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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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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