University of Washington

Leland Stanford Junior University

University of California

University of Chicago

Institute for Research in Biomedicine

University of Utah Research Foundation

Massachusetts Institute of Technology

Harvard College

Yeda Research and Development Co. Ltd.

David Baker

Justin Bloomfield Siegel

Neil P King

Ingrid Swanson Pultz

Kenan Christopher Garcia

Daniel Adriano Silva Manzano

Lance Joseph Stewart

Umut Ulge

Carl Walkey

Jamie Spangler

Shawn Yu

William H Sheffler

Marc J Lajoie

Jacob Bale

Sarel Fleishman

Christine Elaine Tinberg

Elizabeth Joy Stanley

Sarah Jane Wolf

Sydney Rin Anna Gordon

Daniel Ellis

Scott Boyken

Robert A Langan

Alfredo Quijano Rubio

Jorge Fallas

Antonio Lanzavecchia

Michelle Scalley-Kim

David Younger

Benjamin S Glick

Timothy A Whitehead

Daniel E Strongin

Brooke Bevis

Yang Hsia

Elizabeth Gray

Daniel Stetson

Laurent Perez

Clancey Wolf

Jessica Marcandalli

Brooke Fiala

Eric Klavins

George Ueda

Alexandre Zanghellini

Eric Anthony Althoff

Deborah Fuller

Daniela Grabs-Röthlisberger

Wesley Sundquist

Lauren Carter

Vanessa Nguyen

Aaron Arthur Chevalier

Joerg Votteler

Merika Treants Koday

Gabriel Butterfield

Sagar D Khare

Gustav Oberdorfer

Andrew Wollacott

Zibo Chen

Sherry Bermeo

Eva-Maria Strauch

Lucas Nivon

Lin Jiang

Luke Dang

Walter Novak

George M Church

James Michael Thompson

Paul Yager

Patrick S Stayton

James Liao

David S Eisenberg

Stuart A Sievers

Alice Y Ting

Dan S Tawfik

Brian Arthur Kuhlman

Todd O Yeates

Daniel J Mandell

Claudia Yvonne Janda

Jonathan Sockolosky

Mary Elizabeth Lidstrom

Yaacov Ashani

Moshe Goldsmith

Adi Goldenzweig

Justin Feng

Wai Shun Mak

Caitlin E Anderson

Gabriel Jacob Rocklin

Christopher David Bahl

Jason Gilmore

Haim Leader

Izhack Cherny

Per Jr Greisen

Brooke Nickerson

Nidhi Aggarwal

Jiayi Dou

Yu-Ru Lin

Carly Holstein

Jorgen Nelson

Chunfu Xu

Stanley Fields

Benjamin Ward Jester

Erik Procko

Geoffrey Y Berguig

Yifan Song

Disclosed are protein switches that can sequester bioactive peptides and/or binding domains, holding them in an inactive ('off') state, until combined with a second designed polypeptide called the key, which induces a conformational change that activates (“on”) the bioactive peptide or binding domain, components of such protein switches, and their use.

De novo design of protein switches

Disclosed herein are nanostructures and their use, where the nanostructures include

Self-assembling protein nanostructures displaying paramyxovirus and/or pneumovirus F proteins and their use

De novo designed polypeptides that bind to IL-2 receptor βheterodimer (IL-2Rβ), IL-4 receptor αheterodimer (IL-4Rα), or IL-13 receptor α subunit (IL-13Rα) are disclosed, as are methods for using and designing the polypeptides.

De novo design of potent and selective interleukin mimetics

Conditionally active receptor agonists that, when activated, bind to IL-2 receptor βheterodimer (IL-2Rβ), IL-4 receptor αheterodimer (IL-4Rα), or IL-13 receptor a subunit (IL˜13 Rα) are disclosed, as are components of the conditionally active receptor agonists and methods for using the conditionally active receptor agonists.

Split interleukin mimetics and their use

De novo designed polypeptides that bind to IL-2 receptor βγheterodimer (IL-2Rβγ), IL-4 receptor αγheterodimer (IL-4Rαγ), or IL-13 receptor α subunit (IL-13Rα) are disclosed, as are methods for using and designing the polypeptides.

Described herein are polypeptides capable of self-assembling to form homo-oligomers, and methods for designing such polypeptides.

Computational design of self-assembling cyclic protein homo-oligomers

Wnt signaling antagonist and agonist compositions and methods for their use are provided.

Frizzled specific Wnt agonists and antagonists

The application discloses multimeric assemblies packaging one or more active component and their use to carry out nucleic acid regulation or gene editing.

Genome editing reagents and their use

The present invention relates to methods and compositions for the high throughput screening of protein-protein interactions in yeast liquid culture. Protein fusions non-native to yeast may be expressed to replace endogenous sexual agglutination proteins and mediate library-by-library interrogation of protein interactions. The methods and compositions of the invention can be utilized for the characterization of protein interaction networks in high throughput for both binding affinity and specificity, which is crucial for understanding cellular functions, screening therapeutic candidates, and evaluating engineered protein networks.

High throughput protein-protein interaction screening in yeast liquid culture

Disclosed herein are designed heterodimer proteins, monomeric polypeptides capable of forming heterodimer proteins, protein scaffolds including such polypeptides, and methods for using the heterodimer proteins and subunit polypeptides for designing logic gates.

Orthogonal protein heterodimers

Beta-sheet forming polypeptides at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS:1-24 are disclosed, together with their use and methods for designing beta-sheet forming polypeptides.

De novo designed non-local beta sheet proteins

Nanostructures and nanostructure-based vaccines that display antigens capable of eliciting immune responses to infectious agents such as bacteria, viruses, and pathogens are provided. Some vaccines are useful for preventing or decreasing the severity of infection with an infectious agent, including, for example and without limitation, lyme disease, pertussis, herpes virus, orthomyxovirus, paramyxovirus, pneumovirus, filovirus, flavivirus, reovirus, retrovirus, meningococcus, or malaria. The antigens may be attached to the core of the nanostructure either non-covalently or covalently, including as a fusion protein or by other means. Multimeric antigens may optionally be displayed along a symmetry axis of the nanostructure. Also provided are proteins and nucleic acid molecules encoding such proteins, vaccine compositions, and methods of administration.

Self-asssembling nanostructure vaccines

Disclosed herein are nanostructures and their use, where the nanostructures include (a) a plurality of first assemblies, each first assembly comprising a plurality of identical first polypeptides; (b) a plurality of second assemblies, each second assembly comprising a plurality of identical second polypeptides, wherein the second polypeptide differs from the first polypeptide; wherein the plurality of first assemblies non-covalently interact with the plurality of second assemblies to form a nanostructures; and wherein the nanostructure displays multiple copies of one or more paramyxovirus and/or pneumovirus F proteins or antigenic fragments thereof, on an exterior of the nanostructure.

De novo designed polypeptides that bind to IL-2 receptor &#x3b2;heterodimer (IL-2R&#x3b2;), IL-4 receptor &#x3b1;heterodimer (IL-4R&#x3b1;), or IL-13 receptor &#x3b1; subunit (IL-13R&#x3b1;) are disclosed, as are methods for using and designing the polypeptides.

Disclosed herein are macrocyclic polypeptides having no more than 3 ammo acid substitutions compared to the amino acid sequence of any one of SEQ ID NO: 1-2.37 or a mirror image thereof, wherein the polypeptide includes both L and D amino acids, libraries of such polypeptides, and uses thereof.

Macrocyclic polypeptides

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Seattle, WA, United States of America

David Baker