Chemistry-informed Machine Learning Explains Calcium-binding Proteins' Fuzzy Shape for Communicating Changes in the Atomic States of Calcium Ions.

Pengzhi Zhang, Jules Nde, Yossi Eliaz, Nathaniel Jennings, Piotr Cieplak, Margaret S Cheung

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Article in ArXiv, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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6 authors.

Pengzhi ZhangCenter for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA.

Jules NdeDepartment of Physics, University of Washington, Seattle, WA, USA.

Yossi EliazDepartment of Physics, University of Houston, Houston, TX, USA.

Nathaniel JenningsDepartment of Physics, University of Houston, Houston, TX, USA.

Piotr CieplakSanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.

Margaret S CheungDepartment of Physics, University of Washington, Seattle, WA, USA.

Funding

Principles for Tuning Target Selectivity in Signaling ProteinsR01GM097553 · NIGMS · UNIVERSITY OF WASHINGTON · PI CHEUNG, MARGARET SHUN · 2011 to 2022

$2.7M

NIGMS NIH HHS R01 GM097553

6 · The paper itself

Abstract

Proteins' fuzziness are features for communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. Binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit, but it is unclear whether the limited experimental data available can be used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the

Indexed as

calcium-binding proteincalmodulinEF-hand motifgraph theoryion charge statemachine learning explanationmany-body interactions

Identifiers

PMID39108291

PMCPMC11302678

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