Robust Prediction of Enzyme Variant Kinetics with RealKcat.

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Tác giả: Arunraj B, Brisa Calderon-Lopez, Niaz Bahar Chowdhury, Ratul Chowdhury, Sakib Ferdous, Shashank Koneru, Ankur Mali, Mohammed Noor, Abraham Osinuga, Rajib Saha, Karuna Anna Sajeevan, Rahil Salehi, Laura Mariana Santa-Correa, Nabia Shahreen

Ngôn ngữ: eng

Ký hiệu phân loại: 531.113 Kinetics

Thông tin xuất bản: United States : bioRxiv : the preprint server for biology , 2025

Mô tả vật lý:

Bộ sưu tập: NCBI

ID: 673690

 Accurate prediction of kinetic parameters is crucial for understanding known and tailoring novel enzymes for biocatalysis. Current models fail to capture mutation effects on catalytically essential residues, limiting their utility in enzyme design. We grid-searched through ten model architectures (25,671 hyperparameter combinations) to identify a gradient-based additive framework called RealKcat, trained on 27,176 experimental entries curated manually (KinHub-27k) by screening 2,158 articles. Clustering catalytic turnover (𝑘𝑐𝑎𝑡) and substrate affinity (KM) by rational orders of magnitude, RealKcat achieves >
 85% test accuracy, demonstrating highest sensitivity to mutation-induced variability thus far, and is the first-of-its-kind-model to demonstrate complete loss of activity upon deletion of the catalytic apparatus. Finally, state-of-the-art 𝑘𝑐𝑎𝑡 validation accuracy (96%) on alkaline phosphatase (PafA) mutant industrial dataset confirms RealKcat's generalizability in learning per-residue catalytic relevance.
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