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公开(公告)号:US20240263167A1
公开(公告)日:2024-08-08
申请号:US18484871
申请日:2023-10-11
Applicant: University of Washington
Inventor: David BAKER , David YOUNGER , Eric KLAVINS
IPC: C12N15/10
CPC classification number: C12N15/1055
Abstract: 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.
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公开(公告)号:US20240013853A1
公开(公告)日:2024-01-11
申请号:US18348528
申请日:2023-07-07
Applicant: University of Washington
Inventor: David BAKER , Basile WICKY , Lukas MILLES , Alexis COURBET , Robert RAGOTTE , Elias KINFU , Sam TIPPS , Justas DAUPARAS , Ryan KIBLER
IPC: G16B15/20
CPC classification number: G16B15/20
Abstract: Polypeptide are providing that are at least 50% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS:1-37, cyclic homo-oligomers of the polypeptides, and uses thereof.
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公开(公告)号:US20230272446A1
公开(公告)日:2023-08-31
申请号:US18312788
申请日:2023-05-05
Applicant: University of Washington
Inventor: Fabio PARMEGGIANI , TJ BRUNETTE , Po-Ssu HUANG , David BAKER
CPC classification number: C12P21/02 , C07K14/001 , C12N15/70 , C12N2800/101
Abstract: Methods and systems for designing proteins are disclosed, as well as proteins and protein assemblies designed. A computing device can determine a protein repeating unit that includes one or more protein helices and one or more protein loops. The computing device can generate a protein backbone structure with a copy of the protein repeating unit. The computing device can determine whether a distance between a pair of helices of the protein backbone structure is between lower and upper distance thresholds. After determining that the distance between the pair of helices is between the lower and upper distance thresholds, the computing device can: generate a plurality of protein sequences based on the protein backbone structure, select a particular protein sequence of the plurality of protein sequences based on an energy landscape that has information about energy and distance from a target fold of the particular protein sequence, and generate an output based on the particular protein sequence.
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公开(公告)号:US20230142283A1
公开(公告)日:2023-05-11
申请号:US17759175
申请日:2021-03-03
Applicant: University of Washington
Inventor: David BAKER , Matthew BICK , TJ BRUNETTE
CPC classification number: G16B15/20 , G16B35/10 , C12N15/1068 , C07K14/47 , C07K14/001 , C07K2319/00
Abstract: Disclosed herein are junction polypeptides that can be used, for example, to join together protein building blocks via a rigid fusion to generate a wide range of protein shapes; fusion proteins comprising such junction polypeptides, polymers thereof, and methods for designing such junction polypeptides.
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公开(公告)号:US20230065495A1
公开(公告)日:2023-03-02
申请号:US17760165
申请日:2021-02-05
Applicant: University of Washington
Inventor: Jason C. KLIMA , David BAKER
Abstract: Disclosed herein are β-barrel polypeptides including self-complementing multipartite β-barrel polypeptides and circularly permuted β-barrel polypeptides and methods for their design and use in mediating real-time monitoring of polypeptide-polypeptide association and dissociation events.
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公开(公告)号:US20220213153A1
公开(公告)日:2022-07-07
申请号:US17564467
申请日:2021-12-29
Applicant: University of Washington , NEW YORK UNIVERSITY
Inventor: Yang HSIA , Rubul MOUT , Natasha EDMAN , Ivan VULOVIC , Una NATTERMANN , William H. SHEFFLER , TJ BRUNETTE , Young-Jun PARK , Asim BERA , Matthew BICK , Rachel REDLER , Damian EKIERT , Gira BHABHA , David VEESLER , David BAKER
Abstract: The disclosure provides polypeptides as descried herein that including an amino acid sequence at least 50% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS:1-46, oligomers of such polypeptides, methods for using such polypeptides and oligomers, and methods for designing such polypeptides and oligomers.
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公开(公告)号:US20220144895A1
公开(公告)日:2022-05-12
申请号:US17602119
申请日:2020-04-20
Applicant: University of Washington
Inventor: Scott BOYKEN , David BAKER , Zibo CHEN , Alfredo Quijano RUBIO , Neil P. KING , Jason C. KLIMA , Carl WALKEY
IPC: C07K7/08
Abstract: Disclosed herein are polypeptides or polypeptide oligomers, including a buried hydrogen bond network that includes at least (1, 2, 3, 4, 5, 6, 7, 8, or 9) pH sensitive amino acids located (i) at an intra-chain interface between different: structural elements in one polypeptide, or (it) at an inter-chain interface between structural elements present in different chains of a polypeptide oligomer, wherein the polypeptide or polypeptide oligomer is stable above a given pH, and wherein the polypeptide or polypeptide oligomer undergoes a conformational transition when subjected to a pH at or below the given pH.
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公开(公告)号:US20210324011A1
公开(公告)日:2021-10-21
申请号:US17285057
申请日:2019-10-24
Applicant: UNIVERSITY OF WASHINGTON
Inventor: Hao SHEN , Jorge FALLAS , David BAKER
Abstract: Disclosed herein are polypeptides having the amino acid sequence that is 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 full length of the amino acid sequence selected from the group consisting of SEQ ID NO: 1-33 and 36, wherein the polypeptides include at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% of the identified interface residues, and wherein the polypeptides are capable of end-to-end homo-polymerization, homo-polymers of the polypeptides, and related capping and anchor proteins to facilitate homo-polymer formation.
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公开(公告)号:US20210122793A1
公开(公告)日:2021-04-29
申请号:US17078319
申请日:2020-10-23
Applicant: UNIVERSITY OF WASHINGTON
Inventor: Tamuka CHIDYAUSIKU , Enrique MARCOS , Lucas NIVON , Gustav OBERDORFER , David BAKER , Lauren CARTER
Abstract: 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.
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公开(公告)号:US20210115090A1
公开(公告)日:2021-04-22
申请号:US17077692
申请日:2020-10-22
Applicant: UNIVERSITY OF WASHINGTON
Inventor: Robert A. LANGAN , Scott BOYKEN , David BAKER , Walter NOVAK , Marc Joseph LAJOIE , Alfredo QUIJANO RUBIO
Abstract: 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.
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