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

IPD researchers in the Baker group have published in Science a paper entitled “Computational design of self-assembling protein nanomaterials with atomic level accuracy.”  They describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture.  Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed …

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UW to Establish Institute for Protein Design

Dr. Paul Ramsey, CEO of UW Medicine, announces the establishment of the Institute for Protein Design (IPD).   “A major challenge for designing proteins for specific purposes is predicting three-dimensional shape from the amino acid sequence. Dr. David Baker, UW professor of biochemistry and an investigator of the Howard Hughes Medical Institute, has had remarkable success in …

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