Biology subjects

Chen, K.-W.

Publications and source records attributed to Chen, K.-W..

5 recordsLinked to original sources

bioRxiv2025

SAKPE: A Site Attention Kinetic Parameters Prediction Method for Enzyme Engineering

0.The quantitative determination of enzyme kinetic parameters traditionally relies on experimental methods that are both time-intensive and costly. Machine learning models have demonstrated significant potential for predicting enzyme kinetic parameters in recent years. Despite this promise, these methods face challenges, including limited training data, inadequate sensitivity to subtle mutations, and poor alignment with practical enzyme engineering contexts. Here, we introduce SAKPE (Site Attention Kinetic Parameters Prediction Method for Enzyme Engineering), a novel machine-learning framework designed to predict enzyme kinetic parameters with enhanced accuracy in practical application scenarios. By incorporating protein representation, substrate representation, and protein representation with weights for important sites, SAKPE significantly outperforms existing methods in predicting enzymatic kinetic parameters, including turnover number (kcat), Michaelis constant (Km), and inhibition constant (Ki). Incorporating protein representation with weights for important sites enables SAKPE to effectively capture the impact of mutations, especially mutations of important sites and their surrounding amino acids of interest in enzyme engineering, on enzyme kinetics parameters. SAKPE offers a robust and practical tool for predicting enzyme kinetic parameters, providing a superior tool for enzyme engineering scenarios such as enzyme design, directed evolution, and industrial applications.

bioinformatics↗

bioRxiv2025

A De Novo Design Strategy to Convert FAcD from Dimer to Active Monomer

Enzymes largely exist in various oligomeric states, but monomeric enzymes are more conducive to industrial applications. Converting an oligomeric enzyme into an active monomer is a significant challenge. In this study, we present a de novo design strategy to convert fluoroacetate dehalogenase (FAcD) from its native dimeric form to an active monomer. Using the AI-based method ProteinMPNN, we identified critical protein-protein interaction (PPI) sites at the dimer interface. ArDCA, another AI tool, was employed to pinpoint catalytic hotspots. Six mutants, Mu1-Mu6, were designed. Molecular dynamics (MD) simulations, coupled with mass spectrometry, confirmed that these mutants form stable monomers. The pre-reaction state (PRS) model predicted that three of these mutants exhibited catalytic activity. In particular, Mu5 with 11 mutations from the wild-type, was predicted to have high catalytic activity, and was subsequently confirmed by kinetics experiment, with a kcat of 672.2 min-1 and a T5030 > 100 {degrees}C, comparable to the wild-type enzyme (kcat = 676.3 min-1, T5030 = 84 {degrees}C). Notably, the Y149M mutation increased catalytic activity nearly forty-fold, demonstrating the effectiveness of our design strategy.

bioengineering↗

bioRxiv2020

Mitochondrial ROS1 increases mitochondrial fission and respiration in oral squamous cancer carcinoma

Increased ROS1 oncogene expression has been implicated in the invasiveness of human oral squamous cell carcinoma (OSCC). The cellular distribution of ROS1 has long been assumed at the plasma membrane. However, a previous work reported a differential cellular distribution of mutant ROS1 derived from chromosomal translocation, resulting in increased carcinogenesis. We thus hypothesized that cellular distribution of up-regulated ROS1 in OSCC may correlate with invasiveness. We found that ROS1 can localize to mitochondria in the highly invasive OSCC and identified a mitochondria-targeting signal sequence in ROS1. We also demonstrated that ROS1 targeting to mitochondria is required for mitochondrial fission phenotype in the highly invasive OSCC cells. OSCC cells expressing high levels of ROS1 consumed more oxygen and had increased levels of cellular ATP levels. Our results also revealed that ROS1 regulates mitochondrial biogenesis and cellular metabolic plasticity. Together, these findings demonstrate that ROS1 targeting to mitochondria enhances OSCC invasion through regulating mitochondrial morphogenesis and cellular respiratory. Summary StatementThis study discovers a new role for the ROS1 in mitochondrial fission and metabolic activities.

cancer biology↗

bioRxiv2020

PIP3 depletion rescues myoblast fusion defects in human rhabdomyosarcoma cells

Myoblast fusion is required for myotube formation during myogenesis, and defects in myoblast differentiation and fusion have been implicated in a number of diseases, including human rhabdomyosarcoma. While the transcriptional regulation of the myogenic program has been studied extensively, the mechanisms controlling myoblast fusion remain largely unknown. This study identified and characterized the dynamics of a distinct class of blebs, termed bubbling blebs, which are smaller than those that participate in migration. The formation of these bubbling blebs occurred during differentiation and decreased alongside a decline in phosphatidylinositol-(3,4,5)-trisphosphate (PIP3) at the plasma membrane before myoblast fusion. In a human rhabdomyosarcoma-derived (RD) cell line that exhibits strong blebbing dynamics and myoblast fusion defects, PIP3 was constitutively abundant on the membrane during myogenesis. Targeting phosphatase and tensin homolog (PTEN) to the plasma membrane reduced PIP3 levels, inhibited bubbling blebs, and rescued myoblast fusion defects in RD cells. These findings highlight the differential distribution and crucial role of PIP3 during myoblast fusion and reveal a novel mechanism underlying myogenesis defects in human rhabdomyosarcoma. Summary StatementThis study reveals a novel mechanism underlying myogenesis defects in human rhabdomyosarcoma cells involving PIP3, whose depletion with PTEN rescues myoblast fusion defects.

cell biology↗

bioRxiv2019

First report of Telenomus remus parasitizing Spodoptera frugiperda and its natural parasitism in South China

The fall armyworm, Spodoptera frugiperda, is a lepidopteran pest that feeds on many economically important cereal crops such as corn, rice, sorghum, and sugarcane. Native to the Americas, it has become a serious invasive pest in Africa and Asia. Recently, this pest was found invaded China and has spread exceptionally fast across the country. As S. frugiperda will most likely become a major pest in China, Integrated Pest Management strategies, including biological control methods, should be developed to win the battle against it. Here, we report the detection of Telenomus remus parasitizing S. frugiperda eggs in cornfields in South China based on morphological and molecular evidence. Our preliminary surveys indicated that the natural parasitism rates of T. remus on S. frugiperda could reach 30% and 50% for egg masses and per egg mass, respectively. Further application of T. remus against S. frugiperda in biological control programs are discussed.

zoology↗