Engineering topics
Yu, Han
Publications and source records attributed to Yu, Han.
Pathway Evolution Through a Bottlenecking-Debottlenecking Strategy and Machine Learning-Aided Flux Balancing
The evolution of pathway enzymes enhances the biosynthesis of high-value chemicals, crucial for pharmaceutical, and agrochemical applications. However, unpredictable evolutionary landscapes of pathway genes often hinder successful evolution. Here, the presence of complex epistasis is identifued within the representative naringenin biosynthetic pathway enzymes, hampering straightforward directed evolution. Subsequently, a biofoundry-assisted strategy is developed for pathway bottlenecking and debottlenecking, enabling the parallel evolution of all pathway enzymes along a predictable evolutionary trajectory in six weeks. This study then utilizes a machine learning model, ProEnsemble, to further balance the pathway by optimizing the transcription of individual genes. The broad applicability of this strategy is demonstrated by constructing an Escherichia coli chassis with evolved and balanced pathway genes, resulting in 3.65 g L -1 naringenin. The optimized naringenin chassis also demonstrates enhanced production of other flavonoids. This approach can be readily adapted for any given number of enzymes in the specific metabolic pathway, paving the way for automated chassis construction in contemporary biofoundries.
UniKP: a unified framework for the prediction of enzyme kinetic parameters
Prediction of enzyme kinetic parameters is essential for designing and optimizing enzymes for various biotechnological and industrial applications, but the limited performance of current prediction tools on diverse tasks hinders their practical applications. Here, we introduce UniKP, a unified framework based on pretrained language models for the prediction of enzyme kinetic parameters, including enzyme turnover number (k cat ), Michaelis constant (K m ), and catalytic efficiency (k cat / K m ), from protein sequences and substrate structures. A two-layer framework derived from UniKP (EF-UniKP) has also been proposed to allow robust k cat prediction in considering environmental factors, including pH and temperature. In addition, four representative re-weighting methods are systematically explored to successfully reduce the prediction error in high-value prediction tasks. We have demonstrated the application of UniKP and EF-UniKP in several enzyme discovery and directed evolution tasks, leading to the identification of new enzymes and enzyme mutants with higher activity. UniKP is a valuable tool for deciphering the mechanisms of enzyme kinetics and enables novel insights into enzyme engineering and their industrial applications.
Auxiliary sequential deposition enables 19%-efficiency organic solar cells processed from halogen-free solvents
High-efficiency organic solar cells are often achieved using toxic halogenated solvents and additives that are constrained in organic solar cells industry. Therefore, it is important to develop materials or processing methods that enabled highly efficient organic solar cells processed by halogen free solvents. In this paper, we report an innovative processing method named auxiliary sequential deposition that enables 19%-efficiency organic solar cells processed by halogen free solvents. Our auxiliary sequential deposition method is different from the conventional blend casting or sequential deposition methods in that it involves an additional casting of dithieno[3,2-b:2’,3’-d]thiophene between the sequential depositions of the donor (D18-Cl) and acceptor (L8-BO) layers. The auxiliary sequential deposition method enables dramatic performance enhancement from 15% to over 18% compared to the blend casting and sequential deposition methods. Furthermore, by incorporating a branched-chain-engineered acceptor called L8-BO-X, device performance can be boosted to over 19% due to increased intermolecular packing, representing top-tier values for green-solvent processed organic solar cells. Comprehensive morphological and time-resolved characterizations reveal that the superior blend morphology achieved through the auxiliary sequential deposition method promotes charge generation while simultaneously suppressing charge recombination. This research underscores the potential of the auxiliary sequential deposition method for fabricating highly efficient organic solar cells using environmentally friendly solvents.