Design of readers for pathological PTM proteoforms in Alzheimer's disease
Abstract
Alzheimer's disease (AD) is characterized by heterogeneous Tau phosphorylation and aberrant amyloid-beta (Abeta) processing, yet molecular tools that distinguish closely related molecular states of tau and Abeta with predefined specificity remain difficult to develop. Here, we designed de novo protein readers targeting three disease-associated phospho-Tau regions and N-terminal pyroglutamate-modified Abeta (N3pG-Abeta). Screening 192 designs per target identified 51 modification-selective hits among 768 candidates (6.6%). Representative readers exhibited nanomolar to subnanomolar affinities for modified peptides, discriminated authentic modifications from unmodified or substitution-based controls, and preferentially recognized modified full-length targets. We further programmed local modification specificity by interface redesign, generating pT231 readers conditional on the phosphorylation state of neighboring S235 and S237. A 2.0-angstrom crystal structure of an N3pG-Abeta reader closely matched the computational design model (interface C-alpha RMSD = 0.52 angstrom), and redesign of pT231 readers tuned apparent binding affinities from greater than 1 uM to below 1 nM. In a human 3D neuronal culture with both pathological Abeta and tau, selective readers targeting N3pG-Abeta, Tau pT231, and Tau pT217 recognized disease-associated signals, exhibiting colocalization with related antibodies and much higher signal in the AD line than the control. Tau pT231 readers further quantitatively distinguish AD patients and control human brain lysates in dot-blot assays. Together, these results establish genetically encoded readers with programmable specificity for defined Tau and Abeta modification states, enabling molecular-state-resolved detection in human disease models and biological samples, and lay a foundation for controlled pathological molecular perturbation.
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BibTeX
@misc{wu2026design,
title = {{Design of readers for pathological PTM proteoforms in Alzheimer's disease}},
author = {Kejia Wu and Tiana Schantz and Lemuel Chang and Prarthna Chabria and Elaina Bashaw and Thejesh Reddy Kalatturu and Doo Yeon Kim and Anqi Chen and Nathaniel Corley and Asim K. Bera and Alex Kang and Hannah Nguyen and Johnny Mendoza and Xinting Li and Magnus S. Bauer and Misa Baum and Brian C. Kraemer and Yuyu Song and David Baker},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.20.760520},
url = {https://www.biorxiv.org/content/10.64898/2026.10.20.760520v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Design of readers for pathological PTM proteoforms in Alzheimer's disease
AU - Kejia Wu
AU - Tiana Schantz
AU - Lemuel Chang
AU - Prarthna Chabria
AU - Elaina Bashaw
AU - Thejesh Reddy Kalatturu
AU - Doo Yeon Kim
AU - Anqi Chen
AU - Nathaniel Corley
AU - Asim K. Bera
AU - Alex Kang
AU - Hannah Nguyen
AU - Johnny Mendoza
AU - Xinting Li
AU - Magnus S. Bauer
AU - Misa Baum
AU - Brian C. Kraemer
AU - Yuyu Song
AU - David Baker
PY - 2026
DA - 2026/10/20
PB - bioRxiv
DO - 10.64898/2026.10.20.760520
UR - https://www.biorxiv.org/content/10.64898/2026.10.20.760520v1
AB - Alzheimer's disease (AD) is characterized by heterogeneous Tau phosphorylation and aberrant amyloid-beta (Abeta) processing, yet molecular tools that distinguish closely related molecular states of tau and Abeta with predefined specificity remain difficult to develop. Here, we designed de novo protein readers targeting three disease-associated phospho-Tau regions and N-terminal pyroglutamate-modified Abeta (N3pG-Abeta). Screening 192 designs per target identified 51 modification-selective hits among 768 candidates (6.6%). Representative readers exhibited nanomolar to subnanomolar affinities for modified peptides, discriminated authentic modifications from unmodified or substitution-based controls, and preferentially recognized modified full-length targets. We further programmed local modification specificity by interface redesign, generating pT231 readers conditional on the phosphorylation state of neighboring S235 and S237. A 2.0-angstrom crystal structure of an N3pG-Abeta reader closely matched the computational design model (interface C-alpha RMSD = 0.52 angstrom), and redesign of pT231 readers tuned apparent binding affinities from greater than 1 uM to below 1 nM. In a human 3D neuronal culture with both pathological Abeta and tau, selective readers targeting N3pG-Abeta, Tau pT231, and Tau pT217 recognized disease-associated signals, exhibiting colocalization with related antibodies and much higher signal in the AD line than the control. Tau pT231 readers further quantitatively distinguish AD patients and control human brain lysates in dot-blot assays. Together, these results establish genetically encoded readers with programmable specificity for defined Tau and Abeta modification states, enabling molecular-state-resolved detection in human disease models and biological samples, and lay a foundation for controlled pathological molecular perturbation.
SN - 2692-8205
ER -