Výsledky vyhledávání - "David Nedrud"

Akademický článek

DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

Autor: Christian B. Macdonald, David Nedrud, Patrick Rockefeller Grimes, Donovan Trinidad, James S. Fraser, Willow Coyote-Maestas

Publikováno v: Genome Biology, Vol 24, Iss 1, Pp 1-19 (2023)

Abstract Insertions and deletions (indels) enable evolution and cause disease. Due to technical challenges, indels are left out of most mutational scans, limiting our understanding of them in disease, biology, and evolution. We develop a low cost and

Externí odkaz: https://doaj.org/article/11399c52db2f4426b21268f10cf7d139

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Akademický článek

Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling

Autor: Willow Coyote-Maestas, David Nedrud, Antonio Suma, Yungui He, Kenneth A. Matreyek, Douglas M. Fowler, Vincenzo Carnevale, Chad L. Myers, Daniel Schmidt

Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-16 (2021)

Here, the authors perform a large-scale, high-throughput biochemical assay to determine the compatibility of over 300,000 domain recombination variants of the inward rectifier K+ channel Kir2.1. They derive rules for designing domain insertion varian

Externí odkaz: https://doaj.org/article/446c0c0118e64afe931272b243499af9

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Akademický článek

Determinants of trafficking, conduction, and disease within a K+ channel revealed through multiparametric deep mutational scanning

Autor: Willow Coyote-Maestas, David Nedrud, Yungui He, Daniel Schmidt

Publikováno v: eLife, Vol 11 (2022)

A long-standing goal in protein science and clinical genetics is to develop quantitative models of sequence, structure, and function relationships to understand how mutations cause disease. Deep mutational scanning (DMS) is a promising strategy to ma

Externí odkaz: https://doaj.org/article/15c4d948595e4756b6a890ffb7da5841

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Multiparametric domain insertional profiling of Adeno-Associated Virus VP1

Autor: Mareike D. Hoffmann, Alina C. Zdechlik, Yungui He, David Nedrud, George Aslanidi, Wendy Gordon, Daniel Schmidt

Publikováno v: bioRxiv

Evolved properties of Adeno-Associated Virus (AAV), such as broad tropism and immunogenicity in humans, are barriers to AAV-based gene therapy. Previous efforts to re-engineer these properties have focused on variable regions near AAV’s 3-fold prot

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3848cbbbb957670507da90c702717afa
https://europepmc.org/articles/PMC10153220/

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Deep Insertion, Deletion, and Missense Mutation Libraries for Exploring Protein Variation in Evolution, Disease, and Biology

Autor: Christian B. Macdonald, David Nedrud, Patrick Rockefeller Grimes, Donovan Trinidad, James S. Fraser, Willow Coyote-Maestas

Insertions and deletions (indels) are a major source of genetic variation in evolution and the cause of nearly 30% of Mendelian disease. Despite their importance, indels are left out of nearly every systematic mutational scan to date due to technical

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::c0d3c1051ed8660ce8b15749b799d8a4
https://doi.org/10.1101/2022.07.26.501589

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A large‐scale survey of pairwise epistasis reveals a mechanism for evolutionary expansion and specialization of PDZ domains

Autor: Daniel F. Schmidt, David Nedrud, Willow Coyote-Maestas

Publikováno v: Proteins: Structure, Function, and Bioinformatics. 89:899-914

Deep mutational scanning (DMS) facilitates data-driven models of protein structure and function. Here, we adapted Saturated Programmable Insertion Engineering (SPINE) as a programmable DMS technique. We validate SPINE with a reference single mutant d

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9d7321c6e73eedde4bc60aee93a6cba2
https://doi.org/10.1002/prot.26067

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The biophysical basis of protein domain compatibility

Autor: Kenneth A. Matreyek, Antonio Suma, David Nedrud, Yungui He, Douglas M. Fowler, Willow Coyote-Maestas, Vincenzo Carnevale, Daniel F. Schmidt, Chad L. Myers

Understanding the biophysical mechanisms that govern the combination of protein domains into viable proteins is essential for advancing synthetic biology and biomedical engineering. Here, we use massively parallel genotype/phenotype assays to determi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::5fc661cc9702987c58e58b08331e5aa2
https://doi.org/10.1101/2020.12.09.418442

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A survey of pairwise epistasis supports an outside-in hierarchy of clade-specifying and function-defining residues in PSD95 PDZ3

Autor: David Nedrud, Willow Coyote-Maestas, Daniel F. Schmidt

Deep mutational scanning enables data-driven models of protein structure and function. Here, we adapted Saturated Programmable Insertion Engineering as an economical and programmable deep mutational scanning technique. We validate this approach with

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::fb1776917cf66261bee11aedc3bc3033
https://doi.org/10.1101/2020.06.26.174375

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