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Research, news, and commentary from Nature, the international science journal. For daily science news, get Nature Briefing: https://go.nature.com/get-Nature-Briefing
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Nature
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· 15h
Enzyme specificity prediction using cross attention graph neural networks - Nature
Enzymes are the molecular machines of life, and a key property that governs their function is substrate specificity—the ability of an enzyme to recognize and selectively act on particular substrates. This specificity originates from the three-dimensional (3D) structure of the enzyme active site and complicated transition state of the reaction1,2. Many enzymes can promiscuously catalyze reactions or act on substrates beyond those for which they were originally evolved1,3-5. However, millions of known enzymes still lack reliable substrate specificity information, impeding their practical applications and comprehensive understanding of the biocatalytic diversity in nature. Herein, we developed a cross-attention-empowered SE(3)-equivariant graph neural network architecture named EZSpecificity for predicting enzyme substrate specificity, which was trained on a comprehensive tailor-made database of enzyme-substrate interactions at sequence and structural levels. EZSpecificity outperformed the existing machine learning models for enzyme substrate specificity prediction, as demonstrated by both an unknown substrate and enzyme database and seven proof-of-concept protein families. Experimental validation with eight halogenases and 78 substrates revealed that EZSpecificity achieved a 91.7% accuracy in identifying the single potential reactive substrate, significantly higher than that of the state-of-the-art model ESP (58.3%). EZSpecificity represents a general machine learning model for accurate prediction of substrate specificity for enzymes related to fundamental and applied research in biology and medicine.
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Nature
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· 1d
World’s most porous sponges: intricate carbon-trapping powders hit the market
Metal-organic frameworks were the next big thing in chemistry when they were invented more than three decades ago. Now, these intriguing materials are becoming commercial tools for capturing carbon dioxide and harvesting water from the air.
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Nature
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· 1d
Kirigami-inspired parachutes with programmable reconfiguration - Nature
A thin planar disc designed with appropriately patterned cuts transforms itself, due to air flow effects, into an effective parachute exhibiting good positional stability, regardless of its initial orientation.
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